Dynamics of Proteins and Nucleic Acids
This book is a self-contained introduction to the theory of atomic motion in proteins and nucleic acids. An understanding of such motion is essential because it plays a crucially important role in biological activity. The authors, both of whom are well known for their work in this field, describe in detail the major theoretical methods that are likely to be useful in the computer-aided design of drugs, enzymes and other molecules. A variety of theoretical and experimental studies is described and these are critically analyzed to provide a comprehensive picture of dynamic aspects of biomolecular structure and function. The book will be of interest to graduate students and research workers in structural biochemistry (X-ray diffraction and NMR), theoretical chemistry (liquids and polymers), biophysics, enzymology, molecular biology, pharmaceutical chemistry, genetic engineering and biotechnology.
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Structure of proteins nucleic acids and their solvent
Dynamics of proteins nucleic acids and their solvent
Short time dynamics
Local structural transitions
Global structural changes
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active adiabatic mapping algorithm amplitude anharmonic atomic displacements atomic motion atomic positions atoms average backbone basepairs Berendsen biomolecular Biopolymers BPTI Brownian dynamics calculated collective motions collisions configurations conformational constraints correlation covalent covalent bonds described detailed diffusion double helical effects electrostatic energy barriers energy minimization enzyme equation example experimental fluctuations free energy frequency groups Gunsteren Harvey helix hinge bending motions hydrogen bonds interactions ions Journal Karplus kJ/mol Kollman Levitt ligand macromolecules McCammon mean force method molecular dynamics simulation myoglobin nonbonded nonbonded interactions normal mode normal mode analysis Northrup nucleic acids parameters particles polypeptide potential energy function potential function potential of mean Prabhakaran proteins and nucleic pucker rate constant reaction coordinate receptor region relative residues ribose ring rotations scale sidechains solution solvation solvent structure studies substrate surface temperature theoretical thermal thermodynamic Tidor trajectories transitions tRNA tRNAphe typical tyrosine values water molecules X-ray
Page 225 - Calculation of the electric potential in the active site cleft due to a-helix dipoles, J. Mol. Biol. 157:671-679 (1982). 10 21. MY Okamura, G. Feher, and N. Nelson, Reaction centers in: "Photosynthesis,
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