Simple Computer-Aided Approach for the Analyses of the Nuclear-Magnetic-Resonance Spectra of Histones. Fractions Fl, F2al, F2B, Cleaved Halves of F2B and F2B middotDNA

Abstract

A simple method for the computer simulation of high-resolution nuclear magnetic resonance spectra is described and applied to the analyses of salt-induced changes in the spectra of histones. The method is more objective than the earlier approach of visual examination of spectral changes.It allows the information contained in the spectral envelope to be used and has led to some modifications of the earlier proposals of the segments of histones involved in salt-induced conformational changes, interhistone interactions and interactions with DNA. A feature of these newer proposals is their self-consistency, particularly of the results obtained for F2B, the cleaved amino and carboxyl halves of F2B and of F2B * DNA.The direct relationship between the amino-acid sequence of a protein, its three-dimensional structure and its function is now an accepted part of the dogma of molecular biology. I n the case of most proteins, the tertiary structure is determined within quite close limits by the intramolecular interactions between the various parts of its constituent polypeptide chain, and any changes in the shape of the molecule are restricted to small effects resulting from, for example, the binding of substrates, or to the drastic and frequently irreversible process of denaturation. I n the light of this general observation, the group of basic nuclear proteins known as histones stand out as being unusual in that they undergo large and reversible changes in conformation with relatively small changes in solvent conditions. They are further distinguished from most other proteins by the highly asymmetrical way in which residues of differing characters, for example apolar or basic residues, are grouped along the molecular chain, as demonstrated by the sequence for histones F2A1 [I] and F2B [2] and the partial sequence of F1 [3]. Thus the character of one section of a given histone molecule, as expressed in its readinness to form helical conformations or in its ability to interact with other molecules, differs greatly from that of other sections of the same molecule [I-71.These characteristics of the histones lead naturally to the proposal that different parts of the histone Abbreviation. NMR, nuclear magnetic resonance.molecule perform different functions in the structure of chromatin and the complex changes which chromatin undergoes during mitosis. It is therefore of considerable interest to study isolated histone fractions in order to elucidate the properties of individual sections of the molecules and the intramolecular and intermolecular changes which may be induced in them, with a view to the eventual, though as yet remote, solution of the problem of their precise role in the structural changes of the chromosomes.Of the techniques available for studying proteins in solution, nuclear magnetic resonance appears one of the most promising in that it is capable, in t,heory at least, of providing data on each individual residue in the molecule. I n practice, however, even a t the highest frequencies available or projected for t...

The nucleosomal core histone octamer at 3.1 A resolution: a tripartite protein assembly and a left-handed superhelix.

“…The percentage and location of ordered protein found in the new map also correlate well with the findings of Bradbury and coworkers (23)(24)(25), who reported that residues 25-95 of H2A, 37-114 of H2B, 42-110 of H3, and 33-102 of H4 are ordered. Our model includes these residues and extends the structured portion of the octamer by 66 more residues (Fig.…”

“…2). This is slightly in excess of the 62% assigned to structured residues by the earlier studies of Bradbury and associates (23)(24)(25). Within the perspective of viewing this assembly, three distinct shapes can be perceived and the overall mass distribution can be described as tripartite or tetrapartite.…”

Investigation of the conformational and self-aggregational processes of histones using hydrogen and carbon-13 nuclear magnetic resonance

“…This is in contrast to the view expressed by Rattle (1972) andIsenberg (1974a,b), where histone molecules are regarded as completely random coil molecules in the absence of salt.…”

Protein dynamics

“…The slow conformattonal exchange localized around the cystems which bmd the two zmc atoms of the protein observation is confirmed by the analysis of the Bl field strength dependence of the Tl relaxation m the rotating frame The measurement of this so called Tlp relaxation time constant was also recently used m the analysts of slow motion m BPTI [25] A further example of disorder m a DNA bmdmg protein, that of the Antennapedia homeodomam, has more recently been described by Qian et al [26] The existence of extensive flexible regions m histones, known since the pioneermg NMR studies of E M Bradbury [27,28], have been discussed by C Cerf [29] 4. The significance of conformational flexibility A possible functional stgmficance for the disorder observed for residues 20-30 of the B-chain of an msuhn mutant was proposed by M Weiss In a series of msulm analogues such disorder can be seen both by NMR and crystallography and its role m facihtatmg a conformational admstment upon receptor bmdmg represents an attractive hypothesis [30] A somewhat different type of bmdmg site flextbihty was described by G.C.K.…”