Alanine dipeptide solvent effects

The molecular dynamics method has been applied recently to do an extensive study of solvent interactions in a solution of an alanine dipeptide in water[l7b,c]. The effect of solute proximity on dynamic behavior of the solvent, the range of influence of the solvent, the nature of the solvent in the neighborhood of various functional groups in the peptide, as well as the effects of solvent on the peptide dynamics were investigated in these works. 

Stochastic dynamics has been found to be particularly useful for introducing simplified descriptions of the internal motions of complex systems. When applied to small systems (e.g., a peptide or an amino acid sidechain) it is possible to do simulations that extend into the microsecond range, where many important phenomena occur. Simulation studies using this method have been carried out, for example, to explore solvent effects on the dynamics of internal soft degrees of freedom in small biopolymers, e.g., the dynamics of dihedral angle rotations in the alanine dipeptide (see Chapt. IX.B.l). 

Figure 41. Solvent viscosity effects on low-frequency motions of alanine dipeptide. The normalized spectral density for the dihedral angle is plotted versus frequency (ps 1) for (a) dynamics on a vacuum potential surface (see Fig. 58a) (6) dynamics with a potential of mean force (see Fig. 58b) in a solvent of viscosity, y = 1.0 cP (c) dynamics with a potential of mean force (see Fig. 586) in a solvent of viscosity, ij > 1.0 cP.

N. Gresh, G. Tiraboschi, and D. R. Salahub, Biopolymers, 45(6), 405-425 (1998). Conformational Properties of a Model Alanyl Dipeptide and of Alanine-Derived Ohgopeptides Effects of Solvation in Water and in Organic Solvents - A Combined SIBFA/Continuum Reaction Field, ab Initio Self-Consistent Field, and Density Functional Theory Investigation. 

We have been more concerned with the nature of the water around proteins and peptides. To this end we have investigated the structure and energetics of the solvent, both ordered and disordered around the enzyme lysozyme, in the triclinic crystal[l7d]. In addition to lysozyme, we have characterized the water structure and fluctuations in the crystal of a cyclic hexapeptide, (L-Ala-L-Pro-D-Phe)9[20]. and studied the effect of solvent on the conformation of the dipeptide of alanine[2l] and on the equilibria between extended and helical alanine polypeptides such as those discussed in the previous section[22]. The latter systems simulate aqueous solution conditions rather than crystalline environment. 

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