Comparative binding energy (COMBINE) analysis of the substrate
specificity of haloalkane dehalogenase from Xanthobacter
autotrophicus GJ10

J 2001

Comparative binding energy (COMBINE) analysis of the substrate specificity of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10

KMUNÍČEK, Jan; Santos LUENGO; Federico GAGO; Angel Ramirez ORTIZ; Rebecca WADE et. al.

Basic information

Original name

Comparative binding energy (COMBINE) analysis of the substrate specificity of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10

Authors

KMUNÍČEK, Jan; Santos LUENGO; Federico GAGO; Angel Ramirez ORTIZ; Rebecca WADE and Jiří DAMBORSKÝ

Edition

Biochemistry, 2001, 0006-2960

Other information

Language

English

Type of outcome

Article in a journal

Field of Study

10600 1.6 Biological sciences

Country of publisher

United States of America

Confidentiality degree

is not subject to a state or trade secret

References:

URL

Impact factor

Impact factor: 4.114

RIV identification code

RIV/00216224:14310/01:00004531

Organization unit

Faculty of Science

Changed: 15/12/2006 11:21, Mgr. Jan Kmuníček, Ph.D.

Abstract

In the original language

Comparative binding energy (COMBINE) analysis was conducted for eighteen substrates of the haloalkane dehalogenase from Xanthobacter autotrophicus GJ10: 1-chlorobutane; 1-chlorohexane; dichloromethane; 1,2-dichloroethane; 1,2-dichloropropane; 2-chloroethanol; epichlorohydrine; 2-chloroacetonitrile, 2-chloroacetamide and their brominated analogs. The purpose of the COMBINE analysis was to identify the amino acid residues determining the substrate specificity of the haloalkane dehalogenase. This knowledge is essential for the tailoring of this enzyme for biotechnological applications. Complexes of the enzyme with these substrates were modeled and then refined by molecular mechanics energy minimization. The intermolecular enzyme-substrate energy was decomposed into residue-wise van der Waals and electrostatic contributions and complemented by surface area dependent and electrostatic desolvation terms. Partial least-squares projection to latent structures analysis was then used to establish relationships between the energy contributions and the experimental apparent dissociation constants. A model containing van der Waals and electrostatic intermolecular interaction energy contributions calculated using the AMBER force field explained 91 % (73 % cross-validated) of the quantitative variance in the apparent dissociation constants. A model based on van der Waals intermolecular contributions from AMBER and electrostatic interactions derived from the Poisson-Boltzmann equation explained 93 % (74 % cross-validated) of the quantitative variance. COMBINE models predicted correctly the change in apparent dissociation constants upon single-point mutation of DhlA for six enzyme-substrate complexes. The amino acid residues contributing most significantly to the substrate specificity of DhlA were identified; they include Asp124, Trp125, Phe164, Phe172, Trp175, Phe222, Pro223 and Leu263. These residues are suitable targets for modification by site-directed mutagenesis.

Links

LN00A016, research and development project

Name: BIOMOLEKULÁRNÍ CENTRUM

Investor: Ministry of Education, Youth and Sports of the CR, Biomolecular Center

Cite

KMUNÍČEK, Jan; Santos LUENGO; Federico GAGO; Angel Ramirez ORTIZ; Rebecca WADE and Jiří DAMBORSKÝ. Comparative binding energy (COMBINE) analysis of the substrate specificity of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10. Biochemistry. 2001, vol. 40, No 30, p. 8905-8917. ISSN 0006-2960.

@article{371752,
   author = {Kmuníček, Jan and Luengo, Santos and Gago, Federico and Ortiz, Angel Ramirez and Wade, Rebecca and Damborský, Jiří},
   article_number = {30},
   language = {eng},
   issn = {0006-2960},
   journal = {Biochemistry},
   title = {Comparative binding energy (COMBINE) analysis of the substrate specificity of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10},
   url = {http://www.ncbr.chemi.muni.cz/~jiri/ABSTRACTS/biochem01.html},
   volume = {40},
   year = {2001}
}

TY  - JOUR
ID  - 371752
AU  - Kmuníček, Jan - Luengo, Santos - Gago, Federico - Ortiz, Angel Ramirez - Wade, Rebecca - Damborský, Jiří
PY  - 2001
TI  - Comparative binding energy (COMBINE) analysis of the substrate specificity of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10
JF  - Biochemistry
VL  - 40
IS  - 30
SP  - 8905
EP  - 8905
SN  - 00062960
UR  - http://www.ncbr.chemi.muni.cz/~jiri/ABSTRACTS/biochem01.html
N2  - Comparative binding energy (COMBINE) analysis was conducted for eighteen substrates of the haloalkane dehalogenase from Xanthobacter autotrophicus GJ10: 1-chlorobutane; 1-chlorohexane; dichloromethane; 1,2-dichloroethane; 1,2-dichloropropane; 2-chloroethanol; epichlorohydrine; 2-chloroacetonitrile, 2-chloroacetamide and their brominated analogs. The purpose of the COMBINE analysis was to identify the amino acid residues determining the substrate specificity of the haloalkane dehalogenase. This knowledge is essential for the tailoring of this enzyme for biotechnological applications. Complexes of the enzyme with these substrates were modeled and then refined by molecular mechanics energy minimization. The intermolecular enzyme-substrate energy was decomposed into residue-wise van der Waals and electrostatic contributions and complemented by surface area dependent and electrostatic desolvation terms. Partial least-squares projection to latent structures analysis was then used to establish relationships between the energy contributions and the experimental apparent dissociation constants. A model containing van der Waals and electrostatic intermolecular interaction energy contributions calculated using the AMBER force field explained 91 % (73 % cross-validated) of the quantitative variance in the apparent dissociation constants. A model based on van der Waals intermolecular contributions from AMBER and electrostatic interactions derived from the Poisson-Boltzmann equation explained 93 % (74 % cross-validated) of the quantitative variance. COMBINE models predicted correctly the change in apparent dissociation constants upon single-point mutation of DhlA for six enzyme-substrate complexes. The amino acid residues contributing most significantly to the substrate specificity of DhlA were identified; they include Asp124, Trp125, Phe164, Phe172, Trp175, Phe222, Pro223 and Leu263. These residues are suitable targets for modification by site-directed mutagenesis.
ER  -

KMUNÍČEK, Jan; Santos LUENGO; Federico GAGO; Angel Ramirez ORTIZ; Rebecca WADE and Jiří DAMBORSKÝ. Comparative binding energy (COMBINE) analysis of the substrate specificity of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10. \textit{Biochemistry}. 2001, vol.~40, No~30, p.~8905-8917. ISSN~0006-2960.

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