Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations

Journal of the American Chemical Society

Volumn 133, Issue 23, 2011, Pages 8934-8941

  Rosta, Edina ^a   Nowotny, Marcin ^b   Yang, Wei ^a   Hummer, Gerhard ^a  

^a NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

^b INTERNATIONAL INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

ALKOXIDES; CATALYTIC MECHANISMS; FREE ENERGY SURFACE; LEAVING GROUPS; MAGNESIUM IONS; METAL-ION COORDINATION; NONMONOTONIC; NUCLEOPHILIC ATTACK; OVERALL REACTIONS; PH DEPENDENCE; PHOSPHATE GROUP; PHOSPHORANES; PROTON DONORS; PROTON TRANSFER REACTIONS; PROTONATING; REACTION PATHWAYS; RELATIVE MOTION; REPLICA EXCHANGE; RIBONUCLEIC ACID; STRING METHODS; TWO-STEP MECHANISMS; WATER MOLECULE; X RAY CRYSTAL STRUCTURES;

CATALYSIS; CRYSTAL STRUCTURE; FREE ENERGY; MAGNESIUM; MECHANICS; METAL IONS; MOLECULAR MODELING; PROTONS; QUANTUM CHEMISTRY; REACTION INTERMEDIATES; REACTION RATES; RNA;

COORDINATION REACTIONS;

MAGNESIUM ION; NUCLEIC ACID; NUCLEOPHILE; PHOSPHATE; PHOSPHORANE DERIVATIVE; RIBONUCLEASE H; RIBOSE; RNA; THIOL; WATER;

ARTICLE; CATALYSIS; CHEMICAL BOND; CHEMICAL REACTION; FINITE ELEMENT ANALYSIS; HUMAN; MOLECULAR MECHANICS; NONHUMAN; PH; PROTON TRANSPORT; QUANTUM MECHANICS; RNA CLEAVAGE; SIMULATION; SUBSTITUTION REACTION; X RAY CRYSTALLOGRAPHY;

BACILLUS; BIOCATALYSIS; CATALYTIC DOMAIN; HUMANS; HYDROGEN-ION CONCENTRATION; KINETICS; MAGNESIUM; MODELS, MOLECULAR; MOVEMENT; MUTATION; NUCLEIC ACID CONFORMATION; PROTONS; QUANTUM THEORY; RIBONUCLEASE H; RNA; SULFHYDRYL COMPOUNDS; WATER;

EID: 79958776843     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja200173a     Document Type: Article

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