This book focuses on the understanding of enzyme function and optimization gained in the past decade, past enzyme function analysis, enzyme engineering, and growing insights from the simulation work as well and nanotechnology measurement of enzymes in action in vitro or in silico. It presents new insights into the mechanistic function and understanding of enzyme reactions and covers novel structure analysis technologies in conjunction with x-ray and NMR structural methods. The text discusses topics that include single molecules, molecular dynamic simulations of different conformers of enzymes, surface enzyme kinetics, metagenomics and bioinformatics sequence handling, and coupled reactions in nanodevices.

A practical guide to the quantitative analysis of engineered enzymes. Protein Conformational Motions - Enzyme Catalysis. Enzymology meets Nanotechnology: Single-molecule methods for observing enzyme kinetics in real time. Interfacial enzyme function visualized using neutron, x-ray and light scattering methods. Folding dynamics and structural basis of the enzyme mechanism of ubiquitin C-terminal hydroylases. Stabilisation of Enzymes by metal binding: Structures of Alkalophilic Bacillus proteinases and analysis of the second metal binding site of subtilases. Structure and Functional Roles of Surface Binding Sites in Amylolytic Enzymes. Interfacial Enzymes and their Interactions with Surfaces: Molecular Simulation Studies. Sequence, structure, function: What we learn from analyzing protein families. Bioinformatic analysis of protein families to select function-related variable positions. Decoding life secrets in sequences by chemicals. Role of tunnels and gates in enzymatic catalysis. Molecule descriptors for the structureal analysis of enzyme active sites. Hydration effects on enzyme properties in nonaqueous media analysed by MD simulations. Understanding esterase and amidase reaction specificities by molecular modelling. Towards new non-natural TIM-barrel enzymes using computational design and directed evolution approaches. Handling the Numbers Problem in Directed Evolution. Hints from Nature: Metagenomics in Enzyme Engineering. A functional and structural assessment of circularly permuted Bacillus circulans xylanase and Candida antarctica lipase B. Ancestral Reconstruction in Enzymes. High throughput screening or selection methods for evolutionary enzyme engineering. Nanoscale Enzyme Screening Technologies. Computational Enzyme Engineering: Activity Screening using Quantum Chemistry. In silico screening of enzyme variants by molecular dynamics simulation. Kinetic and thermodynamic stability of variant enzymes.