By Charles L. Brooks, Martin Karplus, B. Montgomery Pettitt
Proposing a wide-ranging view of present advancements in protein examine, the papers during this assortment, every one written by means of extremely popular specialists within the box, research a number of points of protein constitution, services, dynamics, and experimentation. themes contain dynamical simulation equipment, the organic function of atom fluctuations, protein folding, impacts on protein dynamics, and quite a few analytical recommendations, akin to X-ray diffraction, vibrational spectroscopy, photodissociation and rebinding kinetics. this is often a part of a chain dedicated to supplying common info on a wide selection of issues in chemical physics in an effort to stimulate new study and to function a textual content for rookies in a specific zone of chemical physics.
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Extra resources for Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics. (Advances in Chemical Physics)(Vol. 71.)
Sample text
The atomic fluctuations required for larger “rigid-body’’ displacements, the sidechain oscillations that play a role in the entrance and exit of ligands in myoglobin, the allosteric transition in hemoglobin, the disorder-order transition in going from inactive trypsinogen to the active enzyme trypsin) there exist detailed theoretical and/or experimental studies of the motions involved. In many other cases, the role of the motion has been inferred only from structural studies that show two or more different conformations.
By solving Newton’s equations of motion to describe how the atomic positions change with respect to time. From the second derivatives of the potential surface, the force constants for small displacements can be evaluated and used to find the normal modes. The normal modes provide an alternative approach to the dynamics in the harmonic limit. In this chapter we outline the nature of the potential functions (force fields) that are generally employed for macromolecules. In the next chapter we describe methods that can be used to determine the dynamics over the wide range of time scales that is of interest.
The potential energy can be used directly to determine the relative stabilities of the different possible structures of the system. To obtain the forces acting on the atoms of the system, the first derivatives of the potential with respect to the atom positions are calculated. , by solving Newton’s equations of motion to describe how the atomic positions change with respect to time. From the second derivatives of the potential surface, the force constants for small displacements can be evaluated and used to find the normal modes.