The oxygen-binding vs. oxygen-consuming paradigm in biocatalysis: structural biology and biomolecular simulation

被引：31

作者：

Baron, Riccardo ^{[1
,2
]}

McCammon, J. Andrew ^{[1
,2
,3
,4
]}

Mattevi, Andrea ^{[5
]}

机构：

[1] Univ Calif San Diego, Dept Chem & Biochem, La Jolla, CA 92093 USA

[2] Univ Calif San Diego, Ctr Theoret Biol Phys, La Jolla, CA 92093 USA

[3] Univ Calif San Diego, Dept Pharmacol, La Jolla, CA 92093 USA

[4] Univ Calif San Diego, Howard Hughes Med Inst, La Jolla, CA 92093 USA

[5] Univ Pavia, Dept Genet & Microbiol, I-27100 Pavia, Italy

来源：

CURRENT OPINION IN STRUCTURAL BIOLOGY | 2009年 / 19卷 / 06期

基金：

美国国家卫生研究院; 美国国家科学基金会;

关键词：

X-RAY CRYSTALLOGRAPHY; CYTOCHROME-C-OXIDASE; MOLECULAR-DYNAMICS; MIGRATION PATHWAYS; ELECTRON-TRANSFER; LIGAND MIGRATION; O-2; SITE; IDENTIFICATION; INTERMEDIATE;

D O I：

10.1016/j.sbi.2009.10.003

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Oxygen biocatalysis and regulation is crucial to a variety of biochemical processes in nature. Oxygen-binding proteins cover only a limited part of oxygen biocatalysis, which involves numerous examples of oxygen-consuming biocatalysts with low oxygen affinities. The integration of experiments with powerful biomolecular simulation opens appealing possibilities to investigate crucial questions on the fascinating relationship between enzyme dynamics and oxygen biocatalysis in new protein structures.

引用

页码：672 / 679

页数：8

共 57 条

[1] Molecular dynamics: Survey of methods for simulating the activity of proteins [J].

Adcock, Stewart A. ;

McCammon, J. Andrew .

CHEMICAL REVIEWS, 2006, 106 (05) :1589-1615

[2] Revealing the moonlighting role of NADP in the structure of a flavin-containing monooxygenase [J].

Alfieri, Andrea ;

Malito, Enrico ;

Orru, Roberto ;

Fraaije, Marco W. ;

Mattevi, Andrea .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008, 105 (18) :6572-6577

[3] Structure of the monooxygenase component of a two-component flavoprotein monooxygenase [J].

Alfieri, Andrea ;

Fersini, Francesco ;

Ruangchan, Nantidaporn ;

Prongjit, Methinee ;

Chaiyen, Pimchai ;

Mattevi, Andrea .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2007, 104 (04) :1177-1182

[4] The kinetics of ligand migration in crystallized myoglobin as revealed by molecular dynamics simulations [J].

Anselmi, Massimiliano ;

Di Nola, Alfredo ;

Amadei, Andrea .

BIOPHYSICAL JOURNAL, 2008, 94 (11) :4277-4281

[5] Multiple pathways guide oxygen diffusion into flavoenzyme active sites [J].

Baron, Riccardo ;

Riley, Conor ;

Chenprakhon, Pirom ;

Thotsaporn, Kittisak ;

Winter, Remko T. ;

Alfieri, Andrea ;

Forneris, Federico ;

van Berkel, Willem J. H. ;

Chaiyen, Pimchai ;

Fraaije, Marco W. ;

Mattevi, Andrea ;

McCammon, J. Andrew .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2009, 106 (26) :10603-10608

[6] Heme-copper oxidases use tunneling pathways [J].

Beratan, David N. ;

Balabin, Ilya A. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008, 105 (02) :403-404

[7] Hemoglobin is an honorary enzyme [J].

Brunori, M .

TRENDS IN BIOCHEMICAL SCIENCES, 1999, 24 (04) :158-161

[8] PENETRATION OF DIOXYGEN INTO PROTEINS STUDIED BY QUENCHING OF PHOSPHORESCENCE AND FLUORESCENCE [J].

CALHOUN, DB ;

VANDERKOOI, JM ;

WOODROW, GV ;

ENGLANDER, SW .

BIOCHEMISTRY, 1983, 22 (07) :1526-1532

[9] PENETRATION OF SMALL MOLECULES INTO PROTEINS STUDIED BY QUENCHING OF PHOSPHORESCENCE AND FLUORESCENCE [J].

CALHOUN, DB ;

VANDERKOOI, JM ;

ENGLANDER, SW .

BIOCHEMISTRY, 1983, 22 (07) :1533-1539

[10] The binding and release of oxygen and hydrogen peroxide are directed by a hydrophobic tunnel in cholesterol oxidase [J].

Chen, Lin ;

Lyubimov, Artern Y. ;

Brammer, Leighanne ;

Vrielink, Alice ;

Sampson, Nicole S. .

BIOCHEMISTRY, 2008, 47 (19) :5368-5377

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