We evaluate the applicability of automated molecular docking techniques and quantum mechanical calculations to the construction of a set of structures of enzyme-substrate complexes for use in Comparative binding energy (COMBINE) analysis to obtain 3D structure-activity relationships. The data set studied consists of the complexes of eighteen substrates docked within the active site of haloalkane dehalogenase (DhlA) from Xanthobacter autotrophicus GJ10. The results of the COMBINE analysis are compared with previously reported data obtained for the same dataset from modelled complexes that were based on an experimentally determined structure of the DhlA-dichloroethane complex. The quality of fit and the internal predictive power of the two COMBINE models are comparable, but better external predictions are obtained with the new approach. Both models show a similar composition of the principal components. Small differences in the relative contributions that are assigned to important residues for explaining binding affinity differences can be directly linked to structural differences in the modelled enzyme-substrate complexes: (i) rotation of all substrates in the active site about their longitudinal axis, (ii) repositioning of the ring of epihalohydrines and the halogen substituents of 1,2-dihalopropanes, and (iii) altered conformation of the long-chain molecules (halobutanes and halohexanes). For external validation, both a novel substrate not included in the training series and two different mutant proteins were used. The results obtained can be useful in the future to guide the rational engineering of substrate specificity in DhlA and other related enzymes.

National Centre for Biomolecular Research Masaryk University Kotlarska 2 611 37 Brno Czech Republic

Zobrazit více v PubMed

Trends Biochem Sci. 2001 Jan;26(1):71-3 PubMed

Biochemistry. 2000 Nov 21;39(46):14082-6 PubMed

Biochemistry. 1999 Dec 7;38(49):16105-14 PubMed

Biochemistry. 1998 Oct 27;37(43):15013-23 PubMed

Nucleic Acids Res. 2000 Jan 1;28(1):235-42 PubMed

Biochemistry. 1999 May 4;38(18):5772-8 PubMed

J Mol Graph. 1990 Mar;8(1):52-6, 29 PubMed

Eur J Biochem. 1995 Mar 1;228(2):403-7 PubMed

J Med Chem. 1998 Mar 12;41(6):836-52 PubMed

J Comput Aided Mol Des. 2000 May;14(4):341-53 PubMed

Biochemistry. 2001 Jul 31;40(30):8905-17 PubMed

Proc Natl Acad Sci U S A. 1997 Aug 5;94(16):8417-20 PubMed

J Med Chem. 1997 Mar 28;40(7):1136-48 PubMed

J Med Chem. 2000 May 4;43(9):1780-92 PubMed

Comb Chem High Throughput Screen. 2001 Dec;4(8):627-42 PubMed

Nature. 1993 Jun 24;363(6431):693-8 PubMed

J Med Chem. 2001 Mar 15;44(6):961-71 PubMed

Biochemistry. 1993 Sep 7;32(35):9031-7 PubMed

J Am Chem Soc. 2003 Feb 12;125(6):1532-40 PubMed

J Biol Chem. 1996 Jun 21;271(25):14747-53 PubMed

J Comput Aided Mol Des. 1990 Mar;4(1):1-105 PubMed

J Mol Graph Model. 1997 Dec;15(6):364-71, 389 PubMed

J Med Chem. 1995 Jul 7;38(14 ):2681-91 PubMed

Protein Eng. 1999 Nov;12(11):989-98 PubMed

J Med Chem. 2002 Oct 24;45(22):4828-37 PubMed

J Am Chem Soc. 2002 Apr 17;124(15):4097-107 PubMed

Biochemistry. 2002 Dec 3;41(48):14272-80 PubMed