Inorganic chemistry, apeptide bond is anamide type ofcovalentchemical bond linking two consecutivealpha-amino acids from C1 (carbon number one) of one alpha-amino acid and N2 (nitrogen number two) of another, along apeptide orprotein chain.[1]
It can also be called aeupeptide bond[1] to distinguish it from anisopeptide bond, which is another type of amide bond between two amino acids.
When two amino acids form adipeptide through apeptide bond,[1] it is a type ofcondensation reaction.[2] In this kind of condensation, two amino acids approach each other, with the non-side chain (C1)carboxylic acidmoiety of one coming near the non-side chain (N2)amino moiety of the other. One loses ahydrogen and oxygen from its carboxyl group (COOH) and the other loses a hydrogen from its amino group (NH2). This reaction produces a molecule of water (H2O) 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 thecarboxyl group of one amino acid molecule reacts with theamino group of the other amino acid molecule, causing the release of a molecule ofwater (H2O), hence the process is adehydration synthesis reaction.
The formation of the peptide bond consumes energy, which, in organisms, is derived fromATP.[3] Peptides andproteins are chains ofamino acids held together by peptide bonds (and sometimes by a fewisopeptide bonds). Organisms useenzymes to producenonribosomal peptides,[4] andribosomes to produce proteins via reactions that differ in details from dehydration synthesis.[5]
Some peptides, likealpha-amanitin, are called ribosomal peptides as they are made by ribosomes,[6] but many arenonribosomal peptides as they are synthesized by specialized enzymes rather than ribosomes. For example, the tripeptideglutathione is synthesized in two steps from freeamino acids, by twoenzymes:glutamate–cysteine ligase (forms anisopeptide bond, which is not a peptide bond) andglutathione synthetase (forms a peptide bond).[7][8]
A peptide bond can be broken byhydrolysis (the addition of water). The hydrolysis of peptide bonds in water releases 8–16 kJ/mol (2–4 kcal/mol) ofGibbs energy.[9] This process is extremely slow, with thehalf life at 25 °C of between 350 and 600 years per bond.[10]
In living organisms, the process is normallycatalyzed byenzymes known as peptidases orproteases, although there are reports of peptide bond hydrolysis caused by conformational strain as the peptide/protein folds into the native structure.[11] This non-enzymatic process is thus not accelerated by transition state stabilization, but rather by ground-state destabilization.
Thewavelength of absorption for a peptide bond is 190–230 nm,[12] which makes it particularly susceptible toUV radiation.
Significant delocalisation of thelone pair of electrons on the nitrogen atom gives the group apartial double-bond character. The partial double bond renders the amide groupplanar, occurring in either thecis ortrans isomers. In the unfolded state of proteins, the peptide groups are free to isomerize and adopt 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 Cα and Cδ atoms ofproline makes the cis and trans isomers nearly equal in energy, as shown in the figure below.
Thedihedral angle associated with the peptide group (defined by the four atoms Cα–C'–N–Cα) is denoted; for the cis isomer (synperiplanar conformation), and for the trans isomer (antiperiplanar conformation). Amide groups can isomerize about the C'–N bond between the cis and trans forms, albeit slowly ( seconds at room temperature). Thetransition states requires that the partial double bond be broken, so that the activation energy is roughly 80 kJ/mol (20 kcal/mol). However, theactivation energy can be lowered (and the isomerizationcatalyzed) 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 inpeptidyl prolyl isomerases (PPIases), which are naturally occurring enzymes that catalyze the cis-trans isomerization of X-Pro peptide bonds.
Conformationalprotein 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 less than similar compounds such asesters. Nevertheless, peptide bonds can undergo chemical reactions, usually through an attack of anelectronegative atom on thecarbonylcarbon, breaking the carbonyl double bond and forming a tetrahedral intermediate. This is the pathway followed inproteolysis and, more generally, in N–O acyl exchange reactions such as those ofinteins. When the functional group attacking the peptide bond is athiol,hydroxyl oramine, the resulting molecule may be called acyclol or, more specifically, a thiacyclol, an oxacyclol or an azacyclol, respectively.
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