APBSmem: A graphical interface for electrostatic calculations at the membrane

PLoS ONE

Volumn 5, Issue 9, 2010, Pages

  Callenberg, Keith M ^a   Choudhary, Om P ^a   de Forest, Gabriel L ^b   Gohara, David W ^c   Baker, Nathan A ^d   Grabe, Michael ^b,e  

^a CARNEGIE MELLON UNIVERSITY   (United States)

^b UNIVERSITY OF PITTSBURGH   (United States)

^c SAINT LOUIS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^e UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTICAL ERROR; ARTICLE; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER MODEL; COMPUTER PROGRAM; COMPUTER SYSTEM; DATA ANALYSIS SOFTWARE; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MEMBRANE POTENTIAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; QUANTITATIVE ANALYSIS; SENSITIVITY ANALYSIS; SOLVATION; STATIC ELECTRICITY;

COMPUTER GRAPHICS; MEMBRANES, ARTIFICIAL; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PROTEIN BINDING; PROTEINS; SOFTWARE; STATIC ELECTRICITY; USER-COMPUTER INTERFACE;

EID: 77958551193     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0012722     Document Type: Article

References (63)

1. Warwicker J, Watson H (1982) Calculation of the electric potential in the active site cleft due to α-helix dipoles. Journal of Molecular Biology 157: 671-679.
2. Zauhar R, Morgan R (1985) A new method for computing the macromolecular electric potential. Journal of Molecular Biology 186: 815-820.
3. Klapper I, Hagstrom R, Fine R, Sharp K, Honig B (1986) Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification. Proteins: Structure, Function, and Genetics 1: 47-59.
4. Warwicker J (1986) Continuum dielectric modelling of the protein-solvent system, and calculation of the long-range electrostatic field of the enzyme phosphoglycerate mutase*. Journal of Theoretical Biology 121: 199-210.
5. Gilson M, Sharp K, Honig B (1987) Calculating electrostatic interactions in biomolecules: method and error assessment. Proceedings of the National Academy of Sciences 9: 327-335.
6. Baker N, Sept D, Joseph S, Holst M, McCammon J (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proceedings of the National Academy of Sciences 98: 10037-10041.
7. Zhou Y, Feig M, Wei G (2008) Highly accurate biomolecular electrostatics in continuum dielectric environments. Journal of Computational Chemistry 29: 87-97.
8. Grant J, Pickup B, Nicholls A (2001) A smooth permittivity function for Poisson-Boltzmann solvation methods. Journal of Computational Chemistry 22: 608-640.
9. Brooks B, Brooks C, III, Mackerell A, Jr., Nilsson L, Petrella R, et al. (2009) CHARMM: the biomolecular simulation program. Journal of Computational Chemistry 30: 1545-1614.
10. Tajkhorshid E, Nollert P, Jensen M, Miercke L, O'Connell J, et al. (2002) Control of the selectivity of the aquaporin water channel family by global orientational tuning. Science 296: 525-530.
11. Bernèche S, Roux B (2001) Energetics of ion conduction through the K+ channel. Nature 414: 73-77.
12. MacCallum J, Moghaddam M, Chan H, Tieleman D (2007) Hydrophobic association of α-helices, steric dewetting, and enthalpic barriers to protein folding. Proceedings of the National Academy of Sciences 104: 6206-6210.
13. Bond P, Faraldo-Gómez J, Deol S, Sansom M (2006) Membrane protein dynamics and detergent interactions within a crystal: A simulation study of OmpA. Proceedings of the National Academy of Sciences 103: 9518-9523.
14. Petrache H, Zuckerman D, Sachs J, Killian J, Koeppe R, II, et al. (2002) Hydrophobic matching mechanism investigated by molecular dynamics simulations. Langmuir 18: 1340-1351.
15. Krepkiy D, Mihailescu M, Freites J, Schow E, Worcester D, et al. (2009) Structure and hydration of membranes embedded with voltage-sensing domains. Nature 462: 473-479.
16. Allen T, Kuyucak S, Chung S (1999) Molecular dynamics study of the KcsA potassium channel. Biophysical Journal 77: 2502-2516.
17. Khelashvili G, Harries D, Weinstein H (2009) Modeling Membrane Deformations and Lipid Demixing upon Protein-Membrane Interaction: The BAR Dimer Adsorption. Biophysical Journal 97: 1626-1635.
18. Khelashvili G, Weinstein H, Harries D (2008) Protein diffusion on charged membranes: a dynamic mean-field model describes time evolution and lipid reorganization. Biophysical Journal 94: 2580-2597.
19. Murray D, Arbuzova A, Hangyás-Mihályné G, Gambhir A, Ben-Tal N, et al. (1999) Electrostatic properties of membranes containing acidic lipids and adsorbed basic peptides: theory and experiment. Biophysical Journal 77: 3176-3188.
20. Murray D, Hermida-Matsumoto L, Buser C, Tsang J, Sigal C, et al. (1998) Electrostatics and the membrane association of Src: theory and experiment. Biochemistry 37: 2145-2159.
21. Murray D, McLaughlin S, Honig B (2001) The role of electrostatic interactions in the regulation of the membrane association of G protein beta gamma heterodimers. Journal of Biological Chemistry 276: 45153-45159.
22. Feig M, Tanizaki S, Sayadi M (2008) Implicit Solvent Simulations of Biomolecules in Cellular Environments. Annual Reports in Computational Chemistry 4: 107-121.
23. Feig M, Im W, Brooks C, III (2004) Implicit solvation based on generalized Born theory in different dielectric environments. The Journal of Chemical Physics 120: 903-911.
24. Im W, Feig M, Brooks C, III (2003) An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins. Biophysical Journal 85: 2900-2918.
25. Tanizaki S, Feig M (2005) A generalized Born formalism for heterogeneous dielectric environments: Application to the implicit modeling of biological membranes. The Journal of Chemical Physics 122: 124706.
26. Tanizaki S, Feig M (2006) Molecular dynamics simulations of large integral membrane proteins with an implicit membrane model. The Journal of Physical Chemistry B 110: 548-556.
27. Denning E, Woolf T (2008) Double Bilayers and Transmembrane Gradients: A Molecular Dynamics Study of a Highly Charged Peptide. Biophysical Journal 95: 3161-3173.
28. Zhang J, Lazaridis T (2006) Calculating the free energy of association of transmembrane helices. Biophysical Journal 91: 1710-1723.
29. Ulmschneider M, Ulmschneider J, Sansom M, Di Nola A (2007) A generalized Born implicit-membrane representation compared to experimental insertion free energies. Biophysical Journal 92: 2338-2349.
30. Nina M, Bernèche S, Roux B (2000) Anchoring of a monotopic membrane protein: the binding of prostaglandin H 2 synthase-1 to the surface of a phospholipid bilayer. European Biophysics Journal 29: 439-454.
31. Roux B, Berneche S, Im W (2000) Ion channels, permeation, and electrostatics: insight into the function of KcsA. Biochemistry 39: 13295-13306.
32. Philippsen A, Im W, Engel A, Schirmer T, Roux B, et al. (2002) Imaging the electrostatic potential of transmembrane channels: atomic probe microscopy of OmpF porin. Biophysical Journal 82: 1667-1676.
33. Faraldo-Gómez J, Roux B, et al. (2004) Electrostatics of ion stabilization in a ClC chloride channel homologue from Escherichia coli. Journal of Molecular Biology 339: 981-1000.
34. Chanda B, Asamoah O, Blunck R, Roux B, Bezanilla F (2005) Gating charge displacement in voltage-gated ion channels involves limited transmembrane movement. Nature 436: 852-856.
35. Jogini V, Roux B (2005) Electrostatics of the intracellular vestibule of K+ channels. Journal of Molecular Biology 354: 272-288.
36. Pathak M, Yarov-Yarovoy V, Agarwal G, Roux B, Barth P, et al. (2007) Closing in on the resting state of the Shaker K+ channel. Neuron 56: 124-140.
37. Robertson J, Palmer L, Roux B (2008) Long-pore electrostatics in inwardrectifier potassium channels. Journal of General Physiology 132: 613-632.
38. Grabe M, Lecar H, Jan Y, Jan L (2004) A quantitative assessment of models for voltage-dependent gating of ion channels. Proceedings of the National Academy of Sciences 101: 17640-17645.
39. Jiang Y, Lee A, Chen J, Cadene M, Chait B, et al. (2002) The open pore conformation of potassium channels. Nature 417: 523-526.
40. Hilf R, Dutzler R (2008) X-ray structure of a prokaryotic pentameric ligandgated ion channel. Nature 452: 375-379.
41. Chatelain F, Alagem N, Xu Q, Pancaroglu R, Reuveny E, et al. (2005) The pore helix dipole has a minor role in inward rectifier channel function. Neuron 47: 833-843.
42. Jo S, Vargyas M, Vasko-Szedlar J, Roux B, Im W (2008) PBEQ-Solver for online visualization of electrostatic potential of biomolecules. Nucleic Acids Research 36: W270-W275.
43. Jmol: an open-source Java viewer for chemical structures in 3D. Available: http://www.jmol.org/.
44. Dolinsky T, Czodrowski P, Li H, Nielsen J, Jensen J, et al. (2007) PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Research 35: W522-W525.
45. Sitkoff D, Sharp K, Honig B (1994) Accurate calculation of hydration free energies using macroscopic solvent models. Journal of Physical Chemistry 98: 1978-1988.
46. MacKerell A, Bashford D, Bellott M, Dunbrack R, Evanseck J, et al. (1998) Allatom empirical potential for molecular modeling and dynamics studies of proteins. Journal of Physical Chemistry B 102: 3586-3616.
47. Swanson J, Wagoner J, Baker N, McCammon J (2007) Optimizing the Poisson dielectric boundary with explicit solvent forces and energies: Lessons learned with atom-centered dielectric functions. Journal of Chemical Theory and Computation 3: 170-183.
48. Wang J, Cieplak P, Kollman P (2000) How well does a restrained electrostatic potential(RESP) model perform in calculating conformational energies of organic and biological molecules? Journal of Computational Chemistry 21: 1049-1074.
49. Green D, Tidor B (2003) Evaluation of ab initio charge determination methods for use in continuum solvation calculations. The Journal of Physical Chemistry B 107: 10261-10273.
50. Schutz C, Warshel A (2001) What are the dielectric "constants" of proteins and how to validate electrostatic models? Proteins: Structure, Function, and Bioinformatics 44: 400-417.
51. Cohen B, McAnaney T, Park E, Jan Y, Boxer S, et al. (2002) Probing protein electrostatics with a synthetic fluorescent amino acid. Science 296: 1700-1703.
52. Silva J, Pan H, Wu D, Nekouzadeh A, Decker K, et al. (2009) A multiscale model linking ion-channel molecular dynamics and electrostatics to the cardiac action potential. Proceedings of the National Academy of Sciences 106: 11102-11106.
53. Choe S, Hecht K, Grabe M (2008) A Continuum Method for Determining Membrane Protein Insertion Energies and the Problem of Charged Residues. Journal of General Physiology 131: 563-573.
54. Lomize M, Lomize A, Pogozheva I, Mosberg H (2006) OPM: orientations of proteins in membranes database. Bioinformatics 22: 623-625.
55. Roux B (1997) Influence of the membrane potential on the free energy of an intrinsic protein. Biophysical Journal 73: 2980-2989.
56. Jackson J (1975) Classical Electrodynamics, Second Edition.
57. Hille B (1984) Ionic channels of excitable membranes. Sunderland, MA. Sinauer Associates Inc, 426pp 174: 289-300.
58. Parsegian A (1969) Energy of an ion crossing a low dielectric membrane: solutions to four relevant electrostatic problems. Nature 221: 844-846.
59. Beckstein O, Tai K, Sansom M (2004) Not ions alone: barriers to ion permeation in nanopores and channels. Journal of the American Chemical Society 126: 14694-14695.
60. Roux B, MacKinnon R (1999) The cavity and pore helices in the KcsA K+ channel: electrostatic stabilization of monovalent cations. Science 285: 100-102.
61. Ujwal R, Cascio D, Colletier J, Faham S, Zhang J, et al. (2008) The crystal structure of mouse VDAC1 at 2.3 Å resolution reveals mechanistic insights into metabolite gating. Proceedings of the National Academy of Sciences 105: 17742-17747.
62. Choudhary OP, Ujwal R, Kowallis W, Coalson R, Abramson J, et al. (2010) The Electrostatics of VDAC: Implications for Selectivity and Gating. Journal of Molecular Biology 396: 580-592.
63. Humphrey W, Dalke A, Schulten K (1996) VMD - Visual Molecular Dynamics. Journal of Molecular Graphics 14: 33-38.