query: where does the energy to form a peptide bond come from

pos: Peptide bond is a dehydration synthesis reaction. The formation of the peptide bond consumes energy, which, in organisms, is derived from ATP. Peptides and proteins are chains of amino acids held together by peptide bonds (and sometimes by a few isopeptide bonds). Organisms use enzymes to produce nonribosomal peptides, and ribosomes to produce proteins via reactions that differ in details from dehydration synthesis. Some peptides, like alpha-amanitin, are called ribosomal peptides as they are made by ribosomes, but many are nonribosomal peptides as they are synthesized by specialized enzymes rather than ribosomes. For example, the tripeptide glutathione is synthesized in two steps

pos: Amino acid and carboxylic acid groups of amino acids can react to form amide bonds, one amino acid molecule can react with another and become joined through an amide linkage. This polymerization of amino acids is what creates proteins. This condensation reaction yields the newly formed peptide bond and a molecule of water. In cells, this reaction does not occur directly; instead, the amino acid is first activated by attachment to a transfer RNA molecule through an ester bond. This aminoacyl-tRNA is produced in an ATP-dependent reaction carried out by an aminoacyl tRNA synthetase. This aminoacyl-tRNA is then a substrate for the

pos: Amino acid activation a considerable part of the energy from the activation reaction. This stored energy provides the majority of the energy needed for peptide bond formation during translation. Each of the 20 amino acids are recognized by its specific aminoacyl-tRNA synthetase. The synthetases are usually composed of one to four protein subunits. The enzymes vary considerably in structure although they all perform the same type of reaction by binding ATP, one specific amino acid and its corresponding tRNA. The specificity of the amino acid activation is as critical for the translational accuracy as the correct matching of the codon with the anticodon.

pos: Bioenergetics the stronger bonds formed when ATP is hydrolyzed (broken down by water) to adenosine diphosphate and inorganic phosphate. Here it is the thermodynamically favorable free energy of hydrolysis that results in energy release; the phosphoanhydride bond between the terminal phosphate group and the rest of the ATP molecule does not itself contain this energy. An organism's stockpile of ATP is used as a battery to store energy in cells. Utilization of chemical energy from such molecular bond rearrangement powers biological processes in every biological organism. Living organisms obtain energy from organic and inorganic materials; i.e. ATP can be synthesized from

neg: Peptide bond (antiperiplanar conformation). Amide groups can isomerize about the C'-N bond between the cis and trans forms, albeit slowly (formula_720 seconds at room temperature). The transition states formula_8 requires that the partial double bond be broken, so that the activation energy is roughly 80 kilojoule/mol (20 kcal/mol). However, the activation energy can be lowered (and the isomerization catalyzed) by changes that favor the single-bonded form, such as placing the peptide group in a hydrophobic environment or donating a hydrogen bond to the nitrogen atom of an X-Pro peptide group. Both of these mechanisms for lowering the activation energy have been observed

neg: Prolyl isomerase include cyclophilin, FKBPs, and parvulin, although larger proteins can also contain prolyl isomerase domains. Proline is unique among the natural amino acids in having a relatively small difference in free energy between the "cis" configuration of its peptide bond and the more common "trans" form. The activation energy required to catalyse the isomerisation between "cis" and "trans" is relatively high: ~20kcal/mol (c.f. ~0kcal/mol for regular peptide bonds). Unlike regular peptide bonds, the X-prolyl peptide bond will not adopt the intended conformation spontaneously, thus, the process of "cis-trans" isomerization can be the rate-limiting step in the process of protein folding. Prolyl

neg: Disulfide simply as "C26–C84" where the disulfide bond is understood and does not need to be mentioned. The prototype of a protein disulfide bond is the two-amino-acid peptide cystine, which is composed of two cysteine amino acids joined by a disulfide bond (shown in Figure 3 in its unionized form). The structure of a disulfide bond can be described by its "χ" dihedral angle between the C−S−S−C atoms, which is usually close to ±90°. The disulfide bond stabilizes the folded form of a protein in several ways: A "disulfide species" is a particular pairing of cysteines in a disulfide-bonded protein and

neg: Peptide bond from free amino acids, by two enzymes: glutamate–cysteine ligase (forms an isopeptide bond, which is not a peptide bond) and glutathione synthetase (forms a peptide bond). A peptide bond can be broken by hydrolysis (the addition of water). In the presence of water they will break down and release 8–16 kilojoule/mol (2–4 kcal/mol) of Gibbs energy. This process is extremely slow, with the half life at 25 °C of between 350 and 600 years per bond. In living organisms, the process is normally catalyzed by enzymes known as peptidases or proteases, although there are reports of peptide bond hydrolysis caused

neg: Peptide bond Peptide bond A peptide bond is an amide type of covalent chemical bond linking two consecutive alpha-amino acids from C1 (carbon number one) of one alpha-amino acid and N2 (nitrogen number two) of another along a peptide or protein chain. It can also be called an eupeptide bond to separate it from an isopeptide bond, a different type of amide bond between two amino acids. When two amino acids form a "dipeptide" through a "peptide bond" it is type of condensation reaction. In this kind of condensation, two amino acids approach each other, with the non-side chain (C1) carboxylic acid

neg: Peptide plane flipping a low-energy pathway between beta sheet and the so-called alpha sheet conformation is suggested to facilitate the early stages of amyloidogenesis. Peptide plane flipping may also be significant in the early stages of protein folding. In protein structures determined by X-ray crystallography, poor peptide-plane geometry has been described as a common problem; many structures in the Protein Data Bank can be identified as needing correction by peptide-plane flips or cis-trans peptide bond isomerization. Conformational diversity in the form of plane flips can sometimes be detected in electron density maps. Peptide plane flipping Peptide plane flipping is a type of conformational

neg: Asparagine peptide lyase which cyclizes to form a succinimide, cleaving its own peptide bond and releasing the intein from the extein. Finally, in the extein the ester or thioester bond is rearranged to form a normal peptide bond. There are three known families of intein-containing proteins (N9, N10 and N11) all of them included in the PD clan, which contains proteolytic enzymes of different catalytic types. The tertiary structure has been solved for the intein V type proton ATPase catalytic subunit ("Saccharomyces cerevisiae"), a member of family N9 and for several inteins from family N10. Asparagine peptide lyase Asparagine peptide lyase are one

neg: Endothermic process energy in the form of heat. Thus in each term (endothermic & exothermic) the prefix refers to where heat goes as the reaction occurs, though in reality it only refers to where the energy goes, without necessarily being in the form of heat. All chemical reactions involve both the breaking of existing and the making of new chemical bonds. A reaction to break a bond always requires the input of energy and so such a process is always endothermic. When atoms come together to form new chemical bonds, the electrostatic forces bringing them together leave the bond with a large

neg: Protein primary structure of the protein, inhibiting its function. The protein is activated by cleaving off the inhibitory peptide. Some proteins even have the power to cleave themselves. Typically, the hydroxyl group of a serine (rarely, threonine) or the thiol group of a cysteine residue will attack the carbonyl carbon of the preceding peptide bond, forming a tetrahedrally bonded intermediate [classified as a hydroxyoxazolidine (Ser/Thr) or hydroxythiazolidine (Cys) intermediate]. This intermediate tends to revert to the amide form, expelling the attacking group, since the amide form is usually favored by free energy, (presumably due to the strong resonance stabilization of the peptide group).

neg: Peptide bond both isomers; however, in the folded state, only a single isomer is adopted at each position (with rare exceptions). The trans form is preferred overwhelmingly in most peptide bonds (roughly 1000:1 ratio in trans:cis populations). However, X-Pro peptide groups tend to have a roughly 30:1 ratio, presumably because the symmetry between the formula_1 and formula_2 atoms of proline makes the cis and trans isomers nearly equal in energy (see figure, below).The dihedral angle associated with the peptide group (defined by the four atoms formula_3) is denoted formula_4; formula_5 for the cis isomer (synperiplanar conformation) and formula_6 for the trans isomer

neg: Protein primary structure can undergo racemization. Although it does not change the sequence, it does affect the chemical properties of the sequence. In particular, the -amino acids normally found in proteins can spontaneously isomerize at the formula_1 atom to form -amino acids, which cannot be cleaved by most proteases. Additionally, proline can form stable trans-isomers at the peptide bond. Finally, the protein can undergo a variety of posttranslational modifications, which are briefly summarized here. The N-terminal amino group of a polypeptide can be modified covalently, e.g., The C-terminal carboxylate group of a polypeptide can also be modified, e.g., Finally, the peptide side chains

neg: Immunophilins common peptide-prolyl isomerase activity. While the majority of the Peptide bonds within proteins exist in trans (planar) conformation because of the partial double-bond nature of the peptide bond, a small fraction occurs in cis. Unlike regular peptide bonds, the X-Pro peptide bond does not adopt the intended trans conformation spontaneously, thus, cis-trans isomerization can be the rate-limiting (slowest) step in the process of protein folding. Immunophilins, with their prolyl isomerase activity, thus function as protein-folding chaperones. Immunophilins In molecular biology, immunophilins are endogenous cytosolic peptidyl-prolyl isomerases (PPI) that catalyze the interconversion between the cis and trans isomers of peptide bonds

neg: P3 peptide in amyloidogenic forms while Aβ does, is that the N-terminal domain Aβ, which is present in Aβ’s sequence but not in p3's one, is known to protect the hydrophobic core of the oligomers from being dissolved by the watered medium. So, p3 peptide oligomers would likely expose hydrophobic residues to water and would be less stable. As a consequence, p3 peptide structural determinants can assemble into fibrils, but no oligomeric forms have been identified. That is why p3 peptide represents the benign form of amyloid. Energy plays a very important role in p3 peptides. While Aβ models have a strong

neg: Proline By contrast, the "cis" and "trans" isomers of the X-Pro peptide bond (where X represents any amino acid) both experience steric clashes with the neighboring substitution and have a much lower energy difference. Hence, the fraction of X-Pro peptide bonds in the "cis" isomer under unstrained conditions is significantly elevated, with "cis" fractions typically in the range of 3-10%. However, these values depend on the preceding amino acid, with Gly and aromatic residues yielding increased fractions of the "cis" isomer. "Cis" fractions up to 40% have been identified for Aromatic-Pro peptide bonds. From a kinetic standpoint, "cis"-"trans" proline isomerization is

neg: Resilin form and cannot be crystallized, which allows the peptide sequence segment to be very soft and highly flexible. Exon 3 encoded peptide takes on the unstructured form before loading, but transforms to an ordered beta-turn structure once stress is applied. Meanwhile, segment encoded by exon 2 serves as a chitin binding domain. It is proposed that as stress is applied, or there is energy input, exon 1 encoded peptide responds immediately due to its high flexibility. Once this occurs, the energy is passed onto exon 3 encoded peptide, which transforms from the unstructured form to beta-turn structure to store energy.

neg: Peptide synthesis new development for producing longer peptide chains is chemical ligation: unprotected peptide chains react chemoselectively in aqueous solution. A first kinetically controlled product rearranges to form the amide bond. The most common form of native chemical ligation uses a peptide thioester that reacts with a terminal cysteine residue. Other methods applicable for covalently linking polypeptides in aqueous solution include the use of split inteins, spontaneous isopeptide bond formation and sortase ligation. In order to optimize synthesis of long peptides, a method was developed in Medicon Valley for converting peptide sequences. The simple pre-sequence (e.g. Lysine (Lysn); Glutamic Acid (Glun); (LysGlu)n)

neg: Serpin inserting into β-sheet A, forming an extra antiparallel β-strand. This converts the serpin from a stressed state, to a lower-energy relaxed state (S to R transition). Serine and cysteine proteases catalyse peptide bond cleavage by a two-step process. Initially, the catalytic residue of the active site triad performs a nucleophilic attack on the peptide bond of the substrate. This releases the new N-terminus and forms a covalent ester-bond between the enzyme and the substrate. This covalent complex between enzyme and substrate is called an acyl-enzyme intermediate. For standard substrates, the ester bond is hydrolysed and the new C-terminus is released

neg: NR58-3.14.3 combined transformation changes the orientation of the amides in the backbone but does not change the position of the amino acid sidechains. The peptide was then cyclised by adding a cysteine to the other end (HO-CLDPKQKWIQC-NH), and oxidisation to form a disulfide bond to give NR58,3-14-3. Like 'Peptide 3', NR58,3-14-3 is a broad-spectrum chemokine inhibitor. It however significantly more active than its earlier analogues migration inhibition potencies of 2.5 to 25 nM vs. CCL2, CCL3, CCL5 and CXCL12 with THP-1 monocytes, and vs. CXCL8 with neutrophils. In addition NR58,3-14-3 does not significantly inhibit leukocte migration due to the other non-chemokine

neg: Beta sheet in the 1930s. He proposed the idea of hydrogen bonding between the peptide bonds of parallel or antiparallel extended β-strands. However, Astbury did not have the necessary data on the bond geometry of the amino acids in order to build accurate models, especially since he did not then know that the peptide bond was planar. A refined version was proposed by Linus Pauling and Robert Corey in 1951. Their model incorporated the planarity of the peptide bond which they previously explained as resulting from keto-enol tautomerization. The majority of β-strands are arranged adjacent to other strands and form an extensive

neg: Davydov soliton excitation with the lattice. The quasiparticle (exciton) Hamiltonian formula_3 is: where the index formula_11 counts the peptide groups along the α-helix spine, the index formula_12 counts each α-helix spine, formula_13 J is the energy of the amide I vibration (CO stretching), formula_14 J is the dipole-dipole coupling energy between a particular amide I bond and those ahead and behind along the same spine, formula_15 J is the dipole-dipole coupling energy between a particular amide I bond and those on adjacent spines in the same unit cell of the protein α-helix, formula_16 and formula_17 are respectively the boson creation and annihilation

neg: Chemical ligation peptides is native chemical ligation. Native chemical ligation has overcome the limitations of the classical synthetic organic chemistry approach to the total synthesis of proteins, and enables the routine total or semi- synthesis of protein molecules. The original chemical ligation methods involved the formation of a non-native bond at the ligation site. Subsequently, native chemical ligation was developed. In native chemical ligation, an unprotected peptide-thioester reacts with a Cys-peptide to give a ligation product with a native amide ('peptide') bond at the ligation site. In this method, the initial thioester-linked ligation product intermediate rearranges to form an amide bond. Native

neg: Solid-phase synthesis synthesised in the opposite direction in cells. In peptide synthesis, an amino-protected amino acid is bound to a solid phase material (most commonly, low cross-linked polystyrene beads), forming a covalent bond between the carbonyl group and the resin, most often an amido or an ester bond. Then the amino group is deprotected and reacted with the carbonyl group of the next amino-protected amino acid. The solid phase now bears a dipeptide. This cycle is repeated to form the desired peptide chain. After all reactions are complete, the synthesised peptide is cleaved from the bead. The protecting groups for the amino

neg: Chymotrypsinogen any other organs. It is activated into its active form by another enzyme called trypsin. This active form is called π-chymotrypsin and is used to create α-chymotrypsin. Trypsin cleaves the peptide bond in chymotrypsinogen between arginine-15 and isoleucine-16. This creates two peptides within π-chymotrypsin molecule held together by a disulfide bond. One of the π-chymotrypsins acts on another by breaking a leucine and serine peptide bond. The activated π-chymotrypsin reacts with other π-chymotrypsin molecules to cleave out two dipeptides, which are, serine-14–arginine-15 and threonine-147–asparagine-148. This reaction yields the α-chymotrypsin. The yield of α-chymotrypsin can be affected by inhibitors such as

neg: Self-assembling peptide of the linker was a surface anchor where a chemical group on the peptide forms a covalent bond with a particular surface. FIGURE 7 : MOLECULAR PAINT/CARPET PEPTIDES. A) A MOLECULAR MODEL OF RADSC-14 PEPTIDES. THEY FORM A 5NM THICK LAYER ON SURFACES AND ALSO TRAPS SPECIFIC MOLECULES ONTO THE SURFACE.B)MOLECULAR MODELS DEMONSTRATING THE LAYERS THAT CAN BE FORMED BY MOLECULAR CARPET PEPTIDES EG6SH (LEFT) AND RADSC-14 (RIGHT). MOLECULAR ‘SWITCH’ PEPTIDES This class of peptides has the unique property of being able to change their molecular structure dramatically. This property is best illustrated using an example. The DAR16-IV peptide, has

neg: Proteolysis smaller polypeptides for laboratory analysis. For example, cyanogen bromide cleaves the peptide bond after a methionine. Similar methods may be used to specifically cleave tryptophanyl, aspartyl, cysteinyl, and asparaginyl peptide bonds. Acids such as trifluoroacetic acid and formic acid may also be used. Like other biomolecules, proteins can also be broken down by high heat alone. At 250 °C, the peptide bond may be easily hydrolyzed, with its half-life dropping to about a minute. Protein may also be broken down without hydrolysis through pyrolysis; small heterocyclic compounds may start to form upon degradation, above 500 °C, polycyclic aromatic hydrocarbon may

neg: Prolyl isomerase Prolyl isomerase Prolyl isomerase (also known as peptidylprolyl isomerase or PPIase) is an enzyme () found in both prokaryotes and eukaryotes that interconverts the "cis" and "trans" isomers of peptide bonds with the amino acid proline. Proline has an unusually conformationally restrained peptide bond due to its cyclic structure with its side chain bonded to its secondary amine nitrogen. Most amino acids have a strong energetic preference for the "trans" peptide bond conformation due to steric hindrance, but proline's unusual structure stabilizes the "cis" form so that both isomers are populated under biologically relevant conditions. Proteins with prolyl isomerase activity

neg: Oligopeptidase metabolizes an oligopeptide. The peptide has first to penetrate into a 4 Å hole on the surface of the enzyme in order to reach an 8,500Å internal cavity, where the active site is located. Even though the size of the peptide is crucial for its docking, the flexibility of both enzyme and ligand seems to play an essential role in determining whether a peptide bond will be hydrolyzed or not. This contrasts with the classical specificity of proteolytic enzymes, which derives from the chemical features of the amino acid side chains around the scissile bond. A number of enzymatic studies

neg: Dipeptide combined in the presence of a coupling agent, which facilitates formation of the amide bond: Subsequent to this coupling reaction, the amine protecting group P and the ester are converted to the free amine and carboxylic acid, respectively. For many amino acids, the ancillary functional groups are protected. The condensation of the amine and the carboxylic acid to form the peptide bond generally employs coupling agents to activate the carboxylic acid. The Bergmann azlactone peptide synthesis is a classic organic synthesis for the preparation of dipeptides. Dipeptides are produced from polypeptides by the action of the hydrolase enzyme dipeptidyl peptidase.

neg: Protein sequencing mass measured to an accuracy of 1 part in 20,000 or better. This is often sufficient to confirm the termini (thus that the protein’s measured mass matches that predicted from its sequence) and infer the presence or absence of many post-translational modifications. Proteolysis does not always yield a set of readily analyzable peptides covering the entire sequence of the POI. The fragmentation of peptides in the mass spectrometer often does not yield ions corresponding to cleavage at each peptide bond. Thus, the deduced sequence for each peptide is not necessarily complete. The standard methods of fragmentation do not distinguish between

neg: De novo peptide sequencing move along the backbone breaking at different sites which result in different fragments. The fragmentation rules are well explained by some publications. Three different types of backbone bonds can be broken to form peptide fragments: alkyl carbonyl (CHR-CO), peptide amide bond (CO-NH), and amino alkyl bond (NH-CHR). When the backbone bonds cleave, six different types of sequence ions are formed as shown in Fig. 1. The N-terminal charged fragment ions are classed as a, b or c, while the C-terminal charged ones are classed as x, y or z. The subscript n is the number of amino acid residues. The

neg: Internal Coordinate Mechanics goal was to develop algorithms for energy optimization of several biopolymers with respect to an arbitrary subset of internal coordinates such as bond lengths, bond angles torsion angles and phase angles. The efficient and general global optimization method which evolved from the original ICM method is still the central piece of the program. It is this basic algorithm which is used for peptide prediction, homology modeling and loop simulations, flexible macromolecular docking and energy refinement. However the complexity of problems related to structure prediction and analysis, as well as the desire for perfection, compactness and consistency, led to the program's

neg: Cyclotide selected residues are labeled on the structure to help orientation. The amino acid sequence (single letter amino acid representation) for this peptide is indicated on the sequence diagram to the right. One of the interesting features of cyclic peptides is that knowledge of the peptide sequence does not reveal the ancestral head and tail; knowledge of the gene sequence is required for this. In the case of kalata B1 the indicated glycine (G) and asparagine (N) amino acids are the terminal residues that are linked in a peptide bond to cyclise the peptide. Cyclotides have been reported to have a

neg: Davydov soliton operator for a quasiparticle at the peptide group. formula_18 The phonon Hamiltonian formula_4 is where formula_21 is the displacement operator from the equilibrium position of the peptide group formula_18, formula_23 is the momentum operator of the peptide group formula_18, M is the mass of each peptide group, and formula_25 N mformula_26 is an effective elasticity coefficient of the lattice (the spring constant of a hydrogen bond). Finally, the interaction Hamiltonian formula_5 is where formula_29 pN is an anharmonic parameter arising from the coupling between the quasiparticle (exciton) and the lattice displacements (phonon) and parameterizes the strength of the exciton-phonon interaction.

neg: Proline gives proline an exceptional conformational rigidity compared to other amino acids. It also affects the rate of peptide bond formation between proline and other amino acids. When proline is bound as an amide in a peptide bond, its nitrogen is not bound to any hydrogen, meaning it cannot act as a hydrogen bond donor, but can be a hydrogen bond acceptor. Peptide bond formation with incoming Pro-tRNA is considerably slower than with any other tRNAs, which is a general feature of N-alkylamino acids. Peptide bond formation is also slow between an incoming tRNA and a chain ending in proline; with

neg: Peptide bond less than similar compounds such as esters. Nevertheless, peptide bonds can undergo chemical reactions, usually through an attack of an electronegative atom on the carbonyl carbon, breaking the carbonyl double bond and forming a tetrahedral intermediate. This is the pathway followed in proteolysis and, more generally, in N-O acyl exchange reactions such as those of inteins. When the functional group attacking the peptide bond is a thiol, hydroxyl or amine, the resulting molecule may be called a cyclol or, more specifically, a thiacyclol, an oxacyclol or an azacyclol, respectively. Peptide bond A peptide bond is an amide type of covalent

neg: Eos (protein) fluorescent protein. The red chromophore, which is generated by cleavage of the peptide backbone, has an absorption maxima at 571 nm and an emission maxima at 581 nm, in its anionic form. The break in the peptide backbone that leads to this chromophore is between His-62 Nα and Cα. The observed red fluorescence occurs due to an extension of the chromophore's π-conjugation where the His-62 imidazole ring connects to the imidazolinone. The hydrogen bond patterns of the red and green chromophores are almost identical. Photochemical conversion occurs due to interactions between the chromophoric unit and residues in its vicinity. Glu-212

neg: Force field (chemistry) form for the total energy in an additive force field can be written as formula_1 where the components of the covalent and noncovalent contributions are given by the following summations: formula_2 formula_3 The bond and angle terms are usually modeled by quadratic energy functions that do not allow bond breaking. A more realistic description of a covalent bond at higher stretching is provided by the more expensive Morse potential. The functional form for dihedral energy is highly variable. Additional, "improper torsional" terms may be added to enforce the planarity of aromatic rings and other conjugated systems, and "cross-terms" that describe

neg: Fumaric acid double bond, and it is an excellent dienophile. Fumaric acid does not combust in a bomb calorimeter under conditions where maleic acid deflagrates smoothly. For teaching experiments designed to measure the difference in energy between the cis- and trans- isomers, a measured quantity of carbon can be ground with the subject compound and the enthalpy of combustion computed by difference. Fumaric acid is found in fumitory ("Fumaria officinalis"), bolete mushrooms (specifically "Boletus fomentarius var. pseudo-igniarius"), lichen, and Iceland moss. Fumarate is an intermediate in the citric acid cycle used by cells to produce energy in the form of adenosine triphosphate

neg: Peptide synthesis removed by washing during aqueous work-up. Carbodiimide activation opens the possibility for racemization of the activated amino acid. Racemization can be circumvented with 'racemization suppressing' additives such as the triazoles 1-hydroxy-benzotriazole (HOBt), and 1-hydroxy-7-aza-benzotriazole (HOAt). These reagents attack the "O"-acylisourea intermediate to form an active ester, which subsequently reacts with the peptide to form the desired peptide bond. Ethyl cyanohydroxyiminoacetate (Oxyma), an additive for carbodiimide coupling, acts as an alternative to HOAt. Some coupling reagents omit the carbodiimide completely and incorporate the HOAt/HOBt moiety as an aminium/uronium or phosphonium salt of a non-nucleophilic anion (tetrafluoroborate or hexafluorophosphate). Examples of aminium/uronium

neg: Asparagine peptide lyase Asparagine peptide lyase Asparagine peptide lyase are one of the seven groups in which proteases, also termed proteolytic enzymes, peptidases, or proteinases, are classified according to their catalytic residue. The catalytic mechanism of the asparagine peptide lyases involves an asparagine residue acting as nucleophile to perform a nucleophilic elimination reaction, rather than hydrolysis, to catalyse the breaking of a peptide bond. The existence of this seventh catalytic type of proteases, in which the peptide bond cleavage occurs by self-processing instead of hydrolysis, was demonstrated with the discovery of the crystal structure of the self-cleaving precursor of the Tsh autotransporter from

neg: Discovery and development of ACE inhibitors Phosphinic peptides are pseudo-peptides where a phosphinic acid bond (PO-CH-) has replaced a peptide bond in the peptide analogue sequence. To some extent the chemical structure of phosphinic peptides is similar to that of intermediates which are produced in hydrolysis of peptides by proteolytic enzymes. The hypothesis has been made that these pseudo-peptides mimic the structure of the enzyme substrates in their transition state and crystallography of zinc proteases in complex with phosphinic peptides supports that hypothesis. RXP 407 is the first N-domain selective phosphinic peptide and was discovered by screening phosphinic peptides libraries. Before the discovery of RXP 407

neg: Collagen helix form of the alpha helix. The three chains are hydrogen bonded to each other. The hydrogen bond donors are the peptide NH groups of glycine residues. The hydrogen bond acceptors are the CO groups of residues on the other chains. The OH group of hydroxyproline also participates in hydrogen bonding. The rise of the collagen helix (superhelix) is 2.9 Å (0.29 nm) per residue. Collagen helix In collagen, the collagen helix, or type-2 helix, is a major shape in secondary structure. It consists of a triple helix made of the repetitious amino acid sequence glycine - X - Y, where

neg: Peptide bond in peptidyl prolyl isomerases (PPIases), which are naturally occurring enzymes that catalyze the cis-trans isomerization of X-Pro peptide bonds. Conformational protein folding is usually much faster (typically 10–100 ms) than cis-trans isomerization (10–100 s). A nonnative isomer of some peptide groups can disrupt the conformational folding significantly, either slowing it or preventing it from even occurring until the native isomer is reached. However, not all peptide groups have the same effect on folding; nonnative isomers of other peptide groups may not affect folding at all. Due to its resonance stabilization, the peptide bond is relatively unreactive under physiological conditions, even

neg: Isopeptide bond through a covalent isopeptide bond. This molecular tool may have applications for "in vivo" protein targeting, fluorescent microscopy, and irreversible attachment for a protein microarray. Isopeptide bond An isopeptide bond is an amide bond that can form for example between the carboxyl group of one amino acid and the amino group of another. At least one of these joining groups is part of the side chain of one of these amino acids. This is unlike in a peptide bond which is sometimes called an "eupeptide" bond, especially when discussing about both of these bond types in the same context to

neg: Proteolysis polypeptide chains linked by two disulfide bonds. Removal of two C-terminal residues from the B-chain then yields the mature insulin. Protein folding occurs in the single-chain Proinsulin form which facilitates formation of the ultimately inter-peptide disulfide bonds, and the ultimately intra-peptide disulfide bond, found in the native structure of insulin. Proteases in particular are synthesized in the inactive form so that they may be safely stored in cells, and ready for release in sufficient quantity when required. This is to ensure that the protease is activated only in the correct location or context, as inappropriate activation of these proteases can

neg: Peptide bond by conformational strain as the peptide/protein folds into the native structure. This non-enzymatic process is thus not accelerated by transition state stabilization, but rather by ground state destabilization. The wavelength of absorption A for a peptide bond is 190–230 nm (which makes it particularly susceptible to UV radiation). Significant delocalisation of the lone pair of electrons on the nitrogen atom gives the group a partial double bond character. The partial double bond renders the amide group planar, occurring in either the cis or trans isomers. In the unfolded state of proteins, the peptide groups are free to isomerize and adopt

neg: Isopeptide bond Isopeptide bond An isopeptide bond is an amide bond that can form for example between the carboxyl group of one amino acid and the amino group of another. At least one of these joining groups is part of the side chain of one of these amino acids. This is unlike in a peptide bond which is sometimes called an "eupeptide" bond, especially when discussing about both of these bond types in the same context to make a distinction between the two. Lysine for example has an amino group on its side chain and glutamic acid has a carboxy group on

neg: De novo peptide sequencing the peptide (the larger mass, the more energy is required), induced energy (higher energy leads to more fragmentation), primary amino acid sequence, mode of dissociation and collision gas. For interpretation, first, look for single amino acid immonium ions (HN=CHR). Corresponding immonium ions for amino acids are listed in Table 1. Ignore a few peaks at the high-mass end of the spectrum. They are ions that undergo neutral molecules losses (HO, NH, CO, HCOOH) from [M+H] ions. Find mass differences at 28 Da since b-ions can form a-ions by loss of CO. Look for b-ions at low-mass end of the spectrum,

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: Thrombin a fragment called fragment 1.2) and leave thrombin, consisting solely of the serine protease domain. As is the case for all serine proteases, prothrombin is converted to active thrombin by proteolysis of an internal peptide bond, exposing a new N-terminal Ile-NH3. The historic model of activation of serine proteases involves insertion of this newly formed N-terminus of the heavy chain into the β-barrel promoting the correct conformation of the catalytic residues. Contrary to crystal structures of active thrombin, hydrogen-deuterium exchange mass spectrometry studies indicate that this N-terminal Ile-NH3 does not become inserted into the β-barrel in the apo form of

neg: De novo peptide sequencing nomenclature was first proposed by Roepstorff and Fohlman, then Biemann modified it and this became the most widely accepted version. Among these sequence ions, a, b and y-ions are the most common ion types, especially in the low-energy collision-induced dissociation (CID) mass spectrometers, since the peptide amide bond (CO-NH) is the most vulnerable and the loss of CO from b-ions. Mass of b-ions = ∑ (residue masses) + 1 (H) Mass of y-ions = ∑ (residue masses) + 19 (HO+H) Mass of a-ions = mass of b-ions – 28 (CO) Double backbone cleavage produces internal ions, acylium-type like HN-CHR-CO-NH-CHR-CO+ or

neg: Potential energy of protein a spring connecting the atoms together. Total potential energy based on bond length is over set S set of pairs of atoms that are connected by chemical bond defined as; E = Σ k(α-α) where: k is the force constant α is the equilibrium length α is the current length for the bond between ith and jth atoms. Just as the potential energy can be written as a quadratic form in the internal coordinates, so it can also be written in terms of generalized forces. The resulting coefficients are termed compliance constants. Like bond length, when three atoms are connected

neg: CNMa CNMa CNMamide (CNMa) is a cyclic neuropeptide identified by computational analysis of Drosophila melanogaster protein sequences and named after its C-terminal ending motif. A gene encoding CNMa was found in most arthropods and comparison among the precursor sequences of several representative species revealed high conservation, particularly in the region of the predicted mature peptide. Two conserved cysteine residues enveloping four amino acids form a disulfide bond and were shown to be important for binding of the peptide to its receptor. Expression of CNMa was confirmed in the larval and adult brain of D. melanogaster but the function of the peptide

neg: Chou's distorted key theory for peptide drugs its scissile bond with some simple chemical procedure, will completely lose its cleavability but it can still tightly bind to the enzyme’s active site. According to Kuo-Chen Chou, the molecule thus modified can be likened to a ‘‘distorted key”, which can be inserted into a lock but can neither open the lock nor automatically get out from it. That is why a molecule modified from a cleavable peptide can spontaneously become a competitive inhibitor against the enzyme. An illustration about Chou’s distorted key theory is given in Fig.3, where panel (a) shows an effective binding of a cleavable peptide to

neg: Lead shielding bond length and a small atomic radius means that many atoms can be packed into a particular lead structure. Because of lead’s density and large number of electrons, it is well suited to scattering x-rays and gamma-rays. These rays form photons, a type of boson, which impart energy onto electrons when they come into contact. Without a lead shield, the electrons within a person’s body would be affected, which could damage their DNA. When the radiation attempts to pass through lead, its electrons absorb and scatter the energy. Eventually though, the lead will degrade from the energy to which it

neg: Born–Haber cycle the element is normally a molecule then we first have to consider its bond dissociation enthalpy (see also bond energy). The energy required to remove one or more electrons to make a cation is a sum of successive ionization energies; for example, the energy needed to form Mg is the ionization energy required to remove the first electron from Mg, plus the ionization energy required to remove the second electron from Mg. Electron affinity is defined as the amount of energy released when an electron is added to a neutral atom or molecule in the gaseous state to form a

neg: Energy carrier are other derivatives of sunlight. Note that although coal, oil and natural gas are derived from sunlight, they are considered primary energy sources which are extracted from the earth (fossil fuels). Natural uranium is also a primary energy source extracted from the earth but does not come from the decomposition of organisms (mineral fuel). Energy carrier An energy carrier is a substance (energy form) or sometimes a phenomenon (energy system) that contains energy that can be later converted to other forms such as mechanical work or heat or to operate chemical or physical processes. Such carriers include springs, electrical batteries,

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: Amino acid a peptide bond formed between the side chain carboxyl of the glutamate (the gamma carbon of this side chain) and the amino group of the cysteine. This dipeptide is then condensed with glycine by glutathione synthetase to form glutathione. In chemistry, peptides are synthesized by a variety of reactions. One of the most-used in solid-phase peptide synthesis uses the aromatic oxime derivatives of amino acids as activated units. These are added in sequence onto the growing peptide chain, which is attached to a solid resin support. The ability to easily synthesize vast numbers of different peptides by varying the types

neg: Potential energy of protein with two chemical bonds, the two bonds tend to form a fixed angle. Any variation from this fixed equilibrium angle contributes to protein potential energy. Total potential energy based on angle is defined as over set S the triplet of atoms that are connected by two chemical bonds; E = Σk(α-α) where: k is the force constant α is the equilibrium angle α is the bond angle The middle bond of three bonds formed by four atoms maintains a certain angle which is also known as torsion is defined over set S the quartet of atoms that are connected by

neg: Internal tide 50 km of the generation site. The lost energy contributes to turbulence and mixing near the generation sites. It is not clear where the energy that leaves the generation site is dissipated, but there are 3 possible processes: 1) the internal tides scatter and/or break at distant midocean topography, 2) interactions with other internal waves remove energy from the internal tide, or 3) the internal tides shoal and break on continental shelves. Briscoe (1975)noted that “We cannot yet answer satisfactorily the questions: ‘where does the internal wave energy come from, where does it go, and what happens to it along

neg: Pancreatic elastase eczema (genetic and histologic studies will be required to investigate the role of ELA1 in these common epidermal disorders.). Pancreatic elastase is formed by activation of proelastase from mammalian pancreas by trypsin. After processing to proelastase, it is stored in the zymogen granules and then activated to elastase in the duodenum by the tryptic cleavage of a peptide bond in the inactive form of the precursor molecule. This process results in the removal of an activation peptide from the N-terminal, that enables the enzyme to adopt its native conformation. Humans have five chymotrypsin-like elastase genes which encode the structurally similar

neg: Peptide plane flipping about the axis defined by the C-C¹ and N-C bond vectors of the peptide group, which are roughly parallel. As an example, the type I and type II beta turns differ by a simple flip of the central peptide group of the turn. The significance of peptide plane flips in the dynamics of the native state has been inferred in some proteins by comparing crystal structures of the same protein in multiple conformations. For example, peptide flips have been described as significant in the catalytic cycle of flavodoxin and in the formation of amyloid structures, where their ability to provide

neg: Asparagine peptide lyase the different families of asparagine peptide lyases. The cleavage mechanism consists in the cyclization of the asparagine, assisted by other active site residues. In certain conditions, the asparagine cyclic structure nucleophilically attacks its C-terminal peptide bond to the main chain forming a new bond to create a stable succinimide, cleaving itself from the main chain and consequently releasing the two halves of the product. No inhibitors are known. The MEROPS protease database includes the following ten families of asparagine peptide lyases, which are included in 6 different clans of proteases. Proteolytic enzymes are classified into families based on sequence similarity.

neg: Hydroxy group carboxy end of the fatty acid. The joining of two aldehyde sugars to form a disaccharide removes the −OH from the carboxy group at the aldehyde end of one sugar. The creation of a peptide bond to link two amino acids to make a protein removes the −OH from the carboxy group of one amino acid. Hydroxyl radicals are highly reactive and undergo chemical reactions that make them short-lived. When biological systems are exposed to hydroxyl radicals, they can cause damage to cells, including those in humans, where they can react with DNA, lipids, and proteins. In 2009, India's Chandrayaan-1

neg: Protein structure defined by patterns of hydrogen bonds between the main-chain peptide groups. They have a regular geometry, being constrained to specific values of the dihedral angles ψ and φ on the Ramachandran plot. Both the α-helix and the β-sheet represent a way of saturating all the hydrogen bond donors and acceptors in the peptide backbone. Some parts of the protein are ordered but do not form any regular structures. They should not be confused with random coil, an unfolded polypeptide chain lacking any fixed three-dimensional structure. Several sequential secondary structures may form a "supersecondary unit". Tertiary structure refers to the three-dimensional

neg: HIV-1 protease deprotonating it. The resulting hydroxyl ion attacks the carbonyl carbon of the peptide bond, forming an intermediate with a transient oxyanion, which is stabilized by the initially protonated Asp25. The oxyanion re-forms a double bond, leading to the cleavage of the peptide bond between the two amino acids, while the initially deprotonated Asp25 undergoes acid catalysis to donate its proton to the amino group, making the amino group a better leaving group for complete peptide bond cleavage and returning to its original deprotonated state. While HIV-1 PR shares many of the same characteristics as a non-viral aspartic protease, some evidence

neg: VIR-576 of the cysteine (C) introduced replacing the methionine (M),both being sulfated amino acids, in the stabilization of its structure. VIR-576 can establish more hydrogen bonds because it has 41 H-bond donors and 56 H-bond acceptors in comparison with the 23 H-bond donors and 30 H-bond acceptors of the VIRIP.Therefore, it's able to form more interactions and react with the gp-41 in a higher intensity than the VIRIP. Another important interaction that we must underline is the disulfide bond established between both cysteines of the two monomers of the VIR-576 which allows the peptide to have more structural stability in the

neg: Protein structure Protein structure Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers specifically polypeptides formed from sequences of amino acids, the monomers of the polymer. A single amino acid monomer may also be called a residue indicating a repeating unit of a polymer. Proteins form by amino acids undergoing condensation reactions, in which the amino acids lose one water molecule per reaction in order to attach to one another with a peptide bond. By convention, a chain under 30 amino acids is often identified as a peptide, rather than a protein. To be able

neg: Bond order potential a chemical bond depends on the bonding environment, including the number of bonds and possibly also angles and bond length. It is based on the Linus Pauling bond order concept and can be written in the form formula_1 This means that the potential is written as a simple pair potential depending on the distance between two atoms formula_2, but the strength of this bond is modified by the environment of the atom formula_3 via the formula_4term. Alternatively, the energy can be written in the form formula_5 where formula_6 is the electron density at the location of atom formula_3. These two

neg: Ingestive behaviors the stomach to the brain via this hormone peptide. This peptide can stimulate thought about food, and is suppressed after food is ingested. Nutrient injection into the blood stream does not suppress ghrelin, so the release of hormone is directed by the digestive system and not by nutrient availability in the blood. These blood levels of ghrelin increase with fasting and are reduced after a meal. Ghrelin antibodies or ghrelin receptor antagonists inhibit eating. Ghrelin also stimulates energy production and signals directly to the hypothalamus regulatory nucli that control energy homeostasis. Hunger is the result of a fall in blood

neg: Polyproline helix peptide bonds. Of the twenty common naturally occurring amino acids, only proline is likely to adopt the "cis" isomer of the peptide bond, specifically the X-Pro peptide bond; steric and electronic factors heavily favor the "trans" isomer in most other peptide bonds. However, peptide bonds that replace proline with another "N"-substituted amino acid (such as sarcosine) are also likely to adopt the "cis" isomer. The PPII helix is defined by (φ,ψ) backbone dihedral angles of roughly (-75°, 150°) and "trans" isomers of the peptide bonds. The rotation angle Ω per residue of any polypeptide helix with "trans" isomers is given

neg: Asparagine peptide lyase at its own N-terminus and C-terminus and releases from the extein, separating it in two fragments. This two fragments are then spliced together and the extein remains as a completely functional protein. The N-terminal residue of the intein domain must be a serine, threonine or cysteine, and it attacks its preceding peptide bond in order to form an ester or a thioester. The first residue of the second portion of the extein must be a serine, threonine or cysteine as well, and this second nucleophile forms a branched intermediary. The C-terminal residue of the intein domain is always an asparagine,

neg: Cell-penetrating peptide results reported in literature are not consistent. Recently, non-covalent strategies have been successfully reported. Secondary amphipathic peptides based on aromatic tryptophan and arginine residues linked with lysine as spacer have been reported under the name of CADY. CADY contains a short peptide sequence of 20 amino acids, with the sequence “Ac-GLWRALWRLLRSLWRLLWRA-cysteamide." This peptide is able to self-assemble in a helical shape with hydrophilic and hydrophobic residues on different side of the molecule, it has two different orientations of the surface that represent the lowest energy and it is able to form complexes with siRNA at different molar ratio varying from

neg: Tracy Bond amnesia. In the films, James Bond is tracking Blofeld in the pre-title credits sequence of "Diamonds Are Forever". The film does not explain why nor does it mention Tracy. Originally, it had been planned that "On Her Majesty's Secret Service" would end with Bond and Tracy driving away from their wedding. The scenes where she was shot were filmed at the same time with the intention that they would form the pre-title sequence of "Diamonds Are Forever". This was rendered inviable when George Lazenby left the role. Subsequent films reference the fact that Bond was previously married, but only fleetingly:

neg: Random coil of adjacent amino acid residues by a peptide bond. This is not actually the case, since the ensemble will be energy weighted due to interactions between amino acid side-chains, with lower-energy conformations being present more frequently. In addition, even arbitrary sequences of amino acids tend to exhibit some hydrogen bonding and secondary structure. For this reason, the term "statistical coil" is occasionally preferred. The conformational entropy associated with the random-coil state significantly contributes to its energetic stabilization and accounts for much of the energy barrier to protein folding. A random-coil conformation can be detected using spectroscopic techniques. The arrangement of

neg: MHC class II HLA gene; each domain is usually encoded by a different exon within the gene, and some genes have further domains that encode leader sequences, transmembrane sequences, etc. These molecules have both extracellular regions as well as a transmembrane sequence and a cytoplasmic tail. The α1 and β1 regions of the chains come together to make a membrane-distal peptide-binding domain, while the α2 and β2 regions, the remaining extracellular parts of the chains, form a membrane-proximal immunoglobulin-like domain. The antigen binding groove, where the antigen or peptide binds, is made up of two α-helixes walls and β-sheet. Because the antigen-binding groove

neg: PEPD the N-terminus of the substrate in a fashion that is yet to be determined. The carbonyl and amide groups of the scissile peptide bond interact with the first metal ion, M1, in addition to His178 and His79, respectively. M1 and Glu204 activate a water molecule to prepare it nucleophilic attack at the carbonyl carbon of the scissile peptide bond. Then, the tetrahedral intermediate (Intermediate II) becomes stabilized from interactions with M1 and His178. Lastly, Glu204 donates a proton to the amine of the leaving peptide (P1’). This leads to the breakdown of the intermediate (Intermediate III), which retains its interactions

neg: Central dogma of molecular biology a peptide bond in such a manner that the main protein "backbone" does not fall apart. This is a case of a protein changing its own primary sequence from the sequence originally encoded by the DNA of a gene. Additionally, most inteins contain a homing endonuclease or HEG domain which is capable of finding a copy of the parent gene that does not include the intein nucleotide sequence. On contact with the intein-free copy, the HEG domain initiates the DNA double-stranded break repair mechanism. This process causes the intein sequence to be copied from the original source gene to the

neg: Prolyl isomerase to note that not every proline peptide bond is critical to the structure or function of a protein, and not every such bond has a significant influence on folding kinetics, especially "trans" bonds. Furthermore, some prolyl isomerases have a degree of sequence specificity and therefore may not catalyze the isomerization of prolines in certain sequence contexts. Prolyl isomerase activity was first discovered using a chymotrypsin-based assay. The proteolytic enzyme chymotrypsin has a very high substrate specificity for the four-residue peptide Ala-Ala-Pro-Phe only when the proline peptide bond is in the "trans" state. Adding chymotrypsin to a solution containing a reporter

neg: Penicillin binding proteins than one of the above reactions. The enzyme has a penicillin-insensitive transglycosylase N-terminal domain (involved in formation of linear glycan strands) and a penicillin-sensitive transpeptidase C-terminal domain (involved in cross-linking of the peptide subunits) and the serine at the active site is conserved in all members of the PBP family. PBPs bind to β-lactam antibiotics because they are similar in chemical structure to the modular pieces that form the peptidoglycan. When they bind to penicillin, the β-lactam amide bond is ruptured to form a covalent bond with the catalytic serine residue at the PBPs active site. This is an irreversible

neg: SEA Native Peptide Ligation nucleophilic addition of one SEA thiol group on the C-terminal carbonyl group of the peptide segment. This results in the migration of the peptide chain from the nitrogen to the sulfur. The overall process of SEA native peptide ligation involves first an "N,S"-acyl shift for in "in situ" formation of a peptide thioester, and later on, after thiol-thioester exchange, an "S,N"-acyl shift for formation of the peptide bond. SEA is an abbreviation of "bis"(2-sulfanylethyl)amido (Scheme 1). SEA ligation involves the reaction of a peptide featuring a C-terminal "bis"(2-sulfanylethyl)amido group with a Cys peptide. This reaction proceeds probably through the formation

neg: Tabtoxin evolutionary relationship between TTR and other GNAT members. The dipeptide toxin contains tabtoxinine-β-lactam (TβL) linked by a peptide bond to threonine produced, the chlorosis-inducing activity occurs only after hydrolysis of the peptide bond by aminopeptidases of plant or bacterial origin. Cleavage of the peptide bond in tabtoxin releases TβL, the toxic moiety. TβL is located at the N terminus, and Thr is at the C terminus, resulting in TβL-Thr. TβL-Thr is hydrolyzed, and the resulting TβL irreversibly inhibits glutamine synthetase, causing characteristic chlorosis in plants. TβL is spontaneously isomerized to tabtoxinine-δ-lactam (TδL), and TblF did not recognize TδL as a

neg: Peptide microarray through an chemoselective bond leading to peptides with the same orientation for interaction profiling. Some alternative procedures describe unspecific covalent binding and adhesive immobilization. However, litographic methods can be used to overcome the problem of excessive number of coupling cycles. Combinatorial synthesis of peptide arrays onto a microchip by laser printing has been described, where a modified colour laser printer is used in combination with conventional solid-phase peptide synthesis chemistry. Amino acids are immobilized within toner particles, and the peptides are printed onto the chip surface in consecutive, combinatorial layers. Melting of the toner upon the start of the coupling

neg: Spark gap equipment from high-voltage transients. The light emitted by a spark does not come from the current of electrons itself, but from the material medium fluorescing in response to collisions from the electrons. When electrons collide with molecules of air in the gap, they excite their orbital electrons to higher energy levels. When these excited electrons fall back to their original energy levels, they emit energy as light. It is impossible for a visible spark to form in a vacuum. Without intervening matter capable of electromagnetic transitions, the spark will be invisible (see vacuum arc). Spark gaps are essential to the

neg: Endothermic process excess of energy (usually in the form of vibrations and rotations). If that energy is not dissipated, the new bond would quickly break apart again. Instead, the new bond can shed its excess energy - by radiation, by transfer to other motions in the molecule, or to other molecules through collisions - and then become a stable new bond. Shedding this excess energy is the exothermicity that leaves the molecular system. Whether a given overall reaction is exothermic or endothermic is determined by the relative contribution of these bond breaking endothermic steps and new bond stabilizing exothermic steps. The concept

neg: Peptide Peptide Peptides (from Gr.: πεπτός, "peptós" "digested"; derived from πέσσειν, "péssein" "to digest") are short chains of amino acid monomers linked by peptide (amide) bonds. The covalent chemical bonds are formed when the carboxyl group of one amino acid reacts with the amino group of another. The shortest peptides are dipeptides, consisting of 2 amino acids joined by a single peptide bond, followed by tripeptides, tetrapeptides, etc. A polypeptide is a long, continuous, and unbranched peptide chain. Hence, peptides fall under the broad chemical classes of biological oligomers and polymers, alongside nucleic acids, oligosaccharides and polysaccharides, etc. Peptides are distinguished

neg: Peptide bond moiety of one coming near the non-side chain (N2) amino moiety of the other. One loses a hydrogen and oxygen from its carboxyl group (COOH) and the other loses a hydrogen from its amino group (NH). This reaction produces a molecule of water (HO) and two amino acids joined by a peptide bond (-CO-NH-). The two joined amino acids are called a dipeptide. The amide bond is synthesized when the carboxyl group of one amino acid molecule reacts with the amino group of the other amino acid molecule, causing the release of a molecule of water (HO), hence the process

neg: Bond-dissociation energy hydrocarbon RH where R is significantly larger than H, for instance, the relationship "D"(R–H) ≈ "DH"°(R–H) – 1.5 kcal/mol is a good approximation. Some textbooks ignore the temperature dependence, while others have defined the bond-dissociation energy to be the reaction enthalpy of homolysis at 298 K. The bond dissociation energy is related to but slightly different from the depth of the associated potential energy well of the bond, "D", known as the "electronic energy". This is due to the existence of a zero-point energy ε for the vibrational ground state, which reduces the amount of energy needed to reach the

neg: Helium compounds ways to make helium reactive are: to convert it into an ion, or to excite an electron to a higher level, allowing it to form excimers. Ionised helium (He), also known as He II, is a very high energy material able to extract an electron from any other atom. He has an electron configuration like hydrogen, so as well as being ionic it can form covalent bonds. Excimers do not last for long, as the molecule containing the higher energy level helium atom can rapidly decay back to a repulsive ground state, where the two atoms making up the bond

neg: Laser propulsion laser electric propulsion, using magnetohydrodynamics to convert laser energy to electricity and to electrically accelerate air around a vehicle for thrust. Laser propulsion Laser propulsion is a form of beam-powered propulsion where the energy source is a remote (usually ground-based) laser system and separate from the reaction mass. This form of propulsion differs from a conventional chemical rocket where both energy and reaction mass come from the solid or liquid propellants carried on board the vehicle. The basic concepts underlying a photon-propelled "sail" propulsion system were developed by Eugene Sanger and the Hungarian physicist György Marx. Propulsion concepts using laser-energized

neg: Alkali metal is an unreactive gas because breaking the strong triple bond in the dinitrogen molecule (N) requires a lot of energy. The formation of an alkali metal nitride would consume the ionisation energy of the alkali metal (forming M ions), the energy required to break the triple bond in N and the formation of N ions, and all the energy released from the formation of an alkali metal nitride is from the lattice energy of the alkali metal nitride. The lattice energy is maximised with small, highly charged ions; the alkali metals do not form highly charged ions, only forming ions

neg: Supramolecular assembly Figure "Representative hydrogen bond patterns in supramolecular assembly". A 1: 1 mixture of cyanuric acid and melamine forms crystal with a highly dense hydrogen-bonding network. This supramolecular aggregates has been used as templates to engineering other crystal structures. Supramolecular assemblies have no specific applications but are the subject of many intriguing reactions. A supramolecular assembly of peptide amphiphiles in the form of nanofibers has been shown to promote the growth of neurons. An advantage to this supramolecular approach is that the nanofibers will degrade back into the individual peptide molecules that can be broken down by the body. By self-assembling

neg: Braun's lipoprotein amino acid signal peptide at the amino terminus. The mature protein is 6 kDa in size. Three monomers of Lpp assemble into a coiled-coil trimer. Large amounts of Braun's lipoprotein is present, more than any other protein in "E. coli". Unlike other lipoproteins, it is linked covalently to the peptidoglycan. Lpp connects the outer membrane to the peptidoglycan. Lpp is anchored to the outer membrane by its amino-terminal lipid group. In "E. coli", one third of Lpp proteins form a peptide bond via the side chain of its carboxy-terminal lysine with diaminopimelic acid in the peptidoglycan layer. The rest of

neg: Ribosomally synthesized and post-translationally modified peptides and is thought to activate the carboxylic acid side chain of a glutamate or aspartate residue via adenylylation. The N-terminal amine formed by the B protein (protease) then reacts with this activated side chain to form the macrocycle-forming isopeptide bond. The exact steps and reaction intermediates in lasso peptide biosynthesis remain unknown due to experimental difficulties associated with the proteins. Commonly, the B protein is referred to as the lasso protease, and the C protein is referred to as the lasso cyclase. Some lasso peptide biosynthetic gene clusters also require an additional protein of unknown function for biosynthesis. Additionally, lasso

neg: Mass driver spacecraft acceleration if available input power is constant (less momentum per unit of energy given to propellant). Electric propulsion methods like mass drivers are systems where energy does not come from the propellant itself. (Such contrasts to chemical rockets where propulsive efficiency varies with the ratio of exhaust velocity to vehicle velocity at the time, but near maximum obtainable specific impulse tends to be a design goal when corresponding to the most energy released from reacting propellants). Although the specific impulse of an electric thruster itself optionally could range up to where mass drivers merge into particle accelerators with fractional-lightspeed