Publications

Chief among the resources produced by the Membrane Protein Structural Dynamics Consortium (MPSDC) are publications co-authored by Consortium team members. These culminate out of research projects undertaken as part of the objectives of the Cores and Projects, and receive funding accordingly. We have made selections of these publications available for viewing, subject to the regulations of the periodicals and journals in which they were published. All publications listed cite the NIH/NIGMS Glue Grant No. GM087519 which funds the MPSDC.

The following are a list of directly related publications which reflect the broad goals and aims of the Consortium Bridges, Pilots, and Cores.

View a complete list of all publications that have been funded by the MPSDC »

2016

Atomic mutagenesis in ion channels with engineered stoichiometry

Lueck JD, Mackey AL, Infield DT, Galpin JD, Li J, Roux B, Ahern CA. Elife 2016 Oct 6;5. pii: e18976. PMID: 27710770. PMID: 24379362. PMCID: PMC5092047.

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From Nanodiscs to Isotropic Bicelles: A Procedure for Solution Nuclear Magnetic Resonance Studies of Detergent-Sensitive Integral Membrane Proteins.

Laguerre A, Löhr F, Henrich E, Hoffmann B, Abdul-Manan N, Connolly PJ, Perozo E, Moore JM, Bernhard F, Dötsch V. Science Structure 2016 Oct 4;24(10):1830-1841. PMID: 27618661. PMCID: PMC5064851.

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Instantaneous ion configurations in the K+ ion channel selectivity filter revealed by 2D IR spectroscopy

Kratochvil HT, Carr JK, Matulef K, Annen AW, Li H, Maj M, Ostmeyer J, Serrano AL, Raghuraman H, Moran SD, Skinner JL, Perozo E, Roux B, Valiyaveetil FI, Zanni MT. Science 2016 Sep 2;353(6303):1040-1044. PMID: 27701114.

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The selectivity of the Na(+)/K(+)-pump is controlled by binding site protonation and self-correcting occlusion

Rui H, Artigas P, Roux B. Elife 2016 Aug 4;5. pii: e16616. PMID: 27490484. PMCID: PMC5026471.

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Combining in Vitro Folding with Cell Free Protein Synthesis for Membrane Protein Expression

Focke PJ, Hein C, Hoffmann B, Matulef K, Bernhard F, Dötsch V, Valiyaveetil FI. Biochemistry 2016 Aug 2;55(30):4212-9. PMID: 27384110. PMCID: PMC5021318.

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Multi-ion free energy landscapes underscore the microscopic mechanism of ion selectivity in the KcsA channel

Medovoy D, Perozo E, Roux B. Biochim Biophys Acta 2016 Jul;1858(7 Pt B):1722-32. PMID: 26896693. PMCID: PMC4939264.

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The Structure of a Sugar Transporter of the Glucose EIIC Superfamily Provides Insight into the Elevator Mechanism of Membrane Transport

McCoy JG, Ren Z, Stanevich V, Lee J, Mitra S, Levin EJ, Poget S, Quick M, Im W, Zhou M. Structure 2016 Jun 7;24(6):956-64. PMID: 27161976. PMC4142352.

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Molecular Basis for Differential Anion Binding and Proton Coupling in the Cl–/H+ Exchanger ClC-ec1

Jiang T, Han W, Maduke M, Tajkhorshid E. J Am Chem Soc. 2016 Mar 9;138(9):3066-75. PMID: 26880377.

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Unfolding of a Temperature-Sensitive Domain Controls Voltage-Gated Channel Activation

Arrigoni C, Rohaim A, Shaya D, Findeisen F, Stein RA, Nurva SR, Mishra S, Mchaourab HS, Minor DL Jr. Cell. 2016 Feb 25;164(5):922-36. PMID: 26919429. PMCID: PMC4769381.

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Revealing an outward-facing open conformational state in a CLC Cl-/H+ exchange transporter

McCoy JG, Ren Z, Stanevich V, Lee J, Mitra S, Levin EJ, Poget S, Quick M, Im W, Zhou M. Elife. 2016 Jan 22;5. [Epub ahead of print]. PMID: 26799336.

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The hitchhiker’s guide to the voltage-gated sodium channel galaxy.

Ahern CA, Payandeh J, Bosmans F, Chanda B. J Gen Physiol. 2016 Jan;147(1):1-24. PMID: 26880377. PMCID: PMCID3918786.

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Conformational Chaperones for Structural Studies of Membrane Proteins Using Antibody Phage Display with Nanodiscs

Dominik PK, Borowska MT, Dalmas O, Kim SS, Perozo E, Keenan RJ, Kossiakoff AA.. Structure. 2015 Dec 28. pii: S0969-2126(15)00503-1. [Epub ahead of print] PMID: 26749445.

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2015

CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model

Qi Y1, Cheng X, Lee J, Vermaas JV, Pogorelov TV, Tajkhorshid E, Park S, Klauda JB, Im W., Hoelz A. Biophys J. 2015 Nov 17;109(10):2012-22. PMID: 26588561. PMCID: PMC4656882.

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Architecture of the fungal nuclear pore inner ring complex

Shen R, Han W, Fiorin G, Islam SM, Schulten K, Roux B., Hoelz A. PLoS Comput Biol. 2015 Oct 27;11(10):e1004368. PMID: 26505197.

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Architecture of the fungal nuclear pore inner ring complex

Stuwe T, Bley CJ, Thierbach K, Petrovic S, Schilbach S, Mayo DJ, Perriches T, Rundlet EJ, Jeon YE, Collins LN, Huber FM, Lin DH, Paduch M, Koide A, Lu V, Fischer J, Hurt E, Koide S, Kossiakoff AA, Hoelz A. Science. 2015 Oct 2;350(6256):56-64. PMID: 26316600.

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A chimeric prokaryotic pentameric ligand-gated channel reveals distinct pathways of activation

Schmandt N, Velisetty P, Chalamalasetti SV, Stein RA, Bonner R, Talley L, Parker MD, Mchaourab HS, Yee VC, Lodowski DT, Chakrapani S. J Gen Physiol. 2015 Oct;146(4):323-40. PMID: 26415570. PMCID: PMC4586589.

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Crystal structures of a double-barrelled fluoride ion channel

Stockbridge RB, Kolmakova-Partensky L, Shane T, Koide A, Koide S, Miller C, Newstead S. Nature. 2015 Sep 24;525(7570):548-51. PMID: 26344196.

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Atomic basis for therapeutic activation of neuronal potassium channels

Kim RY, Yau MC, Galpin JD, Seebohm G, Ahern CA, Pless SA, Kurata HT. Nat Commun. 2015 Sep 3;6:8116. PMID: 26333338. PMCID: PMC4561856.

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Navigating Membrane Protein Structure, Dynamics, and Energy Landscapes Using Spin Labeling and EPR Spectroscopy

Claxton DP, Kazmier K, Mishra S, Mchaourab HS. Methods Enzymol. 2015 Aug 29;564:349-87. PMID: 26205423.

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Mechanism of potassium ion uptake by the Na(+)/K(+)-ATPase

Castillo JP, Rui H, Basilio D, Das A, Roux B, Latorre R, Bezanilla F, Holmgren M. Nat Commun. 2015 Jul 24;6:7622. PMID: 26205423. PMCID: PMC4515779.

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Efficient Exploration of Membrane-Associated Phenomena at Atomic Resolution

Vermaas JV1, Baylon JL, Arcario MJ, Muller MP, Wu Z, Pogorelov TV, Tajkhorshid E. J Membr Biol. 2015 Jun;248(3):563-82. PMID: 25998378. PMCID: PMC4490090.

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Mechanism of the Association between Na+ Binding and Conformations at the Intracellular Gate in Neurotransmitter:Sodium Symporters

Stolzenberg S, Quick M, Zhao C, Gotfryd K, Khelashvili G, Gether U, Loland CJ, Javitch JA, Noskov S, Weinstein H, Shi L. J Biol Chem. 2015 May 29;290(22):13992-4003. PMID: 25869126. PMCID: PMC4447972.

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Computational characterization of structural dynamics underlying function in active membrane transporters

Li J, Wen PC, Moradi M, Tajkhorshid E.. Curr Opin Struct Biol. 2015 Apr;31:96-105. Epub 2015 Apr 27. PMID: 25913536. PMCID: PMC4476910 [Available on 2016-04-27].

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Phage display selections for affinity reagents to membrane proteins in nanodiscs

Dominik PK, Kossiakoff AA. Methods Enzymol. 2015;557:219-45. Epub 2015 Mar 24. PMID: 25950967.

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Room-Temperature Distance Measurements of Immobilized Spin-Labeled Protein by DEER/PELDOR

Meyer V, Swanson MA, Clouston LJ, Boratyński PJ, Stein RA, Mchaourab HS, Rajca A, Eaton SS, Eaton GR. Biophys J. 2015 Mar 10;108(5):1213-9. PMID: 25762332.

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Effects of N-glycosylation on protein conformation and dynamics: Protein Data Bank analysis and molecular dynamics simulation study

Lee HS, Qi Y, Im W. Sci Rep. 2015 Mar 9;;5:8926. PMID: 25748215. PMCID: PMC4352867.

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Structure of the Get3 targeting factor in complex with its membrane protein cargo

Mateja A, Paduch M, Chang HY, Szydlowska A, Kossiakoff AA, Hegde RS, Keenan RJ. Science. 2015 Mar 6;347(6226):1152-5. PMID: 25745174.

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Architecture of the nuclear pore complex coat

Stuwe T, Correia AR, Lin DH, Paduch M, Lu VT, Kossiakoff AA, Hoelz A. Science. 2015 Mar 6;347(6226):1148-52. PMID: 25745173.

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Potential Application of Alchemical Free Energy Simulations to Discriminate GPCR Ligand Efficacy

Lee HS, Seok C, Im W. J Chem Theory Comput. 2015 Feb 11;11(3):1255-1266.

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Multilevel Summation Method for Electrostatic Force Evaluation

Hardy DJ, Wu Z, Phillips JC, Stone JE, Skeel RD, Schulten K. J Chem Theory Comput. 2015 Feb 10;11(2):766-779. PMID: 25691833. PMCID: PMC4325600 [Available on 2015-12-16].

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Transport domain unlocking sets the uptake rate of an aspartate transporter

Akyuz N, Georgieva ER, Zhou Z, Stolzenberg S, Cuendet MA, Khelashvili G, Altman RB, Terry DS, Freed JH, Weinstein H, Boudker O, Blanchard SC. Nature. 2015 Feb 5;518(7537):68-73. PMID: 25652997. PMCID: PMC4351760.

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Simulating the Distance Distribution between Spin-Labels Attached to Proteins

Islam S, Roux B. J. Phys. Chem. B, 2015 Feb 2;119(10). PMID: 25645890.

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13C NMR detects conformational change in the 100-kD membrane transporter ClC-ec1

Abraham SJ, Cheng RC, Chew TA, Khantwal CM, Liu CW, Gong S, Nakamoto RK, Maduke M. J Biomol NMR., 2015 Jan 29. PMID: 25631353.

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Identification of a second substrate-binding site in solute-sodium symporters

Li Z, Lee AS, Bracher S, Jung H, Paz A, Kumar JP, Abramson J, Quick M, Shi L. J Biol Chem., 2015 Jan 2;290(1):127-41. PMID: 25398883. PMCID: PMC4281715.

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2014

Applications for an engineered Protein-G variant with a pH controllable affinity to antibody fragments

Bailey LJ, Sheehy KM, Hoey RJ, Schaefer ZP, Ura M, Kossiakoff AA. J Immunol Methods, 2014 Dec 15;415:24-30. PMID: 25450256. PMCID: PMC4257880.

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A synthetic antibody fragment targeting nicastrin affects assembly and trafficking of γ-secretase

Zhang X, Hoey R, Koide A, Dolios G, Paduch M, Nguyen P, Wu X, Li Y, Wagner SL, Wang R, Koide S, Sisodia SS. J Biol Chem., 2014 Dec 12;289(50):34851-61. PMID: 25352592. PMCID: PMC4263884

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A highly tilted membrane configuration for the prefusion state of synaptobrevin

Blanchard AE, Arcario MJ, Schulten K, Tajkhorshid E. Biophys J., 2014 Nov 4;107(9):2112-21. PMID: 25418096. PMCID: PMC4223215 [Available on 2015/11/4].

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Synthesis of unnatural amino acids functionalized with sterically shielded pyrroline nitroxides

Wang Y, Paletta JT, Berg K, Reinhart E, Rajca S, Rajca A. Org Lett, 2014 Oct 17;16(20):5298-300. PMID: 25324010. PMCID: PMC4201325 [Available on 2015/9/16].

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CHARMM-GUI Membrane Builder toward realistic biological membrane simulations

Wu EL, Cheng X, Jo S, Rui H, Song KC, Dávila-Contreras EM, Qi Y, Lee J, Monje-Galvan V, Venable RM, Klauda JB, Im W. J Comput Chem. 2014 Oct 15;35(27):1997-2004. PMID: 25130509. PMCID: PMC4165794 [Available on 2015/10/15].

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Conformational cycle and ion-coupling mechanism of the Na+/hydantoin transporter Mhp1

Kazmier K, Sharma S, Islam SM, Roux B, Mchaourab HS. Proc Natl Acad Sci U S A. 2014 Oct 14;111(41):14752-7. PMID: 25267652. PMCID: PMC4205665.

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Proof of dual-topology architecture of Fluc F- channels with monobody blockers

Stockbridge RB, Koide A, Miller C, Koide S. Nat Commun. 2014 Oct 7;5:5120. PMID: 25290819.

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xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures

McGreevy R, Singharoy A, Li Q, Zhang J, Xu D, Perozo E, Schulten K. Angew Chem Int Ed Engl. Acta Crystallogr D Biol Crystallogr. 2014 Sep;70(Pt 9):2344-55. PMID: 25195748. PMCID: PMC4157446.

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Total chemical synthesis of biologically active fluorescent dye-labeled Ts1 toxin

Dang B, Kubota T, Correa AM, Bezanilla F, Kent SB. Angew Chem Int Ed Engl. 2014 Aug 18;53(34):8970-4. PMID: 24989851.

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Computational Recipe for Efficient Description of Large-Scale Conformational Changes in Biomolecular Systems

Moradi M, Tajkhorshid E. J Chem Theory Comput. 2014 Jul 8;10(7):2866-2880. PMID: 25018675. PMCID: PMC4089915 [Available on 2015/6/3].

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Not just an oil slick: how the energetics of protein-membrane interactions impacts the function and organization of transmembrane proteins

Mondal S, Khelashvili G, Weinstein H Biophys J. 2014 Jun 3;106(11):2305-16. PMID: 24896109. PMCID: PMC4052241 [Available on 2015/6/3].

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Conformational dynamics of the nucleotide binding domains and the power stroke of a heterodimeric ABC transporter

Mishra S, Verhalen B, Stein RA, Wen PC, Tajkhorshid E, Mchaourab H. eLife 2014 May 16;3:e02740. PMCID: PMC4046567.

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NbIT – a new information theory-based analysis of allosteric mechanisms reveals residues that underlie function in the leucine transporter LeuT

LeVine MV, Weinstein H. PLoS Comput Biol. 2014 May 1;10(5):e1003603. PMID: 24785005. PMCID: PMC4006702.

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Conformational dynamics at the inner gate of KcsA during activation

Hulse RE, Sachleben JR, Wen PC, Moradi M, Tajkhorshid E, Perozo E.. Biochemistry 2014 Apr 29;53(16):2557-9. PMID: 24621378. PMCID: PMC4010282.

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Conformational dynamics of ligand-dependent alternating access in LeuT

Kazmier K, Sharma S, Quick M, Islam SM, Roux B, Weinstein H, Javitch JA, McHaourab HS.. Nat Struct Mol Biol. 2014 Apr 20;21(5):472-9. PMID: 24747939. PMCID: PMC4050370.

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Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model

Das A, Gur M, Cheng MH, Jo S, Bahar I, Roux B.. PLoS Comput Biol. 2014 Apr 3;10(4):e1003521. PMID: 24699246. PMCID: PMC3974643.

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Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain

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.. Nat Struct Mol Biol. 2014 Mar;21(3):244-52. PMID: 24487958. PMCID: PMC4116111.

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CHARMM-GUI PACE CG Builder for Solution, Micelle, and Bilayer Coarse-Grained Simulations

Qi Y, Cheng X, Han W, Jo S, Schulten K, Im W.. J Chem Inf Model. 2014 Mar 24;54(3):1003-9. PMID: 24624945. PMCID: PMCID3985889.

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Single molecule FRET reveals pore size and opening mechanism of a mechano-sensitive ion channel

Wang Y, Liu Y, Deberg HA, Nomura T, Hoffman MT, Rohde PR, Schulten K, Martinac B, Selvin PR. eLife 2014 Feb 18;3:e01834. PMID: 24550255. PMCID: PMC3925968.

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Quantitative analysis of the water occupancy around the selectivity filter of a K+ channel in different gating modes

Weingarth M1, van der Cruijsen EA, Ostmeyer J, Lievestro S, Roux B, Baldus M. J Am Chem Soc. 2014 Feb 5;136(5):2000-7. PMID: 24410583.

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Water access points and hydration pathways in CLC H+/Cl- transporters

Han W, Cheng RC, Maduke MC, Tajkhorshid E. Proceedings of the National Academy of Sciences of the United States of America 2014 Feb 4;111(5):1819-24. PMID: 24379362. PMCID: PMCID3918786

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Structural basis of the alternating-access mechanism in a bile acid transporter

Zhou X, Levin EJ, Pan Y, McCoy JG, Sharma R, Kloss B, Bruni R, Quick M, Zhou M. Nature. 2014 Jan 23;505(7484):569-73. PMID: 24317697. PMCID: PMC4142352.

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How the dynamic properties and functional mechanisms of GPCRs are modulated by their coupling to the membrane environment

Mondal S, Khelashvili G, Johner N, Weinstein H.. Adv Exp Med Biol. 2014;796:55-74. PMID: 24158801.

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2013

Rapid parameterization of small molecules using the Force Field Toolkit

Mayne CG, Saam J, Schulten K, Tajkhorshid E, Gumbart JC. Journal of Computational Chemistry 2013 Dec 15;34(32):2757–2770. PMID: 24000174. PMCID: PMC3874408.

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Hydrogen bonds as molecular timers for slow inactivation in voltage-gated potassium channels

Pless SA, Galpin JD, Niciforovic AP, Kurata HT, Ahern CA.. Elife 2013 Dec 10;2:e01289. PMID: 24327560. PMCID: PMC3852034.

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Mechanistic picture for conformational transition of a membrane transporter at atomic resolution

Moradi, M, Tajkhorshid E. Proceedings of the National Academy of Sciences of the United States of America 2013 Nov 19;110(47):18916-21. PMID: 24191018. PMCID: PMC3839739.

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The membrane protein LeuT in micellar systems: aggregation dynamics and detergent binding to the S2 site

Khelashvili G, LeVine MV, Shi L, Quick M, Javitch JA, Weinstein H. Journal of the American Chemical Society 2013 Sep 25;135(38):14266-75. PMID: 23980525. PMCID: PMC3788620.

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Native chemical ligation at Asx-Cys, Glx-Cys: chemical synthesis and high-resolution X-ray structure of ShK toxin by racemic protein crystallography

Dang B, Kubota T, Mandal K, Bezanilla F, Kent SB.. Journal of the American Chemical Society 2013 Aug 14;135(32):11911-9. PMID: 23919482. PMCID: PMC3838204.

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Importance of lipid-pore loop interface for potassium channel structure and function

van der Cruijsen EA, Nand D, Weingarth M, Prokofyev A, Hornig S, Cukkemane AA, Bonvin AM, Becker S, Hulse RE, Perozo E, Pongs O, Baldus M. Proceedings of the National Academy of Sciences of the USA 2013 Aug 6;110(32):13008-13. PMID: 23882077. PMCID: PMC3740848.

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Automated Force Field Parameterization for Nonpolarizable and Polarizable Atomic Models Based on Ab Initio Target Data

Huang L, Roux B. Journal of Chemical Theory and Computation 2013;9(8). PMID: 24223528. PMCID:3819940.

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Transport dynamics in a glutamate transporter homologue

Akyuz N, Altman RB, Blanchard SC, Boudker O. Nature 2013;502(7469). PMID: 23792560. PMCID: PMC3829612.

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Chloride binding site of neurotransmitter sodium symporters

Kantcheva AK, Quick M, Shi L, Winther AM, Stolzenberg S, Weinstein H, Javitch JA, Nissen P. Proceedings of the National Academy of Sciences of the United States of America 110(21): 8489-94 (2013). PMID: 23641004. PMCID: PMC3666746.

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On the Origin of Large Flexibility of P-glycoprotein in the Inward-Facing State

Wen PC, Verhalen B, Wilkens S, McHaourab H, Tajkhorshid E. Journal of Biological Chemistry 2013;288(26): 19211-20. PMID: 23658020. PMCID: PMC3974643.

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A novel mechanism for fine-tuning open-state stability in a voltage-gated potassium channel

Pless A, Niciforovic A, Galpin J, Nunez J-J, Kurata H, Ahern A. Nature Communications 2013;4:1784. PMID: 23653196. PMCID: PMC3644096.

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Structural Refinement from Restrained-Ensemble Simulations Based on EPR/DEER Data: Application to T4 Lysozyme

Islam S, Stein R, Mchaourab H, Roux B, Weare J. Journal of Physical Chemistry B 2013;117(17):4740-54. PMID: 23510103. PMCID: PMC3684008.

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Restrained-Ensemble Molecular Dynamics Simulations Based on Distance Histograms from Double Electron-Electron Resonance Spectroscopy

Islam S, Roux B. Journal of Physical Chemistry B 2013;117(17):4733-9. PMID: 23510121. PMCID:3683991.

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Generating conformation-specific synthetic antibodies to trap proteins in selected functional states

Paduch M, Koide A, Uysal S, Rizk SS, Koide S, Kossiakoff A. Methods 2013;60(1):3-14. PMID: 23280336. PMCID: PMC3650108.

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On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method

Roux B, Weare J. Journal of Chemical Physics 138(8): 084107 (2013). PMID: 23464140. PMCID: PMC3598863.

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CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application

Jo S, Jiang W, Lee HS, Roux B, Im W. Journal of Chemical Information and Modeling 53(1): 267-277 (2013). PMID: 23205773. PMCID: PMC3557591.

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Structures of a Na+-coupled, substrate-bound MATE multidrug transporter

Lu M, Symersky J, Radchenko M, Koide A, Guo Y, Nie R, Koide S. Proceedings of the National Academy of Sciences of the United States of America 110(6): 2099-104 (2013). PMID: 22143771. PMCID: PMC3251152.

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Visualizing Functional Motions of Membrane Transporters with Molecular Dynamics Simulations

Shaikh SA, Li J, Enkavi G, Wen PC, Huang Z, Tajkhorshid E.. Biochemistry 52(4):569-87 (2013). PMID: 23298176. PMCID: PMC3560430.

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The cost of living in the membrane: A case study of hydrophobic mismatch for the multi-segment protein LeuT

Mondal S, Khelashvili G, Shi L, Weinstein H.. Chemistry and Physics of Lipids 169: 27–38 (2013). PMID: 23376428. PMCID: PMC3631462.

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A common diaryl ether intermediate for the gram-scale synthesis of oxazine and xanthene fluorophores

Anzalone AV, Wang TY, Chen Z, Cornish VW. Angewandte Chemie International Edition 52(2):650-4 (2013). PMID: 23169599. PMCID: PMC3860831.

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2012

Nano-Positioning System for Structural Analysis of Functional Homomeric Proteins in Multiple Conformations

Hyde HC, Sandtner W, Vargas E, Dagcan AT, Robertson JL, Roux B, Correa AM, Bezanilla F. Structure 20(10): 1629-1640 (2012). PMID: 23063010. PMCID: PMC3283816.

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Symmetry-constrained Analysis of Pulsed Double Electron-Electron Resonance (DEER) Spectroscopy Reveals the Dynamic Nature of the KcsA Activation Gate

Dalmas O, Hyde HC, Hulse RE, Perozo E. J Am Chem Soc. 2012 Oct 3;134(39):16360-9. PMID: 22946877. PMCID: PMC3845908.

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Structural intermediates in a model of the substrate translocation path of the bacterial glutamate transporter homologue GltPh

Stolzenberg S, Khelashvili G, Weinstein H. J Phys Chem B. 2012 May 10;116(18):5372-83. PMID: 22494242. PMCID: PMC3350225.

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Accelerating Membrane Insertion of Peripheral Proteins with a Novel Membrane Mimetic Model

Ohkubo YZ, Pogorelov TV, Arcario MJ, Christensen GA and Tajkhorshid E. Biophysical Journal 102(9): 2130-2139 (2012). PMID: 22824277. PMCID: PMC3341550.

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Constraints Imposed by the Membrane Selectively Guide the Alternating Access Dynamics of the Glutamate Transporter GltPh

Lezon TR, Bahar I. Biophysical Journal 102(6): 1331-1340 (2012). PMID: 22455916. PMCID: PMC3283816.

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Determination of Membrane-Insertion Free Energies by Molecular Dynamics Simulations

Gumbart J, Roux B. Biophysical Journal 102(4): 795-801 (2012). PMID: 22385850. PMCID: PMC3283816.

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Target-binding proteins based on the 10th human fibronectin type III domain (10Fn3)

Koide S, Koide A, and Lipovšek D. Methods in Enzymology 503: 135-56 (2012). PMID: 22230568.

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A gate-free pathway for substrate release from the inward-facing state of the Na(+)-galactose transporter

Li J, Tajkhorshid E. Biochimica et Biophysica Acta (BBA) – Biomembranes 1818(2): 263-271 (2012). PMID: 21978597. PMCID: PMC3253917.

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Tracing cytoplasmic Ca2+ ion and water access points in the Ca2+-ATPase

Musgaard M, Thøgersen L, Schiøtt B, Tajkhorshid E. Biophysical Journal 102(2): 268-277 (2012). PMID: 22339863. PMCID: PMC3260667.

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Experimental conditions can obscure the second high-affinity site in LeuT

Quick M, Shi L, Zehnpfennig B, Weinstein H, Javitch JA. Nature Structural & Molecular Biology 19(2): 207-211 (2012). PMID: 22245968. PMCID: PMC3272158.

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Molecular dynamics investigation of the ω-current in the Kv1.2 voltage sensor domains

Khalili-Araghi F, Tajkhorshid E, Roux B, Schulten K. Biophysical Journal 102(2): 258-267 (2012). PMID: 22339862. PMCID: PMC3260662.

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Ion-controlled conformational dynamics in the outward-open transition from an occluded state of LeuT

Zhao C, Stolzenberg S, Gracia L, Weinstein H, Noskov S, Shi L. Biophysical Journal 2012; 103(5): 878-888. PMID: 23009837. PMCID: PMC3433624.

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An adaptive weighted ensemble procedure for efficient computation of free energies and first passage rates

Bhatt D, Bahar I. Journal of Chemical Physics 137(10):104101 (2012). PMID: 22979844. PMCID: PMC3460967.

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Constant electric field simulations of the membrane potential illustrated with simple systems

Gumbart J, Khalili-Araghi F, Sotomayor M, Roux B. Biochimica et Biophysica Acta 2012;1818(2):294-302. PMID: 22001851. PMCID: PMC3575077.

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2011

Energy landscape of the reactions governing the Na+ deeply occluded state of the Na+/K+-ATPase in the giant axon of the Humboldt squid

Castillo JP, De Giorgis D, Basilio D, Gadsby DC, Rosenthal JJ, Latorre R, Holmgren M, Bezanilla F. Proceedings of the National Academy of Sciences of the United States of America 108(51): 20556-61 (2011). PMID: 22143771. PMCID: PMC3251152.

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Toward the fourth dimension of membrane protein structure: Insight into dynamics from spin-labeling EPR spectroscopy

Mchaourab H, Steed P, Kazmier K. Structure 19(11): 1549-61 (2011). PMID: 22078555. PMCID: PMC3224804.

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Quantitative modeling of membrane deformations by multihelical membrane proteins: application to g-protein coupled receptors

Mondal S, Khelashvili G, Shan J, Andersen OS, Weinstein H. Biophysical Journal 101(9): 2092-101 (2011). PMID: 22067146. PMCID: PMC3207176.

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Chemical tags for labeling proteins inside living cells

Jing C, Cornish VW. Accounts of chemical research 44(9): 782-92 (2011). PMID: 21879706. PMCID: PMC3232020.

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Ouabain binding site in a functioning Na+/K+ ATPase

Sandtner W, Egwolf B, Khalili-Araghi F, Sánchez-Rodríguez JE, Roux B, Bezanilla F, Holmgren M. The journal of biological chemistry 286(44): 38177-83 (2011). PMID: 21911500. PMCID: PMC3207469.

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Conformational coupling of the nucleotide-binding and the transmembrane domains in ABC transporters

Wen PC, Tajkhorshid E. Biophysical Journal 101(3): 680-90 (2011). PMID: 21806936. PMCID: PMC3145290.

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Mechanism of activation gating in the full-length KcsA K+ channel

Uysal S, Cuello LG, Cortes DM, Koide S, Kossiakoff AA, Perozo E. Proceedings of the National Academy of Science of the United States of America 108(29): 11896-9 (2011). PMID: 21730186. PMCID: PMC3141920.

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A multipoint hydrogen-bond network underlying KcsA C-type inactivation

Cordero-Morales JF, Jogini V, Chakrapani S, Perozo E. Biophysical Journal 100(10): 2387-93 (2011). PMID: 21575572. PMCID: PMC3093550.

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On the structural basis of modal gating behavior in K(+) channels

Chakrapani S, Cordero-Morales JF, Jogini V, Pan AC, Cortes DM, Roux B, Perozo E. Nature Structural & Molecular Biology 18(1): 67-74 (2010). PMID: 21186363. PMCID: PMC3059741.

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2010

Total chemical synthesis and X-ray structure of kaliotoxin by racemic protein crystallography

Pentelute BL, Mandal K, Gates ZP, Sawaya MR, Yeates TO, Kent SB. Chemical communications (Cambridge, England) 46(43): 8174-6 (2010). PMID: 20877851.

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