Peptide bond

Introduction: A protein is a linear sequence of amino acids linked by peptide bonds together. The peptide bond is a covalent bond between the α-carboxyl group of another and the α-amino group of one amino acid. The peptide bond has partial double bond character and is closely in the trans configuration always. Backbone conformation of a polypeptide is defined by the rotation angles around the Cα–N bond (phi, φ) and Cα–C bond (psi, ψ) of each of its amino acid residues. The sterically permitted values of ψ and φ are visualized in a Ramachandran  plot. When by a peptide bond 2 amino acids are joined they form a dipeptide. In Addition of further amino acids results in long chains called and polypeptides and oligopeptides .

Proteins are linear sequences of amino acids which are linked together by peptide bonds. The peptide bond is a type of chemical, covalent bond formed between the α-amino group of one amino acid and the α-carboxyl group of another amino acid. Once  two  amino  acids  are  joined  together  using  a peptide  bond  to form  a dipeptide, there is yet a free amino group at one end and a free carboxyl group at the other, each of which may in turn be linked to further amino acids. Therefore, to form oligopeptides (up to 25 amino acid residues) and polypeptides (> 25amino acid residues) long, unbranched chains of amino acids can be linked by peptide bonds together.  Note that the polypeptide has a free α-amino group still and a free α-carboxyl group. The Convention has it that peptide chains are written down having the free α-amino group on the left, the free α-carboxyl group on the right  and  a  hyphen  between  the  amino  acids  to  show  the  peptide  bonds.

Therefore, the tripeptide ⁺H3 N-serine–leucine–phenylalanine-COO^– should be written easily as Ser-Leu-Phe or S-L-F.

Figure: (a) Formation of a peptide bond, (b) resonance structures of the peptide bond, (c) peptide units within a polypeptide.

between  the carbon  and nitrogen  the peptide  bond exhibits  partial double- bond character due to the nearness of the carbonyl carbon–oxygen  double-bond permitting  the resonance  structures  in given fig to exist. The C–N bond length is also shorter than usual C–N single bonds because of this.  The  peptide  unit which  is  made  up  of  the  CO–NH  atoms  is  therefore  relatively  planar and rigid  , however, free rotation may take place about the Cα–N and Cα–C bonds (the bonds either  side  of  the  peptide  bond),  allowing  adjacent  peptide  units  to  be  at different angles . Always the hydrogen of the amino group is nearly on the opposite side (trans) of the double bond to the oxygen of the carbonyl group, rather than on the similar side (cis).

The backbone of a protein is a connection sequence of rigid planar peptide groups. Backbone conformation of a polypeptide is defined by  torsion angles or rotation angles about the Cα–N bond (phi, φ) and Cα–C bond (psi, ψ) of each of its amino acid residues.  When  the  polypeptide   chain  is  in  its  planar,  fully extended  (all-trans)  conformation  the φ and ψ angles  are both specified  as 180  , and amplify for a clockwise rotation when viewed from Cα  .The conformational  range  of the torsion  angles, ψ and φ are restricted  by steric hindrance in a polypeptide  backbone  .  The sterically permitted values of ψ and φ can be finding out by calculating the distances between the atoms of a tripeptide at all values of ψ and φ for the central peptide unit. These values are visualized, or else known as a conformation map  or Ramachandran  plot In a steric contour diagram .From given figure it   may be seen that most areas of the Ramachandran  plot (most combinations  of ψ and φ) are conformation ally inaccessible  to a polypeptide  chain.  Three small  regions  of the conformation map are physically accessible to a polypeptide chain Only, and within these regions are the φ–ψ values that generate the right-handed  α-helix, the parallel and antiparallel β-pleated sheets and the collagen helix .

To form a particular shape the polypeptide chain folds up (conformation) in the protein.In the  structure  this conformation  is the three-dimensional arrangement  of atoms  and  is  determined  by  the  amino  acid  sequence.  There are 4 levels of structure in proteins: primary, secondary, tertiary and, sometime quaternary (but not always).

Figure:A segment of a polypeptide chain indicating the torsion angles about the Cα–N bond (φ) and Cα–C bond (ψ).

Figure:Ramachandran plot indicating the allowed angles for poly-L-alanine (grey regions). α, φ–ψ values that generate the right-handed α-helix; β, antiparallel β-pleated sheet; β , parallel β-pleated sheet; C, collagen helix.