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Computational Modeling Core Bibliography

Directly related publications

1. Chakrapani S, Cordero-Morales JF, Jogini V, Pan AC, Cortes DM, Roux B, Perozo E. On the structural basis of modal gating behavior in K(+) channels. Nature structural & molecular biology. 2011;18(1):67-74. doi: 10.1038/nsmb.1968. PubMed PMID: 21186363; PubMed Central PMCID: PMC3059741.

2. Mondal S, Khelashvili G, Shan J, Andersen OS, Weinstein H. Quantitative modeling of membrane deformations by multihelical membrane proteins: application to G-protein coupled receptors. Biophysical journal. 2011;101(9):2092-101. doi: 10.1016/j.bpj.2011.09.037. PubMed PMID: 22067146; PubMed Central PMCID: PMC3207176.

3. Bhatt D, Bahar I. An adaptive weighted ensemble procedure for efficient computation of free energies and first passage rates. The Journal of chemical physics. 2012;137(10):104101. doi: 10.1063/1.4748278. PubMed PMID: 22979844; PubMed Central PMCID: PMC3460967.

4. Gumbart J, Khalili-Araghi F, Sotomayor M, Roux B. Constant electric field simulations of the membrane potential illustrated with simple systems. Biochimica et biophysica acta. 2012;1818(2):294-302. doi: 10.1016/j.bbamem.2011.09.030. PubMed PMID: 22001851; PubMed Central PMCID: PMC3575077.

5. Gumbart J, Roux B. Determination of membrane-insertion free energies by molecular dynamics simulations. Biophysical journal. 2012;102(4):795-801. doi: 10.1016/j.bpj.2012.01.021. PubMed PMID: 22385850; PubMed Central PMCID: PMC3283816.

6. Hyde HC, Sandtner W, Vargas E, Dagcan AT, Robertson JL, Roux B, Correa AM, Bezanilla F. Nano-positioning system for structural analysis of functional homomeric proteins in multiple conformations. Structure. 2012;20(10):1629-40. doi: 10.1016/j.str.2012.08.022. PubMed PMID: 23063010; PubMed Central PMCID: PMC3633233.

7. Khalili-Araghi F, Tajkhorshid E, Roux B, Schulten K. Molecular dynamics investigation of the omega-current in the Kv1.2 voltage sensor domains. Biophysical journal. 2012;102(2):258-67. doi: 10.1016/j.bpj.2011.10.057. PubMed PMID: 22339862; PubMed Central PMCID: PMC3260662.

8. Lezon TR, Bahar I. Constraints imposed by the membrane selectively guide the alternating access dynamics of the glutamate transporter GltPh. Biophysical journal. 2012;102(6):1331-40. doi: 10.1016/j.bpj.2012.02.028. PubMed PMID: 22455916; PubMed Central PMCID: PMC3309413.

9. Li J, Tajkhorshid E. A gate-free pathway for substrate release from the inward-facing state of the Na(+)-galactose transporter. Biochimica et biophysica acta. 2012;1818(2):263-71. doi: 10.1016/j.bbamem.2011.09.011. PubMed PMID: 21978597; PubMed Central PMCID: PMC3253917.

10. Musgaard M, Thogersen L, Schiott B, Tajkhorshid E. Tracing cytoplasmic Ca(2+) ion and water access points in the Ca(2+)-ATPase. Biophysical journal. 2012;102(2):268-77. doi: 10.1016/j.bpj.2011.12.009. PubMed PMID: 22339863; PubMed Central PMCID: PMC3260667.

11. Ohkubo YZ, Pogorelov TV, Arcario MJ, Christensen GA, Tajkhorshid E. Accelerating membrane insertion of peripheral proteins with a novel membrane mimetic model. Biophysical journal. 2012;102(9):2130-9. doi: 10.1016/j.bpj.2012.03.015. PubMed PMID: 22824277; PubMed Central PMCID: PMC3341550.

12. Stolzenberg S, Khelashvili G, Weinstein H. Structural intermediates in a model of the substrate translocation path of the bacterial glutamate transporter homologue GltPh. The journal of physical chemistry B. 2012;116(18):5372-83. doi: 10.1021/jp301726s. PubMed PMID: 22494242; PubMed Central PMCID: PMC3350225.

13. Huang L, Roux B. Automated Force Field Parameterization for Non-Polarizable and Polarizable Atomic Models Based on Target Data. Journal of chemical theory and computation. 2013;9(8). doi: 10.1021/ct4003477. PubMed PMID: 24223528; PubMed Central PMCID: PMC3819940.

14. Islam SM, Stein RA, McHaourab HS, Roux B. Structural refinement from restrained-ensemble simulations based on EPR/DEER data: application to T4 lysozyme. The journal of physical chemistry B. 2013;117(17):4740-54. doi: 10.1021/jp311723a. PubMed PMID: 23510103; PubMed Central PMCID: PMC3684008.

15. Jo S, Jiang W, Lee HS, Roux B, Im W. CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application. Journal of chemical information and modeling. 2013;53(1):267-77. doi: 10.1021/ci300505n. PubMed PMID: 23205773; PubMed Central PMCID: PMC3557591.

16. Kantcheva AK, Quick M, Shi L, Winther AM, Stolzenberg S, Weinstein H, Javitch JA, Nissen P. Chloride binding site of neurotransmitter sodium symporters. Proceedings of the National Academy of Sciences of the United States of America. 2013;110(21):8489-94. doi: 10.1073/pnas.1221279110. PubMed PMID: 23641004; PubMed Central PMCID: PMC3666746.

17. Khelashvili G, LeVine MV, Shi L, Quick M, Javitch JA, Weinstein H. The membrane protein LeuT in micellar systems: aggregation dynamics and detergent binding to the S2 site. Journal of the American Chemical Society. 2013;135(38):14266-75. doi: 10.1021/ja405984v. PubMed PMID: 23980525; PubMed Central PMCID: PMC3788620.

18. Mayne CG, Saam J, Schulten K, Tajkhorshid E, Gumbart JC. Rapid parameterization of small molecules using the Force Field Toolkit. Journal of computational chemistry. 2013;34(32):2757-70. doi: 10.1002/jcc.23422. PubMed PMID: 24000174; PubMed Central PMCID: PMC3874408.

19. Mondal S, Khelashvili G, Shi L, Weinstein H. The cost of living in the membrane: a case study of hydrophobic mismatch for the multi-segment protein LeuT. Chemistry and physics of lipids. 2013;169:27-38. doi: 10.1016/j.chemphyslip.2013.01.006. PubMed PMID: 23376428; PubMed Central PMCID: PMC3631462.

20. Moradi M, Tajkhorshid E. Mechanistic picture for conformational transition of a membrane transporter at atomic resolution. Proceedings of the National Academy of Sciences of the United States of America. 2013;110(47):18916-21. doi: 10.1073/pnas.1313202110. PubMed PMID: 24191018; PubMed Central PMCID: PMC3839739.

21. Roux B, Islam SM. Restrained-ensemble molecular dynamics simulations based on distance histograms from double electron-electron resonance spectroscopy. The journal of physical chemistry B. 2013;117(17):4733-9. doi: 10.1021/jp3110369. PubMed PMID: 23510121; PubMed Central PMCID: PMC3683991.

22. Roux B, Weare J. On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method. The Journal of chemical physics. 2013;138(8):084107. doi: 10.1063/1.4792208. PubMed PMID: 23464140; PubMed Central PMCID: PMC3598863.

23. Shaikh SA, Li J, Enkavi G, Wen PC, Huang Z, Tajkhorshid E. Visualizing functional motions of membrane transporters with molecular dynamics simulations. Biochemistry (Current Topic). 2013;52(4):569-87. doi: 10.1021/bi301086x. PubMed PMID: 23298176; PubMed Central PMCID: PMC3560430.

24. Wen PC, Verhalen B, Wilkens S, McHaourab HS, Tajkhorshid E. On the origin of large flexibility of P-glycoprotein in the inward-facing state. The Journal of biological chemistry. 2013;288(26):19211-20. doi: 10.1074/jbc.M113.450114. PubMed PMID: 23658020; PubMed Central PMCID: PMC3696692.

25. Das A, Gur M, Cheng MH, Jo S, Bahar I, Roux B. Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model. PLoS computational biology. 2014;10(4):e1003521. doi: 10.1371/journal.pcbi.1003521. PubMed PMID: 24699246; PubMed Central PMCID: PMC3974643.

26. Han W, Cheng RC, Maduke MC, Tajkhorshid E. Water access points and hydration pathways in CLC H+/Cl- transporters. Proceedings of the National Academy of Sciences of the United States of America. 2014;111(5):1819-24. doi: 10.1073/pnas.1317890111. PubMed PMID: 24379362; PubMed Central PMCID: PMC3918786.

27. Kazmier K, Sharma S, Quick M, Islam SM, Roux B, Weinstein H, Javitch JA, McHaourab HS. Conformational dynamics of ligand-dependent alternating access in LeuT. Nature structural & molecular biology. 2014;21(5):472-9. doi: 10.1038/nsmb.2816. PubMed PMID: 24747939; PubMed Central PMCID: PMC4050370.

28. LeVine MV, Weinstein H. NbIT–a new information theory-based analysis of allosteric mechanisms reveals residues that underlie function in the leucine transporter LeuT. PLoS computational biology. 2014;10(5):e1003603. doi: 10.1371/journal.pcbi.1003603. PubMed PMID: 24785005; PubMed Central PMCID: PMC4006702.

29. Li Q, Wanderling S, Paduch M, Medovoy D, Singharoy A, McGreevy R, Villalba-Galea CA, Hulse RE, Roux B, Schulten K, Kossiakoff A, Perozo E. Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain. Nature structural & molecular biology. 2014;21(3):244-52. doi: 10.1038/nsmb.2768. PubMed PMID: 24487958; PubMed Central PMCID: PMC4116111.

30. Mishra S, Verhalen B, Stein RA, Wen PC, Tajkhorshid E, McHaourab HS. Conformational dynamics of the nucleotide binding domains and the power stroke of a heterodimeric ABC transporter. eLife. 2014;3:e02740. doi: 10.7554/eLife.02740. PubMed PMID: 24837547; PubMed Central PMCID: PMC4046567.

31. Mondal S, Khelashvili G, Johner N, Weinstein H. How the dynamic properties and functional mechanisms of GPCRs are modulated by their coupling to the membrane environment. Advances in experimental medicine and biology. 2014;796:55-74. doi: 10.1007/978-94-007-7423-0_4. PubMed PMID: 24158801.

32. Mondal S, Khelashvili G, Weinstein H. Not just an oil slick: how the energetics of protein-membrane interactions impacts the function and organization of transmembrane proteins. Biophysical journal. 2014;106(11):2305-16. doi: 10.1016/j.bpj.2014.04.032. PubMed PMID: 24896109; PubMed Central PMCID: PMC4052241.

33. Moradi M, Tajkhorshid E. Computational Recipe for Efficient Description of Large-Scale Conformational Changes in Biomolecular Systems. Journal of chemical theory and computation. 2014;10(7):2866-80. doi: 10.1021/ct5002285. PubMed PMID: 25018675; PubMed Central PMCID: PMC4089915.

34. Qi Y, Cheng X, Han W, Jo S, Schulten K, Im W. CHARMM-GUI PACE CG Builder for solution, micelle, and bilayer coarse-grained simulations. Journal of chemical information and modeling. 2014;54(3):1003-9. doi: 10.1021/ci500007n. PubMed PMID: 24624945; PubMed Central PMCID: PMC3985889.

35. Wang Y, Liu Y, Deberg HA, Nomura T, Hoffman MT, Rohde PR, Schulten K, Martinac B, Selvin PR. Single molecule FRET reveals pore size and opening mechanism of a mechano-sensitive ion channel. eLife. 2014;3:e01834. doi: 10.7554/eLife.01834. PubMed PMID: 24550255; PubMed Central PMCID: PMC3925968.

36. Weingarth M, van der Cruijsen EA, Ostmeyer J, Lievestro S, Roux B, Baldus M. Quantitative analysis of the water occupancy around the selectivity filter of a K+ channel in different gating modes. Journal of the American Chemical Society. 2014;136(5):2000-7. doi: 10.1021/ja411450y. PubMed PMID: 24410583.

37. Wu EL, Cheng X, Jo S, Rui H, Song KC, Davila-Contreras EM, Qi Y, Lee J, Monje-Galvan V, Venable RM, Klauda JB, Im W. CHARMM-GUI Membrane Builder toward realistic biological membrane simulations. Journal of computational chemistry. 2014;35(27):1997-2004. doi: 10.1002/jcc.23702. PubMed PMID: 25130509.

Associate publications

1. Arcario MJ, Ohkubo YZ, Tajkhorshid E. Capturing spontaneous partitioning of peripheral proteins using a biphasic membrane-mimetic model. The journal of physical chemistry B. 2011;115(21):7029-37. doi: 10.1021/jp109631y. PubMed PMID: 21561114; PubMed Central PMCID: PMC3102442.

2. DeChancie J, Shrivastava IH, Bahar I. The mechanism of substrate release by the aspartate transporter GltPh: insights from simulations. Molecular bioSystems. 2011;7(3):832-42. doi: 10.1039/c0mb00175a. PubMed PMID: 21161089; PubMed Central PMCID: PMC3227142.

3. Han DS, Golebiewska U, Stolzenberg S, Scarlata SF, Weinstein H. A dynamic model of membrane-bound phospholipase Cbeta2 activation by Gbetagamma subunits. Molecular pharmacology. 2011;80(3):434-45. doi: 10.1124/mol.111.073403. PubMed PMID: 21693623; PubMed Central PMCID: PMC3164327.

4. Jiang J, Shrivastava IH, Watts SD, Bahar I, Amara SG. Large collective motions regulate the functional properties of glutamate transporter trimers. Proceedings of the National Academy of Sciences of the United States of America. 2011;108(37):15141-6. doi: 10.1073/pnas.1112216108. PubMed PMID: 21876140; PubMed Central PMCID: PMC3174670.

5. Sukumaran M, Rossmann M, Shrivastava I, Dutta A, Bahar I, Greger IH. Dynamics and allosteric potential of the AMPA receptor N-terminal domain. The EMBO journal. 2011;30(5):972-82. doi: 10.1038/emboj.2011.17. PubMed PMID: 21317871; PubMed Central PMCID: PMC3049213.

6. Weinstein H, Scarlata S. The correlation between multidomain enzymes and multiple activation mechanisms–the case of phospholipase Cbeta and its membrane interactions. Biochimica et biophysica acta. 2011;1808(12):2940-7. doi: 10.1016/j.bbamem.2011.08.028. PubMed PMID: 21906583; PubMed Central PMCID: PMC3205958.

7. Zomot E, Bahar I. Protonation of glutamate 208 induces the release of agmatine in an outward-facing conformation of an arginine/agmatine antiporter. The Journal of biological chemistry. 2011;286(22):19693-701. doi: 10.1074/jbc.M110.202085. PubMed PMID: 21487006; PubMed Central PMCID: PMC3103348.

8. Barnard TJ, Gumbart J, Peterson JH, Noinaj N, Easley NC, Dautin N, Kuszak AJ, Tajkhorshid E, Bernstein HD, Buchanan SK. Molecular basis for the activation of a catalytic asparagine residue in a self-cleaving bacterial autotransporter. Journal of molecular biology. 2012;415(1):128-42. doi: 10.1016/j.jmb.2011.10.049. PubMed PMID: 22094314; PubMed Central PMCID: PMC3230255.

9. Dutta A, Shrivastava IH, Sukumaran M, Greger IH, Bahar I. Comparative dynamics of NMDA- and AMPA-glutamate receptor N-terminal domains. Structure. 2012;20(11):1838-49. doi: 10.1016/j.str.2012.08.012. PubMed PMID: 22959625; PubMed Central PMCID: PMC3496038.

10. Khelashvili G, Albornoz PB, Johner N, Mondal S, Caffrey M, Weinstein H. Why GPCRs behave differently in cubic and lamellar lipidic mesophases. Journal of the American Chemical Society. 2012;134(38):15858-68. doi: 10.1021/ja3056485. PubMed PMID: 22931253; PubMed Central PMCID: PMC3469068.

11. Lee HS, Im W. Identification of ligand templates using local structure alignment for structure-based drug design. Journal of chemical information and modeling. 2012;52(10):2784-95. doi: 10.1021/ci300178e. PubMed PMID: 22978550; PubMed Central PMCID: PMC3478504.

12. Levin EJ, Cao Y, Enkavi G, Quick M, Pan Y, Tajkhorshid E, Zhou M. Structure and permeation mechanism of a mammalian urea transporter. Proceedings of the National Academy of Sciences of the United States of America. 2012;109(28):11194-9. doi: 10.1073/pnas.1207362109. PubMed PMID: 22733730; PubMed Central PMCID: PMC3396522.

13. Noinaj N, Easley NC, Oke M, Mizuno N, Gumbart J, Boura E, Steere AN, Zak O, Aisen P, Tajkhorshid E, Evans RW, Gorringe AR, Mason AB, Steven AC, Buchanan SK. Structural basis for iron piracy by pathogenic Neisseria. Nature. 2012;483(7387):53-8. doi: 10.1038/nature10823. PubMed PMID: 22327295; PubMed Central PMCID: PMC3292680.

14. Baylon JL, Lenov IL, Sligar SG, Tajkhorshid E. Characterizing the membrane-bound state of cytochrome P450 3A4: structure, depth of insertion, and orientation. Journal of the American Chemical Society. 2013;135(23):8542-51. doi: 10.1021/ja4003525. PubMed PMID: 23697766; PubMed Central PMCID: PMC3682445.

15. Geyer RR, Musa-Aziz R, Enkavi G, Mahinthichaichan P, Tajkhorshid E, Boron WF. Movement of NH(3) through the human urea transporter B: a new gas channel. American journal of physiology Renal physiology. 2013;304(12):F1447-57. doi: 10.1152/ajprenal.00609.2012. PubMed PMID: 23552862; PubMed Central PMCID: PMC3680674.

16. Kalani MR, Moradi A, Moradi M, Tajkhorshid E. Characterizing a histidine switch controlling pH-dependent conformational changes of the influenza virus hemagglutinin. Biophysical journal. 2013;105(4):993-1003. doi: 10.1016/j.bpj.2013.06.047. PubMed PMID: 23972851; PubMed Central PMCID: PMC3752100.

17. Khalili-Araghi F, Ziervogel B, Gumbart JC, Roux B. Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations. The Journal of general physiology. 2013;142(4):465-75. doi: 10.1085/jgp.201311014. PubMed PMID: 24081985; PubMed Central PMCID: PMC3787774.

18. Khelashvili G, Harries D. How sterol tilt regulates properties and organization of lipid membranes and membrane insertions. Chemistry and physics of lipids. 2013;169:113-23. doi: 10.1016/j.chemphyslip.2012.12.006. PubMed PMID: 23291283; PubMed Central PMCID: PMC3631440.

19. Kosinska Eriksson U, Fischer G, Friemann R, Enkavi G, Tajkhorshid E, Neutze R. Subangstrom resolution X-ray structure details aquaporin-water interactions. Science. 2013;340(6138):1346-9. doi: 10.1126/science.1234306. PubMed PMID: 23766328; PubMed Central PMCID: PMC4066176.

20. Lee HS, Im W. Ligand binding site detection by local structure alignment and its performance complementarity. Journal of chemical information and modeling. 2013;53(9):2462-70. doi: 10.1021/ci4003602. PubMed PMID: 23957286; PubMed Central PMCID: PMC3821077.

21. Li J, Shaikh SA, Enkavi G, Wen PC, Huang Z, Tajkhorshid E. Transient formation of water-conducting states in membrane transporters. Proceedings of the National Academy of Sciences of the United States of America. 2013;110(19):7696-701. doi: 10.1073/pnas.1218986110. PubMed PMID: 23610412; PubMed Central PMCID: PMC3651479.

22. Mondal S, Johnston JM, Wang H, Khelashvili G, Filizola M, Weinstein H. Membrane driven spatial organization of GPCRs. Scientific reports. 2013;3:2909. doi: 10.1038/srep02909. PubMed PMID: 24105260; PubMed Central PMCID: PMC3793225.

23. Moradi M, Tajkhorshid E. Driven Metadynamics: Reconstructing Equilibrium Free Energies from Driven Adaptive-Bias Simulations. The journal of physical chemistry letters. 2013;4(11):1882-7. doi: 10.1021/jz400816x. PubMed PMID: 23795244; PubMed Central PMCID: PMC3688312.

24. Yu H, Schulten K. Membrane sculpting by F-BAR domains studied by molecular dynamics simulations. PLoS computational biology. 2013;9(1):e1002892. doi: 10.1371/journal.pcbi.1002892. PubMed PMID: 23382665; PubMed Central PMCID: PMC3561051.

25. A. BF, N. A, Tajkhorshid E. Thermodynamic Insight into Spontaneous Hydration and Rapid Water Permeation in Aquaporins. Applied Physics Letters. 2014;105(8):083702.

26. Johner N, Mondal S, Morra G, Caffrey M, Weinstein H, Khelashvili G. Protein and lipid interactions driving molecular mechanisms of in meso crystallization. Journal of the American Chemical Society. 2014;136(8):3271-84. doi: 10.1021/ja4129839. PubMed PMID: 24494670; PubMed Central PMCID: PMC3985912.

27. Pogorelov TV, Vermaas JV, Arcario MJ, Tajkhorshid E. Partitioning of amino acids into a model membrane: capturing the interface. The journal of physical chemistry B. 2014;118(6):1481-92. doi: 10.1021/jp4089113. PubMed PMID: 24451004; PubMed Central PMCID: PMC3983343.

28. Vermaas JV, Tajkhorshid E. A microscopic view of phospholipid insertion into biological membranes. The journal of physical chemistry B. 2014;118(7):1754-64. doi: 10.1021/jp409854w. PubMed PMID: 24313792; PubMed Central PMCID: PMC3933253.

29. Vermaas JV, Tajkhorshid E. Conformational heterogeneity of alpha-synuclein in membrane. Biochimica et biophysica acta. 2014;1838:3107–17. doi: 10.1016/j.bbamem.2014.08.012. PubMed PMID: 25135664.

30. Zhou Q, Li J, Yu H, Zhai Y, Gao Z, Liu Y, Pang X, Zhang L, Schulten K, Sun F, Chen C. Molecular insights into the membrane-associated phosphatidylinositol 4-kinase IIalpha. Nature communications. 2014;5:3552. doi: 10.1038/ncomms4552. PubMed PMID: 24675427; PubMed Central PMCID: PMC3974213.

Pending / in press publications

1. Ahn Y, Mahinthichaichan P, Lee JH, Ouyang H, Kaluka D, Yeh S-R, Arjona D, Rousseau DL, Tajkhorshid E, Adelroth P, Gennis RB. Conformational coupling between the active site and residues within the KC-channel of the Vibrio cholerae cbb3-type oxygen reductase. Proceedings of the National Academy of Sciences of the United States of America. 2014.

2. Arcario MJ, Mayne CG, Tajkhorshid E. Atomistic models of general anesthetics for use in in silico biological studies. Journal of Physical Chemistry B. 2014.

3. Arcario MJ, Tajkhorshid E. Membrane-Induced Structural Rearrangement of Talin Subdomains Providing a Molecular Mechanism for Inside-Out Activation of Integrin. Biophysical journal. 2014.

4. Blanchard AE, Arcario MJ, Schulten K, Tajkhorshid E. A Highly Tilted Membrane Configuration FOr Pre-Fusion State of Synaptobrevin. Biophysical journal. 2014.

5. Kazmier K, Sharma R, Islam SM, Roux B, McHaourab HS. Conformational cycle and ion-coupling mechanism of the Na+/hydantoin transporter Mhp1. Proc Natl Acad Sci. 2014.

6. Khelashvili G, Doktorova M, Sahai MA, Johner N, Shi L, Weinstein H. Computational modeling of the N-terminus of the human dopamine transporter2014.

7. Lee HS, Seok C, Im W. Potential Application of Alchemical Free Energy Simulations to Discriminate GPCR Ligand Efficacy. Journal of chemical information and modeling. 2014.

8. Moradi A, Enkavi G, Tajkhorshid E. Thermodynamic Characterization of the Full Transport Cycle in a Secondary Transporter. Science. 2014.

9. Stolzenberg S, Quick M, Zhao C, Johner N, Shi L, Weinstein H. The allosteric interaction network enabling Na+ symport in a neurotransmitter transporter homolog 2014.