Peptide Bond Geometry

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: 351353, 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.

       
  AE  
  EF  
  FB  
  ED  
  FC  
  AEF (in degree)  value may be 114/116  
  EFB (in degree) value may be 123/120  
  AED (in degree)  
  BFC (in degree)  value may be 114/118  
  FCK (in degree)  value may be 111/110.5  
       
        
  DEF (in degree)  
  EFC (in degree)  
  AFE (in degree)  
  AFB (in degree)  
  FEC (in degree)  
  DEC (in degree)  
  DAE (in degree)  
  EAB/KCI (in degree)  
  DAB (in degree)  
  ADE (in degree)  
  EDC (in degree)  
  ADC (in degree)  
  FBC  (in degree)  
  ABF (in degree)  
  ABC (in degree)  
  FCB  (in degree)  
  FCD  (in degree)  
  BCD (in degree)  
  CEF  (in degree)  
  FCE  (in degree)  
  ECD (in degree)  
  BAF (in degree)  
  EAF (in degree)  
  DAF (in degree)  
  EBF (in degree)  
  EBC (in degree)  
  BEF (in degree)  
  DBC (in degree)  
  BDC (in degree)  
  DBA (in degree)  
  BDA (in degree)  
  DAC (in degree)  
  CAB (in degree)  
  DCA (in degree)  
  ACB (in degree)  
  DFC  (in degree)  
  AFD  (in degree)  
  BEC  (in degree)  
  CFK  (in degree)  
  CKF  (in degree)  
       
  If First & Second residue are in the same plane,    
  DCI  (in degree)  
  BCG  (in degree)  
       
       
  AF  
  DF  
  BE  
  CE  
  AB  
  BC  
  CD  
  DA  
  DB  
  AC  
  FK