Realization of the structural fluctuation of biomolecules in solution: Generalized Langevin mode analysis.

Abstract

A new theoretical method, referred to as Generalized Langevin Mode Analysis (GLMA), is proposed to analyze the mode of structural fluctuations of a biomolecule in solution. The method combines the two theories in the statistical mechanics, or the Generalized Langevin theory and the RISM/3D-RISM theory, to calculate the second derivative, or the Hessian matrix, of the free energy surface of a biomolecule in aqueous solution, which consists of the intramolecular interaction among atoms in the biomolecule and the solvation free energy. The method is applied to calculate the wave-number spectrum of an alanine dipeptide in water for which the optical heterodyne-detected Raman-induced spectroscopy (RIKES) spectrum is available to compare with. The theoretical analysis reproduced the main features of the experimental spectrum with respect to the peak positions of the four bands around ~90 cm-1 , ~240 cm-1 , ~370 cm-1 , and 400 cm-1 , observed in the experimental spectrum, in spite that the physics involved in the two spectrum was not exactly the same: the experimental spectrum includes the contributions from the dipeptide and the water molecules interacting with the solute, while the theoretical one is just concerned with the solute molecule, influenced by solvation. Two major discrepancies between the theoretical and experimental spectra, one in the band intensity around ~100 cm-1 , and the other in the peak positions around ~370 cm-1 , are discussed in terms of the fluctuation mode of water molecules interacting with the dipeptide, which is not taken explicitly into account in the theoretical analysis.