Ab initio study of the binding of Trichostatin A (TSA) in the active site of Histone Deacetylase Like Protein (HDLP)

2003 ◽  
Vol 1 (16) ◽  
pp. 2951-2957 ◽  
Author(s):  
Kenno Vanommeslaeghe ◽  
Christian Van Alsenoy ◽  
Frank De Proft ◽  
José C. Martins ◽  
Dirk Tourwé ◽  
...  
Keyword(s):  
Ab Initio ◽  
Histone Deacetylase ◽  
Active Site ◽  
Trichostatin A ◽  
Ab Initio Study

Ab initio study of the physical nature of interactions between enzyme active site fragments in vacuo

2001 ◽  
Vol 3 (5) ◽  
pp. 657-663 ◽  
Author(s):  
W. Andrzej Sokalski ◽  
Paweł Kedzierski ◽  
Jolanta Grembecka
Keyword(s):  
Ab Initio ◽  
Active Site ◽  
Physical Nature ◽  
Ab Initio Study ◽  
Enzyme Active Site

scholarly journals Binding of inhibitors to active-site mutants of CD1, the enigmatic catalytic domain of histone deacetylase 6

2020 ◽  
Vol 76 (9) ◽  
pp. 428-437 ◽  
Author(s):  
Jeremy D. Osko ◽  
David W. Christianson
Keyword(s):  
Crystal Structures ◽  
Histone Deacetylase ◽  
Active Site ◽  
Catalytic Domain ◽  
Trichostatin A ◽  
Histone Deacetylase 6 ◽  
Inhibitor Binding ◽  
Active Site Mutants

The zinc hydrolase histone deacetylase 6 (HDAC6) is unique among vertebrate deacetylases in that it contains two catalytic domains, designated CD1 and CD2. Both domains are fully functional as lysine deacetylases in vitro. However, the in vivo function of only the CD2 domain is well defined, whereas that of the CD1 domain is more enigmatic. Three X-ray crystal structures of HDAC6 CD1–inhibitor complexes are now reported to broaden the understanding of affinity determinants in the active site. Notably, cocrystallization with inhibitors was facilitated by using active-site mutants of zebrafish HDAC6 CD1. The first mutant studied, H82F/F202Y HDAC6 CD1, was designed to mimic the active site of human HDAC6 CD1. The structure of its complex with trichostatin A was generally identical to that with the wild-type zebrafish enzyme. The second mutant studied, K330L HDAC6 CD1, was prepared to mimic the active site of HDAC6 CD2. It has previously been demonstrated that this substitution does not perturb inhibitor binding conformations in HDAC6 CD1; here, this mutant facilitated cocrystallization with derivatives of the cancer chemotherapy drug suberoylanilide hydroxamic acid (SAHA). These crystal structures allow the mapping of inhibitor-binding regions in the outer active-site cleft, where one HDAC isozyme typically differs from another. It is expected that these structures will help to guide the structure-based design of inhibitors with selectivity against HDAC6 CD1, which in turn will enable new chemical biology approaches to probe its cellular function.

Ab initio study of Cd–thiol complexes: application to the modelling of the metallothionein active site

2003 ◽  
Vol 5 (17) ◽  
pp. 3762-3767 ◽  
Author(s):  
Mironel Enescu ◽  
Jean-Philippe Renault ◽  
Stanislas Pommeret ◽  
Jean-Claude Mialocq ◽  
Serge Pin
Keyword(s):  
Ab Initio ◽  
Active Site ◽  
Ab Initio Study

An ab initio study of Se-reacted GaAs(0 0 1) surfaces

1998 ◽  
Vol 184-185 (1-2) ◽  
pp. 80-84 ◽  
Author(s):  
W Faschinger
Keyword(s):  
Ab Initio ◽  
Ab Initio Study

Carrier Transport in 2-D Materials: an Ab Initio Study

2019 ◽  
Author(s):  
Mathieu Luisier ◽  
Aron Szabo ◽  
Cedric Klinkert ◽  
Christian Stieger ◽  
Martin Rau ◽  
...  
Keyword(s):  
Ab Initio ◽  
Carrier Transport ◽  
Ab Initio Study

Ion solvation by dipolar aprotic solvents. An ab initio study

1987 ◽  
Vol 52 (1) ◽  
pp. 6-13 ◽  
Author(s):  
Petr Kyselka ◽  
Zdeněk Havlas ◽  
Ivo Sláma
Keyword(s):  
Ab Initio ◽  
Geometry Optimization ◽  
Molecular Structures ◽  
Dimethyl Sulphoxide ◽  
Ion Solvation ◽  
Interaction Energies ◽  
Ab Initio Study ◽  
Solvation Energies ◽  
Dipolar Aprotic Solvents ◽  
Complete Geometry Optimization

The paper deals with the solvation of Li+, Be2+, Na+, Mg2+, and Al3+ ions in dimethyl sulphoxide, dimethylformamide, acetonitrile, and water. The ab initio quantum chemical method was used to calculate the solvation energies, molecular structures, and charge distributions for the complexes water···ion, acetonitrile···ion, dimethyl sulphoxide···ion, and dimethylformamide···ion. The interaction energies were corrected for the superposition error. Complete geometry optimization was performed for the complex water···ion. Some generalizations are made on the basis of the results obtained.

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