METHODS IN ENZYMOLOGY

By P. LUTIO

CONTENTS 1 COMPUTATIONAL METHODS INTRODUCTION QUANTUM MECHANICS METHODS SCHRÖDINGER EQUATION HARTREE-FOCK THEORY BASIS SETS ELECTRON CORRELATION DENSITY FUNCTIONAL THEORY MULTILEVEL METHODS CLASSICAL MECHANICS STATISTICAL MECHANICS FORCE FIELDS MOLECULAR DYNAMICS FREE ENERGY CALCULATION REFERENCES 2 RADICAL ENZYMES SAM SUPERFAMILY GLYCYL RADICAL ENZYMES SPORE PHOTOPRODUCT LYASE DNA PHOTOLYASES 3 PYRUVATE FORMATE-LYASE STRUCTURE AND ACTIVATION OF PFL SUGGESTED MECHANISMS OF CATALYSIS INHIBITION OF PFL BY SUBSTRATE ANALOGUES A SMALL-MODEL APPROACH IN MODELLING PFL CATALYSIS: FIRST HALF-REACTION COMPUTATIONAL DETAILS RESULTS AND DISCUSSION CONCLUSION A COMPOUND QM/MM PROCEDURE: COMPARATIVE PERFORMANCE ON PFL SYSTEM A MOLECULAR DYNAMICS STUDY OF PFL CATALYSIS: SECOND HALF-REACTION 4 (6-4) PHOTOLYASE THE EPR HYPERFINE STRUCTURE THE PKA VALUES MOLECULAR DYNAMICS STUDY 5 SUMMARY