Molecular Probes: What Is the Range of Their Interaction with the Environment?

Abstract

We performed pressure-tuning hole-burning experiments on a modified cytochrome c protein in a glycerol/buffer glass. The shift and the broadening of the holes were investigated for various frequencies within the inhomogeneous band. On the basis of a simple model, we were able to estimate the interaction range between chromophore and protein. It is approximately 4.5 A. The parameters that enter the model are the compressibility, the static mean-square displacement, the inhomogeneous width, and the average spectral shift per pressure. From this result and from our experiments on pressure-induced denaturing, we conclude that water molecules have to be brought very close to the chromophore during the denaturation process.

Optical Spectroscopy of Biomolecular Dynamics

“…Two lecturers discussed the effect of pressure on the thermodynamics of folding. Joseph Friedrich from the Technical University in Munich (Germany) elaborated on the fascinating elliptic form of the phase diagram of proteins in the temperature-pressure plane and showed how solvent interactions change with pressure, as reflected in the spectra of the chromophore of Zn-cytochrome c. [12] Roland Winter (Dortmund, Germany) showed that temperaturepressure studies, combined with a variety of spectroscopic methods, can be used to parameterize an empirical energy landscape for a folding protein. [13] He also discussed a sophisticated pressure-jump spectrometer and its application to folding.…”

General Framework of Pressure Effects on Structures Formed by Entropically Driven Self-Assembly

“…It has been observed in experiments that denaturation of the native structure (pressure denaturation) [2][3][4][5][6] and dissolution of amyloid-fibrils [7][8][9] and virus assemblies [10] occur at high pressures. A common feature of these phenomena is that the volume change upon the pressure denaturation and dissociation is negative [3,6,10,11].…”

“…The characteristics of the pressure-denatured structure of a protein have been analyzed in detail [2,[4][5][6][12][13][14][15][16]. For example, the pressure dependence of the radius of gyration, R g , of staphylococcal nuclease has been studied using synchrotron X-ray small-angle scattering [2] and small-angle neutron scattering [5].…”

“…In addition, some degree of β-like secondary structure is retained, even above 300 MPa [2], indicating that the pressure-denatured structure is different from the random-coil structure. Some authors have suggested that water has to penetrate into the protein interior to explain the experimental results [4,5,16]. The penetration of water into the protein interior has been observed using molecular dynamics (MD) simulations [13][14][15]-the number of the water molecules in the protein interior increases as the pressure becomes higher.…”

Estimating Hydrogen Bond Energy in Integral Membrane Chromoproteins by High Hydrostatic Pressure Optical Spectroscopy

“…According to Lesch et al (Lesch, Schlichter et al 2004) the integrity of protein complexes can be monitored with sub-nanometer spatial resolution by the so-called molecular probe method. Fig.…”