DelEnsembleElec: Computing ensemble-averaged electrostatics using DelPhi

Communications in Computational Physics

Volumn 13, Issue 1, 2013, Pages 256-268

  Votapka, Lane W ^a   Czapla, Luke ^a   Zhenirovskyy, Maxim ^b   Amaro, Rommie E ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b CLEMSON UNIVERSITY   (United States)

Author keywords

DelEnsembleElec; DelPhi; Ensemble averaged electrostatics; Influenza glycoproteins; Molecular dynamics; Poisson Boltzmann equation

Indexed keywords

EID: 84866318136     PISSN: 18152406     EISSN: 19917120     Source Type: Journal    
DOI: 10.4208/cicp.170711.111111s     Document Type: Conference Paper

References (30)

1. Honig, B. & Nicholls, A. Classical electrostatics in biology and chemistry. Science 268, 1144- 1149 (1995).
2. York, D.M., Darden, T. A. &Pedersen, L. G. The effect of long-range electrostatic interactions in simulations of macromolecular crystals - a comparison of the Ewald and truncated list methods. J Chem Phys 99, 8345-8348 (1993).
3. Greengard, L. & Rokhlin, V. A fast algorithm for particle simulations. J Comput Phys 73, 325-348 (1987).
4. Fogolari, F., Brigo, A. & Molinari, H. The Poisson-Boltzmann equation for biomolecular electrostatics: a tool for structural biology. J Mol Recognit 15, 377-392, doi:10.1002/jmr.577 (2002). (Pubitemid 36101029)
5. Harris, R. C., Bredenberg, J. H., Silalahi, A. R. J., Boschitsch, A. H. & Fenley, M. O. Understanding the physical basis of the salt dependence of the electrostatic binding free energy of mutated charged ligand-nucleic acid complexes. Biophys Chem 156, 79-87, doi:10.1016/j.bpc.2011.02.010 (2011).
6. Rocchia, W. et al. Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects. J Comput Chem 23, 128-137, doi:10.1002/jcc.1161 (2002). (Pubitemid 34063137)
7. Case, D. A. et al. The Amber biomolecular simulation programs. J Comput Chem 26, 1668- 1688, doi:10.1002/jcc.20290 (2005). (Pubitemid 43076180)
8. Brooks, B. R. et al. Charmm - a Program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4, 187-217 (1983).
9. Suydam, I. T. S., C. D.; Pande, V. S.; Boxer, S. G. Electric fields at the active site of an enzyme: direct comparison of experiment with theory. Science 313, 200-204 (2006). (Pubitemid 44066246)
10. Aksimentiev, A. & Schulten, K. Imaging alpha-hemolysin with molecular dynamics: ionic conductance, osmotic permeability, and the electrostatic potential map. Biophys J 88, 3745- 3761, doi:10.1529/biophysj.104.058727 (2005). (Pubitemid 40991090)
11. Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J Mol Graph 14, 33-38, 27-38 (1996). (Pubitemid 26152973)
12. Rocchia, W., Alexov, E. & Honig, B. Extending the applicability of the nonlinear Poisson- Boltzmann equation: Multiple dielectric constants and multivalent ions. J Phys Chem B 105, 6507-6514 (2001). (Pubitemid 35339019)
13. Newhouse, E. I. Mechanism of glycan receptor recognition and specificity switch for avian, swine, and human adapted influenza virus hemagglutinins: a molecular dynamics perspective. J Am Chem Soc 131, 17430-17442 (2009).
14. Xu, D. et al. Distinct glycan topology for avian and human sialopentasaccharide receptor analogues upon binding different hemagglutinins: a molecular dynamics perspective. JMol Biol 387, 465-491, doi:10.1016/j.jmb.2009. 01.040 (2009).
15. Amaro, R. E., Cheng, X., Ivanov, I., Xu, D. &McCammon, J. A. Characterizing loop dynamics and ligand recognition in human- and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free energy calculations. J Am Chem Soc 131, 4702- 4709, doi:10.1021/ja8085643 (2009).
16. Lawrenz,M. et al. Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy. Proteins 78, 2523-2532, doi:10.1002/prot.22761 (2010).
17. Sung, J. C., Van Wynsberghe, A. W., Amaro, R. E., Li, W. W. & McCammon, J. A. Role of secondary sialic acid binding sites in influenza N1 neuraminidase. J Am Chem Soc 132, 2883-2885, doi:10.1021/ja9073672 (2010).
18. Dolinsky, T. J., Nielsen, J. E., McCammon, J. A. & Baker, N. A. PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res 32,W665-667, doi:10.1093/nar/gkh381 (2004). (Pubitemid 38997419)
19. Li, H., Robertson, A. D. & Jensen, J. H. Very fast empirical prediction and rationalization of protein pKa values. Proteins 61, 704-721, doi:10.1002/prot.20660 (2005). (Pubitemid 41753142)
20. Newhouse, E. I. et al. Mechanism of glycan receptor recognition and specificity switch for avian, swine, and human adapted influenza virus hemagglutinins: a molecular dynamics perspective. J Am Chem Soc 131, 17430-17442, doi:10.1021/ja904052q (2009).
21. Phillips, J. C. et al. Scalablemolecular dynamics withNAMD. J Comput Chem26, 1781-1802, doi:Doi 10.1002/Jcc.20289 (2005). (Pubitemid 43078511)
22. Hornak, V. et al. Comparison of multiple amber force fields and development of improved protein backbone parameters. Proteins-Structure Function and Bioinformatics 65, 712-725, doi:Doi 10.1002/Prot.21123 (2006). (Pubitemid 44583220)
23. Scott, E. F., Yuhong, Z., Richard,W. P., Bernard, R. B. Constant pressuremolecular dynamics simulation: the Langevin piston method. J Chem Phys 103, 4613-4621 (1995).
24. Darden, T. Particle mesh Ewald: An N ?log(N) method for Ewald sums in large systems. J Chem Phys 98, 10089-10092 (1993).
25. Andersen, H. C. Rattle: A "velocity" version of the Shake algorithm formolecular dynamics calculations. J Comput Phys 52, 24-34 (1983).
26. Amaro, R. E. S., R. V.; Votapka, L. V.; Li, W. W.; Walker, R. C.; Bush, R. Mechanism of 150-cavity formation in influenza neuraminidase. Nature Commun 2, 388, doi:10.1038/ncomms1390 (2011).
27. Berendsen, H. J. C. Molecular Dynamics with coupling to an external bath. J Chem Phys 81, 3684 (1984).
28. Baker, N. A. Poisson-Boltzmann methods for biomolecular electrostatics.Methods Enzymol 383, 94-118, doi:10.1016/S0076-6879(04)83005-2 (2004). (Pubitemid 38401788)
29. Baker, N. A. & McCammon, J. A. Structural Bioinformatics. 427-440 (John Wiley & Sons, 2003).
30. von Itzstein, M. The war against influenza: discovery and development of sialidase inhibitors. Nat Rev Drug Discov 6, 967-974, doi:10.1038/nrd2400 (2007). (Pubitemid 350201787)