Focus on biological catalysis

In this issue - pv

doi:10.1038/nchembio0809-v

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Focus on biological catalysis

Closing in on catalysis - p515

doi:10.1038/nchembio0809-515

Building on a century of enzymology research and new genome-wide insights into enzyme families, increased interdisciplinary communication and a broad vision will advance our understanding of biological catalysts and enhance our ability to manipulate them.

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Focus on biological catalysis

The far reaches of enzymology - pp516 - 520

Jesse G Zalatan & Daniel Herschlag

doi:10.1038/nchembio0809-516

The scope of enzymology has expanded rapidly over the last century, from an early focus on the chemical and catalytic mechanisms of individual enzymes to more recent efforts to understand enzyme action in the context of dynamic, functional biological systems consisting of many interacting enzymes and proteins. Continuing progress in probing the link between molecular structure and function now promises to pave the way for a deeper understanding of the evolution and behavior of the complex biological systems that govern cellular behavior.

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Focus on biological catalysis

Missing in action: enzyme functional annotations in biological databases - pp521 - 525

Nicholas Furnham, John S Garavelli, Rolf Apweiler & Janet M Thornton

doi:10.1038/nchembio0809-521

Annotations of enzyme function provide critical starting points for generating and testing biological hypotheses, but the quality of functional annotations is hindered by uncertain assignments for uncharacterized sequences and by the relative sparseness of validated experimental data. Given the relentless increase in genomic data, new thinking and validation methods are urgently needed to provide high confidence in enzyme functional assignments.

Full Text - Missing in action: enzyme functional annotations in biological databases | PDF (407 KB) - Missing in action: enzyme functional annotations in biological databases

Focus on biological catalysis

Finding better protein engineering strategies - pp526 - 529

Romas J Kazlauskas & Uwe T Bornscheuer

doi:10.1038/nchembio0809-526

Protein improvement strategies today involve widely varying combinations of rational design with random mutagenesis and screening. To make further progress—defined as making subsequent protein engineering problems easier to solve—protein engineers must critically compare these strategies and eliminate less effective ones.

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Focus on biological catalysis

Vitamins and cofactors: highlights of ESBOC 2009 - pp530 - 533

Edward McDonald

doi:10.1038/nchembio0809-530

The 2009 ESBOC meeting covered advances in synthesis, biosynthesis and biological mechanisms of vitamins and cofactors. Recent exciting developments in the field include the development of 'green' chemistry for manufacture of vitamins, the discovery that some vitamins act directly to regulate gene expression via riboswitches, and initial attempts to exploit the potential of vitamin analogs as therapeutic drugs.

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Focus on biological catalysis

Perry Frey - p534

Catherine Goodman

doi:10.1038/nchembio0809-534

A passion for novel chemistry and experimental surprises has led Perry Frey through 40 years of inspiring enzymology research.

Full Text - Perry Frey | PDF (91 KB) - Perry Frey

A metabolic network described in absolute terms - pp535 - 536

Dietmar Schomburg

doi:10.1038/nchembio0809-535

The parallel determination of more than 100 absolute intracellular metabolite concentrations by isotope-labeled HPLC-MS allowed a comprehensive analysis of the cellular state, its metabolic capacities and modes of regulation. Among other findings, it became obvious that for most enzymes the concentrations were above the K_m values, which indicates a trend toward saturation of most enzyme active sites.

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See also: Article by Bennett et al.

Staring off into chemical space - pp536 - 537

John J Irwin

doi:10.1038/nchembio0809-536

New software to browse chemical space, with structures organized by rings, will enable chemical insight.

Full Text - Staring off into chemical space | PDF (128 KB) - Staring off into chemical space

See also: Brief Communication by Wetzel et al. | Article by Renner et al.

How evolving enzymes can beat the heat and avoid defeat - pp538 - 539

Ichiro Matsumura & Andrei A Ivanov

doi:10.1038/nchembio0809-538

Random mutations usually destabilize protein tertiary structure. Overexpression of the chaperonin GroEL/GroES protects evolving proteins from the destabilizing effects of adaptive mutations and improves the quantity and quality of enzyme variants with modified function.

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Research highlights - pp540 - 541

doi:10.1038/nchembio0809-540

Full Text - Research highlights | PDF (235 KB) - Research highlights

Focus on biological catalysis

A 21^st century revisionist's view at a turning point in enzymology - pp543 - 550

Zachary D Nagel & Judith P Klinman

doi:10.1038/nchembio.204

Abstract - A 21: st: century revisionist's view at a turning point in enzymology | Full Text - A 21st century revisionist's view at a turning point in enzymology | PDF (457 KB) - A 21st century revisionist's view at a turning point in enzymology

Focus on biological catalysis

Enzymatic transition states and dynamic motion in barrier crossing - pp551 - 558

Steven D Schwartz & Vern L Schramm

doi:10.1038/nchembio.202

Abstract - Enzymatic transition states and dynamic motion in barrier crossing | Full Text - Enzymatic transition states and dynamic motion in barrier crossing | PDF (913 KB) - Enzymatic transition states and dynamic motion in barrier crossing | Supplementary information

Focus on biological catalysis

Evolution of efficient pathways for degradation of anthropogenic chemicals - pp559 - 566

Shelley D Copley

doi:10.1038/nchembio.197

Abstract - Evolution of efficient pathways for degradation of anthropogenic chemicals | Full Text - Evolution of efficient pathways for degradation of anthropogenic chemicals | PDF (462 KB) - Evolution of efficient pathways for degradation of anthropogenic chemicals

Focus on biological catalysis

Directed evolution drives the next generation of biocatalysts - pp567 - 573

Nicholas J Turner

doi:10.1038/nchembio.203

Abstract - Directed evolution drives the next generation of biocatalysts | Full Text - Directed evolution drives the next generation of biocatalysts | PDF (629 KB) - Directed evolution drives the next generation of biocatalysts

Erratum: A crowdsourcing evaluation of the NIH chemical probes - p600

Tudor I Oprea, Cristian G Bologa, Scott Boyer, Ramona F Curpan, Robert C Glen, Andrew L Hopkins, Christopher A Lipinski, Garland R Marshall, Yvonne C Martin, Liliana Ostopovici-Halip, Gilbert Rishton, Oleg Ursu, Roy J Vaz, Chris Waller, Herbert Waldmann & Larry A Sklar

doi:10.1038/nchembio0809-600

Full Text - Erratum: A crowdsourcing evaluation of the NIH chemical probes | PDF (39 KB) - Erratum: A crowdsourcing evaluation of the NIH chemical probes