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BioMed Research International
Volume 2013 (2013), Article ID 713585, 12 pages
Improved scFv Anti-HIV-1 p17 Binding Affinity Guided from the Theoretical Calculation of Pairwise Decomposition Energies and Computational Alanine Scanning
1Computational Simulation Modelling Laboratory (CSML), Department of Chemistry and Center of Excellence for Innovation in Chemistry and Materials Science Research Center, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
2Thailand Center of Excellence in Physics, Commission on Higher Education, 328 Sri Ayutthaya Road, Bangkok 10400, Thailand
3Department of Medical Technology, School of Allied Health Sciences, University of Phayao, Phayao 56000, Thailand
4Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
5Biomedical Technology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
6Department of Chemistry, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
Received 30 April 2013; Revised 3 September 2013; Accepted 10 September 2013
Academic Editor: Carmen Domene
Copyright © 2013 Panthip Tue-ngeun et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- A. Wörn and A. Plückthun, “Stability engineering of antibody single-chain Fv fragments,” Journal of Molecular Biology, vol. 305, no. 5, pp. 989–1010, 2001.
- I. Massova and P. A. Kollman, “Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies,” Journal of the American Chemical Society, vol. 121, no. 36, pp. 8133–8143, 1999.
- H. Gohlke, C. Kiel, and D. A. Case, “Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes,” Journal of Molecular Biology, vol. 330, no. 4, pp. 891–913, 2003.
- T. Li, M. Froeyen, and P. Herdewijn, “Computational alanine scanning and free energy decomposition for E. coli type I signal peptidase with lipopeptide inhibitor complex,” Journal of Molecular Graphics & Modelling, vol. 26, no. 5, pp. 813–823, 2008.
- L. Saíz-Urra, M. A. Cabrera, and M. Froeyen, “Exploring the conformational changes of the ATP binding site of gyrase B from Escherichia coli complexed with different established inhibitors by using molecular dynamics simulation: protein-ligand interactions in the light of the alanine scanning and free energy decomposition methods,” Journal of Molecular Graphics & Modelling, vol. 29, no. 5, pp. 726–739, 2011.
- V. S. Lee, P. Tue-ngeun, S. Nangola et al., “Pairwise decomposition of residue interaction energies of single chain Fv with HIV-1 p17 epitope variants,” Molecular Immunology, vol. 47, no. 5, pp. 982–990, 2010.
- H. B. Thorsteinsdottir, T. Schwede, V. Zoete, and M. Meuwly, “How inaccuracies in protein structure models affect estimates of protein-ligand interactions: computational analysis of HIV-I protease inhibitor binding,” Proteins, vol. 65, no. 2, pp. 407–423, 2006.
- S. Huo, I. Massova, and P. A. Kollman, “Computational alanine scanning of the 1:1 human growth hormone-receptor complex,” Journal of Computational Chemistry, vol. 23, no. 1, pp. 15–27, 2002.
- Ó. Villacañas and J. Rubio-Martinez, “Reducing CDK4/6-p16INK4a interface: computational alanine scanning of a peptide bound to CDK6 protein,” Proteins, vol. 63, no. 4, pp. 797–810, 2006.
- 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,” Journal of Physical Chemistry B, vol. 110, no. 22, pp. 10962–10969, 2006.
- L. T. Chong, W. C. Swope, J. W. Pitera, and V. S. Pande, “Kinetic computational alanine scanning: application to p53 oligomerization,” Journal of Molecular Biology, vol. 357, no. 3, pp. 1039–1049, 2006.
- V. Zoete, M. Meuwly, and M. Karplus, “Study of the insulin dimerization: binding free energy calculations and per-residue free energy decomposition,” Proteins, vol. 61, no. 1, pp. 79–93, 2005.
- V. Zoete and M. Meuwly, “Importance of individual side chains for the stability of a protein fold: computational alanine scanning of the insulin monomer,” Journal of Computational Chemistry, vol. 27, no. 15, pp. 1843–1857, 2006.
- A. Malik, A. Firoz, V. Jha, E. Sunderasan, and S. Ahmad, “Modeling the three-dimensional structures of an unbound single-chain variable fragment (scFv) and its hypothetical complex with a Corynespora cassiicola toxin, cassiicolin,” Journal of Molecular Modeling, vol. 16, no. 12, pp. 1883–1893, 2010.
- D. Bordo and P. Argos, “Suggestions for ‘safe’ residue substitutions in site-directed mutagenesis,” Journal of Molecular Biology, vol. 217, no. 4, pp. 721–729, 1991.
- D. Tewari, S. L. Goldstein, A. L. Notkins, and P. Zhou, “cDNA encoding a single-chain antibody to HIV p17 with cytoplasmic or nuclear retention signals inhibits HIV-1 replication,” Journal of Immunology, vol. 161, no. 5, pp. 2642–2647, 1998.
- M. Vieth, J. D. Hirst, A. Kolinski, and C. L. Brooks III, “Assessing energy functions for flexible docking,” Journal of Computational Chemistry, vol. 19, no. 14, pp. 1612–1622, 1998.
- D. A. Case, T. A. Darden, T. E. Cheatham III et al., AMBER 12, University of California, San Francisco, Calif, USA, 2012.
- U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen, “A smooth particle mesh Ewald method,” The Journal of Chemical Physics, vol. 103, no. 19, pp. 8577–8593, 1995.
- P. A. Kollman, I. Massova, C. Reyes et al., “Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models,” Accounts of Chemical Research, vol. 33, no. 12, pp. 889–897, 2000.
- T. Hou, S. Guo, and X. Xu, “Predictions of binding of a diverse set of ligands to gelatinase-A by a combination of molecular dynamics and continuum solvent models,” Journal of Physical Chemistry B, vol. 106, no. 21, pp. 5527–5535, 2002.
- T. Kortemme, D. E. Kim, and D. Baker, “Computational alanine scanning of protein-protein interfaces,” Science's STKE, vol. 2004, no. 219, p. pl2, 2004.
- D. Burdo and P. Argos, “Evolution of protein cores. Constraints in point mutations as observed in globin tertiary structures,” Journal of Molecular Biology, vol. 211, no. 4, pp. 975–988, 1990.