Quaternary structure predictions and estimation of mutational effects on the free energy of dimerization of the OMPLA protein

Journal of Structural Biology

Volumn 163, Issue 2, 2008, Pages 155-162

  Dell'Orco, Daniele ^a   Casciari, Daniele ^a   Fanelli, Francesca ^a  

^a UNIVERSITY OF MODENA AND REGGIO EMILIA   (Italy)

Author keywords

Computational modeling; Molecular recognition; Rigid body docking; ZDOCK

Indexed keywords

MEMBRANE ENZYME; MONOMER; OUTER MEMBRANE PHOSPHOLIPASE A;

AMINO ACID SUBSTITUTION; ARTICLE; DIMERIZATION; ENERGY; ENZYME STRUCTURE; GENE DELETION; GENE MUTATION; GENETIC ASSOCIATION; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN PROTEIN INTERACTION; THERMODYNAMICS;

BACTERIAL OUTER MEMBRANE PROTEINS; DIMERIZATION; MUTATION; PHOSPHOLIPASES A1; PROTEIN BINDING; PROTEIN STRUCTURE, QUATERNARY; SULFINIC ACIDS; THERMODYNAMICS;

EID: 46749089563     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2008.05.006     Document Type: Article

References (22)

1. Bukholm G., Tannaes T., Nedenskov P., Esbensen Y., Grav H.J., Hovig T., Ariansen S., and Guldvog I. Colony variation of Helicobacter pylori: pathogenic potential is correlated to cell wall lipid composition. Scand. J. Gastroenterol. 32 (1997) 445-454
2. Casciari D., Seeber M., and Fanelli F. Quaternary structure predictions of transmembrane proteins starting from the monomer: a docking-based approach. BMC Bioinform. 7 (2006) 340
3. Chen R., and Weng Z. A novel shape complementarity scoring function for protein-protein docking. Proteins 51 (2003) 397-408
4. Chen R., Tong W., Mintseris J., Li L., and Weng Z. ZDOCK predictions for the CAPRI challenge. Proteins 52 (2003) 68-73
5. Dekker N., Tommassen J., and Verheij H.M. Bacteriocin release protein triggers dimerization of outer membrane phospholipase A in vivo. J. Bacteriol. 181 (1999) 3281-3283
6. Dekker N., Tommassen J., Lustig A., Rosenbusch J.P., and Verheij H.M. Dimerization regulates the enzymatic activity of Escherichia coli outer membrane phospholipase A. J. Biol. Chem. 272 (1997) 3179-3184
7. Dell'Orco D., De Benedetti P.G., and Fanelli F. In silico screening of mutational effects on transmembrane helix dimerization: insights from rigid-body docking and molecular dynamics simulations. J. Phys. Chem. B 111 (2007) 9114-9124
8. Dell'Orco D., De Benedetti P.G., and Fanelli F. In silico screening of mutational effects on enzyme-proteic inhibitor affinity: a docking-based approach. BMC Struct. Biol. 7 (2007) 37
9. Dell'Orco D., Seeber M., De Benedetti P., and Fanelli F. Probing fragment complementation by rigid-body docking: in silico reconstitution of calbindin D9k. J. Chem. Inf. Mod. 45 (2005) 1429-1438
10. Dunbrack Jr. R.L., and Karplus M. Backbone-dependent rotamer library for proteins. Application to side-chain prediction. J. Mol. Biol. 230 (1993) 543-574
11. Fanelli F., and Ferrari S. Prediction of MEF2A-DNA interface by rigid body docking: a tool for fast estimation of protein mutational effects on DNA binding. J. Struct. Biol. 153 (2006) 278-283
12. Grant K.A., Belandia I.U., Dekker N., Richardson P.T., and Park S.F. Molecular characterization of pldA, the structural gene for a phospholipase A from Campylobacter coli, and its contribution to cell-associated hemolysis. Infect. Immun. 65 (1997) 1172-1180
13. Heyer L.J., Kruglyak S., and Yooseph S. Exploring expression data: identification and analysis of coexpressed genes. Genome Res. 9 (1999) 1106-1115
14. Horrevoets A.J., Verheij H.M., and de Haas G.H. Inactivation of Escherichia coli outer-membrane phospholipase A by the affinity label hexadecanesulfonyl fluoride. Evidence for an active-site serine. Eur. J. Biochem. 198 (1991) 247-253
15. Ponder J.W., and Richards F.M. Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J. Mol. Biol. 193 (1987) 775-791
16. Scandella C.J., and Kornberg A. A membrane-bound phospholipase A1 purified from Escherichia coli. Biochemistry 10 (1971) 4447-4456
17. Snijder H.J., Kingma R.L., Kalk K.H., Dekker N., Egmond M.R., and Dijkstra B.W. Structural investigations of calcium binding and its role in activity and activation of outer membrane phospholipase A from Escherichia coli. J. Mol. Biol. 309 (2001) 477-489
18. Snijder H.J., Van Eerde J.H., Kingma R.L., Kalk K.H., Dekker N., Egmond M.R., and Dijkstra B.W. Structural investigations of the active-site mutant Asn156Ala of outer membrane phospholipase A: function of the Asn-His interaction in the catalytic triad. Protein Sci. 10 (2001) 1962-1969
19. Snijder H.J., Ubarretxena-Belandia I., Blaauw M., Kalk K.H., Verheij H.M., Egmond M.R., Dekker N., and Dijkstra B.W. Structural evidence for dimerization-regulated activation of an integral membrane phospholipase. Nature 401 (1999) 717-721
20. Stanley A.M., and Fleming K.G. The role of a hydrogen bonding network in the transmembrane beta-barrel OMPLA. J. Mol. Biol. 370 (2007) 912-924
21. Stanley A.M., Chuawong P., Hendrickson T.L., and Fleming K.G. Energetics of outer membrane phospholipase A (OMPLA) dimerization. J. Mol. Biol. 358 (2006) 120-131
22. Sutcliffe M.J., Hayes F.R., and Blundell T.L. Knowledge based modelling of homologous proteins, part ii: rules for the conformations of substituted sidechains. Protein Eng. 1 (1987) 385-392