Protein solvent, effects

Including the solvent around a protein can be done, in principle, by the explicit approach of Chapter 3. Such a treatment, however, is very expensive, in view of the large number of water molecules needed to properly solvate the entire protein. Thus we will consider below two alternative approaches which allow one to effectively represent the solvent. The discussion of these models will be focused on electrostatic aspects where the importance of solvent effects is easily demonstrated. 

The use of computer simulations to study internal motions and thermodynamic properties is receiving increased attention. One important use of the method is to provide a more fundamental understanding of the molecular information contained in various kinds of experiments on these complex systems. In the first part of this paper we review recent work in our laboratory concerned with the use of computer simulations for the interpretation of experimental probes of molecular structure and dynamics of proteins and nucleic acids. The interplay between computer simulations and three experimental techniques is emphasized (1) nuclear magnetic resonance relaxation spectroscopy, (2) refinement of macro-molecular x-ray structures, and (3) vibrational spectroscopy. The treatment of solvent effects in biopolymer simulations is a difficult problem. It is not possible to study systematically the effect of solvent conditions, e.g. added salt concentration, on biopolymer properties by means of simulations alone. In the last part of the paper we review a more analytical approach we have developed to study polyelectrolyte properties of solvated biopolymers. The results are compared with computer simulations. 

In this volume not all stress types are treated. Various aspects have been reviewed recently by various authors e.g. The effects of oxygen on recombinant protein expression by Konz et al. [2]. The Mechanisms by which bacterial cells respond to pH was considered in a Symposium in 1999 [3] and solvent effects were reviewed by de Bont in the article Solvent-tolerant bacteria in biocatalysis [4]. Therefore, these aspects are not considered in this volume. Influence of fluid dynamical stresses on micro-organism, animal and plant cells are in center of interest in this volume. In chapter 2, H.-J. Henzler discusses the quantitative evaluation of fluid dynamical stresses in various type of reactors with different methods based on investigations performed on laboratory an pilot plant scales. S. S. Yim and A. Shamlou give a general review on the effects of fluid dynamical and mechanical stresses on micro-organisms and bio-polymers in chapter 3. G. Ketzmer describes the effects of shear stress on adherent cells in chapter 4. Finally, in chapter 5, P. Kieran considers the influence of stress on plant cells. 

Salvi G, De Los Rios P. Effective interactions cannot replace solvent effects in a lattice model of proteins. Phys Rev Lett 2003 91. 

The racemization of the phosphine (118) has been followed by optical rotation. The lack of a solvent effect indicates that there is little change in dipole moment in the formation of the planar transition state. Circular dichroism has been used to study the interactions of nucleotides with proteins and DNA with a histone. Faraday effects have been reviewed. Refraction studies on chloro-amino-phosphines, fluoro-amino-phosphines, and some chalcogenides are reported. 

Altoe P, Bemardi F, Garavelli M, Orlandi G, Negri F (2005) Solvent effects on the vibrational activity and photodynamics of the green fluorescent protein chromophore a quantum-chemical study. J Am Chem Soc 127 3952-3963... 

O. Tapia, Local field representation of surrounding medium effects. From liquid solvent to protein core effects, in Quantum Theory of Chemical Reaction, Vol. 2, R. Daudel, A. Pullman, L. Salem, and A. Veillard, eds., Reidel, Dordrecht (1980) pp. 25-72. 

The development of biological tools to support DDI studies has paralleled the development of bioanalytical techniques. To better understand in vitro-in vivo (IVIV) correlations, the effects of differences in enzyme preparations and incubation conditions must be understood. Differences between enzyme preparations include nonspecific binding, the ratio of accessory proteins (cytochrome b5 and reductase) to CYPs and genetic variability differences in incubation conditions include buffer strength, the presence of inorganic cations and solvent effects. Understanding how biology influences enzymatic activity is crucial to accurate and consistent prediction of the inhibition potential. 

D. A. Chignell and W. B. Gratzer, Solvent effects on aromatic chromophores and their relation to ultraviolet difference spectra of proteins, J. Phys. Chem. 72, 2934-2941 (1968). 

As a practical matter of cost, studies on solvent isotope effects are usually limited to D/H substituted solvents, although recently a few lsO solvent effects have been measured. Interpretation of enzymatic solvent isotope effects is even more complicated than it is when the isotopic probe is incorporated in the substrate(s). This is because enzyme proteins have many exchangeable protons and, also, this is frequently true for reactants (substrates). Thus the observed isotope effect is the collective result of many different isotopic substitutions, each of which may influence... 

---