Showing papers by "G. N. Ramachandran published in 1968"

Conformation of Polypeptides and Proteins

Abstract: Publisher Summary This chapter deals with the recent developments regarding the description and nature of the conformation of proteins and polypeptides with special reference to the stereochemical aspects of the problem. This chapter considers the parameters that are required for an adequate description of a polypeptide chain. This chapter focuses the attention on what may be called “internal parameters”—that is, those which can be defined in terms of the relationships among atoms or units that form the building blocks of the polypeptide chains. This chapter also provides an account of the mathematical method of utilizing these parameters for calculating the coordinates of all the atoms in a suitable frame of reference, so that all the interatomic distances, and bond angles, can be calculated and their consequences worked out. This chapter observes conformations in amino acids, peptides, polypeptides, and proteins.

Stereochemical criteria for polypeptides and proteins. IV. Standard dimensions for the cis‐peptide unit and conformation of cis‐polypeptides

Abstract: Using potential energy formulas for variation of bond angles and for ω-distortion, the conformation of minimum energy for the cis form of the peptide unit has been worked out. This agrees very well with the corresponding set of atoms in the crystal structure of Leu-Pro-Gly and the dimensions of a standard cis peptide unit are given based on these. The conformational (ϕ,Ψ) map for a cis peptide unit has been worked out from contact criteria, both for a pair of linked units as well as for-helices having constant (ϕ,Ψ). The small allowed region of the helical map contains the conformation experimentally observed for poly-L-proline I.

Possible formation of the left-handed α-helix of poly-L-serine.

Abstract: A conformational study of poly-L-serine has shown that it can exist in the left-handed α-helical form. A study of a pair of peptide units with the serine sidegroup attached to the α carbon atom linking the two units showed that OH O hydrogen bonds between the OH group of the side chain and a carbonyl oxygen of the first peptide group in the backbone can occur in two regions of ϕ, namely, ϕ = 15°-30° for χ1 = 300° and for ϕ = 225°-230° for ϕ = 60°. The latter is close to a possible left-handed helix of poly-L-serine, stabilized by NH O hydrogen bonds. From a study of contact criteria, the best conformation for this helix is found to be ϕ = 227°, Ψ = 238°, χ1 = 65° which has n = 3.65, h = 1.51 A. The NH O hydrogen bond has a length of 2.90 A. (6°) and the OH O hydrogen bond is of length 2.60 A. (0°). There are no other bad short contacts in the structure. The cylindrical coordinates of the atoms, as well as a perspective view of the structure arc given in this paper.