Molecular dynamics simulation of Leishmania major surface metalloprotease GP63 (leishmanolysin)

Proteins: Structure, Function and Genetics

Volumn 64, Issue 2, 2006, Pages 385-390

  Bianchini, Gianluca ^a   Bocedi, Alessio ^a,b   Ascenzi, Paolo ^b,c   Gavuzzo, Enrico ^d   Mazza, Fernando ^a   Aschi, Massimiliano ^a  

^a UNIVERSITY OF L'AQUILA   (Italy)

^b NATIONAL INSTITUTE FOR INFECTIOUS DISEASES L SPALLANZANI   (Italy)

^c ROMA TRE UNIVERSITY   (Italy)

^d CNR   (Italy)

Author keywords

Dynamic domain; Essential dynamics; Leishmania major; Metalloprotease; Molecular dynamics

Indexed keywords

ALANINE; AMINO ACID; ASPARAGINE; ASPARTIC ACID; CYSTEINE; ENZYME PRECURSOR; GLYCINE; HISTIDINE; LEISHMANOLYSIN; LYSINE; METALLOPROTEINASE; PHENYLALANINE; PROLINE; SERINE PROTEINASE; SOLVENT; SURFACE METALLOPROTEASE GP63; THREONINE; TYROSINE; UNCLASSIFIED DRUG; VALINE; WATER;

ALKALINITY; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; BIOINFORMATICS; CRYSTAL STRUCTURE; ENZYME ACTIVATION; ENZYME ACTIVE SITE; ENZYME ACTIVITY; LEISHMANIA MAJOR; MOLECULAR DYNAMICS; MOTION; NONHUMAN; PARASITE VIRULENCE; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN DOMAIN; SEQUENCE ANALYSIS; SIMULATION; STRUCTURE ANALYSIS;

ANIMALS; BINDING SITES; COMPUTER SIMULATION; HUMANS; HYDROGEN-ION CONCENTRATION; LEISHMANIA MAJOR; MATRIX METALLOPROTEINASE 8; METALLOENDOPEPTIDASES; METALLOPROTEASES; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY;

LEISHMANIA MAJOR; LEISHMANIA SP.;

EID: 33745635354     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21009     Document Type: Article

References (30)

1. Cox FEG, editor. Modern parasitology: a textbook of parasitology. Oxford: Blackwell Science; 1993.
2. Gilles HM. Protozoal diseases. London: Arnold; 1999.
3. Desjeux P. Leishmaniasis: current situation and new perspectives. Comp Immunol Infect Dis 2004;27:305-318.
4. Coombs GH, Mottram, JC. In: Hide G, Mottram JC, Coombs GH, Holmes PH, editors. Trypanosomiasis and leishmaniasis: biology and control. Oxford: CAB International; 1997. p. 177-197.
5. Zhang T, Maekawa Y, Hanba J, Dainichi T, Nashed BF, Hisaeda H, Sakai T, Asao T, Himeno K, Good RA, Katunuma N. Lysosomal cathepsin B plays an important role in antigen processing, while cathepsin D is involved in degradation of the invariant chain inovalbumin-immunized mice. Immunology 2000;100:13-20.
6. Zhang T, Maekawa Y, Yasutomo K, Ishikawa H, Fawzy Nashed B, Dainichi T, Hisaeda H, Sakai T, Kasai M, Mizuochi T, Asao T, Katunuma N, Himeno K. Pepstatin A-sensitive aspartic proteases in lysosome are involved in degradation of the invariant chain and antigen-processing in antigen presentino cells of mice infected with Leishmania major. Biochem Biophys Res Commun 2000;276:693-701.
7. Yao C, Donelson JE, Wilson ME. The major surface protease (MSP or GP63) of Leishmania sp. biosynthesis, regulation of expression, and function. Biochem Parasitol 2003;132:1-16.
8. da Silva-Lopez RE, Giovanni De Simone S. Leishmania (Leishmania) amazonensis: purification and characterization of a promastigote serine protease Exp Parasitol 2004;107:173-182.
9. Mottram JC, Coombs GH, Alexander J. Cysteine peptidases as virulence factors of Leishmania. Curr Opin Microbiol 2004;7:375-81.
10. Rafati S, Salmanian AH, Taheri T, Masina S, Schaff C, Taslimi Y, Fasel N. Type I signal peptidase from Leishmania is a target of the immune response in human cutaneous and visceral leishmaniasis. Mol Biochem Parasitol 2004;135:13-20.
11. Singh S, Sivakumar RJ. Challenges and new discoveries in the treatment of leishmaniasis. Infect Chemother 2004;10:307-315.
12. Alves CR, Corte-Real S, Bourguignon SC, Chaves CS, Saraiva EM. Leishmania amazonensis: early proteinase activities during promastigote-amastigote differentiation in vitro. Exp Parasitol 2005;109:38-48.
13. Schlagenhauf E, Etges R, Metcalf P. The crystal structure of the Leishmania major surface proteinase leishmanolysin (gp63). Structure 1998;6:1035-1046.
14. Yiallouros I, Kappelhoff R, Schilling O, Wegmann F, Helms MW, Auge A, Brachtendorf G, Berkhoff EG, Beermann B, Hinz HJ, Konig S, Peter-Katalinic J, Stocker W. Activation mechanism of pro-astacin: role of the pro-peptide, tryptic and autoproteolytic cleavage and importance of precise amino-terminal processing. J Mol Biol 2002;324:237-246.
15. Aschi M, Roccatano D, Di Nola A, Gallina C, Gavuzzo E, Pochetti G, Pieper M, Tschesche H, Mazza F. Computational study of the catalytic domain of human neutrophil collagenase. Specific role of the S-3 and S'(3) subsites in the interaction with a phosphonate inhibitor. J Comput Aided Mol Des 2002;16:213-225.
16. Gavuzzo E, Pochetti G, Mazza F, Gallina C, Gorini B, D'Alessio S, Pieper M, Tschesche H, Tucker PA. Two crystal structures of human neutrophil collagenase, one complexed with a primed- and the other with an unprimed-side inhibitor: implications for drug design. J Med Chem 2000;43:3377-3385.
17. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res. 2000;28:235.
18. Berendsen HJC, van der Spoel D, van Drunen R. GROMACS: a message-passing parallel molecular dynamics implementation. Comp Phys Comm 1995;91:43-56.
19. Berendsen HJC, Postma JPM, van Gunsteren WF, Di Nola A. Molecular dynamics with coupling to an external bath. J Chem Phys 1984;81:3684-3690.
20. Amadei A, Chillemi G, Ceruso M, Grottesi A, Di Nola A. Molecular dynamics simulations with constrained roto-translational motions: theoretical basis and statistical mechanical consistency. J Chem Phys 2000;112:9-23.
21. Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans HJ. In: Pullman B, editor. Intermolecular forces. Dordrecht, The Netherlands: Reidel; 1981. p 331-342.
22. van Gunsteren WF, Billeter SR, Eising AA, Hunemberger PH, Kruger P, Mark AE, Scott VRP, Tironi IG. Biomolecular simulation: the GROMOS96 manual and user guide. Zurich: vdf Hochschlverlag AG an der ETH Zurich; 1996.
23. Hess B, Bekker H, Berendsen HJC, Frajie JGEM. LINGS: a linear constraint solver for molecular simulations. J Comput Chem 1997;18:1463-1472.
24. Darden TA, York DM, Pedersen LG. Particle mesh Ewald: method for Ewald sums in large systems. J Chem Phys 1993;98:10089-10092.
25. Amadei A, Linssen AB, Berendsen HJ. Essential dynamics of proteins. Proteins 1993;17:412-425.
26. Hayward S, Berendsen HJC. Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme. Proteins 1998;30:144-154.
27. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res 2004;32:D23-D26.
28. Hayward S. Identification of specific interactions that drive ligand-induced closure in five enzymes with classic domain movements. J Mol Biol 2004;339:1001-2021.
29. Stoker W, Grams F, Baumann U, Reinemer P, Gomis-Ruth FX, McKay DB, Bode W. The metzincins-topological and sequential relations between the astacins, adamalysins, serralysins, and matrixins (collagenases) define a superfamily of zinc-peptidases. Protein Sci 1995;4:823-840.
30. McGwire BS, O'Connell WA, Chang, K-P, Engman DM. Extracellular release of the glycosylphosphatidylinositol (GPI)-linked Leishmania surface metalloprotease, gp63, is independent of GPI phospholipolysis. J Biol Chem 2002;277:8802.