query: what can change the binding properties of a protein

pos: Ligand (biochemistry) Ligand (biochemistry) In biochemistry and pharmacology, a ligand is a substance that forms a complex with a biomolecule to serve a biological purpose. In protein-ligand binding, the ligand is usually a molecule which produces a signal by binding to a site on a target protein. The binding typically results in a change of conformational isomerism (conformation) of the target protein. In DNA-ligand binding studies, the ligand can be a small molecule, ion, or protein which binds to the DNA double helix. The relationship between ligand and binding partner is a function of charge, hydrophobicity, and molecular structure. The instance of

pos: Ligand (biochemistry) Ligand (biochemistry) In biochemistry and pharmacology, a ligand is a substance that forms a complex with a biomolecule to serve a biological purpose. In protein-ligand binding, the ligand is usually a molecule which produces a signal by binding to a site on a target protein. The binding typically results in a change of conformational isomerism (conformation) of the target protein. In DNA-ligand binding studies, the ligand can be a small molecule, ion, or protein which binds to the DNA double helix. The relationship between ligand and binding partner is a function of charge, hydrophobicity, and molecular structure. The instance of

pos: Protein adsorption the molecular structure of the monomer. By carefully selecting the type or types of mers in a polymer and its manufacturing process, the chemical and physical properties of a polymer can be highly tailored to adsorb specific proteins and cells for a particular application. Protein adsorption often results in significant conformational changes, which refers to changes in the secondary, tertiary, and quartary structures of proteins. In addition to adsorption rates and amounts, orientation and conformation are of critical importance. These conformational changes can affect protein interaction with ligands, substrates, and antigens which are dependent on the orientation of the binding

pos: Binding site Binding site Binding of a ligand to a binding site on protein often triggers a change in conformation in the protein and results in altered cellular function. Hence binding site on protein are critical parts of signal transduction pathways. Types of ligands include neurotransmitters, toxins, neuropeptides, and steroid hormones. Binding sites incur functional changes in a number of contexts, including enzyme catalysis, molecular pathway signaling, homeostatic regulation, and physiological function. Electric charge, steric shape and geometry of the site selectively allow for highly specific ligands to bind, activating a particular cascade of cellular interactions the protein is responsible for. Enzymes

neg: Thermal shift assay of drug binding in a wide range of cells and tissues. CETSA can also be conducted on cell lysates versus intact cells, helping to determine sample penetration of the cell membrane. Thermofluor variant specific for flavin-binding proteins. Analogous to thermofluor binding assays, a small volume of protein solution is heated up and the fluorescence increase is followed as function of temperature. In contrast to Thermofluor, no external fluorescent dye is needed because the flavin cofactor is already present in the flavin-binding protein and its fluorescence properties change upon unfolding. Size exclusion chromatography can be used directly to access protein stability

neg: 8-Anilinonaphthalene-1-sulfonic acid useful. 8-Anilinonaphthalene-1-sulfonic acid 8-Anilinonaphthalene-1-sulfonic acid (ANS), also called 1-anilino-8-naphthalenesulfonate, is an organic compound containing both a sulfonic acid and an amine group. This compound is used as a fluorescent molecular probe. For example, ANS can be used to study conformational changes induced by ligand binding in proteins, as ANS's fluorescent properties will change as it binds to hydrophobic regions on the protein surface. Comparison of the fluorescence in the presence and absence of a particular ligand can thus give information about how the binding of the ligand changes the surface of the protein. Its permeability to mitochondrial membranes makes it

neg: 8-Anilinonaphthalene-1-sulfonic acid 8-Anilinonaphthalene-1-sulfonic acid 8-Anilinonaphthalene-1-sulfonic acid (ANS), also called 1-anilino-8-naphthalenesulfonate, is an organic compound containing both a sulfonic acid and an amine group. This compound is used as a fluorescent molecular probe. For example, ANS can be used to study conformational changes induced by ligand binding in proteins, as ANS's fluorescent properties will change as it binds to hydrophobic regions on the protein surface. Comparison of the fluorescence in the presence and absence of a particular ligand can thus give information about how the binding of the ligand changes the surface of the protein. Its permeability to mitochondrial membranes makes it particularly

neg: Binding domain calcium. Binding domain A binding domain is a protein domain which binds to a specific atom or molecule, such as calcium or DNA. Protein Domain is a part of a protein sequence and a tertiary structure that can change, function, and live by itself for the rest of the protein chain. (Phillips 1). Upon binding, proteins may undergo a conformational change. Binding domains are essential for the function of many proteins. They are essential because they help splice, assemble, and translate proteins. (Yong 1). Examples of binding domains include Zinc finger, which binds to DNA, and EF hand, which binds

neg: Binding domain Binding domain A binding domain is a protein domain which binds to a specific atom or molecule, such as calcium or DNA. Protein Domain is a part of a protein sequence and a tertiary structure that can change, function, and live by itself for the rest of the protein chain. (Phillips 1). Upon binding, proteins may undergo a conformational change. Binding domains are essential for the function of many proteins. They are essential because they help splice, assemble, and translate proteins. (Yong 1). Examples of binding domains include Zinc finger, which binds to DNA, and EF hand, which binds to

neg: SNP annotation splicing pattern. Knowledge base annotation is done based on the information of gene attribute, protein function and its metabolism. In this type of annotation more emphasis is given to genetic variation that disrupts the protein function domain, protein-protein interaction and biological pathway. The non-coding region of genome contain many important regulatory elements including promoter, enhancer and insulator, any kind of change in this regulatory region can change the functionality of that protein. The mutation in DNA can change the RNA sequence and then influence the RNA secondary structure, RNA binding protein recognition and miRNA binding activity. This method mainly identifies

neg: Binding site affinity. Even though the term pocket is used here, similar methods can be used to predict binding sites used in protein-protein interactions that are usually more planar, not in pockets Binding site Binding of a ligand to a binding site on protein often triggers a change in conformation in the protein and results in altered cellular function. Hence binding site on protein are critical parts of signal transduction pathways. Types of ligands include neurotransmitters, toxins, neuropeptides, and steroid hormones. Binding sites incur functional changes in a number of contexts, including enzyme catalysis, molecular pathway signaling, homeostatic regulation, and physiological function.

neg: Protein adsorption site of interest. These conformational changes, as a result of protein adsorption, can also denature the protein and change its native properties. Tissue engineering is a relatively new field that utilizes a scaffolding as a platform upon which the desired cells proliferate. It is not clear what defines an ideal scaffold for a specific tissue type. The considerations are complex and protein adsorption only adds to the complexity. Although architecture, structural mechanics, and surface properties play a key role, understanding degradation and rate of protein adsorption are also key. In addition to the essentials of mechanics and geometry, a suitable

neg: Protein microarray solid surface such as microscope slides, membranes, beads or microtitre plates. The function of this surface is to provide a support onto which proteins can be immobilized. It should demonstrate maximal binding properties, whilst maintaining the protein in its native conformation so that its binding ability is retained. Microscope slides made of glass or silicon are a popular choice since they are compatible with the easily obtained robotic arrayers and laser scanners that have been developed for DNA microarray technology. Nitrocellulose film slides are broadly accepted as the highest protein binding substrate for protein microarray applications. The chosen solid surface

neg: Protein adsorption between molecules can occur, whereas in single-protein solutions intermolecular repulsive interactions dominate. In addition, there is a time-dependent protein spreading, where protein molecules initially make contact with minimal binding sites on the surface. With the increase in protein's residence time on the surface, the protein may unfold for interaction with additional binding sites. This results in a time-dependent increase in the contact points between protein and surface. This further makes desorption less likely. This technique measures a concentration change of proteins in bulk solution before and after adsorption, Δc. Any protein concentration change is attributed to the adsorbed layer, Γ.

neg: Protein–DNA interaction site predictor predict DNA-binding sites and therefore require a three-dimensional structure of the protein, while others use only sequence information and do not require protein structure in order to make a prediction. Structure- and sequence-based prediction of DNA-binding sites in DNA-binding proteins can be performed on several web servers listed below. DISIS predicts DNA binding sites directly from amino acid sequence and hence is applicable for all known proteins. It is based on the chemical-physical properties of the residue and its environment, predicted structural features and evolutionary data. It uses machine learning algorithms. DISIS2 receives the raw amino acid sequence and generates

neg: Protein–DNA interaction site predictor Protein–DNA interaction site predictor Structural and physical properties of DNA provide important constraints on the binding sites formed on surfaces of DNA-binding proteins. Characteristics of such binding sites may be used for predicting DNA-binding sites from the structural and even sequence properties of unbound proteins. This approach has been successfully implemented for predicting the protein–protein interface. Here, this approach is adopted for predicting DNA-binding sites in DNA-binding proteins. First attempt to use sequence and evolutionary features to predict DNA-binding sites in proteins was made by Ahmad et al. (2004) and Ahmad and Sarai (2005). Some methods use structural information to

neg: Protein–DNA interaction site predictor all features from it, such as secondary structure, solvent accessibility, disorder, b-value, protein-protein interaction, coiled coils, and evolutionary profiles, etc. The amount of predicted features is much larger than of DISIS (previous version). Finally, DISIS2 is able to predict DNA-binding residues from protein sequence of DNA-binding proteins. DNABindR predicts DNA binding sites from amino acid sequences using machine learning algorithms. DISPLAR makes a prediction based on properties of protein structure. Knowledge of the protein structure is required BindN makes a prediction based on chemical properties of the input protein sequence. Knowledge of the protein structure is not required. BindN+ is

neg: Protein A/G commonly used to purify, immobilize or detect immunoglobulins. Each of these immunoglobulin-binding proteins has a different antibody binding profile in terms of the portion of the antibody that is recognized and the species and type of antibodies. Protein A/G Protein A/G is a recombinant fusion protein that combines IgG binding domains of both Protein A and Protein G. Protein A/G contains four Fc binding domains from Protein A and two from Protein G, yielding a final mass of 50,460 daltons. The binding of Protein A/G is less pH-dependent than Protein A, but otherwise has the additive properties of Protein A

neg: Binding properties pattern be expressed as follows (in C++): Accomplishing the binding (i.e. connecting the property change notification in an event handler) may be like as follows: Binding properties pattern The Binding properties pattern is combining multiple observers to force properties in different objects to be synchronized or coordinated in some way. This pattern was first described as a technique by Victor Porton. This pattern comes under concurrency patterns. As an alternative to the aspect-oriented implementation of mutual properties, property binding can be proposed. In LibPropC++ C++ library it is implemented too. Some weakness in the LibPropC++ (with property binding): There are two

neg: Bioisostere a simple atom-for-atom switch. For example, a chlorine -Cl group may often be replaced by a trifluoromethyl -CF group, or by a cyano -C≡N group, but depending on the particular molecule used the substitution may result in little change in activity, or either increase or decrease affinity or efficacy depending on what factors are important for ligand binding to the target protein. Another example is aromatic rings, a phenyl -CH ring can often be replaced by a different aromatic ring such as thiophene or naphthalene which may improve efficacy, change specificity of binding, or reduce metabolically labile sites on the

neg: Alpha-ketoglutarate-dependent hydroxylases Eastern Europe that target gamma-butyrobetaine dioxygenase. Many assays were developed to study αKG-dependent dioxygenases so that information such as enzyme kinetics, enzyme inhibition and ligand binding can be obtained. Nuclear magnetic resonance (NMR) spectroscopy is widely applied to study αKG-dependent dioxygenases. For example, assays were developed to study ligand binding, enzyme kinetics, modes of inhibition as well as protein conformational change. Mass spectrometry is also widely applied. It can be used to characterise enzyme kinetics, to guide enzyme inhibitor development, study ligand and metal binding as well as analyse protein conformational change. Assays using spectrophotometry were also used, for example

neg: Hill equation (biochemistry) not be considered a reliable approximation of the number of cooperative ligand binding sites on a receptor except when the binding of the first and subsequent ligands results in extreme positive cooperativity. Unlike more complex models, the relatively simple Hill equation provides little insight into underlying physiological mechanisms of protein-ligand interactions. This simplicity, however, is what makes the Hill equation a useful empirical model, since its use requires little "a priori" knowledge about the properties of either the protein or ligand being studied. Nevertheless, other, more complex models of cooperative binding have been proposed. For more information and examples of

neg: SMiLE-Seq full length, previously uncharacterized transcription factors. Furthermore, SMiLE-seq is able to identify transcription factor binding sites over a wide range of binding affinities, which represents a significant limitation of other technologies. In theory SMiLE-seq is not limited to only protein-DNA interactions and may potentially be utilized to study protein-RNA binding properties once the technology has been developed further. The primary limitation of SMiLE-seq is that the technique can only be used to characterize the binding interactions of previously identified transcription factors, as the method requires "in vitro" transcription and translation of the transcription factors prior to their combination with DNA

neg: Protein–DNA interaction site predictor an upgraded version of BindN that applies support vector machines (SVMs) to sequence-based prediction of DNA or RNA-binding residues from biochemical features and evolutionary information. DP-Bind combines multiple methods to make a consensus prediction based on the profile of evolutionary conservation and properties of the input protein sequence. Profile of evolutionary conservation is automatically generated by the web-server. Knowledge of the protein structure is not required. DBS-PSSM and DBS-Pred predict the DNA-binding in a protein from their sequence information. Protein–DNA interaction site predictor Structural and physical properties of DNA provide important constraints on the binding sites formed on surfaces of

neg: S100A15 thus exemplary for the diversity within the S100 family. Their different properties are compelling reasons to discriminate S100A15 (koebnerisin) and S100A7 (psoriasin) in epithelial homeostasis, inflammation and cancer. Koebnerisin (S100A15) and psoriasin (S100A7) share a common protein in mice encoded by the S100a7a15 (alias: mS100A7, mS100A15, mS100a7a) gene. It can be used to study the significance of the corresponding human proteins for epidermal maturation, inflammation and epithelial carcinogenesis. S100A15 S100 calcium-binding protein A15 (S100A15), also known as koebnerisin and S100 calcium-binding protein A7A (S100A7A), is a protein that in humans is encoded by the "S100A7A" (alias:"S100A15") gene. S100 proteins are

neg: Communication ancient Egypt and looking at the ways they built themselves out of media with very different properties stone and papyrus. Papyrus is what he called 'Space Binding'. it made possible the transmission of written orders across space, empires and enables the waging of distant military campaigns and colonial administration. The other is stone and 'Time Binding', through the construction of temples and the pyramids can sustain their authority generation to generation, through this media they can change and shape communication in their society. In any communication model, noise is interference with the decoding of messages sent over a channel by

neg: Protein A/G Protein A/G Protein A/G is a recombinant fusion protein that combines IgG binding domains of both Protein A and Protein G. Protein A/G contains four Fc binding domains from Protein A and two from Protein G, yielding a final mass of 50,460 daltons. The binding of Protein A/G is less pH-dependent than Protein A, but otherwise has the additive properties of Protein A and G. Protein A/G binds to all subclasses of human IgG, making it useful for purifying polyclonal or monoclonal IgG antibodies whose subclasses have not been determined. In addition, it binds to IgA, IgE, IgM and (to

neg: Methyl-CpG-binding domain protein 2 a mediator of the biological consequences of the methylation signal. It is also reported that MBD2 and MBD3 recruit the NuRD complex to regions of DNA depending on their selective binding of methylated CpG sites. Therefore, MBD2/NuRD and MBD3/NuRD define two distinct protein complexes with different biochemical and functional properties. Methyl-CpG-binding domain protein 2 has been shown to interact with: Methyl-CpG-binding domain protein 2 Methyl-CpG-binding domain protein 2 is a protein that in humans is encoded by the "MBD2" gene. DNA methylation is the major modification of eukaryotic genomes and plays an essential role in mammalian development. Human proteins MECP2,

neg: Sequential model to suggest a single, whole-protein conformational change. The KNF model follows the structural theory of the induced fit model of substrate binding to an enzyme. A slight change in the conformation of an enzyme improves its binding affinity to the transition state of the ligand, thus catalyzing a reaction. This follows the KNF model, which models cooperativity as the changing conformation of the ligand binding site upon ligand binding to another subunit. Two essential assumptions guide the KNF model: The KNF model characterizes enzymes that exhibit what was coined by Koshland and Hamadi in 2002 as i cooperativity. This term

neg: SOBER1 the SOBER1 family are considered closely related to acyl-protein thioesterases, judged by their protein structure. However, a change in their amino acid sequence renders SOBER1's biochemical properties into a deacetylase; in particular the hydrophobic tunnel, which is found in acyl-protein thioesterases, is impaired by additional amino acids in the lid structure of SOBER1, creating a new surface for binding of the acetyl group. So far, the following proteins have been identified as SOBER1 targets: AvrBsT; ACIP1. SOBER1 SOBER1 is an enzyme that catalyzes the biochemical reaction of deacetylation. The SOBER (Suppressor of AvrBsT-elicited resistance) 1 protein is conserved in plants

neg: Bimolecular fluorescence complementation fluorophore will result in a change in the fluorescent intensities or lifetimes of the fluorophores. The yeast two-hybrid (Y2H) is a genetic screening technique that can be used to detect physical (binding) protein–protein or protein–DNA interactions. It tests a 'bait' protein of known function that is fused to the binding domain of the transcription factor GAL4 against potential interacting proteins or a cDNA library that express the GAL4 activation domain (the 'prey'). Bimolecular fluorescence complementation Bimolecular fluorescence complementation (also known as BiFC) is a technology typically used to validate protein interactions. It is based on the association of fluorescent protein

neg: DNM1 DNM1 Dynamin-1 is a protein that in humans is encoded by the "DNM1" gene. This gene encodes a member of the dynamin subfamily of GTP-binding proteins. The encoded protein possesses unique mechanochemical properties used to tubulate and sever membranes, and is involved in clathrin-mediated endocytosis and other vesicular trafficking processes. Actin and other cytoskeletal proteins act as binding partners for the encoded protein, which can also self-assemble leading to stimulation of GTPase activity. More than sixty highly conserved copies of the 3' region of this gene are found elsewhere in the genome, particularly on chromosomes Y and 15. Alternatively spliced

neg: DNM1 transcript variants encoding different isoforms have been described. DNM1 has been shown to interact with: DNM1 Dynamin-1 is a protein that in humans is encoded by the "DNM1" gene. This gene encodes a member of the dynamin subfamily of GTP-binding proteins. The encoded protein possesses unique mechanochemical properties used to tubulate and sever membranes, and is involved in clathrin-mediated endocytosis and other vesicular trafficking processes. Actin and other cytoskeletal proteins act as binding partners for the encoded protein, which can also self-assemble leading to stimulation of GTPase activity. More than sixty highly conserved copies of the 3' region of this

neg: Molecular binding Among the tightest known protein–protein complexes is that between the enzyme angiogenin and ribonuclease inhibitor; the dissociation constant for the human proteins is 5x10 mol/L. Another biological example is the binding protein streptavidin, which has extraordinarily high affinity for biotin (vitamin B7/H, dissociation constant, K ≈10 mol/L). In such cases, if the reaction conditions change (e.g., the protein moves into an environment where biotin concentrations are very low, or pH or ionic conditions are altered), the reverse reaction can be promoted. For example, the biotin-streptavidin interaction can be broken by incubating the complex in water at 70 °C, without damaging

neg: Spanish flu research have already been identified in currently circulating H5N1. This has led some researchers to suggest that other mutations may surface and make the H5N1 virus capable of human-to-human transmission. Another important factor is the change of the HA protein to a binding preference for alpha 2,6 sialic acid (the major form in the human respiratory tract). In avian virus the HA protein preferentially binds to alpha 2,3 sialic acid, which is the major form in the avian enteric tract. It has been shown that only a single amino acid change can result in the change of this binding preference. Altogether,

neg: RING finger domain RNA, protein and/or lipid substrates. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function

neg: Tumor necrosis factor alpha binding causes a conformational change to occur in the receptor, leading to the dissociation of the inhibitory protein SODD from the intracellular death domain. This dissociation enables the adaptor protein TRADD to bind to the death domain, serving as a platform for subsequent protein binding. Following TRADD binding, three pathways can be initiated. The myriad and often-conflicting effects mediated by the above pathways indicate the existence of extensive cross-talk. For instance, NF-κB enhances the transcription of C-FLIP, Bcl-2, and cIAP1 / cIAP2, inhibitory proteins that interfere with death signaling. On the other hand, activated caspases cleave several components of the

neg: Chem-seq be amenable to biotinylation without disruption of its natural binding properties. This is simply not possible with certain small molecules and even when it is, the process can require expertise in organic chemistry. Once synthesized, the binding properties of the biotinylated compound must be tested. To date, this has been accomplished by comparing the binding kinetics of the biotinylated and unmodified compounds, a process that requires prior knowledge of the proteins that the compound binds. The locations of Bio-JQ1 throughout the genome, as determined using Chem-seq, are almost identical to the ChIP-seq derived locations of the JQ1’s known target protein,

neg: Calcium-binding protein 1 decrease in the number of CABP1-expressing cells, specifically in the left dorsolateral prefrontal cortex. This change, however, was compensated on a whole-brain scale by an increase in the protein levels. Calcium-binding protein 1 Calcium binding protein 1 is a protein that in humans is encoded by the CABP1 gene. Calcium-binding protein 1 is a calcium-binding protein discovered in 1999. It has two EF hand motifs and is expressed in neuronal cells in such areas as hippocampus, habenular nucleus of the epithalamus, Purkinje cell layer of the cerebellum, and the amacrine cells and cone bipolar cells of the retina. Calcium-binding protein

neg: Second messenger system to the receptor causes a conformation change in the receptor. This conformation change can affect the activity of the receptor and result in the production of active second messengers. In the case of G protein-coupled receptors, the conformation change exposes a binding site for a "G-protein". The G-protein (named for the GDP and GTP molecules that bind to it) is bound to the inner membrane of the cell and consists of three subunits: alpha, beta and gamma. The G-protein is known as the "transducer." When the G-protein binds with the receptor, it becomes able to exchange a GDP (guanosine diphosphate)

neg: Multi-state modeling of biomolecules multiple mechanisms, including post-translational modifications, ligand binding, conformational change, or formation of new complexes. Similarly, nucleic acids can undergo a variety of transformations, including protein binding, binding of other nucleic acids, conformational change and DNA methylation. In addition, several types of modifications can co-exist, exerting a combined influence on a biological macromolecule at any given time. Thus, a biomolecule or complex of biomolecules can often adopt a very large number of functionally distinct states. The number of states scales exponentially with the number of possible modifications, a phenomenon known as "combinatorial explosion". This is of concern for computational biologists who

neg: Surface plasmon resonance the gold layer. This plasmon can be influenced by the layer just a few nanometer across the gold–solution interface i.e. the bait protein and possibly the prey protein. Binding makes the reflection angle change; formula_6 As SPR biosensors facilitate measurements at different temperatures, thermodynamic analysis can be performed to obtain a better understanding of the studied interaction. By performing measurements at different temperatures, typically between 4 and 40 °C, it is possible to relate association and dissociation rate constants with activation energy and thereby obtain thermodynamic parameters including binding enthalpy, binding entropy, Gibbs free energy and heat capacity. As SPR

neg: GRIK2 to region of the editing site with residues usually in a neighboring intron but can be an exonic sequence. The region that base pairs with the editing region is known as an Editing Complementary Sequence (ECS) ADARs bind interact directly with the dsRNA substrate via their double-stranded RNA binding domains. If an editing site occurs within a coding sequence, the result could be a codon change. This can lead to translation of a protein isoform due to a change in its primary protein structure. Therefore, editing can also alter protein function. A to I editing occurs in a noncoding RNA

neg: COPII side of the endoplasmic reticulum. Sec12, a transmembrane protein found in the ER acts as a Guanine nucleotide exchange factor by stimulating the release of GDP to allow the binding of GTP. Now in a GTP bound state, Sar1p undergoes a conformational change which exposes a hydrophobic tail that can be inserted into the lipid bilayer, binding it to the membrane. Membrane-bound Sar1p recruits the Sec23p/24p complex to form what is collectively known as the pre-budding complex. The pre-budding complex recruits the long, flexible Sec13p/31p complex. Sec13p/31p complexes polymerizes on the cytosolic side of the membrane to form a convex

neg: Ferritin is similar to the mineral ferrihydrite. Each ferritin complex can store about 4500 iron (Fe) ions. Some ferritin complexes in vertebrates are hetero-oligomers of two highly related gene products with slightly different physiological properties. The ratio of the two homologous proteins in the complex depends on the relative expression levels of the two genes. Mitochondrial ferritin was recently identified as a protein precursor, and is classified as a metal-binding protein that is located within the mitochondria. After the protein is taken up by the mitochondria it can be processed into a mature protein and assemble to form functional ferritin shells.

neg: FMN-binding fluorescent protein They noncovalently bind Flavin mononucleotide (FMN) as coenzyme. Due to the bound FMN LOV-domains exhibit an intrinsic fluorescence, which is however very weak. Upon illumination with blue light, LOV-domains undergo a photocyle, during which a covalent bond is formed between a conserved cysteine-residue and the FMN. This causes a conformational change in the protein that is necessary for signal propagation and also leads to the loss of fluorescence. The covalent bond is energetically unfavorable and is cleaved with a protein specific time constant ranging from seconds to hours. In order to make better use of the fluorescence properties of these

neg: Isopeptag its binding partner can be used to permanently link proteins together in the complex environment of a bacterial cell, to target proteins of interest for cellular imaging, and to develop new protein structures. Isopeptag Isopeptag is a 16 amino acid peptide tag (TDKDMTITFTNKKDAE) that can be genetically linked to proteins without interfering with protein folding. What makes the isopeptag different from other peptide tags is that it can bind its binding protein through a permanent and irreversible covalent bond. Other peptide tags generally bind their targets through weak non-covalent interactions, thus limiting their use in applications where molecules experience extreme

neg: CRD-BP CRD-BP The mouse Coding Region Determinant-Binding Protein (CRD-BP) is an RNA-binding protein. CRD-BP belongs to a family of RNA binding proteins that show close a relation to the chicken β-actin zipcode-binding protein ZBP1 and the human forms of the protein IMP-1, IMP-2 and IMP-3. Because of their close relationship, CRD-BP and its orthologs are thought to share the same biochemical properties. Upon binding to its transcripts, CRD-BP plays a role in translation by stabilizing and localizing the transcripts in the cell. Normal expression of CRD-BP has been seen in the early development of the embryo. Conversely, CRD-BP expression in adult

neg: DNA binding site site-specific recombinases (see site-specific recombination) and methyltransferases. DNA binding sites can be thus defined as short DNA sequences (typically 4 to 30 base pairs long, but up to 200 bp for recombination sites) that are specifically bound by one or more DNA-binding proteins or protein complexes. It has been reported that some binding sites have potential to undergo fast evolutionary change. DNA binding sites can be categorized according to their biological function. Thus, we can distinguish between transcription factor-binding sites, restriction sites and recombination sites. Some authors have proposed that binding sites could also be classified according to their most

neg: Förster resonance energy transfer interaction of the two molecules, the acceptor emission will increase because of the intermolecular FRET from the donor to the acceptor. For monitoring protein conformational changes, the target protein is labeled with a donor and an acceptor at two loci. When a twist or bend of the protein brings the change in the distance or relative orientation of the donor and acceptor, FRET change is observed. If a molecular interaction or a protein conformational change is dependent on ligand binding, this FRET technique is applicable to fluorescent indicators for the ligand detection. FRET efficiencies can also be inferred from the

neg: Structural alignment structural alignment methods. These provide comparison of pre-selected parts of proteins (e.g. binding sites, user-defined structural motifs) against binding sites or whole-protein structural databases. The MultiBind and MAPPIS servers allow the identification of common spatial arrangements of physicochemical properties such as H-bond donor, acceptor, aliphatic, aromatic or hydrophobic in a set of user provided protein binding sites defined by interactions with small molecules (MultiBind) or in a set of user-provided protein–protein interfaces (MAPPIS). Others provide comparison of entire protein structures against a number of user submitted structures or against a large database of protein structures in reasonable time (ProBiS). Unlike

neg: RNA thermometer thermometers have been designed with just a simple single-hairpin structure. However, the secondary structure of such short RNA thermometers can be sensitive to mutation, as a single base change can render the hairpin inactive "in vivo". RNA thermometers are found in the 5' UTR of messenger RNA, upstream of a protein-coding gene. Here they are able to occlude the ribosome binding site (RBS) and prevent translation of the mRNA into protein. As temperature increases, the hairpin structure can 'melt' and expose the RBS or Shine-Dalgarno sequence to permit binding of the small ribosomal subunit (30S), which then assembles other translation

neg: Ligand (biochemistry) with regards to what sort of binding has been observed. The etymology stems from "ligare", which means 'to bind'. Ligand binding to a receptor protein alters the conformation by affecting the three-dimensional shape orientation. The conformation of a receptor protein composes the functional state. Ligands include substrates, inhibitors, activators, and neurotransmitters. The rate of binding is called affinity, and this measurement typifies a tendency or strength of the effect. Binding affinity is actualized not only by host-guest interactions, but also by solvent effects that can play a dominant, steric role which drives non-covalent binding in solution. The solvent provides a

neg: Isopeptag Isopeptag Isopeptag is a 16 amino acid peptide tag (TDKDMTITFTNKKDAE) that can be genetically linked to proteins without interfering with protein folding. What makes the isopeptag different from other peptide tags is that it can bind its binding protein through a permanent and irreversible covalent bond. Other peptide tags generally bind their targets through weak non-covalent interactions, thus limiting their use in applications where molecules experience extreme forces. The isopeptags covalent binding to its target overcomes these barriers and allows target proteins to be studied in harsher molecular environments. The isopeptag was developed by dissecting the pilin protein (Spy0128) from

neg: Myristoylation the protein, these processes can be highly coordinated and closely controlled. This defines myristoylation as a “molecular switch”. Both a hydrophobic myristoyl group and a “basic patch”, or highly positive regions on the protein characterize myristoyl-electrostatic switches. The basic patch allows for favorable electrostatic interactions to occur between the negatively charged phospholipid-heads of the membrane and the positive surface of the associating protein. This allows tighter association and directed localization of proteins. Myristoyl-conformational switches can come in several forms. Ligand binding to a myristoylated protein with its myristoyl group sequestered can result in a conformational change in the protein resulting

neg: SLC25A1 tricarboxylate transport protein. The tricarboxylate transport protein exists in two states: a cytoplasmic state where it accepts malate from the cytoplasm and a matrix state where it accepts citrate from the mitochondrial matrix. A single binding site is present near the center of the cavity of the tricarboxylate transport protein, which can be either exposed to the cytosol or the mitochondrial matrix depending on the state. A substrate induced conformational change occurs when citrate enters from the matrix side and binds to the central cavity of the tricarboxylate transport protein. This conformational change opens a gate on the cytosolic side

neg: Affibody molecule capable of specific binding to different target proteins with almost good affinity, while retaining the favorable folding and stability properties, and ease of bacterial expression of the parent molecule. The original Affibody protein scaffold was designed based on the Z domain (the immunoglobulin G binding domain) of protein A. These molecules are the newly developed class of scaffold proteins derived from the randomization of 13 amino acids of located in two alpha-helices involved in the binding activity of the parent protein domain. Lately, amino acids outside of the binding surface have been substituted in the scaffold to create a surface

neg: Protein up only 3% and 20%, respectively. The set of proteins expressed in a particular cell or cell type is known as its proteome. The chief characteristic of proteins that also allows their diverse set of functions is their ability to bind other molecules specifically and tightly. The region of the protein responsible for binding another molecule is known as the binding site and is often a depression or "pocket" on the molecular surface. This binding ability is mediated by the tertiary structure of the protein, which defines the binding site pocket, and by the chemical properties of the surrounding amino

neg: Clearance (pharmacology) of these equations can be found in e.g Rang and Dale's Pharmacology For substances that exhibit substantial plasma protein binding, clearance is generally dependent on the total concentration (free + protein-bound) and not the free concentration. Most plasma substances have primarily their free concentrations regulated, which thus remains the same, so extensive protein binding increases total plasma concentration (free + protein-bound). This decreases clearance compared to what would have been the case if the substance did not bind to protein. However, the mass removal rate is the same, because it depends only on concentration of free substance, and is independent

neg: Corticotropin-releasing hormone receptor 1 be biologically significant. CRF is 70% homologous with the second human CRF receptor family, CRF; the greatest divergence between the two lies at the N-terminus of the protein. CRF is activated through the binding of CRF or a CRF-agonist. The ligand binding and subsequent receptor conformational change depends on three different sites in the second and third extracellular domains of CRF. In the majority of tissues, CRF is coupled to a stimulatory G-protein that activates the adenylyl cyclase signaling pathway, and ligand-binding triggers an increase in cAMP levels. However, the signal can be transmitted along multiple signal transduction cascades, according

neg: Plasmodium falciparum erythrocyte membrane protein 1 had unusually large-sized cell membrane proteins, and these proteins had antibody-binding (antigenic) properties. An elusive protein, its chemical structure and molecular properties were revealed only after a decade, in 1995. It is now established that there is not one but a large family of PfEMP1 proteins, genetically regulated (encoded) by a group of about 60 genes called "var". Each "P. falciparum" is able to switch on and off specific "var" genes to produce a functionally different protein, rendering evasion from the host's immune system. RBCs carrying PfEMP1 on their surface stick to endothelial cells, which facilitates further binding with uninfected

neg: Aldehyde tag explored the strategy of producing protein-protein conjugates with the help of the aldehyde tag. Their aim was to connect full length human IgG (hIgG) to the human growth hormone (hGH). These protein-protein conjugates can be superior to monomeric proteins in terms of serum half life in protein therapeutics and, additionally, have appealing dual binding properties. In order to achieve protein fusion, the five-residue aldehyde tag (CxPxR) was incooperated into hIgG and hGH. In hIgG, the aldehyde tag was introduced at the C termini of the two heavy chains, resulting in two possible conjugation sites. FGE then oxidizes the cysteine residue

neg: Enzyme catalysis; instead, the enzyme contains sites to bind and orient catalytic cofactors. Enzyme structures may also contain allosteric sites where the binding of a small molecule causes a conformational change that increases or decreases activity. A small number of RNA-based biological catalysts called ribozymes exist, which again can act alone or in complex with proteins. The most common of these is the ribosome which is a complex of protein and catalytic RNA components. Enzymes must bind their substrates before they can catalyse any chemical reaction. Enzymes are usually very specific as to what substrates they bind and then the chemical

neg: Genetics amino acid sequences, some changes can dramatically change the properties of a protein by destabilizing the structure or changing the surface of the protein in a way that changes its interaction with other proteins and molecules. For example, sickle-cell anemia is a human genetic disease that results from a single base difference within the coding region for the β-globin section of hemoglobin, causing a single amino acid change that changes hemoglobin's physical properties. Sickle-cell versions of hemoglobin stick to themselves, stacking to form fibers that distort the shape of red blood cells carrying the protein. These sickle-shaped cells no longer

neg: Aconitase in both 5' and 3' regions, but only to RNA in the apo form, without the Fe-S cluster. Expression of IRE-BP in cultured cells has revealed that the protein functions either as an active aconitase, when cells are iron-replete, or as an active RNA-binding protein, when cells are iron-depleted. Mutant IRE-BPs, in which any or all of the three Cys residues involved in Fe-S formation are replaced by serine, have no aconitase activity, but retain RNA-binding properties. Aconitase is inhibited by fluoroacetate, therefore fluoroacetate is poisonous. Fluoroacetate, in the citric acid cycle,can innocently enter as fluorocitrate. However, aconitase cannot bind

neg: Protein function prediction beyond spatial proximity). To deal with the situation that many protein sequences have no solved structures, some function prediction servers such as RaptorX are also developed that can first predict the 3D model of a sequence and then use structure-based method to predict functions based upon the predicted 3D model. In many cases instead of the whole protein structure, the 3D structure of a particular motif representing an active site or binding site can be targeted. The Structurally Aligned Local Sites of Activity (SALSA) method, developed by Mary Jo Ondrechen and students, utilizes computed chemical properties of the individual amino

neg: Point mutation properties of the amino acid remain the same (e.g., hydrophobic, hydrophilic, etc.). At times, a change to one amino acid in the protein is not detrimental to the organism as a whole. Most proteins can withstand one or two point mutations before their function changes. Non-conservative mutations result in an amino acid change that has different properties than the wild type. The protein may lose its function, which can result in a disease in the organism. For example, sickle-cell disease is caused by a single point mutation (a missense mutation) in the beta-hemoglobin gene that converts a GAG codon into

neg: Point mutation to a ribosomal binding site, it can be used to initiate translation. The likely effect is additional amino acids added to the amino terminus of the original protein. Frame-shift mutations are also possible in start-gain mutations, but typically do not affect translation of the original protein. Start-loss is a point mutation in a transcript's AUG start codon, resulting in the reduction or elimination of protein production. Missense mutations code for a different amino acid. A missense mutation changes a codon so that a different protein is created, a non-synonymous change. Conservative mutations result in an amino acid change. However, the

neg: ERBB3 dimerization loop required for dimer formation. The cytoplasmic domain contains a juxtamembrane segment, a kinase domain, and a C-terminal domain. Unliganded receptor adopts a conformation that inhibits dimerization. Binding of neuregulin to the ligand binding subdomains (I and III) induces a conformational change in ErbB3 that causes the protrusion of the dimerization loop in subdomain II, activating the protein for dimerization. ErbB3 has been shown to bind the ligands heregulin and NRG-2. Ligand binding causes a change in conformation that allows for dimerization, phosphorylation, and activation of signal transduction. ErbB3 can heterodimerize with any of the other three ErbB family

neg: Protein isoform region of DNA near a gene that serves as an initial binding site—resulting in slightly modified transcripts and protein isoforms. Generally, one protein isoform is labeled as the canonical sequence based on criteria such as its prevalence and similarity to orthologous—or functionally analogous—sequences in other species. Isoforms are assumed to have similar functional properties, as most have similar sequences, and share some to most exons with the canonical sequence. However, some isoforms show much greater divergence (for example, through trans-splicing), and can share few to no exons with the canonical sequence. In addition, they can have different biological effects—for example,

neg: IQGAP1 binding does not by itself construct an interesting story. Far more important is the outcome of the binding event. Does binding change the target protein’s localization? Does it activate the target, or in some way change the target (or effector molecule’s) conformation? As a scaffolding protein, IQGAP1 binds and regulates many targets—its role is to integrate and mediate signaling from diverse pathways and insulate key pathway members from crosstalk. Scaffolds organize signaling pathways—help regulate how various extracellular signals can be transduced by the same canonical pathway members into various cellular outputs. Generally, scaffolds regulate output, localization, and selectivity of pathways.

neg: Poly(A)-binding protein Mutations of poly(A)-binding protein nuclear 1 (PABPN1) can cause OPMD (oculopharyngeal muscular dystrophy). What makes the PABPN1 protein so different than all other genes with disease causing expanded polyalanine tracts, is that it is not a transcription factor. Instead, PABPN1 is involved in the polyadenylation of mRNA precursors. Mutations in PABPN1 that cause this disorder, result when the protein has an extended polyalanine tract (12-17 alanines long vs. the expected amount of 10). The extra alanines cause PABPN1 to aggregate and form clumps within muscles because they are not able to be broken down. These clumps are believed to disrupt

neg: Lactose permease periplasm. On binding, a large conformational change takes place which makes the sugar binding site accessible from the cytoplasm. Mechanism: hydronium ions from the outside of the cell binds to a carboxyl group on the enzyme that allows it to undergo a conformational change. This form of lactose permease can bind lactose from outside the cell. The enzyme then everts and lactose is transported inward. The X-ray crystal structure was first solved in 2003 by J. Abramson "et al." Lactose permease Lactose permease is a membrane protein which is a member of the major facilitator superfamily. Lactose permease can be

neg: Binding site protein's affinity for substrate is negative modulation. At the active site, a substrate binds to an enzyme to induce a chemical reaction. Substrates, transition states, and products can bind to the active site, as well as any competitive inhibitors. For example, in the context of protein function, the binding of calcium to troponin in muscle cells can induce a conformational change in troponin. This allows for tropomyosin to expose the actin-myosin binding site to which the myosin head binds to form a cross-bridge and induce a muscle contraction. In the context of the blood, an example of competitive binding is

neg: Protein engineering design or semi-ration design, the libraries of mutant proteins must be screened to determine which mutants show enhanced properties. Phage display methods are one option for screening proteins. This method involves the fusion of genes encoding the variant polypeptides with phage coat protein genes. Protein variants expressed on phage surfaces are selected by binding with immobilized targets in vitro. Phages with selected protein variants are then amplified in bacteria, followed by the identification of positive clones by enzyme linked immunosorbent assay. These selected phages are then subjected to DNA sequencing. Cell surface display systems can also be utilized to screen

neg: RNA-binding protein database number of experiments will lead you to the research articles which are related to the protein. Also, in this database you can search experiments which are related to specific RNA binding sequence. Furthermore, this site can help you predict the binding sites for your sequence. RNA-binding protein database The RNA-binding Proteins Database (RBPDB) is a biological database of RNA-binding protein specificities that includes experimental observations of RNA-binding sites. The experimental results included are both in vitro and in vivo from primary literature. It includes four metazoan species, which are "Homo sapiens", "Mus musculus", "Drosophila melanogaster", and "Caenorhabditis elegans". RNA-binding domains

neg: Perilipin-3 increase the affinity of this protein for its cargo. The mannose-6-phosphate receptor-binding properties of TIP47 are disputed, despite the designation of M6PRBP1 as TIP47's gene symbol. TIP47 protein is most commonly described in the scientific literature as a coat protein for lipid droplets. TIP47 belongs to the peripilin protein family and shares significant homology with the other genes of this family, including perilipin and adipophilin. M6PRBP1 has been shown to interact with both Mannose 6-phosphate receptors. Perilipin-3 Mannose-6-phosphate receptor binding protein 1 (M6PRBP1) is a protein which in humans is encoded by the "M6PRBP1" gene. Its gene product, as well

neg: Squamosa promoter binding protein Squamosa promoter binding protein The SQUAMOSA promoter binding protein-like (SBP or SPL) family of transcription factors are defined by a plant-specific DNA-binding domain. The founding member of the family was identified based on its specific "in vitro" binding to the promoter of the snapdragon SQUAMOSA gene. SBP proteins are thought to be transcriptional activators. SPB proteins have roles in leaf development, vegetative phase change, flower and fruit development, plant architecture, sporogenesis, Gibberelic acid signaling and toxin response. The domain contains 10 conserved cysteine and histidine residues that probably are zinc ligands. The SBP domain is a highly conserved DNA-binding domain.

neg: Calcium-binding protein firing state of neurons, such as the voltage-dependent potassium channel. Compartmentalization of calcium binding proteins such as calretinin and calbindin-28 kDa has been noted within cells, suggesting that these proteins perform distinct functions in localized calcium signaling. It also indicates that in addition to freely diffusing through the cytoplasm to attain a homogeneous distribution, calcium binding proteins can bind to cellular structures through interactions that are likely important for their functions. Calcium Binding Protein Modulator Agonists Calcium Binding Protein Modulator Antagonists Calcium Binding Protein Modulator Inhibitors Additional Calcium Binding Protein Modulators Calcium-binding protein Calcium-binding proteins are proteins that participate in

neg: Conserved sequence may be conserved to different extents, as the degeneracy of the genetic code means that synonymous mutations in a coding sequence do not affect the amino acid sequence of its protein product. Amino acid sequences can be conserved to maintain the structure or function of a protein or domain. Conserved proteins undergo fewer amino acid replacements, or are more likely to substitute amino acids with similar biochemical properties. Within a sequence, amino acids that are important for folding, structural stability, or that form a binding site may be more highly conserved. The nucleic acid sequence of a protein coding gene

neg: Hyalin Hyalin Hyalin is a protein released from the cortical granules of a fertilized animal egg. The released hyalin modifies the extracellular matrix of the fertilized egg to block other sperm from binding to the egg, and is known as the slow-block to polyspermy. All animals have this slow-block mechanism. Hyalin is a large, acidic protein which aids in embryonic development. The protein has strong adhesive properties which can help with cell differentiation and as a polyspermy prevention component. It forms the hyaline layer which covers the surface of the egg after insemination. Its physical structure has a major and minor

neg: Hyalin Hyalin Hyalin is a protein released from the cortical granules of a fertilized animal egg. The released hyalin modifies the extracellular matrix of the fertilized egg to block other sperm from binding to the egg, and is known as the slow-block to polyspermy. All animals have this slow-block mechanism. Hyalin is a large, acidic protein which aids in embryonic development. The protein has strong adhesive properties which can help with cell differentiation and as a polyspermy prevention component. It forms the hyaline layer which covers the surface of the egg after insemination. Its physical structure has a major and minor

neg: Viral protein viral nonstructural proteins such as NS5A, NS5B, and NS3, are also recruited to the complex, and NS4B interacts with them and binds to viral RNA. The immune response of a host to an infected cell can be adjusted through the immunomodulatory properties of viral nonstructural proteins. Viral nonstructural protein NS1 in the West Nile virus prevents complement activation through its binding to a complement control protein, factor H. As a result, complement recognition of infected cells is reduced, and infected cells remain unharmed by the host's immune system. Viral regulatory and accessory proteins have many functions. These viral proteins control

neg: Binding properties pattern loops can be eliminated by blocking the signal, or comparing the assigned value with the property value before assignment, or eliminating unnecessary assignments. Binding properties of different types can be achieved through Type Conversions. Binding properties with transformations can be achieved through reducing the transformation function to the problem of binding properties, and the function can be imaginary consider as Type Conversions. Properties are being kept synchronized automatically. Between library calls they always have the values expressed by the EqualityConstraints. Property changes watching mechanism acquires some resources. Code sketch for one-way binding may look like as follows: Two-way binding can

neg: Avidin study disagreed with prior assumptions "that the binding site of avidin is destroyed on heat denaturation". The biotin-binding properties of avidin were exploited during the development of idrabiotaparinux, a long-acting low molecular weight heparin used in the treatment of venous thrombosis. Due to the long-acting nature of idraparinux, concerns were made about the clinical management of bleeding complications. By adding a biotin moiety to the idraparinux molecule, idrabiotaparinux was formed; its anticoagulant activity in the setting of a bleeding event can be reversed through an intravenous infusion of avidin. Avidin Avidin is a tetrameric biotin-binding protein produced in the oviducts

neg: C10orf35 throughout the brain. The c10orf35 protein has been experimentally shown by Affinity Capture-MS to interact with 7 other proteins as shown below. C10orf35 Chromosome 10 open reading frame 35 (c10orf35) is a gene that in humans, encodes for a protein-binding, transmembrane protein. The protein contains the domain of unknown function 4605 (DUF4605) which belongs to the protein family pfam15378. This gene is located at locus 10q22.1. The physical properties of the c10orf35 protein were analyzed, and the molecular weight was predicted to be 13.2 kdal, and the isoelectric point was predicted to be 11.5. The properties of DUF4605 were also

neg: RHOT1 The EF-hand motifs serve as binding sites for the adaptor protein Milton and the kinesin heavy chain. These domains can also bind calcium ions, and the binding results in a conformational change that dissociates the mitochondrial surface from kinesin. RHOT1 is a member of the Rho GTPase family and one of two isoforms of the protein Miro: RHOT1 (Miro1) and RHOT2 (Miro2). Compared to the rest of the Rho GTPase family, the Miro isoforms are considered atypical due to their different regulation. Moreover, the Miro isoforms are only expressed in the mitochondria. Miro associates with Milton (TRAK1/2) and the motor

neg: Cofactor (biochemistry) enzyme can "grasp" the coenzyme to switch it between different catalytic centers. Cofactors can be divided into two major groups: organic Cofactors, such as flavin or heme, and inorganic cofactors, such as the metal ions Mg, Cu, Mn, or iron-sulfur clusters. Organic cofactors are sometimes further divided into "coenzymes" and "prosthetic groups". The term coenzyme refers specifically to enzymes and, as such, to the functional properties of a protein. On the other hand, "prosthetic group" emphasizes the nature of the binding of a cofactor to a protein (tight or covalent) and, thus, refers to a structural property. Different sources give

neg: Emetine be administered in a hospital so that adverse events can be addressed. Dehydroemetine is a synthetically produced antiprotozoal agent similar to emetine in its anti-amoebic properties and structure (they differ only in a double bond next to the ethyl group), but it produces fewer side effects. Cephaeline is a desmethyl analog of emetine also found in ipecac root. Emetine dihydrochloro hydrate is used in the laboratory to block protein synthesis in eukaryotic cells. It does this by binding to the 40S subunit of the ribosome. This can thus be used in the study of protein degradation in cells. Mutants resistant

neg: Squamosa promoter binding protein It is approximately 80 amino acids in length and contains a zinc finger motif with two zinc-binding sites: Cys-Cys-His-Cys and Cys-Cys-Cys-His. It has a three-stranded antiparallel beta-sheet. Squamosa promoter binding protein The SQUAMOSA promoter binding protein-like (SBP or SPL) family of transcription factors are defined by a plant-specific DNA-binding domain. The founding member of the family was identified based on its specific "in vitro" binding to the promoter of the snapdragon SQUAMOSA gene. SBP proteins are thought to be transcriptional activators. SPB proteins have roles in leaf development, vegetative phase change, flower and fruit development, plant architecture, sporogenesis, Gibberelic acid

neg: Eos (protein) spectroscopic properties, therefore, it is likely that the structural modifications which arise from separation of interfaces have little to no effect on the structure of the fluorophore-binding site. Many different fusion proteins have been created using EosFP and its engineered variants. These fusion proteins allow for the tracking of proteins within living cells while retaining complex biological functions like protein-protein interactions and protein-DNA interactions. Eos fusion constructs include those with recombination signal-binding protein (RBP) and cytokeratin. Studies have shown that it is favourable to attach the protein of interest to the N-terminal side of the EosFP label. These fusion constructs

neg: (+)-CPCA by the lack of knowledge about the 3D structure of these targets. In cases where the 3D structure of the binding site in a target protein is not well defined, as is the case for the monoamine transporter proteins, one can perform ligand-based design to develop a pharmacophore. That is, by studying the conformational properties of a series of pharmacologically similar compounds, one can form hypotheses regarding the pharmacophore. Most of the potent tropane-based inhibitors, inc. coca, are believed to have at least 3 major interactions with the transporter binding site: one ionic or H-bonding interaction at the basic nitrogen,

neg: S100A1 (residues 27–29 and 68–70). Upon binding calcium, helix 3 of S100A1 re-orients from being relatively antiparallel to helix 4 to being roughly perpendicular. This conformational change is different from most EF hands, in that the entering helix, and not the exiting helix, moves. This conformational change exposes a large hydrophobic pocket between helix 3, 4, and the hinge region of S100A1 that is involved in virtually all calcium-dependent target protein interactions. These biophysical properties seem to be well conserved across the S100 family of proteins. Helix 3, 4, and the hinge region are the most divergent areas between individual S100

neg: DLG4 three times over in PSD-95. PDZ domains are short peptide binding sequences commonly found at the C-terminus of interacting proteins. The three copies within the gene have different binding partners, due to amino acid substitutions within the PSD-95 protein and its ligands. The SH3 domain is again a protein-protein interaction domain. Its family generally bind to PXXP sites, but in MAGUKs it is known to bind to other sites as well. One of the most well known features is that it can form an intramolecular bond with the GUK domain, creating what is known as a GUK-SH3 'closed' state. The

neg: Pro-hevein Pro-hevein Pro-hevein (Alternative name: Major hevein, gene name: HEV1) is a wound-induced and a lectin-like protein from "Hevea brasiliensis" (rubber tree) where it is involved in the coagulation of latex. The 187 amino-acid propeptide pro-hevein is cleaved in two fragments: a N-terminal 43 amino-acid Hevein bearing a chitin-binding type-1 domain (also known as CBM18 carbohydrate-binding module) that binds to chitin and a 138 amino-acid Win-like protein bearing a Barwin domain. It has antifungal properties. Hevein is the main IgE-binding epitope of the major latex allergen prohevein as are hevein-like protein domains in fruit class I chitinases. Therefore it is a

neg: Streptogramin A to the chain, followed by hydroxylation and dehydration to form dehydroproline, which is thought to occur through a reverse Michael-type reaction. By themselves, streptogramins A and B are bacteriostatic. However, when used in conjunction with one another, the streptogramins can inhibit bacterial growth and are bactericidal. Streptogramin A first binds to the peptidyl transferase domain of the 50s ribosomal subunit, preventing the early events of elongation. The binding of streptogramin A causes a conformational change that increases the ribosomal binding activity of streptogramin B 100-fold. Upon binding the ribosome (which streptogramin B can accomplish at any stage of protein synthesis),

neg: C10orf35 C10orf35 Chromosome 10 open reading frame 35 (c10orf35) is a gene that in humans, encodes for a protein-binding, transmembrane protein. The protein contains the domain of unknown function 4605 (DUF4605) which belongs to the protein family pfam15378. This gene is located at locus 10q22.1. The physical properties of the c10orf35 protein were analyzed, and the molecular weight was predicted to be 13.2 kdal, and the isoelectric point was predicted to be 11.5. The properties of DUF4605 were also analyzed, and the molecular weight was predicted to be 6.0 kdal. The isoelectric point was predicted to be 6.9, which is significantly

neg: Synthetic biology of binding oxygen with similar properties as hemoglobin, yet did not bind carbon monoxide. A similar protein structure was generated to support a variety of oxidoreductase activities. Another group generated a family of G-protein coupled receptors that could be activated by the inert small molecule clozapine-N-oxide but insensitive to the native ligand, acetylcholine.Novel functionalities or protein specificity can also be engineered using computational approaches. One study was able to use two different computational methods – a bioinformatics and molecular modeling method to mine sequence databases, and a computational enzyme design method to reprogram enzyme specificity. Both methods resulted in designed

neg: Intrinsically disordered proteins that protein dynamics may be highly relevant for such systems. Despite their lack of stable structure, IDPs are a very large and functionally important class of proteins. In some cases, IDPs can adopt a fixed three-dimensional structure after binding to other macromolecules. Overall, IDPs are different from structured proteins in many ways and tend to have distinct properties in terms of function, structure, sequence, interactions, evolution and regulation. In the 1930s -1950s, the first protein structures were solved by protein crystallography. These early structures suggested that a fixed three-dimensional structure might be generally required to mediate biological functions of proteins.

neg: Agglutinin Agglutinin An agglutinin is a substance in the blood that causes particles to coagulate and aggregate; that is, to change from fluid-like state to a thickened-mass (solid) state. Agglutinins can be antibodies that cause antigens to aggregate by binding to the antigen-binding sites of antibodies. Agglutinins can also be any substance other than antibodies, such as sugar-binding protein lectins. When an agglutinin is added to a uniform suspension of particles, such as bacteria or blood, in a test tube (in vitro), agglutinin binds to the agglutinin-specific structure on the particle causing the particles to aggregate and fall to the bottom,

neg: Regulator of G protein signaling Plants have RGS proteins but do not have canonical G protein-coupled receptors. Thus G proteins and GTPase accelerating proteins appear to have evolved before any known G protein activator. RGS domains can be found within the same protein in combination with a variety of other domains, including: DEP for membrane targeting (), PDZ for binding to GPCRs (), PTB for phosphotyrosine-binding (), RBD for Ras-binding (), GoLoco for guanine nucleotide inhibitor activity (), PX for phosphoinositide-binding (), PXA that is associated with PX (), PH for phosphatidylinositol-binding (), and GGL (G protein gamma subunit-like) for binding G protein beta subunits