Description Theoretical chemistry has been an area of tremendous expansion and development over the past decade; from an approach where we were able
to treat only a few atoms quantum mechanically or make fairly crude molecular dynamics simulations, into a discipline with an accuracy
and predictive power that has rendered it an essential complementary tool to experiment in basically all areas of science.
This
volume gives a flavour of the types of problems in biochemistry that theoretical calculations can solve at present, and illustrates the
tremendous predictive power these approaches possess.
A wide range of computational approaches, from classical MD and Monte Carlo
methods, via semi-empirical and DFT approaches on isolated model systems, to Car-Parinello QM-MD and novel hybrid QM/MM studies are covered.
The systems investigated also cover a broad range; from membrane-bound proteins to various types of enzymatic reactions as well as inhibitor
studies, cofactor properties, solvent effects, transcription and radiation damage to DNA.
Audience
For experimental and research chemists and biochemists who use theoretical and computational techniques in their work.
Contents
The Structure and Function of Blue Copper Proteins (U. Ryde,
M.H.M. Olsson and K. Pierloot). Introduction. Methods.
Geometry. Electronic spectra. Reorganisation energies. Reduction potentials. Related proteins. Protein strain. Concluding remarks.
Myoglobin (D. Karancsi-Menyhard, G. Keserü and G. Náray-Szabó). Introduction. Conformation and
structural dynamics. Complexes with various ligands. Photodissociation. Recombination. Ligand migration.
Mechanisms for
Enzymatic Reactions Involving Formation or
Cleavage of O-O Bonds (P.E.M. Siegbahn and M.R.A. Blomberg). Introduction. Methods
and models. Formation of O2. O-O bond cleavage. Conclusions.
Catalytic Reactions of Radical Enzymes (F.
Himo and L.A.
Eriksson). Introduction. Methodology. Galactose oxidase. Pyruvate formate-lyase. Ribonucleotide reductase. Concluding
remarks.
Theoretical Studies of Coenzyme B12-Dependent Carbon-Skeleton Rearrangements (D.M. Smith, S.D.
Wetmore and L. Radom). Introduction. Background. Evaluation of theoretical techniques. 2-Methyleneglutarate mutase. Methylmalonyl-CoA
mutase. Glutamate mutase. Comparison of the models for B12-dependent carbon-skeleton mutases. The partial-proton-transfer
concept. Conclusions.
Simulations of Enzymatic Systems: Perspectives from Car-Parinello Molecular Dynamics Simulations (P.
Carloni and U. Rothlisberger). Introduction. Principles of the Car-Parinello method. Car-Parinello modelling of biological systems.
Applications to non-enzymatic systems. Applications to enzymes. Outlook.
Computational Enzymology: Protein Tyrosine Phosphatase
Reactions (K. Kolmodin, V. Luzhkov and J. Åqvist). Introduction. Protein tyrosine phosphatase reactions. The empirical
valence bond method. Reaction free energy profile of the LMPTP. Substrate trapping in cysteine to serine mutated PTPases. Prediction
of a ligand induced conformational change in the active site of CDC25A. Kinetic isotope effects in phosphoryl transfer reactions.
Monte
Carlo Simulations of HIV-1 Protease Binding Dynamics and Thermodynamics with Ensembles of Protein Conformations: Incorporating Protein
Flexibility in Deciphering Mechanisms of Molecular Recognition (G.M. Verkhivker, D. Bouzida, D.K. Gehlhaar, P.A. Rejto, L. Schaffer,
S. Arthurs, A.B. Colson, S.T. Freer, V. Larson, B.A: Luty, T. Marrone and P.W. Rose). Structural models for molecular recognition.
Structure-based analysis of HIV-1 protease-inhibitor binding. Structure-based computational models of ligand-protein binding dynamics
and molecular docking. Computer simulations of ligand-protein binding. Computer simulations of HIV-1 protease-inhibitor binding dynamics
and thermodynamics. Conclusions.
Protein-DNA Interactions in the Initiation of Transcription: The Role of Flexibility and Dynamics of the TATA Recognition Sequence
and the TATA Box Binding Protein (N. Pastor and H. Weinstein). TBP and transcription. TATA box sequence specific recognition.
Dynamics effects in complex stabilization. Towards the preinitiation complex assembly. Concluding remarks.
A Multi-Component
Model for Radiation Damage to DNA
from its Components (S.D. Wetmore, L.A. Eriksson and R.J.
Boyd). Introduction. Characterization
of DNA radiation products. Full DNA studies. Multi-component model for DNA radiation damage. Concluding remarks.
New Computational
Strategies for the Quantum Mechanical Study of Biological Systems in Condensed Phases (C. Adamo,
M. Cossi, N. Rega and V. Barone).
Introduction. The density functional model. Vibrational averaging. Solvent effects. Applications. Concluding remarks.
Modelling
Enzyme-Ligand Interactions (M.J. Ramos, A. Melo
and E.S. Henriques). Introduction. Strategies in enzyme-ligand design. The
enzyme-ligand complex in motion. A quantum insight into the study of enzyme-ligand interactions. Conclusions.
The QM/MM Approach
to Enzymatic Reactions (A.J.
Mulholland). Introduction. Theory. QM/MM methods. Techniques for reaction modelling. Practical
aspects of modelling enzyme reactions. Some recent applications. Conclusions.
Quinones and Quinoidal Radicals in Photosynthesis (R.A. Wheeler). Introduction. Tests of computational methods for calculating properties of quinoidal radicals. Calculated
properties of quinoidal radicals important in photosynthesis. Semiquinone radical anions in plant photosystem II. Conclusion and future
directions.
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