Computational Study of IAG-Nucleoside Hydrolase:  Determination of the Preferred Ground State Conformation and the Role of Active Site Residues†

Biochemistry ◽  
2005 ◽  
Vol 44 (21) ◽  
pp. 7805-7817 ◽  
Author(s):  
Devleena Mazumder-Shivakumar ◽  
Thomas C. Bruice
Keyword(s):  
Ground State ◽  
Active Site ◽  
Computational Study ◽  
Active Site Residues ◽  
Nucleoside Hydrolase

scholarly journals The mechanistic role of active site residues in non-stereo haloacid dehalogenase E (DehE)

2019 ◽  
Vol 90 ◽  
pp. 219-225 ◽  
Author(s):  
Muhammad Hasanuddin Zainal Abidin ◽  
Khairul Bariyyah Abd Halim ◽  
Fahrul Huyop ◽  
Tengku Haziyamin Tengku Abdul Hamid ◽  
Roswanira Abdul Wahab ◽  
...  
Keyword(s):  
Active Site ◽  
Active Site Residues ◽  
Haloacid Dehalogenase

Mechanism of Thioredoxin-Catalyzed Disulfide Reduction. Activation of the Buried Thiol and Role of the Variable Active-Site Residues

2008 ◽  
Vol 112 (8) ◽  
pp. 2511-2523 ◽  
Author(s):  
Alexandra T. P. Carvalho ◽  
Marcel Swart ◽  
Joost N. P. van Stralen ◽  
Pedro A. Fernandes ◽  
Maria J. Ramos ◽  
...  
Keyword(s):  
Active Site ◽  
Active Site Residues ◽  
Disulfide Reduction

Molecular dynamics study of active-site interactions with tetracoordinate transients in acetylcholinesterase and its mutants

2001 ◽  
Vol 353 (3) ◽  
pp. 645-653 ◽  
Author(s):  
Istvan J. ENYEDY ◽  
Ildiko M. KOVACH ◽  
Akos BENCSURA
Keyword(s):  
Molecular Dynamics ◽  
Glutamic Acid ◽  
Active Site ◽  
Indole Ring ◽  
Active Site Residues ◽  
Parallel Simulations ◽  
Electrostatic Stabilization ◽  
Carbenium Ion ◽  
Dynamics Simulations

The role of active-site residues in the dealkylation reaction in the PSCS diastereomer of 2-(3,3-dimethylbutyl)methylphosphonofluoridate (soman)-inhibited Torpedo californicaacetylcholinesterase (AChE) was investigated by full-scale molecular dynamics simulations using CHARMM: > 400ps equilibration was followed by 150–200ps production runs with the fully solvated tetracoordinate phosphonate adduct of the wild-type, Trp84Ala and Gly199Gln mutants of AChE. Parallel simulations were carried out with the tetrahedral intermediate formed between serine-200 Oγ of AChE and acetylcholine. We found that the NεH in histidine H+-440 is positioned to protonate the oxygen in choline and thus promote its departure. In contrast, NεH in histidine H+-440 is not aligned for a favourable proton transfer to the pinacolyl O to promote dealkylation, but electrostatic stabilization by histidine H+-440 of the developing anion on the phosphonate monoester occurs. Destabilizing interactions between residues and the alkyl fragment of the inhibitor enforce methyl migration from Cβ to Cα concerted with C—O bond breaking in soman-inhibited AChE. Tryptophan-84, phenyalanine-331 and glutamic acid-199 are within 3.7–3.9 Å (1 Å=10-10 m) from a methyl group in Cβ, 4.5–5.1 Å from Cβ and 4.8–5.8 Å from Cα, and can better stabilize the developing carbenium ion on Cβ than on Cα. The Trp84Ala mutation eliminates interactions between the incipient carbenium ion and the indole ring, but also reduces its interactions with phenylalanine-331 and aspartic acid-72. Tyrosine-130 promotes dealkylation by interacting with the indole ring of tryptophan-84. Glutamic acid-443 can influence the orientation of active-site residues through tyrosine-421, tyrosine-442 and histidine-440 in soman-inhibited AChE, and thus facilitate dealkylation.

Topological role of cytochrome P450 2D6 active site residues

2006 ◽  
Vol 447 (1) ◽  
pp. 53-58 ◽  
Author(s):  
Robert A.B. van Waterschoot ◽  
Peter H.J. Keizers ◽  
Chris de Graaf ◽  
Nico P.E. Vermeulen ◽  
Richard A. Tschirret-Guth
Keyword(s):  
Cytochrome P450 ◽  
Active Site ◽  
Cytochrome P450 2D6 ◽  
Active Site Residues ◽  
P450 2D6
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