Peptide bonds are formed when the
carboxyl carbon of
first amino acid is joined to the amino nitrogen of the second amino
acid with release of one molecule of water. This C-N bond, though a
single bond, has about 30-40% double bond characteristics. The bond
length is about 10% less than the usual C-N bond length due to the
resonance structure of the C-N to C=N+. The bond is
rigid and hardly any rotation is allowed. However, rotation is
permissible around N-Cα
(Ramchandran angle φ ,about -58°) and
Cα -C(Ramchandran
angle ψ, about -47°) . The shaded regions are planar
and the side groups and H jot out. In the above picture, A is alpha
carbon, E is carbonyl carbon, D is carbonyl oxygen, F is amino
nitrogen, B is hydrogen, C is next alpha carbon. A,E,D,F,B,C
(6 atoms) lie in one plane and form 1 unit. C,K,G,J,I,H
are also planar ( not necessarily in same plane as AEDFBC ) with C
common for both. Bold letters are carbon atoms. The orientation is
trans in nature.
C--C-N-C-C-N-C.......are
the backbone structure of the polypeptides. In the first
residue, there are 4 atoms in the backbone, in the second 3, third 3
and 4th 3, thus aggregating 13. One repeat turn of the α-
helix (called Pitch) covers 3.6 residues, approximately ending at H
of the 4th plane. Hence, 13th atom becomes the H instead of
Cα . Total turn of
angles is 110.5*3 +HCI /CAB = 331.5 + 31.34 = 362 degree approxi.
So we call the α- helix as 3.613 - Helix.
For every n amino
acids linked in a protein there are n −
1 peptide bonds. The free energy of peptide bond hydrolysis and
formation in aqueous solution defines the equilibrium position
between peptide and amino acid hydrolysis products. Yet few
experimental values exist.
The equilibrium of this reaction lies on the side of
hydrolysis rather than synthesis. Hence, the biosynthesis of peptide
bonds requires an input of free energy. Nonetheless, peptide bonds
are quite stable
kinetically; the
lifetime of a peptide bond in aqueous solution in the absence of a
catalyst approaches 1000 years.
With a minimum of assumptions, this paper deduces the free energies
of hydrolysis of a variety of peptide bonds. Formation of a di-peptide
from two amino acids is about eight times more difficult than
subsequent condensations of an amino acid to a di-peptide or longer
chain. Condensation of an amino acid to a peptide of any size is
five times more difficult than joining two smaller peptides of at
least di-peptide size. Thus in an abiogenesis scenario, there is a
kind of nucleation in peptide bond formation with the initial
condensation of two amino acids to yield a di-peptide more difficult
than subsequent condensations to a growing chain. © 1998 John Wiley
& Sons, Inc. Biopoly 45: 351–353, 1998
Similar to many ureas, N-carbamoylamino acids were shown to be
hydrolyzed in aqueous solution through elimination mechanisms at
close to neutral pH, the nucleophilic attack of water being a minor
process. Two competing elimination mechanisms can take place
involving either cyanate or isocyanate transient intermediates.
Peptide formation was observed and attributed to the latter pathway
through the intermediacy of amino acid N-carboxyanhydride (NCA).
Eventually, cyanate and its precursors (including urea) unexpectedly
behave as amino acid activating agents because of their ability in
amino acid carbamoylation. Owing to its ability to generate a
background prebiotic production of NCAs on the primitive Earth, this
reaction is suggested to have contributed to the origin of life
process.
The reaction of cyanate with C-terminal carboxyl groups of peptides
in aqueous solution was considered as a potential pathway for the
abiotic formation of peptide bonds under the condition of the
primitive Earth. The catalytic effect of dicarboxylic acids on
cyanate hydrolysis was definitely attributed to intramolecular
nucleophilic catalysis by the observation of the 1H-NMR signal of
succinic anhydride when reacting succinic acid with KOCN in aqueous
solution (pH 2.2-5.5). The formation of amide bonds was noticed when
adding amino acids or amino acid derivatives into the solution. The
reaction of N-acyl aspartic acid derivatives was observed to proceed
similarly and the scope of the cyanate-promoted reaction was
analyzed from the standpoint of prebiotic peptide formation. The
role of cyanate in activating peptide C-terminus constitutes a proof
of principle that intra-molecular reactions of adducts of peptides
C-terminal carboxyl groups with activating agents represent a
pathway for peptide activation in aqueous solution, the relevance of
which is discussed in connexion with the issue of the emergence of
homo-chirality. |