By Charles L. Brooks, Martin Karplus, B. Montgomery Pettitt

Providing a wide-ranging view of present advancements in protein study, the papers during this assortment, each one written by means of extremely popular specialists within the box, learn numerous facets of protein constitution, features, dynamics, and experimentation. themes comprise dynamical simulation equipment, the organic function of atom fluctuations, protein folding, affects on protein dynamics, and numerous analytical options, equivalent to X-ray diffraction, vibrational spectroscopy, photodissociation and rebinding kinetics. this is often a part of a chain dedicated to supplying basic info on a wide selection of issues in chemical physics with a purpose to stimulate new learn and to function a textual content for newcomers in a selected region of chemical physics.

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Additional info for Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics. (Advances in Chemical Physics)(Vol. 71.)

Example text

RN) and with the dissipative and random forces defined in Eqs. 10 and 11, respectively. In certain applications of the stochastic dynamics approach, the potential of mean force can be obtained by analysis of a full dynamical simulation. For example, the distribution function for one part of a protein (such as the orientation of a sidechain) is evaluated and then used to determine the potential of mean force. Alternatively, when all of the solvent or bath degrees of freedom are to be eliminated, the statistical mechanical theory for the equilibrium structure of polar fluids109J12-115a can be employed.

Often it is desirable to attempt such fits with a variety of weighting factors in the least-squares procedure to assure that a wellbalanced parameterization results. Experience has shown that useful information can be obtained by employing the presently available functional forms and parameter sets. Illustrations of the applications to dynamic and thermodynamic simulations are given in subsequent chapters. However, it must always be remembered that whatever the precision of the motional or thermodynamic properties obtained from the simulation methods, the ultimate accuracy of the results depends on the potential function that was used.

Two separate molecules interact with each other only through the nonbonded interactions unless reactions are being considered. Thus nonbonded interactions are common to both intermolecular and intramolecular potentials, whereas the other terms are strictly intramolecular. The important nonbonded interactions between atoms consist of a part that accounts for the excluded volume, the repulsive van der Waals term already mentioned, a part that models the dispersion attraction, and a part that characterizes the electrostatic interaction due to the partial charge and higher electric moments associated with each atom.

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