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.

Conformation of Polypeptides and Proteins

Properties of lactic acid based polymers and their correlation with composition

The 1.9-A-resolution crystal structure of the nucleosome core particle containing 147 DNA base pairs reveals the conformation of nucleosomal DNA with unprecedented accuracy. The DNA structure is remarkably different from that in oligonucleotides and non-histone protein-DNA complexes. The DNA base-pair-step geometry has, overall, twice the curvature necessary to accommodate the DNA superhelical path in the nucleosome. DNA segments bent into the minor groove are either kinked or alternately shifted. The unusual DNA conformational parameters induced by the binding of histone protein have implications for sequence-dependent protein recognition and nucleosome positioning and mobility. Comparison of the 147-base-pair structure with two 146-base-pair structures reveals alterations in DNA twist that are evidently common in bulk chromatin, and which are of probable importance for chromatin fibre formation and chromatin remodelling.

The structure of DNA in the nucleosome core

Poly(lactic acid) crystallization

We describe a computer program we have been developing to build models of molecules and calculate their interactions using empirical energy approaches. The program is sufficiently flexible and general to allow modeling of small molecules, as well as polymers. As an illustration, we present applications of the program to study the conformation of actinomycin D. In particular, we study the rotational isomerism about the D-Val-, L-Pro, and L-Pro-Sar amide bonds as well as comparing the energy and structure of the Sobell model and the x-ray structure of actinomycin D.

AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions

The predominant role of van der Waal interactions in determining the helical conformations of a simple synthetic linear polymer, as well as helical polypeptides, was pointed out in systematic studies by Liquori et al.1,2. In the case of homopolypeptides the conformational analysis carried out on the basis of a simple semiempirical function describing the van der Waal pairwise interactions between the non directly bonded atoms lead to the conclusion that only five helices are allowed (Rα, β, γ, δ, Lα).2,3

In view of the close similarities with poly-L-alanine, we have investigated by x-ray and conformational analysis the molecular conformation of poly(S-lactic acid) which has recently been described by Kleine and Kleine4 and Schuls and Schwaab5 and studied in solution by Goodman and D'Alagni.6 In fact, this polymer may be related to the polypeptide by the interchange of a peptide bond with ester bond along the main chain. This operation is expected to involve only a relatively small change in the steric interaction within the possible helical conformation, but obviously rules out any possibility of hydrogen bonding.

P. De Santis

Papers

Molecular conformation of poly(S‐lactic acid)

Conformational Analysis of Regular Enantiomeric Sequences

An example of a Collett-Wolf source

Dual role of DNA intrinsic curvature and flexibility in determining nucleosome stability.

A theoretical model of DNA curvature