The Reaction Coordinate of a Bacterial GH47 α-Mannosidase: A Combined Quantum Mechanical and Structural Approach

2012 ◽  
Vol 51 (44) ◽  
pp. 10997-11001 ◽  
Author(s):  
Andrew J. Thompson ◽  
Jerome Dabin ◽  
Javier Iglesias-Fernández ◽  
Albert Ardèvol ◽  
Zoran Dinev ◽  
...  
Keyword(s):  
Structural Approach ◽  
Reaction Coordinate ◽  
Quantum Mechanical

Inside Back Cover: The Reaction Coordinate of a Bacterial GH47 α-Mannosidase: A Combined Quantum Mechanical and Structural Approach (Angew. Chem. Int. Ed. 44/2012)

2012 ◽  
Vol 51 (44) ◽  
pp. 11171-11171
Author(s):  
Andrew J. Thompson ◽  
Jerome Dabin ◽  
Javier Iglesias-Fernández ◽  
Albert Ardèvol ◽  
Zoran Dinev ◽  
...  
Keyword(s):  
Structural Approach ◽  
Reaction Coordinate ◽  
Quantum Mechanical ◽  
Back Cover

scholarly journals Innenrücktitelbild: The Reaction Coordinate of a Bacterial GH47 α-Mannosidase: A Combined Quantum Mechanical and Structural Approach (Angew. Chem. 44/2012)

2012 ◽  
Vol 124 (44) ◽  
pp. 11333-11333
Author(s):  
Andrew J. Thompson ◽  
Jerome Dabin ◽  
Javier Iglesias-Fernández ◽  
Albert Ardèvol ◽  
Zoran Dinev ◽  
...  
Keyword(s):  
Structural Approach ◽  
Reaction Coordinate ◽  
Quantum Mechanical

The Reaction Coordinate of a Bacterial GH47 α-Mannosidase: A Combined Quantum Mechanical and Structural Approach

2012 ◽  
Vol 124 (44) ◽  
pp. 11159-11163 ◽  
Author(s):  
Andrew J. Thompson ◽  
Jerome Dabin ◽  
Javier Iglesias-Fernández ◽  
Albert Ardèvol ◽  
Zoran Dinev ◽  
...  
Keyword(s):  
Structural Approach ◽  
Reaction Coordinate ◽  
Quantum Mechanical

scholarly journals Conformational Analysis of the Mannosidase Inhibitor Kifunensine: A Quantum Mechanical and Structural Approach

ChemBioChem ◽  
2017 ◽  
Vol 18 (15) ◽  
pp. 1496-1501 ◽  
Author(s):  
Alexandra Males ◽  
Lluís Raich ◽  
Spencer J. Williams ◽  
Carme Rovira ◽  
Gideon J. Davies
Keyword(s):  
Conformational Analysis ◽  
Structural Approach ◽  
Quantum Mechanical

Analysis of the Reaction Coordinate of α-l-Fucosidases: A Combined Structural and Quantum Mechanical Approach

2010 ◽  
Vol 132 (6) ◽  
pp. 1804-1806 ◽  
Author(s):  
Alicia Lammerts van Bueren ◽  
Jennifer Fayers-Kerr ◽  
Bo Luo ◽  
Yongmin Zhang ◽  
Matthieu Sollogoub ◽  
...  
Keyword(s):  
Reaction Coordinate ◽  
Quantum Mechanical ◽  
Mechanical Approach ◽  
Quantum Mechanical Approach

Calculating approximate quantum mechanical rates without an a priori reaction coordinate

2002 ◽  
Vol 116 (19) ◽  
pp. 8376 ◽  
Author(s):  
Yisroel Brumer ◽  
Andrei A. Golosov ◽  
Zong Da Chen ◽  
David R. Reichman
Keyword(s):  
A Priori ◽  
Reaction Coordinate ◽  
Quantum Mechanical

scholarly journals Quantum Mechanical/Molecular Mechanical Analysis of the Catalytic Mechanism of Phosphoserine Phosphatase

Molecules ◽  
2018 ◽  
Vol 23 (12) ◽  
pp. 3342 ◽  
Author(s):  
Dieter Krachtus ◽  
Jeremy Smith ◽  
Petra Imhof
Keyword(s):  
Free Energy ◽  
Proton Transfer ◽  
Active Site ◽  
Catalytic Mechanism ◽  
Free Energy Calculations ◽  
Reaction Coordinate ◽  
Reaction Pathways ◽  
Quantum Mechanical ◽  
Energy Calculation ◽  
Phosphoserine Phosphatase

Phosphoserine phosphatase (PSP), a member of the haloacid dehalogenase (HAD) superfamily that comprises the vast majority of phosphotransferases, is likely a steady-state regulator of the level of d-serine in the brain. The proposed catalytic cycle of PSP consists of a two-step mechanism: formation of a phospho-enzyme intermediate by phosphate transfer to Asp11 and its subsequent hydrolysis. Our combined quantum mechanical/molecular mechanical (QM/MM) calculations of the reaction pathways favour a dissociative mechanism of nucleophilic substitution via a trigonal-planar metaphosphate-like configuration for both steps, associated with proton transfer to the leaving group or from the nucleophile. This proton transfer is facilitated by active site residue Asp13 that acts as both a general base and a general acid. Free energy calculation on the reaction pathways further support the structural role of the enzymatic environment and the active site architecture. The choice of a proper reaction coordinate along which to bias the free energy calculations can be guided by a projection of the canonical reaction coordinate obtained from a chain-of-state optimisation onto important internal coordinates.

Structural approach to instructional problems.

1977 ◽  
Vol 32 (1) ◽  
pp. 33-53 ◽  
Author(s):  
Joseph M. Scandura
Keyword(s):  
Structural Approach
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