Protein structure solvent effects

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 the structurally coupled QM/MM implementation of Zhang et al. [55, 56], in which the QM/MM boundary was treated by use of the pseudobond approach [55, 57], the QM/MM minimization of the QM part is combined with FEP calculations. In this procedure the energy profile of the enzyme reaction is first determined by use of QM/MM energy minimizations. The structures and charges of the QM atoms are then used, in the same manner as in the QM/FE method, to determine the role of environment on the energy profile of the reaction. In this way the effects of a large number of MM conformations of protein and solvent environment can be included in the total energies. 

R. W. Cowgill, Fluorescence and protein structure X. Reappraisal of solvent and structural effects, Biochim. Biophys. Acta 133, 6-18 (1967). 

When 18-crown-6 was co-lyophilized with a-chymotrypsin, a 470-fold activation was seen over the free enzyme in the transesterification of APEE with 1-propanol in cyclohexane (Scheme 3.2) [96]. There was a low apparent specificity for the size and macrocyclic nature of the crown ether additives, suggesting that, during lyophilization, 18-crown-6 protects the overall native conformation and acts as a lyoprotectant. To examine this global effect, FTIR was used to examine the effect of crown ethers on the secondary structure of enzymes. In one study [98], subtilisin Carlsberg was shown to retain its secondary structure in 1,4-dioxane when lyophi-lized in a 1 1 ratio with 18-crown-6. In addition, examination of FTIR spectra from varying incubation temperatures indicated that an increase in crown ether content in the final enzyme preparation resulted in a decreased denaturation temperature in the solvent, indicating a more flexible protein structure. 

Recall that stable protein crystals contain a large amount of both ordered and disordered water molecules. As a result, the proteins in the crystal are still in the aqueous state, subject to the same solvent effects that stabilize the structure in solution. Viewed in this light, it is less surprising that proteins retain their solution structure in the crystal. 

A major problem in predicting protein structure is the computational intractability. A short, 100-residue protein will contain at least 100 side-chain-to-side-chain or side-chain-to-solvent interactions. The orientation of each of these interactions will lead to cascading effects throughout the protein. Comparative modeling, threading algorithms, and de novo predictions seek to predict protein structure in reasonable execution times. 

Hydrophobic forces The hydrophobic effect is the name given to those forces that cause nonpolar molecules to minimize their contact with water. This is clearly seen with amphipathic molecules such as lipids and detergents which form micelles in aqueous solution (see Topic El). Proteins, too, find a conformation in which their nonpolar side chains are largely out of contact with the aqueous solvent, and thus hydrophobic forces are an important determinant of protein structure, folding and stability. In proteins, the effects of hydrophobic forces are often termed hydrophobic bonding, to indicate the specific nature of protein folding under the influence of the hydrophobic effect. 

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