• Corpus ID: 94697400

Computer Modeling of Chemical Reactions in Enzymes and Solutions

  title={Computer Modeling of Chemical Reactions in Enzymes and Solutions},
  author={Arieh Warshel},
Basic Principles of Chemical Bonding. Chemical Reactions in the Gas Phase and in Simple Solvent Models. Chemical Reaction in All--Atom Solvent Models. Potential Surfaces and Simulations of Macromolecules. Modeling Reactions in Enzymes: An Introduction. General Acid Catalysis and Electrostatic Stabilization in the Catalytic Reaction of Lysozyme. Serine Proteases and the Examination of Different Mechanistic Options. Simulating Metalloenzymes. How Do Enzymes Really Work? Index. 

Computational enzymology.

Computer simulations and modelling can provide detailed, atomic-level insight into the fundamental mechanisms of biological catalysts and potential practical applications include interpretation of experimental data, catalyst design and drug development.

Computer Simulation of the Triosephosphate Isomerase Catalyzed Reaction (*)

The calculations clearly demonstrate the important catalytic effects associated with stabilization of charged high energy intermediates and reduction of reorganization energy, which are likely to be general principles of enzyme catalyzed charge transfer and separation reactions.

Computational Studies of Enzyme-Catalyzed Reactions: Where Are We in Predicting Mechanisms and in Understanding the Nature of Enzyme Catalysis?

Although the preorganization free energy contains a large entropic contribution, entropy effects on going from the enzyme−substrate noncovalent complex to the transition state for the reaction are expected to be generally small and not very different in enzyme and in solution.

How Enzymes Work: Analysis by Modern Rate Theory and Computer Simulations

A framework for understanding the effects of lowering of the activation free energy and changes in the generalized transmission coefficient on enzyme catalysis is presented, and the contributions of the different factors are identified and quantified by computer simulations.

Simulating enzyme reactions: Challenges and perspectives

  • M. Field
  • Computer Science
    J. Comput. Chem.
  • 2002
Some of the processes that need to be investigated if enzyme catalysis is to be understood are outlined, the current state‐of‐the‐art in enzyme simulation work is reviewed, and challenges for the future are highlighted.

Computational modeling of enzymatic keto-enol isomerization reactions

Abstract. Catalysis of proton abstraction from nonacidic carbon atoms adjacent to a carbonyl or carboxylate group is a fundamental reaction in enzymology that has been extensively studied during the

Quantum Mechanical Modeling: A Tool for the Understanding of Enzyme Reactions

In this review, an overview to non-specialists on various enzyme models as well as established computational methods are given and applications to some specific cases are described.



Evaluation of Activation-Free Energies

    Factors That Are Not So Effective in Enzyme Catalysis [209] 9.2.1. It Is Hard to Reduce Activation Free Energies in Enzymes by Steric Strain

      Entropic Factors Should be Related to Well-Defined Potential Surfaces [217] 9.3.2. Entropic Factors in Model Compounds and Their Relevance to Enzyme Catalysis

        All-Atom Models for Proton Transfer Reactions in Enzymes

          Linear Free-Energy

            Calculation of Solvation Energies by Free-Energy Perturbation Methods [80] 3.3.1. Direct Calculations of Free Energy Converge Very

              Appendix B-Four Electrons/Three Orbitals VB Treatment

                Molecular Dynamics and Phase Space Exploration

                  Some Relevant Computer Programs

                    Normal Modes Analysis of Large Molecules