Protein-solvent system

A factor of 6.25 was used to convert nitrogen content to protein. Solvent systems used included (1) O.OIM phosphate buffer, pH 7.2 (2) O.OIM carbonate buffer, pH 10.0 (3) Phosphate buffer + 1% 2-mercaptoethanol (2-ME) (4) Phosphate buffer + 1% sodium dodecyl sulfate (SDS) and (5) Phosphate buffer + 1% 2-ME +1% SDS. 

In protein structure prediction, potentials are used to assign an energy-like quantity to a conformation of a protein molecule. If this quantity enables us to distinguish the native state of a protein, the potential is regarded as a reasonable model for a protein-solvent system. The rationale behind this relies on two assumptions (a) a solved protein in its native state can be described by an ensemble of closely related conformations, and (b) in this state the system is in the global minimum of free energy. Virtually all techniques designed for structure prediction are based on these principles [3,4]. 

Several factors compensate the protein-solvent system for the loss of chain entropy required by folding ... 

We can reasonably assume two major contributions to the difference in specific volume between the unfolded and folded states of a protein. The first contribution is that arising from the decrease in solvent-excluded volume when the tightly, but of course not perfectly, packed protein folded structure is disrupted. Water molecules enter this volume, thereby decreasing the overall volume of the protein solvent system. The magnitude of this contribution is a specific property of the protein, both in its folded and unfolded state. The second contribution arises from the change in the volume of the water molecules that hydrate the newly exposed protein surface area, relative to their volume in the bulk. Much of our present understanding of the contribution of differential hydration volume has come from recent studies of model compounds and proteins based on PPC. This technique, developed by Brandts and coworkers [17] and recently reviewed by us [16,18], is based on the measurement of the heat released or absorbed upon small (e.g., 0.5 MPa) pressure... 

The interplay of these factors is difficult to evaluate quantitatively in the general protein-solvent system. Some useful qualitative conclusions, however, may be arrived at in certain extreme cases. 

From an operational point of view, the influence of electrostatic interactions in a particular protein-solvent system can be greatly diminished, often... 

The equilibrium state of any process involving an enthalpy change must be affected by temperature. The conformational transitions in proteins discussed in Section Pf,E are a case in point. The transition from the native to the denatured form in a nonaqueous solvent is usually an endothermic process, and a decrease in temperature will favor the native form. In such cases, it is possible that the disruption of the native conformation in a given protein-solvent system, which observed at room temperatures, may be reversed at sufficiently low temperatures. [On the other hand, particularly in mixed solvents, the transition from an ordered to a disordered state may be an exothemic process (Doty and Yang, 1956 Foss and Schellman, 1959), and the reverse effect of temperature may be ob-... 

In cases in which a sharp question can be formulated and so suggest a test of a mechanism of solvent participation, site-directed mutagenesis provides an experimental tool, perhaps appropriately guided by computer simulation of the protein—solvent system. The participation of fixed or random (percolative) network structures in proton movement is... 

H. Nakamura, /. Phys. Soc. Japan, 57, 3702 (1988). Numerical Calculations of Reaction Fields of Protein-Solvent Systems. 

Protein-Solvent System and Calculation of the Long-Range Electrostatic Field of the Enzyme Phosphoglycerate Mutase. 

The theoretical background to classical electrostatics is first reviewed, beginning with the physical basis for the electrostatic response of a protein/solvent system to a charge distribution, and ways of modelling this response. Consistent classical electrostatic frameworks for describing a protein/solvent system are then described. In addition the methods must be able to model temperature, pH and ionic strength effects if these affect the property of interest. Of particular importance is the way one may extract experimentally observable properties from such models. 

Protein solubility is a thermodynamic characteristic of the protein/solvent system dehned as the concentration of soluble protein in equilibrium with the solid phase at a given pH, temperature, and solvent composition (Flynn, 1984 Arakawa and Timashelf, 1985 Middaugh and Volkin, 1992). For practical purposes, solubility of proteins can be dehned as the maximum amount of protein that remains in a visibly clear solution (i.e. does not show protein precipitates, crystals, gels, or hazy soluble aggregates), or does not sediment at 30,000 g centrifugation for 30 min (Schein, 1990 Ducruix and Reis-Kautt, 1990). 

Undoubtedly, the realism of any simulation of a protein-solvent system will be further enhanced if all parts of the system experience thermal motion. Because water molecules interact most strongly with polar side chains and because the conformation of long polar side chains may be subject to considerable thermal disorder, flexibility of side chains, in particular, is a major aspect of protein-solvent interaction. Thermal motion of side chains could be provided for rather simply by rigid-body internal rotation of side chains about side-chain single bonds as part of the Monte Carlo process. 

As mentioned in section 16.3.1, rate constant calculations often rest on the determination of the activation free-energy which is usually deduced from the free-energy profile of the system as a function of the reaction coordinate. The reaction coordinate x is a function xif) of the coordinates of the atoms of the system chosen so as to follow the reaction advancement. In an ensemble of protein + solvent systems in equilibrium at temperature T, the x value distribution is characterized by the probability density p(x) given by ... 

This chapter provides an introductory overview of the approaches used to predict ionization states of titratable residues in proteins, based on the assumption that the difference in protonation behavior of a given group isolated in solution, for which the ionization constant is assumed to be known, and the protonation behavior in the protein environment is purely electrostatic in origin. Calculations of the relevant electrostatic free energies are based on the Poisson-Boltzmann (PB) model of the protein-solvent system and the finite difference solution to the corresponding Poisson-Boltzmaim equation. We also discuss some relevant pH-dependent properties that can be determined experimentally. The discussion is limited to models that treat the solvent and the solute as continuous dielectric media. Alternative approaches based on microscopic simulations, which can be useful for small molecules (e.g., see Refs. 19-24) are not covered here because they are, in general, too time intensive for proteins. The present treatment is intended to be simple and pedagogic. 

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