Structural and Mechanistic Enzymology: Bringing Together Experiments and Computing

Both strategies for investigation (computational and experimental) in structural and mechanistic Enzymology have developed to some extent independently. However, over the last few years a trend has emerged for strengthening their integration. This combination not only brings together computations and experiments focused on the same enzymatic problems, but also provides complementary insights into the investigated properties and has a powerful synergy effect. This thematic volume of Advances in Protein Chemistry and Structural Biology focuses on the recent success in structural and mechanistic enzymology and has its main emphasis on explaining the enzyme phenomena by using both the experimental and computational approaches. The selected contributions demonstrate how the application of a variety of experimental techniques and modeling methods helps further the understanding of enzyme dynamics, mechanism, inhibition, and drug design.

Focuses on the recent success in structural and mechanistic enzymologyHas its main emphasis on explaining the enzyme phenomena by using both the experimental and computational approachesDemonstrates how the application of a variety of experimental techniques and modeling methods helps further the understanding of enzyme dynamics, mechanism, inhibition, and drug design

1. Structural and Computational Enzymology: Bringing Experiments and Computations Together

Tatyana Karabencheva and Christo Christov

2. Structural and Functional Analysis of Proteins by High-Speed Atomic Force Microscopy

Arivazhagan Rajendran, Masayuki Endo and Hiroshi Sugiyama

3. Reaction Intermediates Discovered in Crystal Structures of Enzymes

Irene T. Weber, Johnson Agniswamy, Guoxing Fu, Chen-Hsiang Shen and Robert W. Harrison

4. Structural, Functional and Mutagenesis Studies of UDP-Glycosyltransferases

Vatsala Malik and Gary W Black

5. Vipoxin and its Components: Structure – Function Relationship

S. D. Petrova, V. N. Atanasov and K. Balashev

6. Experimental and Theoretical Studies of Enzyme-Catalyzed Hydrogen Transfer Reactions

Zhen Wang, Daniel Roston and Amnon Kohen

7. Protein Flexibility and Enzymatic Catalysis

M. Kokkinidis, N. M. Glykos and V. E. Fadouloglou

8. Molecular Modeling of Inhibitors of Human DNA Methyltransferase with a Crystal Structure: Discovery of a Novel DNMT1 Inhibitor

Jakyung Yoo, Joo Hee Kim, Keith D. Robertson and José L. Medina-Franco

9. In Silico Strategies Towards Enzyme Function and Dynamics

Sílvia G. Estácio

10. Dynamic Simulations as a Complement to Experimental Studies of Enzyme Mechanisms

Andrew Christofferon, Lifeng Zhao and Qiang Pei

11. The Increasing Role of QM/MM in Drug Discovery

Alessio Lodola and Marco De Vivo

12. Probing Allostery and Binding Cooperativity of the Catalytic Subunit of Protein Kinase A by NMR Spectroscopy and Molecular Dynamics Simulations

Larry R. Masterson, Alessandro Cembran, Lei Shi and Gianluigi Veglia

13. Using a Combination of Computational and Experimental Techniques to Understand the Molecular Basis for Protein Allostery Wanting Jiao and Emily J. Parker