Structure
Research ArticleVolume changes on protein folding
Introduction
The volume changes that occur on protein folding are directly related to the forces responsible for the stability of proteins. They are the result of the differences in the molecular interactions that occur within folded proteins and those that occur between unfolded proteins and water. More than 20 years ago, several groups determined experimentally the extent of volume changes that occur on folding [1], [2], [3]. These experiments were carried out to test the hydrophobic model for protein stability [4]: the results were not those expected.
It was found that on protein folding the volume changes are very small (< 0.5%) at normal pressures but large and positive at high pressures — i.e. at low pressures the folded and unfolded states occupy the same volume but at high pressure the unfolded state is more compact. Models of the hydrophobic effect, based on the transfer of non-polar solutes from water to organic solvent, predict that the volume changes on folding would be positive at low pressure and negative at high pressure — i.e. the unfolded state should be more compact at low pressure and less compact at high pressure [4].
A consequence of the failure of the solution transfer models to account for the observed volume changes was that the molecular mechanisms that underlay the changes were not understood [1], [2], [3]. However, as Kauzmann has argued [5], for any model of protein stability to be successful it must account for these observations.
Soon after these experiments, Richards introduced a procedure for determining directly the volumes of residues buried in the interior of protein structures [6]. Its application to the early protein crystal structures showed clearly that their interiors are close-packed as in crystals of amino acids [6], [7]. Though this discovery has been important for subsequent calculations and experiments on protein stability it raised a new problem: the total protein volumes given by these calculations were significantly larger than the volumes determined by solution experiments [6].
Here we provide an explanation for the volume changes on protein folding. This explanation is based upon a redetermination of the volumes residues occupy in folded proteins (which demonstrates that they are smaller than previously thought) and a comparison of these new volumes with the volumes residues occupy in solution.
Section snippets
Redetermination of the mean volumes of residues in protein interiors
The current values for the mean volumes of residues buried in protein interiors were determined from the atomic coordinates of 15 proteins (the set of structures that was available at the time) [7]. Much more accurate and extensive crystallographic data are now available and we used these to redetermine the volumes of buried residues.
We initially took 119 different proteins from the protein structure data bank [8]. All had different sequences, were determined at high resolution (between 1.0 å
Biological implications
On protein folding, residues are transferred from solution to the close-packed interior of the molecule. This change produces different effects on different groups: aliphatic groups occupy smaller volumes in proteins than they do in solution; polar groups occupy larger volumes. Examination of the surfaces buried in a wide range of proteins shows that the proportions of these groups that become buried is essentially constant and are such that the positive and negative volume changes cancel each
Acknowledgements
We thank Drs JT Edsall, FM Richards, RL Baldwin and M Han for discussions of our results and J Goodfellow and TH Lilley for information. MG is supported by an Damon-Runyon Walter-Winchell Fellowship.
Dedication
This paper is dedicated to John Edsall on the sixtieth anniversary of his paper with Cohn, McKeekin and Blanchard [14] on the volumes of residues in solution.
Yehouda Harpaz, Cambridge Centre for Protein Engineering, Hills Road, Cambridge, CB2 2QH, UK.
Mark Gerstein, MRC Laboratory of Molecular Biology and Cambridge Centre for Protein Engineering, Hills Road, Cambridge CB2 2QH, UK and Beckman Laboratories for Structural Biology, Department of Cell Biology, Stanford Medical School, Stanford, CA 94305, USA.
Cyrus Chothia, MRC Laboratory of Molecular Biology and Cambridge Centre for Protein Engineering, Hills Road, Cambridge CB2 2QH, UK.
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Yehouda Harpaz, Cambridge Centre for Protein Engineering, Hills Road, Cambridge, CB2 2QH, UK.
Mark Gerstein, MRC Laboratory of Molecular Biology and Cambridge Centre for Protein Engineering, Hills Road, Cambridge CB2 2QH, UK and Beckman Laboratories for Structural Biology, Department of Cell Biology, Stanford Medical School, Stanford, CA 94305, USA.
Cyrus Chothia, MRC Laboratory of Molecular Biology and Cambridge Centre for Protein Engineering, Hills Road, Cambridge CB2 2QH, UK.