Journal Article10.1002/CHIN.201336244
Computational Enzyme Design
253
Abstract: Recent developments in computational chemistry and biology have come together in the "inside-out" approach to enzyme engineering. Proteins have been designed to catalyze reactions not previously accelerated in nature. Some of these proteins fold and act as catalysts, but the success rate is still low. The achievements and limitations of the current technology are highlighted and contrasted to other protein engineering techniques. On its own, computational "inside-out" design can lead to the production of catalytically active and selective proteins, but their kinetic performances fall short of natural enzymes. When combined with directed evolution, molecular dynamics simulations, and crowd-sourced structure-prediction approaches, however, computational designs can be significantly improved in terms of binding, turnover, and thermal stability.
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References
The Protein Data Bank
Helen M. Berman,John D. Westbrook,Zukang Feng,Gary L. Gilliland,Talapady N. Bhat,Helge Weissig,Ilya N. Shindyalov,Philip E. Bourne +7 more
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Protein production by auto-induction in high-density shaking cultures
TL;DR: Investigation of factors that affect stability, growth, and induction of T7 expression strains in shaking vessels led to the recognition that sporadic, unintended induction of expression in complex media, previously reported by others, is almost certainly caused by small amounts of lactose.
6.2K
The hydrogen bond in the solid state.
TL;DR: The hydrogen bond is the most important of all directional intermolecular interactions, operative in determining molecular conformation, molecular aggregation, and the function of a vast number of chemical systems ranging from inorganic to biological.
5.8K
Engineering the third wave of biocatalysis
Uwe T. Bornscheuer,Gjalt W. Huisman,Romas J. Kazlauskas,Romas J. Kazlauskas,Stefan Lutz,Jeffrey C. Moore,Karen Robins +6 more
TL;DR: Applications of protein-engineered biocatalysts ranging from commodity chemicals to advanced pharmaceutical intermediates that use enzyme catalysis as a key step are discussed.
2.3K
Structure of hen egg-white lysozyme. A three-dimensional Fourier synthesis at 2 Angstrom resolution.
C. C. F. Blake,D. F. Koenig,D. F. Koenig,G. A. Mair,A. C. T. North,D. C. Phillips,V. R. Sarma +6 more
TL;DR: Structure of Hen Egg-White Lysozyme: A Three-dimensional Fourier Synthesis at 2 A Resolution as mentioned in this paper, 3D Fourier synthesis at 2 a resolution.
1.6K