Time scales and fluctuations of protein dynamics metmyoglobin in aqueous solution

Dynamic motions in biological systems are thought to play a very important role in determining their functionality and material properties [1]. Both theoretical and experimental methods of studying kinetics and molecular dynamics have become valuable tools for understanding biomolecular function [2]. The fundamental fluctuations in both main-chain and side-chain positions provide a wealth of detail into structures and mechanisms responsible for the various functional roles that proteins play. 

While current computer simulations give a level of detail that is not presently available from experiments, discrepancies both among various simulations [3,4] and with observable properties exist. The cause of the observed disagreement may be due in some cases to treatment of environmental influences around the protein [5]. Other problems between theoretical studies may include parameter differences [6] and sample preparations. 

Since a number of relatively complete reviews of protdn molecular dynamics exist [1,2], it seems appropriate to illustrate a single example in some detail to highlight the successes and weaknesses of this sort of theoretical investigation. To this end, in this contribution, we present a representative 150 ps molecular dynamics simulation of metmyoglobin in water. Myoglobin has been the object of extensive experimental [7] and theoretical [2] studies and hence serves as a useful case for comparing molecular simulation methodologies and experiments. 

In section 7.2, we describe the general methods used in this dynamic simulation of metmyoglobin in water. Since the principle of solving Newton s equations of motion for a given force field is commonly appreciated, the reader interested in more details is referred to [2]. Following this, we present comparisons of our results with experimental data and with previous computer simulations which do not include explicit water molecules. The final section presents a discussion about the present study. 

NVTsimulation was then carried out on the system and, as we will describe in the later sections, the system actually achieved equilibrium-like properties considerably later in the simulation. While temperature and energy fluctuations occur with this algorithm, the average of the temperature of the system holds constant without drift. 

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Time scales and fluctuations of protein dynamics metmyoglobin in aqueous solution... 

L. A. Findsen, S. Subramaniam, V. Lounnas, and B. M. Pettitt, in Principles of Molecular Recognition, A. D. Buckingham, Ed., Chapman Hall, London, 1993, pp. 168-193. Time Scales and Fluctuations of Protein Dynamics Metmyoglobin in Aqueous Solution. 

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