Electrostatic complementarity between proteins and ligands. 1. Charge disposition, dielectric and interface effects

SummaryElectrostatic interactions have always been considered an important factor governing ligand-receptor interactions. Previous work in this field has established the existence of electrostatic complementarity between the ligand and its receptor site. However, this property has not been treated rigorously, and the description remains largely qualitative. In this work, 34 data sets of high quality were chosen from the Brookhaven Protein Databank. The electrostatic complementarity has been calculated between the surface potentials; complementarity is absent between adjacent or neighbouring atoms of the ligand and the receptor. There is little difference between complementarities on the total ligand surface and the interfacial region. Altering the homogeneous dielectric to distance-dependent dielectrics reduces the complementarity slightly, but does not affect the pattern of complementarity.

[1]  T. Steitz,et al.  Structure of a complex of catabolite gene activator protein and cyclic AMP refined at 2.5 A resolution. , 1987, Journal of molecular biology.

[2]  R. M. Burnett,et al.  Structure of the semiquinone form of flavodoxin from Clostridum MP. Extension of 1.8 A resolution and some comparisons with the oxidized state. , 1978, Journal of molecular biology.

[3]  R. Dixon,et al.  Crystallographic analysis of a complex between human immunodeficiency virus type 1 protease and acetyl-pepstatin at 2.0-A resolution. , 1991, The Journal of biological chemistry.

[4]  Haruki Nakamura,et al.  Protein-protein interactions on the surface of immunoglobulin molecules , 1989 .

[5]  L. Delbaere,et al.  Structures of product and inhibitor complexes of Streptomyces griseus protease A at 1.8 A resolution. A model for serine protease catalysis. , 1980, Journal of molecular biology.

[6]  C. Giessner-Prettre,et al.  On the molecular electrostatic potentials obtained with CNDO and INDO wave functions , 1974 .

[7]  Haruki Nakamura,et al.  Visualization of electrostatic recognition by enzymes for their ligands and cofactors , 1985 .

[8]  S J Oatley,et al.  Crystal structures of Escherichia coli dihydrofolate reductase: the NADP+ holoenzyme and the folate.NADP+ ternary complex. Substrate binding and a model for the transition state. , 1990, Biochemistry.

[9]  A Wlodawer,et al.  Structure at 2.5-A resolution of chemically synthesized human immunodeficiency virus type 1 protease complexed with a hydroxyethylene-based inhibitor. , 1991, Biochemistry.

[10]  P C Moody,et al.  Structure of holo-glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus at 1.8 A resolution. , 1987, Journal of molecular biology.

[11]  T A Jones,et al.  Crystallographic refinement of human serum retinol binding protein at 2Å resolution , 1990, Proteins.

[12]  R. Huber,et al.  Molecular structure of the bilin binding protein (BBP) from Pieris brassicae after refinement at 2.0 A resolution. , 1987, Journal of molecular biology.

[13]  J M Blaney,et al.  Electrostatic potential molecular surfaces. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[14]  A Wlodawer,et al.  Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 A resolution. , 1989, Science.

[15]  Philip M. Dean,et al.  Electrostatic complementarity between proteins and ligands. 2. Ligand moieties , 1994, J. Comput. Aided Mol. Des..

[16]  R F Standaert,et al.  Atomic structure of FKBP-FK506, an immunophilin-immunosuppressant complex , 1991, Science.

[17]  F A Quiocho,et al.  Sugar-binding and crystallographic studies of an arabinose-binding protein mutant (Met108Leu) that exhibits enhanced affinity and altered specificity. , 1991, Biochemistry.

[18]  R. DesJarlais,et al.  Inhibition of human immunodeficiency virus-1 protease by a C2-symmetric phosphinate. Synthesis and crystallographic analysis. , 1993, Biochemistry.

[19]  S J Remington,et al.  1.9-A structures of ternary complexes of citrate synthase with D- and L-malate: mechanistic implications. , 1991, Biochemistry.

[20]  G A Petsko,et al.  Crystallographic analysis of the complex between triosephosphate isomerase and 2-phosphoglycolate at 2.5-A resolution: implications for catalysis. , 1990, Biochemistry.

[21]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

[22]  P. Dean,et al.  Molecular recognition: 3d surface structure comparison by gnomonic , 1987 .

[23]  P. Dean,et al.  Statistical method for surface pattern-making between dissimilar molecules: electrostatic potentials and accessible surfaces , 1986 .

[24]  M. Katharine Holloway,et al.  X-Ray Crystal Structure of the HIV Protease Complex with L-700,417, an Inhibitor with Pseudo C2 Symmetry , 1991 .

[25]  P. Karplus,et al.  Atomic structure of ferredoxin-NADP+ reductase: prototype for a structurally novel flavoenzyme family. , 1991, Science.

[26]  W G Hol,et al.  Crystal structure of p-hydroxybenzoate hydroxylase complexed with its reaction product 3,4-dihydroxybenzoate. , 1988, Journal of Molecular Biology.

[27]  A M Hassell,et al.  Hydroxyethylene isostere inhibitors of human immunodeficiency virus-1 protease: structure-activity analysis using enzyme kinetics, X-ray crystallography, and infected T-cell assays. , 1992, Biochemistry.

[28]  J L Sussman,et al.  Refined crystal structure of dogfish M4 apo-lactate dehydrogenase. , 1989, Journal of molecular biology.

[29]  K. Diederichs,et al.  The refined structure of the complex between adenylate kinase from beef heart mitochondrial matrix and its substrate AMP at 1.85 A resolution. , 1991, Journal of molecular biology.

[30]  U Heinemann,et al.  Three-dimensional structure of the ribonuclease T1 2'-GMP complex at 1.9-A resolution. , 1988, The Journal of biological chemistry.

[31]  Philip M. Dean,et al.  Electrostatic complementarity between proteins and ligands. 3. Structural basis , 1994, J. Comput. Aided Mol. Des..

[32]  Y. Lindqvist,et al.  Refined structure of spinach glycolate oxidase at 2 A resolution. , 1989, Journal of molecular biology.

[33]  S. Addelman,et al.  Fitting straight lines when both variables are subject to error. , 1978, Life sciences.

[34]  William H. Press,et al.  Numerical Recipes: FORTRAN , 1988 .

[35]  J. Kraut,et al.  Crystal structures of recombinant human dihydrofolate reductase complexed with folate and 5-deazafolate. , 1990, Biochemistry.

[36]  A Wlodawer,et al.  X-ray crystallographic structure of a complex between a synthetic protease of human immunodeficiency virus 1 and a substrate-based hydroxyethylamine inhibitor. , 1990, Proceedings of the National Academy of Sciences of the United States of America.