Insight into the self-association of key enzymes from pathogenic species

European Biophysics Journal

Volumn 34, Issue 5, 2005, Pages 469-476

  Perugini, Matthew A ^a   Griffin, Michael D W ^b,c   Smith, Brian J ^d   Webb, Lauren E ^a   Davis, Antony J ^d   Handman, Emanuela ^d   Gerrard, Juliet A ^b  

^a University of Melbourne ^*  (Australia)

^b UNIVERSITY OF CANTERBURY   (New Zealand)

^c NZ Inst Crop Food Research Limited   (New Zealand)

^d WALTER AND ELIZA HALL INSTITUTE OF MEDICAL RESEARCH   (Australia)

Author keywords

Analytical ultracentrifugation; Binding; Bioinformatics; Drug discovery; Enzyme; Leishmania; Protein protein interactions; Sedimentation; Structural modeling

Indexed keywords

ANTIINFECTIVE AGENT; DIHYDRODIPICOLINATE SYNTHASE; ENZYME; LYSINE; MANNOSE; OLIGOMER; TETRAMER; UNCLASSIFIED DRUG;

AMINO ACID ANALYSIS; ARTICLE; BACTERICIDAL ACTIVITY; BIOSYNTHESIS; CHEMICAL ANALYSIS; CRYSTALLIZATION; DATA ANALYSIS; DIFFUSION; HUMAN; LEISHMANIA; MICROORGANISM; MOLECULAR MODEL; NONHUMAN; OLIGOMERIZATION; PATHOGENICITY; PROTEIN PROTEIN INTERACTION; SAMPLE; SEDIMENTATION; SPECIES; ULTRACENTRIFUGATION; VELOCITY; WILD TYPE;

ANIMALS; BIOPHYSICS; COMPUTATIONAL BIOLOGY; DIMERIZATION; ENZYMES; ESCHERICHIA COLI; GUANOSINE DIPHOSPHATE; HYDRO-LYASES; LEISHMANIA; LYSINE; MODELS, MOLECULAR; NUCLEOTIDYLTRANSFERASES; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, TERTIARY; PSEUDOMONAS AERUGINOSA; SOFTWARE; STREPTOCOCCUS PNEUMONIAE; ULTRACENTRIFUGATION;

EID: 22844439302     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00249-005-0491-y     Document Type: Article

References (36)

1. Andrews P (1964) Estimation of the molecular weights of proteins by sephadex gel-filtration. Biochem J 91:222-233
2. Blankenfeldt W, Asuncion M, Lam JS, Naismith JH (2000) The structural basis of the catalytic mechanism and regulation of glucose-1-phosphate thymidylyltransferase (RmlA). EMBO J 19:6652-6663
3. Boggetto N, Reboud-Ravaux M (2002) Dimerization inhibitors of HIV-1 protease. Biol Chem 383:1321-1324
4. Davis AJ, Murray HW, Handman E (2004a) Drugs against leishmaniasis: a synergy of technology and partnerships. Trends Parasitol 20:73-76
5. Davis AJ, Perugini MA, Smith BJ, Stewart JD, Ilg T, Hodder AN, Handman E (2004b) Properties of GDP-mannose pyrophosphorylase, a critical enzyme and drug target in Leishmania mexicana. J Biol Chem 279:12462-12468
6. Dobson RCD, Valegard K, Gerrard JA (2004) The crystal structure of three site-directed mutants of Escherichia coli dihydrodipicolinate synthase: further evidence for a catalytic triad. J Mol Biol 338:329-339
7. Eisenberg D, Luthy R, Bowie JU (1997) VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol 277:396-404
8. Fenton AW, Paricharttanakul NM, Reinhart GD (2004) Disentangling the web of allosteric communication in a homotetramer: heterotropic activation in phosphofructokinase from Escherichia coli. Biochemistry 43:14104-14110
9. Gabb HA, Jackson RM, Sternberg MJ (1997) Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol 272:106-120
10. Handman E (1992) Host-parasite interactions in leishmaniasis. Adv Mol Cell Biol 5:133-155
11. Handman E (2001) Leishmaniasis: current status of vaccine development. Clin Microbiol Rev 14:229-243
12. van Holde KE, Hansen JC (1998) Analytical ultracentrifugation from 1924 to the present: a remarkable history. Chemtracts Biochem Mol Biol 11:933-943
13. Hubbard SJ, Thornton JM (1993) NACCESS. Computer Program, Department of Biochemistry and Molecular Biology, University College London
14. Hutton CA, Southwood TJ, Turner JJ (2003) Inhibitors of lysine biosynthesis as antibacterial agents. Mini Rev Med Chem 3:115-127
15. Jackson RM, Gabb HA, Sternberg MJ (1998) Rapid refinement of protein interfaces incorporating solvation: application to the docking problem. J Mol Biol 276:265-285
16. Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637
17. Kraulis P (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallog 24:946-950
18. Laue TM, Shah BD, Ridgeway TM, Pelletier SL (1992) Computer-aided interpretation of analytical sedimentation data for proteins. In: Analytical ultracentrifugation in biochemistry and polymer science. The Royal Society of Chemistry, Cambridge, pp 90-125
19. Luthy R, Bowie JU, Eisenberg D (1992) Assessment of protein models with three-dimensional profiles. Nature 356:83-85
20. Marianayagam NJ, Sunde M, Matthews JM (2004) The power of two: protein dimerization in biology. Trends Biochem Sci 29:618-625
21. Martz F, Wilczynska M, Kleczkowski LA (2002) Oligomerisation status, with the monomer as the active species, defines catalytic efficiency of UDP-glucose pyrophosphorylase. Biochem J 367:295-300
22. Merritt EA, Bacon DJ (1997) Raster3D: photorealistic molecular graphics. Methods Enzymol 277:505-524
23. Mirwaldt C, Korndorfer I, Huber R (1995) The crystal structure of dihydrodipicolinate synthase from Escherichia coli at 2.5 Å resolution. J Mol Biol 246:227-239
24. Moont G, Gabb HA, Sternberg MJ (1999) Use of pair potentials across protein interfaces in screening predicted docked complexes. Proteins 35:364-373
25. Nooren IMA, Thornton JM (2003) Diversity of protein-protein interaction. EMBO J 22:3486-3492
26. Perugini MA, Schuck P, Hewlett GJ (2000) Self-association of human apolipoprotein E3 and E4 in the presence and absence of phospholipid. J Biol Chem 275:36758-36765
27. Perugini MA, Schuck P, Howlett GJ (2002) Differences in the binding capacity of human apolipoprotein E3 and E4 to size-fractionated lipid emulsions. Eur J Biochem 269:5939-5949
28. Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234:779-815
29. Schagger H, Cramer WA, von Jagow G (1994) Analysis of molecular masses and oligomeric states of protein complexes by blue native electrophoresis and isolation of membrane protein complexes by two-dimensional native electrophoresis. Anal Biochem 217:220-230
30. Schuck P (2000) Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and Lamm equation modeling. Biophys J 78:1606-1619
31. Schuck P, Perugini MA, Gonzales NR, Howlett GJ, Schubert D (2002) Size-distribution analysis of proteins by analytical ultracentrifugation: strategies and application to model systems. Biophys J 82:1096-1111
32. Shi J, Blundell TL, Mizuguchi K (2001) FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol 310:243-257
33. Singh SK, Maithal K, Balaram H, Balaram P (2001) Synthetic peptides as inactivators of multimeric enzymes: inhibition of Plasmodium falciparum triosephosphate isomerase by interface peptides. FEBS Lett 501:19-23
34. Sulzenbacher G, Gal L, Peneff C, Fassy F, Bourne Y (2001) Crystal structure of Streptococcus pneumoniae N-acetylglucosamine-1-phosphate uridyltransferase bound to acetyl-coenzyme A reveals a novel active site architecture. J Biol Chem 276:11844-11851
35. Vistica J, Dam J, Balbo A, Yikilmaz E, Mariuzza RA, Rouault TA, Schuck P (2004) Sedimentation equilibrium analysis of protein interactions with global implicit mass conservation constraints and systematic noise decomposition. Anal Biochem 326:234-256
36. Yonetani T, Park S, Tsuneshige A, Imai K, Kanaori K (2002) Global allostery model of hemoglobin. Modulation of O2 affinity, cooperativity, and Bohr effect by heterotropic allosteric effectors. J Biol Chem 277:34508-34520