Bridging the Gap Between Theory and Experiment to Derive a Detailed Understanding of Hammerhead Ribozyme Catalysis - Progress in Molecular Biology and Translational Science - page 24

CHAPTER TWO

Bridging the Gap Between Theory
and Experiment to Derive a
Detailed Understanding of
Hammerhead Ribozyme Catalysis

, † , Kin-Yiu Wong * , † , ‡ , George M. Giambasu * , † ,

Tai-Sung Lee *

, †
* Center for Integrative Proteomics Research and BioMaPS Institute for Quantitative Biology, Rutgers, The
State University of New Jersey, Piscataway, New Jersey, USA
† Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway,
New Jersey, USA
‡ Department of Physics, High Performance Cluster Computing Centre, Institute of Computational and
Theoretical Studies, Hong Kong Baptist University, Kowloon Tong, Hong Kong

Darrin M. York *

Contents
1. Introduction 26

2. A Metal Ion Story with a Happy Ending 29

2.1 Discrepancies between biochemical and crystallographic data 29

2.2 The crystal structures of the full-length (extended) HHR 31

2.3 Probing metal ion-binding modes in HHR with molecular simulation 32

2.4 Results 37

2.5 The big picture 41

3. Finding the Catalytic Reaction Path Through Multidimensional Free-Energy
Surfaces

42

3.1 Results 43

3.2 Summary 47

3.3 Simulation setup and protocol 47

4. HHR Uses Specific Cation-Binding Modes to Reach Its Catalytically Active
Conformation 49

4.1 Results 49

4.2 Discussion 60

4.3 Simulation setup and protocols 62

5. Computational Mutagenesis of Key Residues of HHR 63

5.1 Results 64

5.2 Discussion 79

5.3 Simulation setup and protocol 83

6. Conclusion 83

Acknowledgments 84

References 84