Solvent accessibility properties of complex proteins

NaturePublished 1 July 1979

Stephen R. Sprang, Dan Yang, Robert J. Fletterick

DOI10.1038/280333a0

Source URL

Citations28

SJR quartileQ1

SJR score18.29

SNIP10.16

TL;DR

The results of solvent accessibility calculations for the large (195,000 Mr) dimeric enzyme phosphorylase a and other multidomain, multisubunit proteins are presented.

Abstract

AN important factor in the thermodynamics of protein folding is the partition of amino acid residues between the solvent environment and the protein core. The extent of the interaction between the folded polypeptide and the surrounding medium can be measured by determining the solvent accessible surface area as defined by Lee and Richards1. In this communication we present the results of solvent accessibility calculations for the large (195,000 Mr) dimeric enzyme phosphorylase a and other multidomain, multisubunit proteins. These results are discussed in the light of the generalisations concerning protein solvent—accessible surface area and shape which have been based on data derived from low molecular weight proteins.

Keywords

Materials ScienceBiochemistry, Genetics and Molecular Biology

Journal of Molecular BiologyThe interpretation of protein structures: Estimation of static accessibility

5,888 Citations1971B. Lee, F.M. Richards

The accessibility of atoms in the twenty common amino acids in model tripeptides of the type Ala-X-Ala are given for defined conformation and the larger non-polar amino acids tend to be more “buried” in the native form of all three proteins.

Journal of Molecular BiologyThe nature of the accessible and buried surfaces in proteins

1,161 Citations1976Cyrus Chothia

The accessible surface areas have been calculated for the individual residues in 12 proteins, and for the extended chains, the secondary structures and tertiary structure of six proteins and it is shown that the accessible surface area of folded proteins is simply proportional to the two-thirds power of their molecular weight.

NaturePrinciples of protein–protein recognition

1,046 Citations1975Cyrus Chothia, Joël Janin

Results indicate that hydrophobicity is the major factor stabilising protein–protein association, while complementarity plays a selective role in deciding which proteins may associate.

NatureHydrophobic bonding and accessible surface area in proteins

887 Citations1974Cyrus Chothia

The hydrophobic bond is the term used by Kauzmann to describe the gain in free energy on the transfer of non-polar residues from an aqueous environment to the interior of proteins.

NatureStructural invariants in protein folding

869 Citations1975Cyrus Chothia

An analysis of 15 protein structures indicates: first, the loss of accessible surface area by monomeric proteins on folding—proportional to hydrophobic energy—is a simple function of molecular weight.

NatureSurface and inside volumes in globular proteins

711 Citations1979Joël Janin

The study of the accessibility to solvent of amino acid residues in several proteins confirmed the early observation that polar residues are found mostly on the surface and non-polar residues mostly inside globular protein structures, but the accessibility shows systematic variations with the molecular weight.

BiochemistryRole of hydrophobicity in the binding of coenzymes

132 Citations1978Joël Janin, Cyrus Chothia

It is demonstrated that hydrophobicity is the major source of stabilization free energy in FMN binding to flavodoxin and in NAD binding to the two dehydrogenases: it contributes 25 to 30 kcal/mol to the free energy of dissociation, more than required in order to compensate for the loss of six degrees of translational/rotational freedom by the coenzyme.

NatureAccessible area, packing volumes and interaction surfaces of globular proteins

128 Citations1976David C. Teller

It is demonstrated that accessible surface area of monomeric proteins varies as the 2/3 power of the molecular weight.