Polypeptide chain modes

The eigenvectors of polypeptide chain modes, as in the case of NMA, can be described by PEDs in terms of symmetry coordinates, which in turn are related to internal coordinates. A list of the internal coordinates for (Ala) is given in Table IV, and the local symmetry coordinates are given in Table V (Moore and Krimm, 1976b). These serve as the general local symmetry coordinates for most polypeptide chain structures [for the particular set for (Gly) I, see Dwivedi and Krimm (1982a)]. 

Flavoenzymes are widespread in nature and are involved in many different chemical reactions. Flavoenzymes contain a flavin mononucleotide (FMN) or more often a flavin adenine dinucleotide (FAD) as redox-active prosthetic group. Both cofactors are synthesized from riboflavin (vitamin B2) by microorganisms and plants. Most flavoenzymes bind the flavin cofactor in a noncovalent mode (1). In about 10% of aU flavoenzymes, the isoalloxazine ring of the flavin is covalently linked to the polypeptide chain (2, 3). Covalent binding increases the redox potential of the flavin and its oxidation power, but it may also be beneficial for protein stability, especially in flavin-deficient environments. 

P sheet A mode of protein folding in which two polypeptide chains (/ strands) lie side by side and either parallel or antiparallel with respect to the direction of the NH-Cq-CO group. Hydrogen bonds are formed from a carbonyl group of one chain to an amide nitrogen atom of the other chain and vice versa. 

We illustrate the results of a normal-mode calculation on a small molecule by discussing the normal vibrations of N-methylacetamide (NMA), the simplest molecule containing a trans peptide group analogous to that in a polypeptide chain. A study of this molecule provides insights into the general nature of the so-called amide modes of the peptide group. 

The preceding discussions have established the theoretical basis for computing the normal modes of vibration of a polypeptide chain molecule. Throughout the discussion we have assumed knowledge of the structure of the molecule and of its vibrational potential energy function. It is now necessary to examine these two kinds of inputs, and in particular to understand how we can obtain a polypeptide force field that might serve to predict the vibrational frequencies of an arbitrary chain conformation. 

It is worth noting from Table XIII that the approximate force field gives a good reproduction of the frequencies and eigenvectors of the non-CHs modes of the side-chain point-mass model of the a helix. This approximation should therefore be satisfactory for reproducing the amide modes of an a-helical polypeptide chain in, for example, a globular protein. 

The conformations considered above have referred to polypeptide chains all of whose residues are achiral, such as (Gly) or (Aib) , or have the same chirality, L or n, throughout. There is an important class of polypeptides, of which the transmembrane ion-channel gramicidin A (GA) is an example, in which the chirality of adjacent residues alternates along the chain. Although a-helix structures are possible (Hesselink and Scheraga, 1972), l,d sequences favor new kinds of conformations. The normal-mode analyses of these structures (Naik and Krimm, 1986a) permit a detailed characterization of their vibrational spectra. 

The goal of a vibrational spectroscopic study of a polypeptide molecule is to derive structural information from spectral parameters, such as band frequencies, intensities, and polarizations. In the past, the frequencies of the amide modes were the main diagnostic quantities, with structural insights being obtained from correlational studies based on observed spectra of known polypeptide chain structures. 

---