Biomolecular conformation

Urry, D. W., Ohnishi, M. Spectroscopic Approaches to Biomolecular Conformation, p. 263, (ed. Urry, D. W.), American Medical Association Press, Chicago, Illinois 1970... 

Most descriptions of the dynamics of molecular or particle motion in solution require a knowledge of the frictional properties of the system. This is especially true for polymer solutions, colloidal suspensions, molecular transport processes, and biomolecular conformational changes. Particle friction also plays an important role in the calculation of diffusion-influenced reaction rates, which will be discussed later. Solvent multiparticle collision dynamics, in conjunction with molecular dynamics of solute particles, provides a means to study such systems. In this section we show how the frictional properties and hydrodynamic interactions among solute or colloidal particles can be studied using hybrid MPC-MD schemes. 

In cases when the slow manifold is higher than one-dimensional (which is likely to be the case for complex biomolecular conformational changes), the guiding vector es is to be calculated for each initial configuration, or, if there is little variation in the slow direction for certain initial regions, a single es can be applied to some or all of the initial points. 

Kaltashov, I.A. Eyles, S.J. Studies of biomolecular conformations and conformational dynamics by mass spectrometry. Mass Spectrom. Rev. 2002, 21, 37-71. 

Doniach, S. (2001). Changes in biomolecular conformation seen by small angle X-ray scattering. Chem. Rev. 101, 1763-1778. 

The problems being addressed in recent work carried out in various laboratories include the fundamental nature of the solute-water intermolecular forces, the aqueous hydration of biological molecules, the effect of solvent on biomolecular conformational equilibria, the effect of biomolecule - water interactions on the dynamics of the waters of hydration, and the effect of desolvation on biomolecular association 17]. The advent of present generation computers have allowed the study of the structure and statistical thermodynamics of the solute in these systems at new levels of rigor. Two methods of computer simulation have been used to achieve this fundamental level of inquiry, the Monte Carlo and the molecular dynamics methods. 

Urry, D. W., and Ohnishi, M. Spectroscopic approaches to biomolecular conformation (ed. D. W. Urry) Chap. VII, pp. 263—303. Oiks American Medical Association 1970. 

Sampling of the biomolecular conformations is usually performed using MD simulations or Monte Carlo methods (61, 62). The protonation state of titrateable amino acids can be treated with constant pH dynamics, QM/MM calculations, or continuum electrostatics methods (61, 62). Formation of a protein-protein encounter complex is often studied using Brownian dynamics (63). Studies of protein-protein docking involve electrostatic potential analysis and, more recently, protein flexibility models, for example normal mode analysis (64). 

Multiscale Modelling in Molecular Dynamics Biomolecular Conformations as Metastable States ... 

E. Meerbach et al. Multiscale Modelling in Molecular Dynamics Biomolecular Conformations as Metastable States, Lect. Notes Phys. 703, 495-517 (2006)... 

C. Schiitte and W. Huisinga (2003) Biomolecular conformations can be identified as metastable sets of molecular dynamics. In Handbook of Numerical Analysis (P. G. Ciaret and J.-L. Lions, eds.). Computational Chemistry, North-Holland... 

A. Fischer, S. Waldhausen, I. Horenko, E. Meerbach, and C. Schiitte (2004) Identification of biomolecular conformations from incomplete torsion angle observations by hidden Markov models. Journal of computational Physics (submitted)... 

A. Markelz, S. Whitmire, J. Hillebrecht and R. Birge, THz time domain spectroscopy of biomolecular conformational modes, Phys. Med. Biol. 47(21), 3797-3805 (2002). 

The living organism is replete with particulate structures, such as membranes, mitochondria, nuclei, and connective tissue containing insoluble elastin. These structures contain molecules which either are not soluble or when solubilized would not necessarily reflect the conformation of interest within the particle. Accordingly, one would like to develop techniques for assessing biomolecular conformations in particulate systems. Progress has been made, in this connection, with the optical rotation methods. ... 

This work demonstrated (a) that there are distortions in the CD of particulate systems (this had not previously been appreciated and the distorted spectra had been interpreted in terms of unique conformational features), (b) that the distorted spectra can be calculated and hence corrected, and (c) that there is a measurable differential scatter of left and right circularly polarized light by optically active particles. Thus, in addition to correcting spectra for suspensions of particulate systems that may be interpreted in terms of biomolecular conformation, the third point makes it possible to obtain an optical rotatory dispersion spectrum for the particle surface. In the case of membranes this will allow determination of relative amounts of surface area which are covered by ordered protein. This information coupled with the CD spectrum for the whole membrane will provide considerable information on the structure of membranes. 

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