NUST - PG Courses

CSE-914 Computational Enzymology

Campus	RCMS
Programs	PG
Session	Fall Semester 2016
Course Title	Computational Enzymology
Course Code	CSE-914
Credit Hours	3-0
Pre-Requisutes	Computational Chemistry, Biochemistry
Course Objectives	Decommention: This course combines lectures and laboratory exercises to teach the enzymatic structure and function with particular emphasis on computational biocatalysis. The course provides a broad understanding of the theory, with emphasis on the application of computational methods to enzymatic reaction mechanisms. Laboratory exercises provide hand-on training on practical methods in computational enzymology. Objectives: On completion, students will have comprehensive knowledge and understanding of a) the structure and function of enzymes, b) enzyme kinetics, c) enzymatic reaction mechanisms, d) computational methods in enzymology and e) the practical knowledge of computational enzymology.
Detail Content	Enzyme Structure and Function Overview of Protein Chemistry Enzyme Commission Nomenclature Enzymatic and Non-Enzymatic Catalysis Catalytic Approaches Adopted by Enzymes Enzyme kinetics Steady state kinetics Isotope effects Transient Phase kinetics pH-Rate profiles Allosteric Regulations Computational Methods in Enzymology Hybrid Potentials for Large Bio-molecular Systems Conformational Search on High-Dimensional Energy Surface Conjugate Peak Refinement Method Boundary Interactions at the QM/MM Interface Combined Quantum Mechanical/Classical Molecular Dynamics Simulations Reaction Mechanisms revealed by QM/MM investigations Biomolecular Motors RAS-GAP Signaling protein EcoRV enzyme Lactate and Maltate Dehydrogenases Acetylcholinestrase Carbonic Anhydrase Ni-Fe Hydrogeanse HIV Protease Challenges in Enzyme Modeling lab work, workshops practice Energy Minimization Techniques Molecular Dynamics Simulations Rotamase Catalysis in FK506 Binding Protein (FKBP)
Text/Ref Books	Kiani FA, Fischer S: The Catalytic Strategy of P–O Bond Cleaving Enzymes: Comparing EcoRV and Myosin in Molecular Catalysts: Structure and Functional Design. With a foreword by Nobel Laureate Roald Hofmann Wiley-VCH Verlag GmbH & Co. KgaA, 2014, 359-376. Mulholland AJ, Grant IM: Computational Enzymology: Insights into Enzyme Mechanism and Catalysis from Modeling in Challenges and advances in Computational Chemistry and Physics. 2007, 4:275-304. Zhu X, Yang Y, Yu H: In silico enzyme modeling, Australian Biochemist 2014, 45:12-15. Frey PA, Hegeman AD: Enzyme Reaction Mechanisms, Oxford University Press, 2007. Buchholz K, Bornscheuer UT: Biocatalysts and Enzyme Technology, Wiley-Blackwell, 2012. Hou CT, Shaw J-F: Biocatalysis and Biomolecular Engineering, Wiley, 2010. Warshel A: Computer Simulations of Enzyme Catalysis: Methods, Progress, and Insights Annu Rev Biophys Biomol Struct, 32: 425-443. Warshel A, Sharma PK, Kato M, Xiang Y, Liu H, Olsson MHM: Electrostatic Basis for Enzyme Catalysis, Chem Rev 2006, 106:3210−3235 Kamerlin SCL, Warshel A: At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis? Proteins Struct Funct Bioinf 2010, 78:1339–1375. Warshel A: Molecular Dynamics Simulations of Biological Reactions, Acc Chem Res 2002, 35:385–395. Olsson MHM, Parson WW, Warshel A: Dynamical Contributions to Enzyme Catalysis: Critical Tests of A Popular Hypothesis, Chem Rev 2006, 106:1737−1756 Friesner RA, Guallar V: Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis, Annu Rev Phys Chem 2005, 56:389-427 DOI: 10.1146/annurev.physchem.55.091602.094410 Senn HM, Thiel W: QM/MM studies of enzymes, Curr Opin Chem Biol, 2007, 11:182–187 Senn HM, Thiel W: QM/MM Methods for Bio-molecular Systems, Angew Chem Intl Ed 2009, 48:1198–1229.
Time Schedule
Faculty/Resource Person	Associate Professor - Dr Farooq Ahmed Kiani