Published August 28, 2009 | Version 15475
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Recent Advances on Computational Proteomics

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In this work we report the recent progresses that have been achieved by our group in the last half decade on the field of computational proteomics. Specifically, we discuss the application of Molecular Dynamics Simulations and Electronic Structure Calculations in drug design, in the clarification of the structural and dynamic properties of proteins and enzymes and in the understanding of the catalytic and inhibition mechanism of cancer-related enzymes. A set of examples illustrate the concepts and help to introduce the reader into this important and fast moving field.

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References

  • J. A. McCammon, B. R. Gelin, and M. Karplus, "Dynamics of folded proteins," Nature, vol. 267, pp. 585-590, 1977.
  • M. Karplus and J. A. McCammon, "Molecular dynamics simulations of biomolecules," Nat. Struct. Biol., vol. 9, pp. 646-652, 2002.
  • A. Warshel, "Molecular dynamics simulations of biological reactions," Acc. Chem. Res., vol. 35, pp. 385-395, 2002.
  • S. J. Weiner, P. A. Kollman, D. A. Case, U. C. Singh, C. Ghio, G. Alagona, et al., "A new force-field for molecular mechanical simulation of nucleic-acids and proteins," J. Am. Chem. Soc., vol. 106, pp. 765- 784, 1984.
  • S. J. Weiner, P. A. Kollman, D. T. Nguyen, and D. A. Case, "An allatom force field for simulations of protein and nucleic acids," J. Comput. Chem., vol. 7, pp. 230-252, 1986.
  • W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Fergunson, et al., "A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules," J. Am. Chem. Soc., vol. 117, pp. 5179-5197, 1995.
  • B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, "CHARMM - a programm for macromolecular energy, minimization, and dynamics calculations," J. Comput. Chem., vol. 4, pp. 187-217, 1983.
  • A. D. MacKerell, D. Bashford, M. Bellott, R. L. Dunbrack, J. D. Evanseck, M. J. Field et al., "All-atom empirical potential for molecular modeling and dynamics studies of proteins," J. Phys. Chem. B, vol. 102, pp. 3586-3616, 1998.
  • A. D. MacKerell, N. Banavali, and N. Foloppe, "Development and current status of the CHARMM force field for nucleic acids," Biopolymers, vol. 56, pp. 257-265, 2000. [10] W. L. Jorgensen and J. Tirado-Rives, "The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin," J. Am. Chem. Soc., vol. 110, pp. 1657-1666, 1988. [11] J. Pranata, S. G. Wierschke, and W. L. Jorgensen, "Opls Potential Functions for Nucleotide Bases - Relative Association Constants of Hydrogen-Bonded Base-Pairs in Chloroform," J. Am. Chem. Soc., vol. 113, pp. 2810-2819, 1991. [12] W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives, "Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids," J. Am. Chem. Soc., vol. 118, pp. 11225-11236, 1996. [13] A. T. Marques, P. A. Fernandes, and M. J. Ramos, "Molecular dynamics simulations of the amyloid-beta binding alcohol dehydrogenase (ABAD) enzyme," Bioorgan. Med. Chem., vol. 16, pp. 9511-9518, 2008. [14] N. F. Bras, N. M. F. S. Cerqueira, P. A. Fernandes, and M. J. Ramos, "Carbohydrate-binding modules from family 11: Understanding the binding mode of polysaccharides," Int. J. Quantum Chem., vol. 108, pp. 2030-2040, 2008. [15] A. Viegas, N. F. Bras, N. M. F. S. Cerqueira, P. A. Fernandes, J. A. M. Prates, C. M. G. A. Fontes, et al., "Molecular determinants of ligand specificity in family 11 carbohydrate binding modules - an NMR, X-ray crystallography and computational chemistry approach," FEBS J., vol. 275, pp. 2524-2535, 2008. [16] A. T. P. Carvalho, M. Swart, J. N. P. van Stralen, P. A. Fernandes, M. J. Ramos, and F. M. Bickelhaupt, "Mechanism of thioredoxin-catalyzed disulfide reduction. Activation of the buried thiol and role of the variable active-site residues," J. Phys. Chem. B, vol. 112, pp. 2511-2523, 2008. [17] A. T. P. Carvalho, P. A. Fernandes, and M. J. Ramos, "Insights on resistance to reverse transcriptase: The different patterns of interaction of the nucleoside reverse transcriptase inhibitors in the deoxyribonucleotide triphosphate binding site relative to the normal substrate," J. Med. Chem., vol. 49, pp. 7675-7682, 2006. [18] S. F. Sousa, P. A. Fernandes, and M. J. Ramos, "Enzyme Flexibility and the Catalytic Mechanism of Farnesyltransferase: Targeting the Relation," J. Phys. Chem. B, vol. 112, pp. 8681-8691, 2008. [19] S. F. Sousa, P. A. Fernandes, and M. J. Ramos, "Molecular Dynamics Simulations on the Critical States of the Farnesyltransferase Enzyme," Bioorg. Med. Chem., pp. (10.1016/j.bmc.2009.03.055), 2009. [20] S. F. Sousa, P. A. Fernandes, and M. J. Ramos, "Molecular dynamics analysis of farnesyltransferase: A closer look into the amino acid behavior," Int. J. Quant. Chem., vol. 108, pp. 1939-1950, 2008. [21] N. M. F. S. Cerqueira, N. F. Bras, P. A. Fernandes, and M. J. Ramos, "MADAMM: A multistaged docking with an automated molecular modeling protocol," Proteins, vol. 74, pp. 192-206, 2009. [22] S. F. Sousa, P. A. Fernandes, and M. J. Ramos, "Unraveling the mechanism of the farnesyltransferase Enzyme," J. Biol. Inorg. Chem., vol. 10, pp. 3-10, 2005. [23] S. F. Sousa, P. A. Fernandes, and M. J. Ramos, "Farnesyltransferase inhibitors: A detailed chemical view on an elusive biological problem," Curr. Med. Chem., vol. 15, pp. 1478-1492, 2008. [24] S. F. Sousa, P. A. Fernandes, and M. J. Ramos, "The Search for the Mechanism of the Reaction Catalyzed by Farnesyltransferase," Chemistry, 2009. [25] S. F. Sousa, P. A. Fernandes, and M. J. Ramos, "Farnesyltransferase-- New Insights into the Zinc-Coordination Sphere Paradigm: Evidence for a Carboxylate-Shift Mechanism," Biophys. J., vol. 88, pp. 483-494,2005. [26] S. F. Sousa, P. A. Fernandes, and M. J. Ramos, "Farnesyltransferase: Theoretical Studies on Peptide Substrate Entrance - Thiol or Thiolate Coordination?," J. Mol. Struct. (Theochem), vol. 729, pp. 125-129, 2005. [27] S. F. Sousa, P. A. Fernandes, and M. J. Ramos, "The carboxylate-shift in zinc enzymes: a computational study," J. Am. Chem. Soc., vol. 129, pp. 1378-1385, 2007. [28] S. F. Sousa, P. A. Fernandes, and M. J. Ramos, "Theoretical Studies on Farnesyltransferase: The Distances Paradox Explained," Proteins, vol. 66, pp. 205-218, 2007. [29] M. J. Ramos and P. A. Fernandes, "Computational enzymatic catalysis," Acc. Chem. Res., vol. 41, pp. 689-698, 2008. [30] S. B. Long, P. J. Casey, and L. S. Beese, "Reaction path of protein farnesyltransferase at atomic resolution," Nature, vol. 419, pp. 645-650, 2002. [31] H. W. Park, S. R. Boduluri, J. F. Moomaw, P. J. Casey, and L. S. Beese, "Crystal Structure of Protein Farnesyltransferase at 2.25 Angstrom Resolution," Science, vol. 275, pp. 1800-1804, 1997. [32] D. A. Tobin, J. S. Pickett, H. L. Hartman, C. A. Fierke, and J. E. Penner-Hahn, "Structural characterization of the zinc site in protein farnesyltransferase," J. Am. Chem. Soc., vol. 125, pp. 9962-9969,2003. [33] S. F. Sousa, P. A. Fernandes, and M. J. Ramos, "Theoretical Studies on Farnesyltransferase: Evidence for Thioether Product Coordination to the Active-Site Zinc Sphere," J. Comput. Chem., vol. 28, pp. 1160-1168, 2007. [34] N. M. F. S. A. Cerqueira, S. Pereira, P. A. Fernandes, and M. J. Ramos, "Overview of ribonucleotide reductase inhibitors: an appealing target in anti-tumour therapy," Curr. Med. Chem., vol. 12, pp. 1283-1294, 2005. [35] N. M. F. S. A. Cerqueira, P. A. Fernandes, L. A. Eriksson, and M. J. Ramos, "New insights into a critical biological control step of the mechanism of ribonucleotide reductase," J. Mol. Struct. (Theochem), vol. 709, pp. 53-65, 2004. [36] N. M. F. S. A. Cerqueira, P. A. Fernandes, L. A. Eriksson, and M. J. Ramos, "Ribonucleotide activation by enzyme ribonucleotide reductase: understanding the role of the enzyme," J. Comput. Chem., vol. 25, pp. 2031-2037, 2004. [37] N. M. F. S. A. Cerqueira, P. A. Fernandes, L. A. Eriksson, and M. J. Ramos, "Dehydration of ribonucleotides catalysed by ribonucleotide reductase: the role of the enzyme," Biophys. J., vol. 90, pp. 2109-2119, 2006. [38] P. A. Fernandes, L. A. Eriksson, and M. J. Ramos, "The reduction of ribonucleotides catalyzed by the enzyme ribonucleotide reductase," Theor. Chem. Acc., vol. 108, pp. 352-364, 2002. [39] S. Pereira, N. M. F. S. A. Cerqueira, P. A. Fernandes, and M. J. Ramos, "Computational studies on class I ribonucleotide reductase: Understanding the mechanism of action and inhibition of a cornerstone enzyme for the treatment of cancer," Eur. Biophys. J., vol. 35, pp. 125- 135, 2006. [40] P. A. Fernandes and M. J. Ramos, "Theoretical studies on the mode of inhibition of ribonucleotide reductase by 2'-substituted substrate analogues," Chem. Eur. J., vol. 9, pp. 5916-5925, 2003. [41] N. M. F. S. Cerqueira, P. A. Fernandes, and M. J. Ramos, "Enzyme ribonucleotide reductase: Unraveling an enigmatic paradigm of enzyme inhibition by furanone derivatives," J. Phys. Chem. B, vol. 110, pp. 21272-21281, 2006. [42] S. Pereira, P. A. Fernandes, and M. J. Ramos, "Theoretical study of ribonucleotide reductase mechanism-based inhibition by 2'-azido-2'- deoxyribonucleoside 5'-diphosphates," J. Comput. Chem., vol. 25, pp. 227-237, 2004. [43] S. Pereira, P. A. Fernandes, and M. J. Ramos, "Mechanism for ribonucleotide reductase inactivation by the anticancer drug gemcitabine," J. Comput. Chem., vol. 25, pp. 1286-1294, 2004. [44] S. Pereira, P. A. Fernandes, and M. J. Ramos, "Theoretical study on the inhibition of ribonucleotide reductase by 2'-mercapto-2'- deoxyribonucleoside-5," J. Am. Chem. Soc., vol. 127, pp. 5174-5179, 2005. [45] P. A. Fernandes and M. J. Ramos, "Theoretical studies on the mechanism of inhibition of Ribonucleotide Reductase by (E)-2'- Fluoromethylene-2'-deoxycitidine-5'-diphosphate," J. Am. Chem. Soc., vol. 125, pp. 6311-6322, 2003. [46] A. Ghosh, "Just how good is DFT?," J. Biol. Inorg. Chem., vol. 11, pp. 671-673, 2006. [47] N. E. Schultz, Y. Zhao, and D. G. Truhlar, "Density functionals for inorganometallic and organometallic chemistry," J. Phys. Chem. A, vol. 109, pp. 11127-11143, 2005. [48] P. Hohenberg and W. Kohn, "Inhomogeneous Electron Gas," Phys. Rev. B, vol. 136, pp. B864, 1964. [49] Y. Zhao and D. G. Truhlar, "Density functionals with broad applicability in chemistry," Acc. Chem. Res., vol. 41, pp. 157-167, 2008. [50] S. F. Sousa, P. A. Fernandes, and M. J. Ramos, "General Performance of Density Functionals," J. Phys. Chem A, vol. 111, pp. 10439-10452, 2007. [51] S. F. Sousa, P. A. Fernandes, and M. J. Ramos, "Comparative assessment of theoretical methods for the determination of geometrical properties in biological zinc complexes," J. Phys. Chem. B, vol. 111, pp. 9146-9152, 2007. [52] P. Jurecka, J. Cerny, P. Hobza, and D. R. Salahub, "Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations," J. Comput. Chem., vol. 28, pp. 555-569, 2007. [53] A. Karton, A. Tarnopolsky, J. F. Lamere, G. C. Schatz, and J. M. L. Martin, "Highly Accurate First-Principles Benchmark Data Sets for the Parametrization and Validation of Density Functional and Other Approximate Methods. Derivation of a Robust, Generally Applicable, Double-Hybrid Functional for Thermochemistry and Thermochemical Kinetics," J. Phys. Chem. A, vol. 112, pp. 12868-12886, 2008. [54] Y. Zhao and D. G. Truhlar, "Density functionals for noncovalent interaction energies of biological importance," J. Chem. Theor. Comput., vol. 3, pp. 289-300, 2007. [55] T. van Mourik, "Assessment of Density Functionals for Intramolecular Dispersion-Rich Interactions," J. Chem. Theor. Comput., vol. 4, pp. 1610-1619, 2008. [56] R. Peverati and K. K. Baldridge, "Implementation and Performance of DFT-D with Respect to Basis Set and Functional for Study of Dispersion Interactions in Nanoscale Aromatic Hydrocarbons," J. Chem. Theor. Comput., vol. 4, pp. 2030-2048, 2008. [57] N. F. Bras, S. A. Moura-Tamames, P. A. Fernandes, and M. J. Ramos, "Mechanistic Studies on the Formation of Glycosidase-Substrate and Glycosidase-Inhibitor Covalent Intermediates," J. Comput. Chem., vol. 29, pp. 2565-2574, 2008. [58] I. S. Moreira, P. A. Fernandes, and M. J. Ramos, "Hot spots-A review of the protein-protein interface determinant amino-acid residues," Proteins, vol. 68, pp. 803-812, 007. [59] S. Jones and J. M. Thornton, "Principles of protein-protein interactions," Proc. Natl. Acad. Sci. USA, vol. 93, pp. 13-20, 1996. [60] A. A. Bogan and K. S. Thorn, "Anatomy of hot spots in protein interfaces," J. Mol. Biol., vol. 280, pp. 1-9, 1998. [61] T. Clackson and J. A. Wells, "A Hot-Spot of Binding-Energy in A Hormone-Receptor Interface," Science, vol. 267, pp. 383-386, 1995. [62] W. L. Delano, "Unraveling hot spots in binding interfaces: progress and challenges," Curr. Opin. Struct. Biol., vol. 12, pp. 14-20, 2002. [63] I. S. Moreira, P. A. Fernandes, and M. J. Ramos, "Detailed microscopic study of the full ZipA : FtsZ interface," Proteins, vol. 63, pp. 811-821, 2006. [64] I. S. Moreira, P. A. Fernandes, and M. J. Ramos, "Unraveling the importance of protein-protein interaction: Application of a computational alanine-scanning mutagenesis to the study of the IgG1 streptococcal protein G (C2 fragment) complex," J. Phys. Chem. B, vol. 110, pp. 10962-10969, 2006. [65] I. S. Moreira, P. A. Fernandes, and M. J. Ramos, "Hot spot computational identification: Application to the complex formed between the hen egg white lysozyme (HEL) and the antibody HyHEL- 10," Int. J. Quant. Chem., vol. 107, pp. 299-310, 2007. [66] I. S. Moreira, P. A. Fernandes, and M. J. Ramos, "Hot spot occlusion from bulk water: A comprehensive study of the complex between the lysozyme HEL and the antibody FVD1.3," J. Phys. Chem. B, vol. 111, pp. 2697-2706, 2007. [67] I. S. Moreira, P. A. Fernandes, and M. J. Ramos, "Unravelling Hot Spots: a comprehensive computational mutagenesis study," Theor. Chem. Acc., vol. 117, pp. 99-113, 2007. [68] I. S. Moreira, P. A. Fernandes, and M. J. Ramos, "Accuracy of the numerical solution of the Poisson-Boltzmann equation," J. Mol. Struct. (Theochem), vol. 729, pp. 11-18, 2005. [69] I. S. Moreira, P. A. Fernandes, and M. J. Ramos, "Computational alanine scanning mutagenesis - An improved methodological approach," J. Comput. Chem., vol. 28, pp. 644-654, 2007. [70] T. Kortemme and D. Baker, "A simple physical model for binding energy hot spots in protein-protein complexes," Proc. Natl. Acad. Sci. USA, vol. 99, pp. 14116-14121, 2002. [71] E. Guney, N. Tuncbag, O. Keskin, and A. Gursoy, "HotSprint: database of computational hot spots in protein interfaces," Nucleic Acids Res., vol. 36, pp. D662-D666, 2008. [72] S. J. Darnell, D. Page, and J. C. Mitchell, "An automated decision-tree approach to predicting protein interaction hot spots," Proteins, vol. 68, pp. 813-823, 2007. [73] D. A. Case, T. A. Darden, T. E. Cheatham III, C. L. Simmerling, J. Wang, R. E. Duke, et al., "AMBER 8," University of California, San Francisco, 2004. [74] M. R. Shirts, J. W. Pitera, W. C. Swope, and V. S. Pande, "Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins," J. Chem. Phys., vol. 119, pp. 5740-5761, 2003. [75] J. W. Pitera and W. F. van Gunsteren, "A comparison of non-bonded scaling approaches for free energy calculations," Mol. Simul., vol. 28, pp. 45-65, 2002. [76] A. Blondel, "Ensemble variance in free energy calculations by thermodynamic integration: Theory, optimal "Alchemical" path, and practical solutions," J. Comput. Chem., vol. 25, pp. 985-993, 2004. [77] P. A. Kollman, I. Massova, C. Reyes, B. Kuhn, S. H. Huo, L. Chong, M. Lee, T. Lee, Y. Duan, W. Wang, O. Donini, P. Cieplak, J. Srinivasan, D. A. Case, and T. E. Cheatham, "Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models," Acc. Chem. Res., vol. 33, pp. 889-897, 2000. [78] M. A. S. Perez, P. A. Fernandes, and M. J. Ramos, "Drug design: New inhibitors for HIV-1 protease based on Nelfinavir as lead," J. Mol. Graph. Model., vol. 26, pp. 634-642, 2007. [79] W. Wang and P. A. Kollman, "Computational study of protein specificity: The molecular basis of HIV-1 protease drug resistance," Proc. Natl. Acad. Sci. USA, vol. 98, pp. 14937-14942, 2001. [80] S. Gupta, L. M. Rodrigues, A. P. Esteves, A. M. F. Oliveira-Campos, M. S. J. Nascimento, N. Nazareth, H. Cidade, M. P. Neves, F. Fernandes, M. Pinto, N. M. F. S. A. Cerqueira, and N. Bras, "Synthesis of N-aryl-5- amino-4-cyanopyrazole derivatives as potent xanthine oxidase inhibitors," Eur. J. Med. Chem., vol. 43, pp. 771-780, 2007. [81] M. L. Lamb and W. L. Jorgensen, "Computational approaches to molecular recognition," Curr. Opin. Chem. Biol., vol. 1, pp. 449-457, 1997. [82] C. N. Cavasotto and N. Singh, "Docking and high throughput docking: Successes and the challenge of protein flexibility," Curr. Comput. Aided Drug Des., vol. 4, pp. 221-234, 2008. [83] S. F. Sousa, P. A. Fernandes, and M. J. Ramos, "Protein-ligand docking: Current status and future challenges," Proteins, vol. 65, pp. 15-26, 2006. [84] N. Brooijmans and I. D. Kuntz, "Molecular recognition and docking algorithms," Ann. Rev. Biophys. Biomol. Struct., vol. 32, pp. 335-373, 2003.