Local Compressibilities of proteins: Comparison of optical experiments and simulations for horse heart cytochrome c

¹ Physik-Department E14, Lehrstuhl für Physik Weihenstephan

^* To whom correspondence should be addressed. E-mail: christina.scharnagl{at}physik.blm.tu-muenchen.de.

Submitted on December 1, 2004
Revised on January 4, 2005
Accepted on 1 April 2005

	Abstract

Spectroscopy with probe molecules yields local information on the environment of the probe. In this paper we compare local compressibilities of cytochrome c as obtained from molecular dynamics simulations with experimental results as obtained from spectroscopic measurements. The simulations show that the protein-core around the heme is much less compressible in a glycerol/water solvent than in pure water. The pocket is also much less compressible than the protein as a whole, although the compressibility of the water inside the rather incompressible protein-core is almost liquid-like. We show, that the local compressibility values capture the collective correlations of local volume fluctuations with volume fluctuations in the surrounding protein-solvent system. The decoupling of the volume fluctuations of the core from the solvent shell explains the reduction of the heme-core-compressibility in glycerol/water solvent. This decoupling could be traced back to the suppression of the exchange between pocket-water and hydration-shell-water upon addition of glycerol as cosolvent.

Key Words: compressibilities of proteins, cosolvent, hole burning spectroscopy, molecular dynamic simulations, protein hydration, volume fluctuation