Local compressibilities of proteins: comparison of optical experiments and simulations for horse heart cytochrome-c.
Spectroscopy with probe molecules yields local information on the environment of the probe. In this article 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 liquidlike. 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 co-solvent.
Scharnagl
Christina
C
Physik-Department E14, Lehrstuhl für Physik Weihenstephan, Technische Universität München, Freising, Germany. christina.scharnagl@physik.blm.tu-muenchen.de
Reif
Maria
M
Friedrich
Josef
J
D000042:Absorption; D000465:Algorithms; D000818:Animals; D003198:Computer Simulation; D045304:Cytochromes c / Q000737:chemistry*; D005990:Glycerol / Q000737:chemistry; D006418:Heme / Q000737:chemistry; D006736:Horses; D008958:Models, Molecular; D009206:Myocardium / Q000378:metabolism*; D011166:Porphyrins / Q000737:chemistry; D011312:Pressure; D011506:Proteins / Q000737:chemistry*; D012984:Software; D012997:Solvents / Q000737:chemistry; D013053:Spectrophotometry; D013314:Stress, Mechanical; D013696:Temperature; D013718:Tensile Strength; D014443:Tyrosine / Q000737:chemistry; D014867:Water / Q000737:chemistry
D011166:Porphyrins; D011506:Proteins; D012997:Solvents; D014867:Water; D014443:Tyrosine; D006418:Heme; D045304:Cytochromes c; D005990:Glycerol