The X-ray crystal structure of the nucleosome core particle of chromatin shows in atomic detail how the histone protein octamer is assembled and how 146 base pairs of DNA are organized into a superhelix around it. Both histone/histone and histone/DNA interactions depend on the histone fold domains and additional, well ordered structure elements extending from this motif. Histone amino-terminal tails pass over and between the gyres of the DNA superhelix to contact neighbouring particles. The lack of uniformity between multiple histone/DNA-binding sites causes the DNA to deviate from ideal superhelix geometry.

Crystal structure of the nucleosome core particle at 2.8 Å resolution

Reviewing the thermodynamic parameters characterizing self-association and ligand binding of proteins at 25 OC, we find AGO, AHo, AS\", and ACpo are often all of negative sign. It is thus not possible to account for the stability of association complexes of proteins on the basis of hydrophobic interactions alone. We present a conceptual model of protein association consisting of two steps: the mutual penetration of hydration layers causing disordering of the solvent followed by further short-range interactions. The net AGO for the complete association process is primarily determined by the positive entropy change accompanying the first step and the negative enthalpy change of the second step. On the basis of the thermochemical behavior of small molecule interactions, we conclude that the strengthening of hydrogen bonds in the I n the past decade, a complete thermodynamic description of the self-association of many proteins and their interactions From the Laboratory of Molecular Biology (P.D.R.) and Laboratory of Nutrition and Endocrinology (S.S.), National Institute of Arthritis, Metabolism and Digestive Diseases, National Institutes of Health, Bethesda, Maryland 20205. Received September 23, 1980. low dielectric macromolecular interior and van der Waals' interactions introduced as a consequence of the hydrophobic effect are the most important factors contributing to the observed negative values of AHo and ASo and hence to the stability of protein association complexes. The X-ray crystallographic structures of these complexes are consonant with this analysis. The tendency for protein association reactions to become entropy dominated and/or entropy-enthalpy assisted at low temperatures and enthalpy dominated at high temperatures (a consequence of the typically negative values of AC,\") arises from the diminution of the hydrophobic effect with increasing temperature which is a general property of the solvent, water. with small molecular substrates has become available. Concomitantly, X-ray crystallography has provided a detailed picture of some of these associations, and this has stimulated a number of theoretical studies (Levitt & Warshel, 1975; Gelin & Karplus, 1975; Chothia & Janin, 1975), based upon energetic considerations, to account for these structures. The This article not subject to U S . Copyright. Published 1981 by the American Chemical Society T H E R M O D Y N A M I C S O F P R O T E I N A S S O C I A T I O N V O L . 2 0 , N O . 1 1 , 1 9 8 1 3097 Table I: Thermodynamics of Protein Association' association process A G \" ~ AiY A s o , A c p o (kcal mol-') (kcal mol-l) (cal K-I mol-') (cal K-I mol-I) refb trypsin (bovine) + inhibitor (soybean) -14.6 8.6 78 -440 c, d deoxyhemoglobin S gelation -3.4 2.0 18 -200 e, f lysozyme self-association (indefinite) -3.9 -6 .4 -8.3 g glucagon trimerization -12.1 -3 1 -64 -430 h, i hemoglobin t haptoglobin -11.5 -3 3 -7 3 -940 i a-chymotrypsin dimerization -7.1 -35 -9 5 k, I S-peptide + S-protein (ribonuclease) -13 -40 -90 -1100 m, n All thermodynamic parameters expressed per mole of complex formed except the indefinite association cases of hemoglobin S and lysozyme for which the mole refers to the monomeric protein reacted. Unitary entropy and free energy are given for processes of defined stoichiometry. Standard states are hypothetical 1 M protein, pH at which the reaction was measured. All pHs were close to 7 except for trypsin, pH 5, haptoglobin, pH 5.5, and glucagon, pH 10.5. All data for 25 \"C except glucagon, T = 30 \"C. ence is to calorimetric work and the second is to X-ray crystallographic structure determination. al. (1974). e Rosset al. (1977). Wishner e t al. (1975). g Banerjee et al. (1975). Johnson et al. (1979). * Sasaki et al. (1975). For each entry, the first referSweet et Baugh & Trowbridge (1972). Lavialle et al. (1974). Shiao & Sturtevant (1969). lVandlen &Tulinsky (1973). Hearn et al. (1971). Wyckoff e t al. (1970). methodology and problems involved in such calculations have been critically reviewed by NBmethy & Scheraga (1977). In this paper we review the thermodynamics of protein association processes for the examples best characterized in terms of their chemistry and structure. From this survey we find that the thermodynamic parameters AGO, Ai?, AS\", and ACpo are predominantly of negative sign. This result poses severe difficulties for interpretations of protein association based upon the entropically driven hydrophobic effect. The aim of this paper is to attempt to account for the signs and magnitudes of these thermodynamic parameters for protein association reactions in terms of known molecular forces and the thermochemistry of small molecule interactions.

Thermodynamics of protein association reactions: forces contributing to stability

Publisher Summary This chapter investigates the anatomy and taxonomy of protein structures. A protein is a polypeptide chain made up of amino acid residues linked together in a definite sequence. Amino acids are “handed,” and naturally occurring proteins contain only L-amino acids. A simple mnemonic for that purpose is the “corncrib.” The sequence of side chains determines all that is unique about a particular protein, including its biological function and its specific three-dimensional structure. The major possible routes to knowledge of three-dimensional protein structure are prediction from the amino acid sequence and analysis of spectroscopic measurements such as circular dichroism, laser Raman spectroscopy, and nuclear magnetic resonance. The analysis and discussion of protein structure is based on the results of three-dimensional X-ray crystallography of globular proteins. The basic elements of protein structures are discussed. The most useful level at which protein structures are to be categorized is the domain, as there are many cases of multiple-domain proteins in which each separate domain resembles other entire smaller proteins. The simplest type of stable protein structure consists of polypeptide backbone wrapped more or less uniformly around the outside of a single hydrophobic core. The outline of the taxonomy is also provided in the chapter.

The anatomy and taxonomy of protein structure.

Prediction of the secondary structure of proteins from their amino acid sequence.

Twenty-Five Years of the Nucleosome, Fundamental Particle of the Eukaryote Chromosome

Crystal structure of sickle-cell deoxyhemoglobin at 5 A resolution.

A table has been compiled of the spatial disposition of the amino acid residues in the human deoxy hemoglobin tetramer. The table also indicates regions of possible contact between residues in each subunit and possible contacts between subunits.

Location of amino acid residues in human deoxy hemoglobin

The structure of the (H2A-H2B-H3-H4)2 histone octamer has been determined by means of x-ray crystallographic techniques at a resolution of 3.3 angstroms. The octamer is a prolate ellipsoid 110 angstroms long and 65 to 70 angstroms in diameter, and its general shape is that of a rugby ball. The size and shape are radically different from those determined in earlier studies. The most striking feature of the histone octamer is its tripartite organization, that is, a central (H3-H4)2 tetramer flanked by two H2A-H2B dimers. The DNA helix, placed around the octamer in a path suggested by the features on the surface of the protein, appears like a spring holding the H2A-H2B dimers at either end of the (H3-H4)2 tetramer.

https://science.sciencemag.org/content/sci/228/4699/546.full.pdf

Crystallographic structure of the octameric histone core of the nucleosome at a resolution of 3.3 Å

Structure of deoxyhemoglobin A crystals grown from polyethylene glycol solutions.

Refinement of a molecular model for lamprey hemoglobin from Petromyzon marinus.

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