Molecular Modeling and Dynamics of Bioinorganic Systems

ISBN-13: 9789401061742 / Angielski / Miękka / 2012 / 470 str.

Lucia Banci;Peter Comba

Opis

A unique selection of papers on the most recent progress in the modelling of biological molecules containing metal ions.
New approaches and techniques in this field are allowing researchers to discuss structures, electronic properties and reaction mechanisms of metalloproteins on the basis of computational studies. The book discusses different approaches in the development of new force fields and their application to the computation of the structures, electronic properties and dynamics of bioinorganic compounds as well as quantum mechanical and integrated QM/MM methods for understanding the function of metalloenzymes and the calculation of electrostatic interactions.

Spis treści

Preface. 1. Solution Structures of Proteins Containing Paramagnetic Metal Ions; I. Bertini, A. Rosato. 2. Modeling of Structures and Molecular Properties of Transition Metal Compounds - Toward Metalloprotein Modeling; P. Comba. 3. Extending Molecular Mechanics Methods to the Descriptions of Transition Metal Complexes and Bond-Making and -Breaking Processes; C.R. Landis, et al. 4. A Novel Molecular Mechanics Strategy for Transition Metals Bound to Biological Molecules; R.J. Deeth, et al. 5. Computational Analysis of Inorganic and Bio-Inorganic Nickel Complexes; C. Csiki, et al. 6. Molecular Modeling of Platinum Complexes with Oligonucleotides: Methodological Lessons and Structural Insights; M.-A. Elizondo-Riojas, et al. 7. Metal Cations in Biological Systems: Modeling Metal Ions in Ionophores and DNA; P. Kollman. 8. The Role of Ca2+ in the Binding of Carbohydrates to C-Type Lectins as Revealed by Molecular Mechanics and Molecular Dynamics Calculations; C.-W. von der Lieth. 9. Molecular Dynamics Calculations on Metalloproteins; L. Banci, G.G. Savellini. 10. The Effective Crystal Field Methodology as used to Incorporate Transition Metals into Molecular Mechanics; A.L. Tchougréeff. 11. Quantum Chemical Studies of Transition Metal Catalyzed Enzyme Reactions; P.E.M. Siegbahn. 12. Ab Initio and Density Functional Theory Applied to Models for the Oxo Transfer Reaction of Dioxomolybdenum Enzymes; S. Zaric, M.B. Hall. 13. Quantum Mechanical Modeling of Active Sites in Metalloproteins. Electrostatic Coupling to the Protein/Solvent Environment; J. Li, et al. 14. Semi-Empirical MOCalculations on Enzyme Reaction Mechanisms; T. Clark, et al. 15. Normal Mode Analysis of Proteins to Interpret Resonant and Inelastic Scattering of &ggr; Quanta; E.W. Knapp, et al. 16. Computer Simulations of the Action of Metalloenzymes; A. Warshel. 17. The Role of the Protein in Modulating Cofactor Electrochemistry in Proteins: The Calculation of Electrostatic Forces; M.R. Gunner, E. Alexov. 18. Molecular Dynamics Study of H93G Sperm Whale Deoxymyoglobin Mutants with Exogenous Proximal Ligands; W. Nowak. 19. The Role of Electrostatics at the Catalytic Metal Binding Site in Xylose Isomerase Action; B. Asbóth, et al. 20. Copper(II) and Zinc(II) Complexes of Peptides as Models for Collagenase Inhibitors; K. Várnagy, H. Süli-Vargha. Subject Index.