Interaction of malaria parasite-inhibitory antibodies with the merozoite surface protein MSP119 by computational docking

Proteins: Structure, Function and Genetics

Volumn 66, Issue 3, 2007, Pages 513-527

  Autore, Flavia ^a   Melchiorre, Sara ^a   Kleinjung, Jens ^b   Morgan, William D ^b   Fraternali, Franca ^a,c  

^a UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^b NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

^c KING'S COLLEGE LONDON   (United Kingdom)

Author keywords

Antibody antigen complex; Docking; Malaria; Molecular dynamics; MSP1 (merozoite surface protein 1); NMR; Plasmodium falciparum

Indexed keywords

EPITOPE; MALARIA VACCINE; MEROZOITE SURFACE PROTEIN 1; MONOCLONAL ANTIBODY;

ANTIBODY SPECIFICITY; ANTIGEN ANTIBODY COMPLEX; ANTIGEN ANTIBODY REACTION; BINDING SITE; CARBOXY TERMINAL SEQUENCE; CONFERENCE PAPER; ERYTHROCYTE; HOST PARASITE INTERACTION; MOLECULAR DYNAMICS; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PARASITE DEVELOPMENT; PLASMODIUM FALCIPARUM; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN;

AMINO ACID SEQUENCE; ANIMALS; ANTIBODIES, PROTOZOAN; ANTIGEN-ANTIBODY COMPLEX; COMPUTER SIMULATION; HUMANS; MALARIA; MEROZOITE SURFACE PROTEIN 1; PLASMODIUM; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID;

PLASMODIUM FALCIPARUM;

EID: 33846198406     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21212     Document Type: Conference Paper

References (54)

1. Engers HD, Godal T. Malaria vaccine development: current status. Parasitol Today 1998;14:56-64.
2. Holder AA. Proteins on the surface of the malaria parasite and cell invasion. Parasitology 1994;108 Suppl:S5-S18.
3. Barnwell JW, Galinski MR. The adhesion of malaria merozoite proteins to erythrocytes: a reflection of function? Res Immunol 1991;142:666-672.
4. Holder AA, Guevara Patino JA, Uthaipibull C, Syed SE, Ling IT, Scott-Finnigan T, Blackman MJ. Merozoite surface protein 1 , immune evasion, and vaccines against asexual blood stage malaria. Parassitologia 1999;41:409-414.
5. McBride JS, Heidrich HG. Fragments of the polymorphic Mr 185,000 glycoprotein from the surface of isolated Plasmodium falciparum merozoites form an antigenic complex. Mol Biochem Parasitol 1987;23:71-84.
6. Holder AA, Sandhu JS, Hillman Y, Davey LS, Nicholls SC, Cooper H, Lockyer MJ. Processing of the precursor to the major merozoite surface antigens of Plasmodium falciparum. Parasitology 1987;94:199-208.
7. Holder AA, Riley EM. Human immune response to MSP-1. Parasitol Today 1996;12:173,174.
8. Blackman MJ, Heidrich HG, Donachie S, McBride JS, Holder AA. A single fragment of a malaria merozoite surface protein remains on the parasite during red cell invasion and is the target of invasion-inhibiting antibodies. J Exp Med 1990;172:379-382.
9. Blackman MJ, Scott-Finnigan TJ, Shai S, Holder AA. Antibodies inhibit the protease-mediated processing of a malaria merozoite surface protein. J Exp Med 1994;180:389-393.
10. Guevara Patino JA, Holder AA, McBride JS, Blackman MJ. Antibodies that inhibit malaria merozoite surface protein-1 processing and erythrocyte invasion are blocked by naturally acquired human antibodies. J Exp Med 1997;186:1689-1699.
11. Nwuba RI, Sodeinde O, Anumudu CI, Omosun YO, Odaibo AB, Holder AA, Nwagwu M. The human immune response to Plasmodium falciparum includes both antibodies that inhibit merozoite surface protein-1 secondary processing and blocking antibodies. Infect Immun 2002;70:5328-5331.
12. Morgan WD, Birdsall B, Frenkiel TA, Gradwell MG, Burghaus PA, Syed SE, Uthaipibull C, Holder AA, Feeney J. Solution structure of an EGF module pair from the Plasmodium, falciparum merozoite surface protein 1. J Mol Biol 1999;289:113-122.
13. Chitarra V, Holm I, Bentley GA, Pétres S, Longacre S. The crystal structure of C-terminal merozoite surface protein-1 at 1.8 A resolution, a highly protective malaria vaccine candidate. Mol Cell 1999;3:457-464.
14. Carman SC, Simcoke WN, Stowers AW, Garboczi DN. Structure of the C-terminal domains of merozoite surface protein-1 from Plasmodium knowlesi reveals a novel histidine binding site. J Biol Chem 2003;278:7264-7269.
15. Pizarro JC, Chitarra V, Verger D, Holm I, Pétres S, Dartevelle S, Nato F, Longacre S, Bentley GA. Crystal structure of a Fab complex formed with PfMSP1-19, the C-terminal fragment of merozoite surface protein 1 from Plasmodium falciparum: a malaria vaccine candidate. J Mol Biol 2003;328:1091-1103.
16. Jennings RM. Murine and human antibody responses to Plasmodium falciparum merozoite surface protein-1. PhD Thesis, London: University College London; 2004.
17. Uthaipibull C, Aufiero B, Syed SE, Hansen B, Guevara Patino JA, Angov E, Ling IT, Fegeding K, Morgan WD, Ockenhouse C, Birdsall B, Feeney J, Lyon JA, Holder AA. Inhibitory and blocking monoclonal antibody epitopes on merozoite surface protein 1 of the malaria parasite Plasmodium falciparum. J Mol Biol 2001;307:1381-1394.
18. Morgan WD, Frenkiel TA, Lock MJ, Grainger M, Holder AA. Precise epitope mapping of malaria parasite inhibitory antibodies by TROSY NMR cross-saturation. Biochemistry 2005;44:518-523.
19. Morgan WD, Lock MJ, Frenkiel TA, Grainger M, Holder AA. Malaria parasite-inhibitory antibody epitopes on Plasmodium falciparum merozoite surface protein-1(19) mapped by TROSY NMR. Mol Biochem Parasitai 2004;138:29-36.
20. Wodak SJ, Méndez R. Prediction of protein-protein interactions: the CAPRI experiment, its evaluation and implications. Curr Opin Struct Biol 2004;14:242-249.
21. Chen R, Li L, Weng Z. ZDOCK: an initial-stage protein-docking algorithm. Proteins 2003;52:80-87.
22. Chen R, Weng Z. A novel shape complementarity scoring function for protein-protein docking. Proteins 2003;51:397-408.
23. Berendsen HJC, van der Spoel D, van Drunen R. GROMACS: A message-passing parallel molecular dynamics implementation. Comput Phys Commun 1995;91:43-56.
24. Chen R, Tong W, Mintseris J, Li L, Weng Z. ZDOCK predictions for the CAPRI challenge. Proteins 2003;52:68-73.
25. Ehrlich LP, Nilges M, Wade RC. The impact of protein flexibility on protein-protein docking. Proteins 2005;58:126-133.
26. Smith GS, Sternberg MJE, Bates PA. The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking. J Mol Biol 2005;347:1077-1101.
27. Notredame C, Higgins DG, Heringa J. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000;302:205-217.
28. Huang X, Miller W. A time-efficient, linear-space local similarity algorithm. Adv Appl Math 1991;12:337-357.
29. Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 1988;85:2444-2448.
30. Schwede T, Kopp J, Guex N, Peitsch MC. SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res 2003;31:3381-3385.
31. Sun SW, Bhat TN, Navia MA, Cohen GH, Rao DN, Rudikoff S, Davies DR. The galactan-binding immunoglobulin Fab J539: an X-ray diffraction study at 2.6-Aresolution. Proteins 1986;1:74-80.
32. Chitarra V, Alzari PM, Bentley GA, Bhat TN, Eiselé JL, Houdusse A, Lescar J, Souchon H, Poljak RJ. Three-dimensional structure of a heteroclitic antigen-antibody cross-reaction complex. Proc Natl Acad Sci USA 1993;90:7711-7715.
33. Love RA, Villafranca JE, Aust RM, Nakamura KK, Jue RA, Major JG, Radhakrishnan R, Butler WF. How the anti-(metal chelate) antibody CHA255 is specific for the metal ion of its antigen: X-ray structures for two Fab'/hapten complexes with different metals in the chelate. Biochemistry 1993;32:10950-10959.
34. Alzari PM, Spinelli S, Mariuzza RA, Boulot G, Poljak RJ, Jarvis JM, Milstein C. Three-dimensional structure determination of an anti-2- phenyloxazolone antibody: the role of somatic mutation and heavy/light chain pairing in the maturation of an immune response. EMBO J 1990;9:3807-3814.
35. Chen R, Weng Z. Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins 2002;47: 281-294.
36. Kleinjung J, Romein J, Lin K, Heringa J. Contact-based sequence alignment. Nucleic Acids Res 2004;32:2464-2473.
37. Team RDC. R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2005.
38. Daura X, Mark AE, van Gunsteren WF. Parametrization of aliphatic CHn united atoms of GROMOS96 force field. J Comput Chem 1998;19:535-547.
39. Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J, Pullman B. Interaction models for water in relation to protein hydration. In: Pullman B, editor. Intermolecular forces. Dordrecht: Reidel; 1981. pp 331-342.
40. Berendsen HJC, Postma JPM, van Gunsteren WF, Dinola A, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys 1984;81:3684-3690.
41. Hess B, Bekker H, Berendsen HJC, Fraaije J. LINCS: a linear constraint solver for molecular simulations. J Comput Chem 1997;18:1463-1472.
42. Darden T, Perera L, Li L, Pedersen L. New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations. Struct Fold Des 1999;7(3).
43. Tironi IG, Sperb R, Smith PE, Vangunsteren WF. A generalized reaction field method for molecular-dynamics simulations. J Chem Phys 1995;102:5451-5459.
44. Kleinjung J, Fraternali F. POPSCOMP: an automated interaction analysis of biomolecular complexes. Nucleic Acids Res 2005; 33:W342-W346. (Web server issue).
45. Fraternali F, Cavallo L. Parameter optimized surfaces (POPS): analysis of key interactions and conformational changes in the ribosome. Nucleic Acids Res 2002;30:2950-2960.
46. Cavallo L, Kleinjung J, Fraternali F. POPS: a fast algorithm for solvent accessible surface areas at atomic and residue level. Nucleic Acids Res 2003;31:3364-3366.
47. Morea V, Tramontano A, Rustici M, Chothia C, Lesk AM. Conformations of the third hypervariable region in the VH domain of immunoglobulins. J Mol Biol 1998;275:269-294.
48. Torino J, Stadler E, Skern T, Auer H, Kanzler O, Betzel C, Blaas D, Fita I. Three-dimensional structure of the Fab fragment of a neutralizing antibody to human rhinovirus serotype 2. Protein Sci 1992;1:1154-1161.
49. Saul FA, Poljak RJ. Crystal structure of human immunoglobulin fragment Fab New refined at 2.0 A resolution. Proteins 1992;14: 363-371.
50. Zdanov A, Li Y, Bundle DR, Deng SJ, MacKenzie CR, Narang SA, Young NM, Cygler M. Structure of a single-chain antibody variable domain (Fv) fragment complexed with a carbohydrate antigen at 1.7-A resolution. Proc Natl Acad Sci USA 1994;91: 6423-6427.
51. Prasad L, Sharma S, Vandonselaar M, Quail JW, Lee JS, Waygood EB, Wilson KS, Dauter Z, Delbaere LT. Evaluation of mutagenesis for epitope mapping. Structure of an antibody-protein antigen complex. J Biol Chem 1993;268:10705-10708.
52. Chothia C, Lesk AM, Tramontano A, Levitt M, Smith-Gill SJ, Air G, Sherriff S, Padlan EA, Davies D, Tulip WR, Colman PM, Spinelli S, Alzari PM, Poljak J. Conformations of immunoglobulin hypervariable regions. Nature 1989;342:877-883.
53. Aloy P, Russel RB. Structural systems biology: modelling protein interactions. Nat Rev Mol Cell Biol 2006;7:188-197.
54. Chappel JA, Holder AA. Monoclonal antibodies that inhibit Plasmodium falciparum invasion in vitro recognise the first growth factor-like domain of merozoite surface protein-1. Mol Biochem Parasitol 1993;60:303-311.