Exploring the pH-dependent substrate transport mechanism of FocA using molecular dynamics simulation

Biophysical Journal

Volumn 105, Issue 12, 2013, Pages 2714-2723

  Lv, Xiaoying ^a   Liu, Huihui ^a   Ke, Meng ^a   Gong, Haipeng ^a  

^a TSINGHUA UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CARRIER PROTEIN; ESCHERICHIA COLI PROTEIN; FOCA PROTEIN, E COLI; FORMIC ACID; FORMIC ACID DERIVATIVE;

AMINO ACID SEQUENCE; ARTICLE; CHEMISTRY; ESCHERICHIA COLI; METABOLISM; MOLECULAR DYNAMICS; MOLECULAR GENETICS; PH; TRANSPORT AT THE CELLULAR LEVEL;

AMINO ACID SEQUENCE; BIOLOGICAL TRANSPORT; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; FORMATES; HYDROGEN-ION CONCENTRATION; MEMBRANE TRANSPORT PROTEINS; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA;

EID: 84890617295     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2013.11.006     Document Type: Article

References (42)

1. S. Leonhartsberger, I. Korsa, and A. Böck The molecular biology of formate metabolism in enterobacteria J. Mol. Microbiol. Biotechnol. 4 2002 269 276
2. M.H. Saier Jr., and B.H. Eng G.B. Young Phylogenetic characterization of novel transport protein families revealed by genome analyses Biochim. Biophys. Acta 1422 1999 1 56
3. G. Sawers, and J. Heider A. Böck Expression and operon structure of the sel genes of Escherichia coli and identification of a third selenium-containing formate dehydrogenase isoenzyme J. Bacteriol. 173 1991 4983 4993
4. M. Jormakka, and S. Törnroth S. Iwata Molecular basis of proton motive force generation: structure of formate dehydrogenase-N Science 295 2002 1863 1868
5. R.G. Sawers Formate and its role in hydrogen production in Escherichia coli Biochem. Soc. Trans. 33 2005 42 46
6. L. Beyer, and C. Doberenz R.G. Sawers Coordination of FocA and pyruvate formate-lyase synthesis in Escherichia coli demonstrates preferential translocation of formate over other mixed-acid fermentation products J. Bacteriol. 195 2013 1428 1435
7. R. Rossmann, G. Sawers, and A. Böck Mechanism of regulation of the formate-hydrogenlyase pathway by oxygen, nitrate, and pH: definition of the formate regulon Mol. Microbiol. 5 1991 2807 2814
8. M. Kaiser, and G. Sawers Pyruvate formate-lyase is not essential for nitrate respiration by Escherichia coli FEMS Microbiol. Lett. 117 1994 163 168
9. Y. Wang, and Y. Huang Y. Shi Structure of the formate transporter FocA reveals a pentameric aquaporin-like channel Nature 462 2009 467 472
10. W. Lü, and N.J. Schwarzer O. Einsle Structural and functional characterization of the nitrite channel NirC from Salmonella typhimurium Proc. Natl. Acad. Sci. USA 109 2012 18395 18400
11. A.D. MacKerell Jr., and D. Bashford M. Karplus All-atom empirical potential for molecular modeling and dynamics studies of proteins J. Phys. Chem. Lett 102 1998 3586 3616
12. W. Lü, and J. Du S.L. Andrade The formate channel FocA exports the products of mixed-acid fermentation Proc. Natl. Acad. Sci. USA 109 2012 13254 13259
13. W. Lü, and J. Du O. Einsle The formate/nitrite transporter family of anion channels Biol. Chem. 394 2013 715 727
14. A.B. Waight, J. Love, and D.N. Wang Structure and mechanism of a pentameric formate channel Nat. Struct. Mol. Biol. 17 2010 31 37
15. Z. Feng, T. Hou, and Y. Li Concerted movement in pH-dependent gating of FocA from molecular dynamics simulations J. Chem. Inf. Model. 52 2012 2119 2131
16. W. Lü, and J. Du O. Einsle pH-dependent gating in a FocA formate channel Science 332 2011 352 354
17. N. Eswar, and B. Webb A. Sali Comparative protein structure modeling using MODELLER Curr. Protoc. Protein Sci. 2007 Chapter 2, Unit 2.9
18. J.C. Phillips, and R. Braun K. Schulten Scalable molecular dynamics with NAMD J. Comput. Chem. 26 2005 1781 1802
19. K. Vanommeslaeghe, and E. Hatcher A.D. Mackerell Jr. CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields J. Comput. Chem. 31 2010 671 690
20. U. Essmann, and L. Perera L.G.A. Pedersen A smooth particle mesh Ewald method J. Chem. Phys. 103 1995 8577 8593
21. J. Hsin, and A. Arkhipov K. Schulten Using VMD: an introductory tutorial Curr. Protoc. Bioinformatics 2008 Chapter 5, Unit 5.7
22. W. Humphrey, A. Dalke, and K. Schulten VMD: visual molecular dynamics J. Mol. Graph. 14 1996 33 38 27-28
23. E. Darve, D. Rodríguez-Gómez, and A. Pohorille Adaptive biasing force method for scalar and vector free energy calculations J. Chem. Phys. 128 2008 144120
24. E. Darve, and A. Pohorille Calculating free energies using average force J. Chem. Phys. 115 2001 9169 9183
25. E. Darve, M. Wilson, and A. Pohorille Calculating free energies using a scaled-force molecular dynamics algorithm Mol. Simul. 28 2002 113 144
26. D. Rodriguez-Gomez, E. Darve, and A. Pohorille Assessing the efficiency of free energy calculation methods J. Chem. Phys. 120 2004 3563 3578
27. S. Izrailev, and S. Stepaniants K. Schulten Molecular dynamics study of unbinding of the avidin-biotin complex Biophys. J. 72 1997 1568 1581
28. R. Zwanzig High-temperature equation of state by a perturbation method. II. Polar gases J. Chem. Phys. 23 1955 1915 1922
29. P. Kollman Free energy calculations: applications to chemical and biochemical phenomena Chem. Rev. 93 1993 2395 2417
30. T.C. Beutler, and A.E. Mark W.F. van Gunsteren Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations Chem. Phys. Lett. 222 1994 529 539
31. M. Zacharias, T.P. Straatsma, and J.A. McCammon Separation - shifted scaling, a new scaling method for Lennard-Jones interactions in thermodynamic integration J. Chem. Phys. 100 1994 9025 9031
32. A. Pohorille, C. Jarzynski, and C. Chipot Good practices in free-energy calculations J. Phys. Chem. B 114 2010 10235 10253
33. C. Bennett Efficient estimation of free energy differences from Monte Carlo data J. Comput. Phys. 22 1976 245 268
34. Case, D. A., T. A. Darden, T. E. Cheattham, III, C. L. Simmerling, J. Wang, R. E. Duke, R. Luo, R. C. Walker, W. Zhang, K. M. Merz, B. Roberts, S. Hayik, A. E. Roitberg, G. Seabra, J. Swails, A. W. Goetz, I. Kolossvary, K. F. Wong, F. Paesani, J. Vanicek, R. M. Wolf, J. Liu, X. Wu, S. R. Brozell, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, J. Wang, M.-J. Hsieh, G. Cui, D. R. Roe, D. H. Mathews, M. G. Seetin, R. Salomon-Ferrer, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, and P. A. Kollman. 2012. AMBER 12.
35. R.C. Walker, M.F. Crowley, and D.A. Case The implementation of a fast and accurate QM/MM potential method in Amber J. Comput. Chem. 29 2008 1019 1031
36. J.J. Stewart Optimization of parameters for semiempirical methods V: modification of NDDO approximations and application to 70 elements J. Mol. Model. 13 2007 1173 1213
37. P. Jurecka, and J. Cerný 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. 28 2007 555 569
38. O.S. Smart, J.M. Goodfellow, and B.A. Wallace The pore dimensions of gramicidin A Biophys. J. 65 1993 2455 2460
39. O.S. Smart, and J.G. Neduvelil M.S. Sansom HOLE: a program for the analysis of the pore dimensions of ion channel structural models J. Mol. Graph. 14 1996 354 360 376
40. R. Gamini, and M. Sotomayor K. Schulten Cytoplasmic domain filter function in the mechanosensitive channel of small conductance Biophys. J. 101 2011 80 89
41. ++: a server for estimating pKas and adding missing hydrogens to macromolecules Nucleic Acids Res. 33 Web Server issue 2005 W368 W371
42. C.J. IIIingworth, and C. Domene Many-body effects and simulations of potassium channels Proc. Roy. Soc. A: Math., Phys. and Eng. Sci. 465 2009 1701 1706