Artículos de revistas
Analysis Of Molecular Targets Of Mycobacterium Tuberculosis By Analytical Ultracentrifugation
Registro en:
Current Medicinal Chemistry. , v. 18, n. 9, p. 1276 - 1285, 2011.
9298673
10.2174/092986711795029537
2-s2.0-79952787283
Autor
Borges J.C.
Ramos C.H.I.
Institución
Resumen
The interest in analytical ultracentrifugation (AUC) to analyze protein structural parameters and interactions has increased in the past decades as a result of several developments on new generation instrumentation and data analysis tools. In this article, we review AUC principles and applications to study proteins, emphasizing molecular targets of Mycobacterium tuberculosis. © 2011 Bentham Science Publishers Ltd. 18 9 1276 1285 Ralston, G., (1993) Introduction to Analytical Ultracentrifugation, , Beckman Instruments Inc.: Fullerton Laue, T.M., Stafford III, W.F., Modern applications of analytical ultracentrifugation (1999) Annual Review of Biophysics and Biomolecular Structure, 28, pp. 75-100. , DOI 10.1146/annurev.biophys.28.1.75 Laue, T., Biophysical studies by ultracentrifugation (2001) Current Opinion in Structural Biology, 11 (5), pp. 579-583. , DOI 10.1016/S0959-440X(00)00250-5 Harding, S.E., Winzor, D.J., Sedimentation equilibrium in the analytical ultracentrifuge (2001) Protein-Ligand Interactions: Hydrodynamics and Calorimetry: Partical Approach, pp. 105-135. , Harding, S. E., Chowdhry, B. Z., Eds. Oxford University Press: Oxford Winzor, D.J., Harding, S.E., Basic principles of sedimentation velocity (2001) Protein-Ligand Interactions: Hydrodynamics and Calorimetry: Partical Approach, pp. 75-104. , Harding, S. E., Chowdhry, B. Z., Eds. Oxford University Press: Oxford Lebowitz, J., Lewis, M.S., Schuck, P., Modern analytical ultracentrifugation in protein science: A tutorial review (2002) Protein Science, 11 (9), pp. 2067-2079. , DOI 10.1110/ps.0207702 Howlett, G.J., Minton, A.P., Rivas, G., Analytical ultracentrifugation for the study of protein association and assembly (2006) Current Opinion in Chemical Biology, 10 (5), pp. 430-436. , DOI 10.1016/j.cbpa.2006.08.017, PII S1367593106001244, Analytical Techniques/Mechanisms Svedberg, T., Fahraeus, R., A new method for the determination of the molecular weight of the proteins (1926) J. Am. Chem. Soc., 48 (1), pp. 430-438 Svedberg, T., Ultra centrifugal dispersion determination in protein solutions (1930) Kollid Z., 51 (1), pp. 10-24 Svedberg, T., Pedersen, K.O., (1940) The Ultracentrifuge, , Clarendon Press: Oxford Tanford, C., Reynolds, J., (2001) Naturés Robots, a Story of Proteins, , 1st ed. Oxford University Press: New York Giebeler, R., The optima XL-A: A new analytical ultracentrifuge with a novel precision absorption optical system (1992) Analytical Ultracentrifugation in Biochemistry and Polymer Science, pp. 16-25. , Harding, S., Rowe AJ, Horton JC, Eds. Royal Society of Chemistry: Cambridge Yphantis, D.A., Lary, J.W., Stavord, W.F., Liu, S., Olsen, P.H., Hayes, D.B., Moody, T.P., Laue, T., On line data acquisition for the Rayleigh interference optical system of the analytical ultracentrifuge (1994) Modern Analytical Ultracentrifugation, pp. 209-226. , Schuster, T. M., Laue, T. M., Eds. Birkhäuser: Boston Furst, A., The XL-I analytical ultracentrifuge with Rayleigh interference optics (1997) European Biophysics Journal, 25 (5-6), pp. 307-310. , DOI 10.1007/s002490050043 Schmidt, B., Riesner, B., A fuorescence detection system for the analytical ultracentrifuge and its application to proteins, nucleic acids, viroids and viruses (1992) Analytical Ultracentrifugation in Biochemistry and Polymer Science, pp. 176-207. , Harding, S. E., Rowe, A. J., Horton, J. C., Eds. The Royal Society of Chemistry: Cambridge MacGregor, I.K., Anderson, A.L., Laue, T.M., Fluorescence detection for the XLI analytical ultracentrifuge (2004) Biophysical Chemistry, 108 (1-3), pp. 165-185. , DOI 10.1016/j.bpc.2003.10.018, PII S0301462203003041 Einstein, A., The motion of elements suspended in static liquids as claimed in the molecular kinetic theory of heat (1905) Ann. Phys., 17 (8), pp. 549-560 Cantor, C.R., Schimmel, P.R., Size and shape of macromolecules (1980) Biophysical Chemistry, Part II: Techniques for the Study of Biological Structure and Function, pp. 539-590. , McCombs L. W., Ed. W.H. Freeman Company: New York Teller, D.C., Swanson, E., De Haon, C., The translational friction coefficient of proteins (1979) Methods Enzymol., 61, pp. 104-124 Eisenberg, D., Crothers, D., Bridging the macroscopic and microscopic (1979) Physical Chemistry with application to the Life Sciences, pp. 700-745. , Forkner M., Ed. The Benjamin/Cummings Publishing Company: Menlo Park Lamm, O., Die Differentialgleichung der Ultrazentrifugierung (1929) Ark. Mat. Astr. Fys, 21 B (2), pp. 1-4 Borges, J.C., Ramos, C.H.I., Characterization of nucleotide-induced changes on the quaternary structure of human 70 kDa heat shock protein Hsp70.1 by analytical ultracentrifugation (2009) BMB Rep., 42 (3), pp. 166-171 Borges, J.C., Pereira, J.H., Vasconcelos, I.B., Dos Santos, G.C., Olivieri, J.R., Ramos, C.H.I., Palma, M.S., De Azevedo Jr., W.F., Phosphate closes the solution structure of the 5-enolpyruvylshikimate-3- phosphate synthase (EPSPS) from Mycobacterium tuberculosis (2006) Archives of Biochemistry and Biophysics, 452 (2), pp. 156-164. , DOI 10.1016/j.abb.2006.05.008, PII S0003986106001779 Berkowitz, S.A., Role of analytical ultracentrifugation in assessing the aggregation of protein biopharmaceuticals (2006) AAPS J., 8 (3), pp. E590-E605 Liu, J., Andaya, J.D., Shire, S.J., A critical review of analytical ultracentrifugation and field flow fractionation methods for measuring protein aggregation (2006) AAPS Journal, 8 (3), pp. E580-E589. , http://www.aapsj.org/view.asp?art=aapsj080367, DOI 10.1208/aapsj080367, 67 Philo, J.S., Is any measurement method optimal for all aggregate sizes and types? (2006) AAPS J., 8 (3), pp. E564-E571 Balbo, A., Brown, P., Schuck, P., (2007) Experimental Protocol for Sedimentation Equilibrium Analytical Ultracentrifugation., , https://sedfitsedphat.nibib.nih.gov/tools/Protocols/ SedimentationEquilibrium.pdf, (Accessed March 20, 2010) Balbo, A., Brown, A.K., Schuck, P., (2008) Experimental Protocol for Sedimentation Velocity Analytical Ultracentrifugation., , https://sedfitsedphat.nibib.nih.gov/tools/Protocols/ SedimentationVelocity.pdf, (Accessed March 20, 2010) Schirf, V., Planken, K.L., Center for analytical ultracentrifugation of macromolecular assemblies (2008) Analytical Ultracentrifuge User Guide, 1. , http://ultrascan.uthscsa.edu/AUCuserGuideVolume-1-Hardware.pdf, Hardware. (Accessed March 18 2010) Balbo, A., Zhao, H., Brown, P., Schuck, P., Assembly loading, and alignment of an analytical ultracentrifuge sample cell (2009) JoVE, p. 33. , http://www.jove.com/index/details.stp?id=1530, (Accessed April 01 2010) Gabrielson, J.P., Arthur, K.K., Stoner, M.R., Winn, B.C., Kendrick, B.S., Razinkov, V., Svitel, J., Ridgeway, R., Precision of protein aggregation measurements by sedimentation velocity analytical ultracentrifugation in biopharmaceutical applications (2010) Anal. Biochem., 396 (2), pp. 231-241 Terrak, M., Wu, G., Stafford, W.F., Lu, R.C., Dominguez, R., Two distinct myosin light chain structures are induced by specific variations within the bound IQ motifs - Functional implications (2003) EMBO Journal, 22 (3), pp. 362-371. , DOI 10.1093/emboj/cdg058 Baldwin, R.L., Sedimentation coefficients of small molecules- methods of measurement based on the refractive-index gradient curve- The sedimentation coefficient of polyglucose-A (1953) Biochem. J., 55 (4), pp. 644-648 Goldberg, R.J., Sedimentation in the ultracentrifuge (1953) J. Phys. Chem., 57 (2), pp. 194-202 Milthorpe, B.K., Jeffrey, P.D., Nichol, L.W., Direct analysis of sedimentation equilibrium results obtained with polymerizing systems (1975) Biophys. Chem., 3 (2), pp. 169-176 Rowe, A.J., The concentration dependence of transport processes: a general description applicable to the sedimentation, translational diffusion, and viscosity coefficients of macromolecular solutes (1977) Biopolymers, 16 (12), pp. 2595-2611 Van Holde, K.E., Weischet, W.O., Boundary analysis of sedimentation-velocity experiments with monodisperse and paucidisperse solutes (1978) Biopolymers, 17 (6), pp. 1387-1403. , DOI 10.1002/bip.1978.360170602 Holladay, L.A., Approximate solution to the lamm equation (1979) Biophys. Chem., 10 (2), pp. 187-190 Johnson, M.L., Correia, J.J., Yphantis, D.A., Halvorson, H.R., Analysis of data from the analytical ultra-centrifuge by non-linear least-squares techniques (1981) Biophys. J., 36 (3), pp. 575-588 Johnson, M.L., Faunt, L.M., Parameter-estimation by least-squares methods (1992) Methods Enzymol., 210, pp. 1-37 Stafford, W.F., Boundary analysis in sedimentation transport experiments- A procedure for obtaining sedimentation coefficient distributions using the time derivative of the concentration profile (1992) Anal. Biochem., 203 (2), pp. 295-301 Hansen, J.C., Lebowitz, J., Demeler, B., Analytical ultracentrifugation of complex macromolecular systems (1994) Biochemistry, 33 (45), pp. 13155-13163. , DOI 10.1021/bi00249a001 Stafford, W.F., Boundary analysis in sedimentation velocity experiments (1994) Methods Enzymol., 240, pp. 478-501 Behlke, J., Ristau, O., Molecular mass determination by sedimentation velocity experiments and direct fitting of the concentration profiles (1997) Biophysical Journal, 72 (1), pp. 428-434 Demeler, B., Saber, H., Hansen, J.C., Identification and interpretation of complexity in sedimentation velocity boundaries (1997) Biophysical Journal, 72 (1), pp. 397-407 Philo, J.S., An improved function for fitting sedimentation velocity data for low- molecular-weight solutes (1997) Biophysical Journal, 72 (1), pp. 435-444 Demeler, B., Saber, H., Determination of molecular parameters by fitting sedimentation data to finite-element solutions of the Lamm equation (1998) Biophysical Journal, 74 (1), pp. 444-454 Schuck, P., Sedimentation analysis of noninteracting and self-associating solutes using numerical solutions to the Lamm equation (1998) Biophysical Journal, 75 (3), pp. 1503-1512 Winzor, D.J., Jacobsen, M.P., Wills, P.R., Direct analysis of sedimentation equilibrium distributions reflecting complex formation between dissimilar reactants (1998) Biochemistry, 37 (8), pp. 2226-2233. , DOI 10.1021/bi972211v Carruthers, L.M., Schirf, V.R., Demeler, B., Hansen, J.C., Sedimentation velocity analysis of macromolecular assemblies (2000) Methods in Enzymology, 321, pp. 66-80 Philo, J.S., Sedimentation equilibrium analysis of mixed associations using numerical constraints to impose mass or signal conservation (2000) Methods in Enzymology, 321, pp. 100-120 Schuck, P., Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and Lamm equation modeling (2000) Biophysical Journal, 78 (3), pp. 1606-1619 Schuck, P., Perugini, M.A., Gonzales, N.R., Hewlett, G.J., Schubert, D., Size-distribution analysis of proteins by analytical ultracentrifugation: Strategies and application to model systems (2002) Biophysical Journal, 82 (2), pp. 1096-1111 Schuck, P., On the analysis of protein self-association by sedimentation velocity analytical ultracentrifugation (2003) Analytical Biochemistry, 320 (1), pp. 104-124. , DOI 10.1016/S0003-2697(03)00289-6 Stafford, W.F., Sherwood, P.J., Analysis of heterologous interacting systems by sedimentation velocity: Curve fitting algorithms for estimation of sedimentation coefficients, equilibrium and kinetic constants (2004) Biophysical Chemistry, 108 (1-3), pp. 231-243. , DOI 10.1016/j.bpc.2003.10.028, PII S0301462203003090 Brown, P.H., Balbo, A., Schuck, P., On the analysis of sedimentation velocity in the study of protein complexes (2009) Eur. Biophys. J. Biophys. Lett., 38 (8), pp. 1079-1099 Brookes, E., Demeler, B., Rosano, C., Rocco, M., The implementation of SOMO (SOlution MOdeller) in the UltraScan analytical ultracentrifugation data analysis suite: Enhanced capabilities allow the reliable hydrodynamic modeling of virtually any kind of biomacromolecule (2010) Eur. Biophys. J., 39 (3), pp. 423-435 Philo, J.S., (2006) SEDNTERP, , http://jphilo.mailway.com/download.htm, (Accessed March 24, 2010) Cohn, E.J., Edsall, E.T., (1943) Proteins, Amino Acids, and Peptides as Ions and Dipolar Ions, , Reinhold Publ. Co.: New York Maher, D., Dye, C., Floyd, K., Pantoja, A., Lonnroth, K., Reid, A., Nathanson, E., Espinal, M., Planning to improve global health: The next decade of tuberculosis control (2007) Bulletin of the World Health Organization, 85 (5), pp. 341-347. , http://www.who.int/bulletin/volumes/85/5/06-037820.pdf, DOI 10.2471/BLT.06.037820 Raviglione, M., Revised international definitions in tuberculosis control (2001) International Journal of Tuberculosis and Lung Disease, 5 (3), pp. 213-215 Global tuberculosis control: Surveillance, planning, financing (2009) WHO Report, , World Health Organization Dye, C., Watt, C.J., Bleed, D.M., Hosseini, S.M., Raviglione, M.C., Evolution of tuberculosis control and prospects for reducing tuberculosis incidence, prevalence, and deaths globally (2005) Journal of the American Medical Association, 293 (22), pp. 2767-2775. , http://jama.ama-assn.org/cgi/reprint/293/22/2767.pdf, DOI 10.1001/jama.293.22.2767 Pablos-Mendez, A., Raviglione, M.C., Laszlo, A., Binkin, N., Rieder, H.L., Bustreo, F., Cohn, D.L., Nunn, P., Global Surveillance for Antituberculosis-Drug Resistance, 1994-1997 (1998) New England Journal of Medicine, 338 (23), pp. 1641-1649. , DOI 10.1056/NEJM199806043382301 Stokstad, E., Infectious disease- Drug-resistant TB on the rise (2000) Science, 287 (5462), p. 2391 Gopal, B., Haire, L.F., Cox, R.A., Colston, M.J., Major, S., Brannigan, J.A., Smerdon, S.J., Dodson, G., The crystal structure of NusB from Mycobacterium tuberculosis (2000) Nature Structural Biology, 7 (6), pp. 475-478. , DOI 10.1038/75876 Gopal, B., Papavinasasundaram, K.G., Dodson, G., Colston, M.J., Major, S.A., Lane, A.N., Spectroscopic and thermodynamic characterization of the transcription antitermination factor NusE and its interaction with NusB from Mycobacterium tuberculosis (2001) Biochemistry, 40 (4), pp. 920-928. , DOI 10.1021/bi0018279 Curti, E., Smerdon, S.J., Davis, E.O., Characterization of the helicase activity and substrate specificity of Mycobacterium tuberculosis UvrD (2007) Journal of Bacteriology, 189 (5), pp. 1542-1555. , DOI 10.1128/JB.01421-06 Long, M.C., Escuyer, V., Parker, W.B., Identification and Characterization of a Unique Adenosine Kinase from Mycobacterium tuberculosis (2003) Journal of Bacteriology, 185 (22), pp. 6548-6555. , DOI 10.1128/JB.185.22.6548-6555.2003 Carroll, K.S., Gao, H., Chen, H.Y., Stout, C.D., Leary, J.A., Bertozzi, C.R., A conserved mechanism for sulfonucleotide reduction (2005) PLoS Biol., 3 (8), pp. 1418-1435 Zhou, X., Lou, Z., Fu, S., Yang, A., Shen, H., Li, Z., Feng, Y., Rao, Z., Crystal structure of ArgP from Mycobacterium tuberculosis confirms two distinct conformations of full-length LysR transcriptional regulators and reveals its function in DNA binding and transcriptional regulation (2010) J. Mol. Biol., 396 (4), pp. 1012-1024 Cox, R.J., Sutherland, A., Vederas, J.C., Bacterial diaminopimelate metabolism as a target for antibiotic design (2000) Bioorganic and Medicinal Chemistry, 8 (5), pp. 843-871. , DOI 10.1016/S0968-0896(00)00044-4, PII S0968089600000444 Mitsakos, V., Dobson, R.C.J., Pearce, F.G., Devenish, S.R., Evans, G.L., Burgess, B.R., Perugini, M.A., Hutton, C.A., Inhibiting dihydrodipicolinate synthase across species: Towards specificity for pathogens? (2008) Bioorg. Med. Chem. Lett., 18 (2), pp. 842-844 Kefala, G., Evans, G.L., Griffin, M.D.W., Devenish, S.R.A., Pearce, F.G., Perugini, M.A., Gerrard, J.A., Dobson, R.C.J., Crystal structure and kinetic study of dihydrodipicolinate synthase from Mycobacterium tuberculosis (2008) Biochemical Journal, 411 (2), pp. 351-360. , DOI 10.1042/BJ20071360 Goulding, C.W., Apostol, M.I., Sawaya, M.R., Phillips, M., Parseghian, A., Eisenberg, D., Regulation by oligomerization in a mycobacterial folate biosynthetic enzyme (2005) Journal of Molecular Biology, 349 (1), pp. 61-72. , DOI 10.1016/j.jmb.2005.03.023, PII S0022283605002925 Semavina, M., Beckett, D., Logan, T.M., Metal-linked dimerization in the iron-dependent regulator from Mycobacterium tuberculosis (2006) Biochemistry, 45 (41), pp. 12480-12490. , DOI 10.1021/bi060797s Brown, A.K., Meng, G., Ghadbane, H., Scott, D.J., Dover, L.G., Nigou, J., Besra, G.S., Futterer, K., Dimerization of inositol monophosphatase Mycobacterium tuberculosis SuhB is not constitutive, but induced by binding of the activator Mg 2+ (2007) BMC Struct. Biol., 7 Kruh, N.A., Rawat, R., Ruzsicska, B.P., Tonge, P.J., Probing mechanisms of resistance to the tuberculosis drug isoniazid: Conformational changes caused by inhibition of InhA, the enoyl reductase from Mycobacterium tuberculosis (2007) Protein Science, 16 (8), pp. 1617-1627. , http://www.proteinscience.org/cgi/reprint/16/8/1617, DOI 10.1110/ps.062749007 Marrakchi, H., Ducasse, S., Labesse, G., Montrozier, H., Margeat, E., Emorine, L., Charpentier, X., Quemard, A., MabA (FabG1), a Mycobacterium tuberculosis protein involved in the long-chain fatty acid elongation system FAS-II (2002) Microbiology, 148 (4), pp. 951-960 Chopra, T., Banerjee, S., Gupta, S., Yadav, G., Anand, S., Surolia, A., Roy, R.P., Gokhale, R.S., Novel intermolecular iterative mechanism for biosynthesis of mycoketide synthase by a bimodular polyketide synthase (2008) PLoS Biol., 6 (7), pp. 1584-1598 Garzon, D., Bond, P.J., Faraldo-Gomez, J.D., Predicted structural basis for CD1c presentation of mycobacterial branched polyketides and long lipopeptide antigens (2009) Mol. Immunol., 47 (2-3), pp. 253-260 Alibhai, M.F., Stallings, W.C., Closing down on glyphosate inhibition - With a new structure for drug discovery (2001) Proceedings of the National Academy of Sciences of the United States of America, 98 (6), pp. 2944-2946. , DOI 10.1073/pnas.061025898 Dias, M.V.B., Borges, J.C., Ely, F., Pereira, J.H., Canduri, F., Ramos, C.H.I., Frazzon, J., De Azevedo Jr., W.F., Structure of chorismate synthase from Mycobacterium tuberculosis (2006) Journal of Structural Biology, 154 (2), pp. 130-143. , DOI 10.1016/j.jsb.2005.12.008, PII S1047847705002911 Sasso, S., Ramakrishnan, C., Gamper, M., Hilvert, D., Kast, P., Characterization of the secreted chorismate mutase from the pathogen mycobacterium tuberculosis (2005) FEBS J., 272 (2), pp. 375-389 Vivan, A.L., Caceres, R.A., Abrego, J.R.B., Borges, J.C., Neto, J.R., Ramos, C.H., De Azevedo, W.F., Santos, D.S., Structural studies of prephenate dehydratase from Mycobacterium tuberculosis H37Rv by SAXS, ultracentrifugation, and computational analysis (2008) Proteins-Struct. Funct. Bioinf., 72 (4), pp. 1352-1362 Colfen, H., Laue, T.M., Wohlleben, W., Schilling, K., Karabudak, E., Langhorst, B.W., Brookes, E., Demeler, B., The open AUC project (2010) Eur. Biophys. J., 39 (3), pp. 347-359