Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory
Abstract
It is fundamental for the flourishing biological cells that membrane proteins mediate the process. Membrane-embedded transporters move ions and larger solutes across membranes; receptors mediate communication between the cell and its environment and membrane-embedded enzymes catalyze chemical reactions. Understanding these mechanisms of action requires knowledge of how the proteins couple to their fluid, hydrated lipid membrane environment. Here, we present here current studies in computational and experimental membrane protein biophysics, and show how they address outstanding challenges in understanding the complex environmental effects on the structure, function, and dynamics of membrane proteins.
- Authors:
-
more »
- Academy of Athens (Greece)
- Univ. of California, Davis, CA (United States); RMIT Univ., Melbourne (Australia)
- Univ. of California, Irvine, CA (United States)
- Univ. of Nice Sophia Antipolis and French National Center for Scientific Research (France)
- Zuse Inst. of Berlin (Germany)
- Rutgers Univ., Camden, NJ (United States)
- Univ. College, Dublin (Ireland)
- Temple Univ., Philadelphia, PA (United States)
- Univ. of Granada (Spain)
- Linnaeus Univ., Kalmar (Sweden)
- IBPC and CNRS, Paris (France)
- Univ. of Lorraine, Nancy (France); Lomonosov Moscow State Univ. (Russia)
- Univ. of Athens (Greece)
- Univ. of Southampton (United Kingdom)
- Univ. of Alberta, Edmonton, AB (Canada)
- Pompeu Fabra Univ., Barcelona (Spain)
- Univ. of Lorraine and CNRS, Nancy (France)
- Univ. of Nice Sophia Antipolis and French National Center for Scientific Research (France)
- Johns Hopkins Univ., Baltimore, MD (United States)
- Univ. of Cambridge (United Kingdom)
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Free Univ. of Berlin (Germany)
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE; National Science Foundation (NSF)
- OSTI Identifier:
- 1265906
- Grant/Contract Number:
- AC05-00OR22725
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Journal of Membrane Biology
- Additional Journal Information:
- Journal Volume: 248; Journal Issue: 4; Journal ID: ISSN 0022-2631
- Publisher:
- Springer
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Cournia, Zoe, Allen, Toby W., Andricioaei, Ioan, Antonny, Bruno, Baum, Daniel, Brannigan, Grace, Buchete, Nicolae-Viorel, Deckman, Jason T., Delemotte, Lucie, del Val, Coral, Friedman, Ran, Gkeka, Paraskevi, Hege, Hans-Christian, Hénin, Jérôme, Kasimova, Marina A., Kolocouris, Antonios, Klein, Michael L., Khalid, Syma, Lemieux, M. Joanne, Lindow, Norbert, Roy, Mahua, Selent, Jana, Tarek, Mounir, Tofoleanu, Florentina, Vanni, Stefano, Urban, Sinisa, Wales, David J., Smith, Jeremy C., and Bondar, Ana-Nicoleta. Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory. United States: N. p., 2015.
Web. doi:10.1007/s00232-015-9802-0.
Cournia, Zoe, Allen, Toby W., Andricioaei, Ioan, Antonny, Bruno, Baum, Daniel, Brannigan, Grace, Buchete, Nicolae-Viorel, Deckman, Jason T., Delemotte, Lucie, del Val, Coral, Friedman, Ran, Gkeka, Paraskevi, Hege, Hans-Christian, Hénin, Jérôme, Kasimova, Marina A., Kolocouris, Antonios, Klein, Michael L., Khalid, Syma, Lemieux, M. Joanne, Lindow, Norbert, Roy, Mahua, Selent, Jana, Tarek, Mounir, Tofoleanu, Florentina, Vanni, Stefano, Urban, Sinisa, Wales, David J., Smith, Jeremy C., & Bondar, Ana-Nicoleta. Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory. United States. https://doi.org/10.1007/s00232-015-9802-0
Cournia, Zoe, Allen, Toby W., Andricioaei, Ioan, Antonny, Bruno, Baum, Daniel, Brannigan, Grace, Buchete, Nicolae-Viorel, Deckman, Jason T., Delemotte, Lucie, del Val, Coral, Friedman, Ran, Gkeka, Paraskevi, Hege, Hans-Christian, Hénin, Jérôme, Kasimova, Marina A., Kolocouris, Antonios, Klein, Michael L., Khalid, Syma, Lemieux, M. Joanne, Lindow, Norbert, Roy, Mahua, Selent, Jana, Tarek, Mounir, Tofoleanu, Florentina, Vanni, Stefano, Urban, Sinisa, Wales, David J., Smith, Jeremy C., and Bondar, Ana-Nicoleta. Thu .
"Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory". United States. https://doi.org/10.1007/s00232-015-9802-0. https://www.osti.gov/servlets/purl/1265906.
@article{osti_1265906,
title = {Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory},
author = {Cournia, Zoe and Allen, Toby W. and Andricioaei, Ioan and Antonny, Bruno and Baum, Daniel and Brannigan, Grace and Buchete, Nicolae-Viorel and Deckman, Jason T. and Delemotte, Lucie and del Val, Coral and Friedman, Ran and Gkeka, Paraskevi and Hege, Hans-Christian and Hénin, Jérôme and Kasimova, Marina A. and Kolocouris, Antonios and Klein, Michael L. and Khalid, Syma and Lemieux, M. Joanne and Lindow, Norbert and Roy, Mahua and Selent, Jana and Tarek, Mounir and Tofoleanu, Florentina and Vanni, Stefano and Urban, Sinisa and Wales, David J. and Smith, Jeremy C. and Bondar, Ana-Nicoleta},
abstractNote = {It is fundamental for the flourishing biological cells that membrane proteins mediate the process. Membrane-embedded transporters move ions and larger solutes across membranes; receptors mediate communication between the cell and its environment and membrane-embedded enzymes catalyze chemical reactions. Understanding these mechanisms of action requires knowledge of how the proteins couple to their fluid, hydrated lipid membrane environment. Here, we present here current studies in computational and experimental membrane protein biophysics, and show how they address outstanding challenges in understanding the complex environmental effects on the structure, function, and dynamics of membrane proteins.},
doi = {10.1007/s00232-015-9802-0},
journal = {Journal of Membrane Biology},
number = 4,
volume = 248,
place = {United States},
year = {Thu Jun 11 00:00:00 EDT 2015},
month = {Thu Jun 11 00:00:00 EDT 2015}
}
Web of Science
Works referenced in this record:
Allosteric regulation of rhomboid intramembrane proteolysis
journal, July 2014
- Arutyunova, Elena; Panwar, Pankaj; Skiba, Pauline M.
- The EMBO Journal, Vol. 33, Issue 17
Local anesthetic and antiepileptic drug access and binding to a bacterial voltage-gated sodium channel
journal, August 2014
- Boiteux, C.; Vorobyov, I.; French, R. J.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 36
Lateral opening of a translocon upon entry of protein suggests the mechanism of insertion into membranes
journal, September 2010
- Egea, P. F.; Stroud, R. M.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 40
Crystal Structure of the Mammalian GIRK2 K+ Channel and Gating Regulation by G Proteins, PIP2, and Sodium
journal, September 2011
- Whorton, Matthew R.; MacKinnon, Roderick
- Cell, Vol. 147, Issue 1
Equilibrium thermodynamics from basin-sampling
journal, January 2006
- Bogdan, Tetyana V.; Wales, David J.; Calvo, Florent
- The Journal of Chemical Physics, Vol. 124, Issue 4
Energy landscapes: calculating pathways and rates
journal, January 2006
- Wales, David J.
- International Reviews in Physical Chemistry, Vol. 25, Issue 1-2
Mechanism of Voltage Gating in Potassium Channels
journal, April 2012
- Jensen, M. O.; Jogini, V.; Borhani, D. W.
- Science, Vol. 336, Issue 6078
Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides
journal, April 2012
- Seo, Mikyung; Rauscher, Sarah; Pomès, Régis
- Journal of Chemical Theory and Computation, Vol. 8, Issue 5
Insights into Aβ Aggregation: A Molecular Dynamics Perspective
journal, March 2013
- Shea, Joan-Emma; Urbanc, Brigita
- Current Topics in Medicinal Chemistry, Vol. 12, Issue 22
Probabilistic Local Features in Uncertain Vector Fields with Spatial Correlation
journal, June 2012
- Petz, Christoph; Pöthkow, Kai; Hege, Hans-Christian
- Computer Graphics Forum, Vol. 31, Issue 3pt2
Structure of a complex of the ATPase SecA and the protein-translocation channel
journal, October 2008
- Zimmer, Jochen; Nam, Yunsun; Rapoport, Tom A.
- Nature, Vol. 455, Issue 7215
Wild type and mutants of the HET-s(218-289) prion show different flexibility at fibrillar ends: a simulation study
text, January 2014
- Friedman, Ran; Caflisch, Amedeo
- Wiley-Blackwell
Energy landscapes for diffusion: Analysis of cage-breaking processes
journal, October 2008
- de Souza, Vanessa K.; Wales, David J.
- The Journal of Chemical Physics, Vol. 129, Issue 16
Single molecule unfolding and stretching of protein domains inside a solid-state nanopore by electric field
journal, April 2013
- Freedman, Kevin J.; Haq, S. Raza; Edel, Joshua B.
- Scientific Reports, Vol. 3, Issue 1
Effect of ivermectin on γ-aminobutyric acid-induced chloride currents in mouse hippocampal embryonic neurones
journal, July 1994
- Kru˚šek, Jan; Zemkova´, Hana
- European Journal of Pharmacology, Vol. 259, Issue 2
Repetitive Pulling Catalyzes Co-translocational Unfolding of Barnase During Import Through a Mitochondrial Pore
journal, July 2005
- Tian, Pu; Andricioaei, Ioan
- Journal of Molecular Biology, Vol. 350, Issue 5
Dynamics of SecY Translocons with Translocation-Defective Mutations
journal, July 2010
- Bondar, Ana-Nicoleta; del Val, Coral; Freites, J. Alfredo
- Structure, Vol. 18, Issue 7
The energy landscape as a unifying theme in molecular science
journal, December 2004
- Wales, David J.
- Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 363, Issue 1827
Tuning voltage-gated channel activity and cellular excitability with a sphingomyelinase
journal, September 2013
- Combs, David J.; Shin, Hyeon-Gyu; Xu, Yanping
- The Journal of General Physiology, Vol. 142, Issue 4
Probing the Effects of Membrane Cholesterol in the Torpedo californica Acetylcholine Receptor and the Novel Lipid-exposed Mutation αC418W in Xenopus Oocytes
journal, September 2001
- Santiago, John; Guzmán, Gisila R.; Rojas, Legier V.
- Journal of Biological Chemistry, Vol. 276, Issue 49
Thermodynamics and Kinetics of Aggregation for the GNNQQNY Peptide
journal, December 2007
- Strodel, Birgit; Whittleston, Chris S.; Wales, David J.
- Journal of the American Chemical Society, Vol. 129, Issue 51
How Translocons Select Transmembrane Helices
journal, June 2008
- White, Stephen H.; von Heijne, Gunnar
- Annual Review of Biophysics, Vol. 37, Issue 1
Membrane Simulations of OpcA: Gating in the Loops?
journal, January 2007
- Bond, Peter J.; Derrick, Jeremy P.; Sansom, Mark S. P.
- Biophysical Journal, Vol. 92, Issue 2
Effect of local anaesthetics on steroid-nicotinic acetylcholine receptor interactions in native membranes of Torpedo marmorata electric organ
journal, September 1990
- Arias, H. R.; Sankaram, M. B.; Marsh, D.
- Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1027, Issue 3
Cholesterol and the Golgi apparatus
journal, September 1993
- Bretscher, M.; Munro, S.
- Science, Vol. 261, Issue 5126
Determination of RNA Orientation during Translocation through a Biological Nanopore
journal, January 2006
- Butler, Tom Z.; Gundlach, Jens H.; Troll, Mark A.
- Biophysical Journal, Vol. 90, Issue 1
Cytochrome Display on Amyloid Fibrils
journal, February 2006
- Baldwin, Andrew J.; Bader, Reto; Christodoulou, John
- Journal of the American Chemical Society, Vol. 128, Issue 7
Membrane Insertion of a Potassium-Channel Voltage Sensor
journal, March 2005
- Hessa, T.
- Science, Vol. 307, Issue 5714
The Alzheimer β-peptide shows temperature-dependent transitions between left-handed 31-helix, β-strand and random coil secondary structures: Structural transitions of Alzheimer β-peptide
journal, July 2005
- Danielsson, Jens; Jarvet, Jüri; Damberg, Peter
- FEBS Journal, Vol. 272, Issue 15
A? Oligomers ? a decade of discovery
journal, June 2007
- Walsh, Dominic M.; Selkoe, Dennis J.
- Journal of Neurochemistry, Vol. 101, Issue 5
The Role of Molecular Simulations in the Development of Inhibitors of Amyloid β-Peptide Aggregation for the Treatment of Alzheimer’s Disease
journal, April 2012
- Lemkul, Justin A.; Bevan, David R.
- ACS Chemical Neuroscience, Vol. 3, Issue 11
Cholesterol effects on nicotinic acetylcholine receptor
journal, November 2007
- Barrantes, Francisco J.
- Journal of Neurochemistry, Vol. 103, Issue s1
Structure of the transmembrane region of the M2 protein H+ channel
journal, November 2001
- Wang, Junfeng; Kim, Sanguk; Kovacs, Frank
- Protein Science, Vol. 10, Issue 11
Structural analysis of a rhomboid family intramembrane protease reveals a gating mechanism for substrate entry
journal, November 2006
- Wu, Zhuoru; Yan, Nieng; Feng, Liang
- Nature Structural & Molecular Biology, Vol. 13, Issue 12
G protein-coupled receptors: novel targets for drug discovery in cancer
journal, December 2010
- Lappano, Rosamaria; Maggiolini, Marcello
- Nature Reviews Drug Discovery, Vol. 10, Issue 1
Halothane-induced changes in acetylcholine receptor channel kinetics are attenuated by cholesterol
journal, April 1986
- Lechleiter, James; Wells, Michael; Gruener, Raphael
- Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 856, Issue 3
Simulation of activation free energies in molecular systems
journal, August 1996
- Neria, Eyal; Fischer, Stefan; Karplus, Martin
- The Journal of Chemical Physics, Vol. 105, Issue 5
Molecular Interactions of Alzheimer's Aβ Protofilaments with Lipid Membranes
journal, August 2012
- Tofoleanu, Florentina; Buchete, Nicolae-Viorel
- Journal of Molecular Biology, Vol. 421, Issue 4-5
Crystal structure of a rhomboid family intramembrane protease
journal, October 2006
- Wang, Yongcheng; Zhang, Yingjiu; Ha, Ya
- Nature, Vol. 444, Issue 7116
Structure-Guided Design of AMP Mimics That Inhibit Fructose-1,6-bisphosphatase with High Affinity and Specificity
journal, December 2007
- Erion, Mark D.; Dang, Qun; Reddy, M. Rami
- Journal of the American Chemical Society, Vol. 129, Issue 50
Growth of β2-microglobulin-related amyloid fibrils by non-esterified fatty acids at a neutral pH
journal, November 2008
- Hasegawa, Kazuhiro; Tsutsumi-Yasuhara, Shinobu; Ookoshi, Tadakazu
- Biochemical Journal, Vol. 416, Issue 2
Voltage-gated ion channel modulation by lipids: Insights from molecular dynamics simulations
journal, May 2014
- Kasimova, Marina A.; Tarek, Mounir; Shaytan, Alexey K.
- Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1838, Issue 5
Free Energy Calculations on the Two Drug Binding Sites in the M2 Proton Channel
journal, July 2011
- Gu, Ruo-Xu; Liu, Limin Angela; Wei, Dong-Qing
- Journal of the American Chemical Society, Vol. 133, Issue 28
Two pools of cholesterol in acetylcholine receptor-rich membranes from Torpedo
journal, February 1987
- Leibel, Wayne S.; Firestone, Leonard L.; Legler, Dwight C.
- Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 897, Issue 2
Imaging α-Hemolysin with Molecular Dynamics: Ionic Conductance, Osmotic Permeability, and the Electrostatic Potential Map
journal, June 2005
- Aksimentiev, Aleksij; Schulten, Klaus
- Biophysical Journal, Vol. 88, Issue 6
Interactive Extraction and Tracking of Biomolecular Surface Features
journal, June 2013
- Krone, M.; Reina, G.; Schulz, C.
- Computer Graphics Forum, Vol. 32, Issue 3pt3
Computational models for the prediction of polypeptide aggregation propensity
journal, October 2006
- Caflisch, A.
- Current Opinion in Chemical Biology, Vol. 10, Issue 5
Mechanism of potassium-channel selectivity revealed by Na+ and Li+ binding sites within the KcsA pore
journal, November 2009
- Thompson, Ameer N.; Kim, Ilsoo; Panosian, Timothy D.
- Nature Structural & Molecular Biology, Vol. 16, Issue 12
Effective energy function for proteins in lipid membranes
journal, June 2003
- Lazaridis, Themis
- Proteins: Structure, Function, and Genetics, Vol. 52, Issue 2
Dual Effect of Phosphatidyl (4,5)-Bisphosphate PIP 2 on Shaker K + Channels
journal, August 2012
- Abderemane-Ali, Fayal; Es-Salah-Lamoureux, Zeineb; Delemotte, Lucie
- Journal of Biological Chemistry, Vol. 287, Issue 43
Coupling of Retinal, Protein, and Water Dynamics in Squid Rhodopsin
journal, October 2010
- Jardón-Valadez, Eduardo; Bondar, Ana-Nicoleta; Tobias, Douglas J.
- Biophysical Journal, Vol. 99, Issue 7
Embedding Aβ42 in Heterogeneous Membranes Depends on Cholesterol Asymmetries
journal, August 2013
- Liguori, Nicoletta; Nerenberg, Paul S.; Head-Gordon, Teresa
- Biophysical Journal, Vol. 105, Issue 4
Force distributions in a triangular lattice of rigid bars
text, January 2005
- Tighe, Brian P.; Socolar, Joshua E. S.; Schaeffer, David G.
- arXiv
Crystal Structure of the Human K2P TRAAK, a Lipid- and Mechano-Sensitive K+ Ion Channel
journal, January 2012
- Brohawn, S. G.; del Marmol, J.; MacKinnon, R.
- Science, Vol. 335, Issue 6067
Crystal Structure of a Mammalian Voltage-Dependent Shaker Family K+ Channel
journal, August 2005
- Long, S. B.
- Science, Vol. 309, Issue 5736
The importance of solvation in the design of ligands targeting membrane proteins
journal, January 2011
- González, Angel; Murcia, Marta; Benhamú, Bellinda
- MedChemComm, Vol. 2, Issue 3
The force network ensemble for granular packings
journal, January 2010
- Tighe, Brian P.; Snoeijer, Jacco H.; Vlugt, Thijs J. H.
- Soft Matter, Vol. 6, Issue 13
Principles of activation and permeation in an anion-selective Cys-loop receptor
journal, May 2011
- Hibbs, Ryan E.; Gouaux, Eric
- Nature, Vol. 474, Issue 7349
Rigorous Free Energy Calculations in Structure-Based Drug Design
journal, July 2010
- Michel , Julien; Foloppe, Nicolas; Essex, Jonathan W.
- Molecular Informatics, Vol. 29, Issue 8-9
Alzheimer Aβ peptide interactions with lipid membranes: Fibrils, oligomers and polymorphic amyloid channels
journal, September 2012
- Tofoleanu, Florentina; Buchete, Nicolae-Viorel
- Prion, Vol. 6, Issue 4
Fibril elongation mechanisms of HET-s prion-forming domain: Topological evidence for growth polarity
journal, August 2011
- Baiesi, Marco; Seno, Flavio; Trovato, Antonio
- Proteins: Structure, Function, and Bioinformatics, Vol. 79, Issue 11
Characterization of the outer membrane protein OprF of Pseudomonas aeruginosa in a lipopolysaccharide membrane by computer simulation
journal, February 2009
- Straatsma, T. P.; Soares, T. A.
- Proteins: Structure, Function, and Bioinformatics, Vol. 74, Issue 2
Jamming, Yielding, and Rheology of Weakly Vibrated Granular Media
journal, September 2011
- Dijksman, Joshua A.; Wortel, Geert H.; van Dellen, Louwrens T. H.
- Physical Review Letters, Vol. 107, Issue 10
Structural mechanism of C-type inactivation in K+ channels
journal, July 2010
- Cuello, Luis G.; Jogini, Vishwanath; Cortes, D. Marien
- Nature, Vol. 466, Issue 7303
Deciphering ionic current signatures of DNA transport through a nanopore
journal, January 2010
- Aksimentiev, Aleksei
- Nanoscale, Vol. 2, Issue 4
Spontaneous diabetes mellitus in transgenic mice expressing human islet amyloid polypeptide.
journal, July 1996
- Janson, J.; Soeller, W. C.; Roche, P. C.
- Proceedings of the National Academy of Sciences, Vol. 93, Issue 14
The Role of L1 Loop in the Mechanism of Rhomboid Intramembrane Protease GlpG
journal, December 2007
- Wang, Yongcheng; Maegawa, Saki; Akiyama, Yoshinori
- Journal of Molecular Biology, Vol. 374, Issue 4
Perspectives on: Ion selectivity
journal, April 2011
- Andersen, Olaf S.
- The Journal of General Physiology, Vol. 137, Issue 5
A Specific Cholesterol Binding Site Is Established by the 2.8 Å Structure of the Human β2-Adrenergic Receptor
journal, June 2008
- Hanson, Michael A.; Cherezov, Vadim; Griffith, Mark T.
- Structure, Vol. 16, Issue 6
Ion conduction and conformational flexibility of a bacterial voltage-gated sodium channel
journal, February 2014
- Boiteux, Céline; Vorobyov, Igor; Allen, Toby W.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 9
The free energy landscape and dynamics of met-enkephalin
journal, November 2003
- Evans, David A.; Wales, David J.
- The Journal of Chemical Physics, Vol. 119, Issue 18
Statistical Mechanical Theory of Transport Processes. VII. The Coefficient of Thermal Conductivity of Monatomic Liquids
journal, May 1954
- Zwanzig, Robert W.; Kirkwood, John G.; Oppenheim, Irwin
- The Journal of Chemical Physics, Vol. 22, Issue 5
Negative Conductance Caused by Entry of Sodium and Cesium Ions into the Potassium Channels of Squid Axons
journal, November 1972
- Bezanilla, F.
- The Journal of General Physiology, Vol. 60, Issue 5
Hydrogen bond dynamics in membrane protein function
journal, April 2012
- Bondar, Ana-Nicoleta; White, Stephen H.
- Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1818, Issue 4
Optimization of Receptor-G Protein Coupling by Bilayer Lipid Composition I: KINETICS OF RHODOPSIN-TRANSDUCIN BINDING
journal, September 2001
- Mitchell, Drake C.; Niu, Shui-Lin; Litman, Burton J.
- Journal of Biological Chemistry, Vol. 276, Issue 46
Critical Scaling and Aging in Cooling Systems Near the Jamming Transition
journal, April 2009
- Head, David A.
- Physical Review Letters, Vol. 102, Issue 13
Lipids revert inert Aβ amyloid fibrils to neurotoxic protofibrils that affect learning in mice
journal, December 2007
- Martins, Ivo Cristiano; Kuperstein, Inna; Wilkinson, Hannah
- The EMBO Journal, Vol. 27, Issue 1
Soluble Protofibrils as Metastable Intermediates in Simulations of Amyloid Fibril Degradation Induced by Lipid Vesicles
text, January 2010
- Friedman, R.; Pellarin, R.; Caflisch, A.
- American Chemical Society
On the selective ion binding hypothesis for potassium channels
journal, October 2011
- Kim, I.; Allen, T. W.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 44
Soluble Protofibrils as Metastable Intermediates in Simulations of Amyloid Fibril Degradation Induced by Lipid Vesicles
journal, December 2009
- Friedman, Ran; Pellarin, Riccardo; Caflisch, Amedeo
- The Journal of Physical Chemistry Letters, Vol. 1, Issue 2
Uncovering the intimate relationship between lipids, cholesterol and GPCR activation
journal, December 2011
- Oates, Joanne; Watts, Anthony
- Current Opinion in Structural Biology, Vol. 21, Issue 6
Jamming, Yielding and Rheology of Weakly Vibrated Granular Media
text, January 2011
- Dijksman, J. A.; Wortel, G. H.; van Dellen, L. T. H.
- arXiv
Regulation of receptor function by cholesterol
journal, October 2000
- Burger, K.; Gimpl, G.; Fahrenholz, F.
- Cellular and Molecular Life Sciences, Vol. 57, Issue 11
Amyloid Aggregation on Lipid Bilayers and Its Impact on Membrane Permeability
journal, March 2009
- Friedman, Ran; Pellarin, Riccardo; Caflisch, Amedeo
- Journal of Molecular Biology, Vol. 387, Issue 2
Conformational transition of Sec machinery inferred from bacterial SecYE structures
journal, October 2008
- Tsukazaki, Tomoya; Mori, Hiroyuki; Fukai, Shuya
- Nature, Vol. 455, Issue 7215
Endogenous neurosteroids regulate GABAA receptors through two discrete transmembrane sites
journal, November 2006
- Hosie, Alastair M.; Wilkins, Megan E.; da Silva, Helena M. A.
- Nature, Vol. 444, Issue 7118
Lipid-Dependent GPCR Dimerization
book, October 2013
- Goddard, Alan D.; Dijkman, Patricia M.; Adamson, Roslin J.
- Methods in Cell Biology
The crystal structure of a voltage-gated sodium channel
journal, July 2011
- Payandeh, Jian; Scheuer, Todd; Zheng, Ning
- Nature, Vol. 475, Issue 7356
Origins of ion selectivity in potassium channels from the perspective of channel block
journal, April 2011
- Nimigean, Crina M.; Allen, Toby W.
- The Journal of General Physiology, Vol. 137, Issue 5
Helix Self-Assembly from Anisotropic Molecules
journal, August 2007
- Fejer, Szilard N.; Wales, David J.
- Physical Review Letters, Vol. 99, Issue 8
Discrete Ba2+ block as a probe of ion occupancy and pore structure in the high-conductance Ca2+ -activated K+ channel.
journal, November 1988
- Neyton, J.; Miller, C.
- The Journal of General Physiology, Vol. 92, Issue 5
Ensemble Theory for Force Networks in Hyperstatic Granular Matter
text, January 2004
- Snoeijer, Jacco H.; Vlugt, Thijs J. H.; Ellenbroek, Wouter G.
- arXiv
Coarse-Grained Biomolecular Simulation with REACH: Realistic Extension Algorithm via Covariance Hessian
journal, November 2007
- Moritsugu, Kei; Smith, Jeremy C.
- Biophysical Journal, Vol. 93, Issue 10
Increased membrane cholesterol reduces the potentiation of GABAA currents by neurosteroids in dissociated hippocampal neurones
journal, September 1998
- Sooksawate, T.; Simmonds, M. A.
- Neuropharmacology, Vol. 37, Issue 9
Molecular Dynamics and NMR Spectroscopy Studies of E. coli Lipopolysaccharide Structure and Dynamics
journal, September 2013
- Wu, Emilia L.; Engström, Olof; Jo, Sunhwan
- Biophysical Journal, Vol. 105, Issue 6
Lipid-protein interactions in reconstituted membranes containing acetylcholine receptor
journal, November 1983
- Ellena, Jeffrey F.; Blazing, Michael A.; McNamee, Mark G.
- Biochemistry, Vol. 22, Issue 24
Structure of the amantadine binding site of influenza M2 proton channels in lipid bilayers
journal, February 2010
- Cady, Sarah D.; Schmidt-Rohr, Klaus; Wang, Jun
- Nature, Vol. 463, Issue 7281
Reduced Lateral Mobility of Lipids and Proteins in Crowded Membranes
journal, April 2013
- Goose, Joseph E.; Sansom, Mark S. P.
- PLoS Computational Biology, Vol. 9, Issue 4
Lipids as Modulators of Proteolytic Activity of BACE: INVOLVEMENT OF CHOLESTEROL, GLYCOSPHINGOLIPIDS, AND ANIONIC PHOSPHOLIPIDS IN VITRO
journal, August 2005
- Kalvodova, Lucie; Kahya, Nicoletta; Schwille, Petra
- Journal of Biological Chemistry, Vol. 280, Issue 44
Visual Analysis of Dynamic Protein Cavities and Binding Sites
conference, March 2014
- Krone, Michael; Kauker, Daniel; Reina, Guido
- 2014 IEEE Pacific Visualization Symposium (PacificVis)
Proteolysis inside the Membrane Is a Rate-Governed Reaction Not Driven by Substrate Affinity
journal, December 2013
- Dickey, Seth W.; Baker, Rosanna P.; Cho, Sangwoo
- Cell, Vol. 155, Issue 6
Curvature, Lipid Packing, and Electrostatics of Membrane Organelles: Defining Cellular Territories in Determining Specificity
journal, November 2012
- Bigay, Joëlle; Antonny, Bruno
- Developmental Cell, Vol. 23, Issue 5
The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations
journal, July 2007
- Marrink, Siewert J.; Risselada, H. Jelger; Yefimov, Serge
- The Journal of Physical Chemistry B, Vol. 111, Issue 27
Calculation of Relative Binding Free Energy Differences for Fructose 1,6-Bisphosphatase Inhibitors Using the Thermodynamic Cycle Perturbation Approach
journal, July 2001
- Reddy, M. Rami; Erion, Mark D.
- Journal of the American Chemical Society, Vol. 123, Issue 26
The rhomboid protease family: a decade of progress on function and mechanism
journal, January 2011
- Urban, Sinisa; Dickey, Seth W.
- Genome Biology, Vol. 12, Issue 10
Structural basis for lipid modulation of nicotinic acetylcholine receptor function
journal, December 2004
- Barrantes, F. J.
- Brain Research Reviews, Vol. 47, Issue 1-3
Free Energy Calculations Reveal the Origin of Binding Preference for Aminoadamantane Blockers of Influenza A/M2TM Pore
journal, December 2012
- Gkeka, Paraskevi; Eleftheratos, Stelios; Kolocouris, Antonios
- Journal of Chemical Theory and Computation, Vol. 9, Issue 2
Dynamic channels in biomolecular systems: Path analysis and visualization
conference, October 2012
- Lindow, Norbert; Baum, Daniel; Bondar, Ana-Nicoleta
- 2012 IEEE Symposium on Biological Data Visualization (BioVis)
Potential role of caveolin-1-positive domains in the regulation of the acetylcholine receptor's activable pool: Implications in the pathogenesis of a novel congenital myasthenic syndrome
journal, May 2008
- Baez, Carlos; Martinez-Ortiz, Yaiza; Otero-Cruz, Jose D.
- Channels, Vol. 2, Issue 3
Reconstitution of acetylcholine receptor from Torpedo californica with highly purified phospholipids: Effect of α-tocopherol, phylloquinone, and other terpenoid quinones
journal, March 1980
- Kilian, Patricia L.; Dunlap, Carolyn R.; Mueller, Paul
- Biochemical and Biophysical Research Communications, Vol. 93, Issue 2
Electrophysiological evidence for heptameric stoichiometry of ion channels formed by Staphylococcus aureus alpha-toxin in planar lipid bilayers
journal, September 2000
- Krasilnikov, Oleg V.; Merzlyak, Petr G.; Yuldasheva, Liliya N.
- Molecular Microbiology, Vol. 37, Issue 6
Structural basis of PIP2 activation of the classical inward rectifier K+ channel Kir2.2
journal, August 2011
- Hansen, Scott B.; Tao, Xiao; MacKinnon, Roderick
- Nature, Vol. 477, Issue 7365
Computational approaches to molecular recognition
journal, December 1997
- Lamb, Michelle L.; Jorgensen, William L.
- Current Opinion in Chemical Biology, Vol. 1, Issue 4
In Silico Partitioning and Transmembrane Insertion of Hydrophobic Peptides under Equilibrium Conditions
journal, October 2011
- Ulmschneider, Jakob P.; Smith, Jeremy C.; White, Stephen H.
- Journal of the American Chemical Society, Vol. 133, Issue 39
Experimentally determined hydrophobicity scale for proteins at membrane interfaces
journal, October 1996
- Wimley, William C.; White, Stephen H.
- Nature Structural & Molecular Biology, Vol. 3, Issue 10
Enzymatic analysis of a rhomboid intramembrane protease implicates transmembrane helix 5 as the lateral substrate gate
journal, April 2007
- Baker, R. P.; Young, K.; Feng, L.
- Proceedings of the National Academy of Sciences, Vol. 104, Issue 20
Catalysis of Na+ permeation in the bacterial sodium channel NaVAb
journal, June 2013
- Chakrabarti, N.; Ing, C.; Payandeh, J.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 28
Slowing down single-molecule trafficking through a protein nanopore reveals intermediates for peptide translocation
journal, January 2014
- Mereuta, Loredana; Roy, Mahua; Asandei, Alina
- Scientific Reports, Vol. 4, Issue 1
Membrane permeabilization by Islet Amyloid Polypeptide
journal, July 2009
- Engel, Maarten F. M.
- Chemistry and Physics of Lipids, Vol. 160, Issue 1
Impaired Processing of Human Pro-Islet Amyloid Polypeptide Is Not a Causative Factor for Fibril Formation or Membrane Damage in Vitro
journal, November 2009
- Khemtémourian, Lucie; Lahoz Casarramona, Gemma; Suylen, Dennis P. L.
- Biochemistry, Vol. 48, Issue 46
Rhodopsin Exhibits a Preference for Solvation by Polyunsaturated Docosohexaenoic Acid
journal, April 2003
- Feller, Scott E.; Gawrisch, Klaus; Woolf, Thomas B.
- Journal of the American Chemical Society, Vol. 125, Issue 15
Visualizing dynamic molecular conformations
conference, January 2002
- Schmidt-Ehrenberg, J.; Baum, D.; Hege, H. -C.
- VIS2002. IEEE Visualization 2002., IEEE Visualization, 2002. VIS 2002.
Simulations of rigid bodies in an angle-axis framework
journal, January 2009
- Chakrabarti, Dwaipayan; Wales, David J.
- Physical Chemistry Chemical Physics, Vol. 11, Issue 12
The effect of cholesterol on agonist-induced flux in reconstituted acetylcholine receptor vesicles
journal, December 1980
- Dalziel, A. W.; Rollins, E. S.; McNamee, M. G.
- FEBS Letters, Vol. 122, Issue 2
Excursion of a single polypeptide into a protein pore: simple physics, but complicated biology
journal, March 2008
- Mohammad, Mohammad M.; Movileanu, Liviu
- European Biophysics Journal, Vol. 37, Issue 6
Phospholipid chain immobilization and steriod rotational immobilization in acetylcholine receptor-rich membranes from torpedo marmorata
journal, June 1981
- Marsh, D.; Watts, A.; Barrantes, F. J.
- Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 645, Issue 1
Solubilisation of the ?-Aminobutyric Acid/Benzodiazepine Receptor from Rat Cerebellum: Optimal Preservation of the Modulatory Responses by Natural Brain Lipids
journal, November 1987
- Bristow, David R.; Martin, Ian L.
- Journal of Neurochemistry, Vol. 49, Issue 5
Molecular basis of voltage gating of OmpF porin
journal, October 2002
- Robertson, Kindal M.; Tieleman, D. Peter
- Biochemistry and Cell Biology, Vol. 80, Issue 5
Diffusible, nonfibrillar ligands derived from A 1-42 are potent central nervous system neurotoxins
journal, May 1998
- Lambert, M. P.; Barlow, A. K.; Chromy, B. A.
- Proceedings of the National Academy of Sciences, Vol. 95, Issue 11
Stability and membrane interactions of an autotransport protein: MD simulations of the Hia translocator domain in a complex membrane environment
journal, February 2013
- Holdbrook, Daniel A.; Piggot, Thomas J.; Sansom, Mark S. P.
- Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1828, Issue 2
Channelopathies linked to plasma membrane phosphoinositides
journal, April 2010
- Logothetis, Diomedes E.; Petrou, Vasileios I.; Adney, Scott K.
- Pflügers Archiv - European Journal of Physiology, Vol. 460, Issue 2
Exploring cavity dynamics in biomolecular systems
journal, November 2013
- Lindow, Norbert; Baum, Daniel; Bondar, Ana-Nicoleta
- BMC Bioinformatics, Vol. 14, Issue S19
Influence of the membrane potential on the free energy of an intrinsic protein
journal, December 1997
- Roux, B.
- Biophysical Journal, Vol. 73, Issue 6
Unfolding of Proteins and Long Transient Conformations Detected by Single Nanopore Recording
journal, April 2007
- Oukhaled, G.; Mathé, J.; Biance, A. -L.
- Physical Review Letters, Vol. 98, Issue 15
PIP 2 Is a Necessary Cofactor for Ion Channel Function: How and Why?
journal, June 2008
- Suh, Byung-Chang; Hille, Bertil
- Annual Review of Biophysics, Vol. 37, Issue 1
Architectural and thermodynamic principles underlying intramembrane protease function
journal, July 2012
- Baker, Rosanna P.; Urban, Sinisa
- Nature Chemical Biology, Vol. 8, Issue 9
Rhomboid Protease Dynamics and Lipid Interactions
journal, March 2009
- Bondar, Ana-Nicoleta; del Val, Coral; White, Stephen H.
- Structure, Vol. 17, Issue 3
Neurosteroids: endogenous regulators of the GABAA receptor
journal, June 2005
- Belelli, Delia; Lambert, Jeremy J.
- Nature Reviews Neuroscience, Vol. 6, Issue 7
Structural basis for the function and inhibition of an influenza virus proton channel
journal, January 2008
- Stouffer, Amanda L.; Acharya, Rudresh; Salom, David
- Nature, Vol. 451, Issue 7178
Modulation of Alzheimer’s Aβ Protofilament-Membrane Interactions by Lipid Headgroups
journal, January 2015
- Tofoleanu, Florentina; Brooks, Bernard R.; Buchete, Nicolae-Viorel
- ACS Chemical Neuroscience, Vol. 6, Issue 3
Thermal Unfolding of Proteins Probed at the Single Molecule Level Using Nanopores
journal, April 2012
- Payet, Linda; Martinho, Marlène; Pastoriza-Gallego, Manuela
- Analytical Chemistry, Vol. 84, Issue 9
PIP2 controls voltage-sensor movement and pore opening of Kv channels through the S4-S5 linker
journal, August 2012
- Rodriguez-Menchaca, A. A.; Adney, S. K.; Tang, Q. -Y.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 36
Role of Cholesterol and Polyunsaturated Chains in Lipid−Protein Interactions: Molecular Dynamics Simulation of Rhodopsin in a Realistic Membrane Environment
journal, April 2005
- Pitman, Michael C.; Grossfield, Alan; Suits, Frank
- Journal of the American Chemical Society, Vol. 127, Issue 13
Reconstitution of acetylcholine receptor function in lipid vesicles of defined composition
journal, January 1983
- Ochoa, Enrique L. M.; Dalziel, Adam W.; McNamee, Mark G.
- Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 727, Issue 1
A Predicted Binding Site for Cholesterol on the GABAA Receptor
journal, May 2014
- Hénin, Jérôme; Salari, Reza; Murlidaran, Sruthi
- Biophysical Journal, Vol. 106, Issue 9
Dynamics of Unfolded Protein Transport through an Aerolysin Pore
journal, March 2011
- Pastoriza-Gallego, Manuela; Rabah, Leila; Gibrat, Gabriel
- Journal of the American Chemical Society, Vol. 133, Issue 9
Coarse-Grained Models for Protein Folding and Aggregation
book, January 2012
- Derreumaux, Philippe
- Methods in Molecular Biology
Critical Scaling of Shear Viscosity at the Jamming Transition
journal, October 2007
- Olsson, Peter; Teitel, S.
- Physical Review Letters, Vol. 99, Issue 17
The crystal structure of the rhomboid peptidase from Haemophilus influenzae provides insight into intramembrane proteolysis
journal, January 2007
- Lemieux, M. Joanne; Fischer, Sarah J.; Cherney, Maia M.
- Proceedings of the National Academy of Sciences, Vol. 104, Issue 3
Disaccharides Impact the Lateral Organization of Lipid Membranes
journal, November 2014
- Moiset, Gemma; López, Cesar A.; Bartelds, Rianne
- Journal of the American Chemical Society, Vol. 136, Issue 46
Structure of Rhomboid Protease in a Lipid Environment
journal, March 2011
- Vinothkumar, Kutti R.
- Journal of Molecular Biology, Vol. 407, Issue 2
Transmembrane Structures for Alzheimer’s Aβ 1−42 Oligomers
journal, September 2010
- Strodel, Birgit; Lee, Jason W. L.; Whittleston, Christopher S.
- Journal of the American Chemical Society, Vol. 132, Issue 38
Initial Response of the Potassium Channel Voltage Sensor to a Transmembrane Potential
journal, February 2009
- Treptow, Werner; Tarek, Mounir; Klein, Michael L.
- Journal of the American Chemical Society, Vol. 131, Issue 6
Jamming Transition as Probed by Quasistatic Shear Flow
journal, May 2009
- Heussinger, Claus; Barrat, Jean-Louis
- Physical Review Letters, Vol. 102, Issue 21
Virtual Screening in Drug Discovery - A Computational Perspective
journal, August 2007
- Reddy, A. Srinivas; Pati, S. Priyadarshini; Kumar, P. Praveen
- Current Protein & Peptide Science, Vol. 8, Issue 4, p. 329-351
Inhibition of peptide aggregation by lipids: Insights from coarse-grained molecular simulations
journal, February 2011
- Hung, Andrew; Yarovsky, Irene
- Journal of Molecular Graphics and Modelling, Vol. 29, Issue 5
Removal of phospho-head groups of membrane lipids immobilizes voltage sensors of K+ channels
journal, February 2008
- Xu, Yanping; Ramu, Yajamana; Lu, Zhe
- Nature, Vol. 451, Issue 7180
Wild type and mutants of the HET-s(218-289) prion show different flexibility at fibrillar ends: A simulation study: Wild Type and Mutants of HET-s(218-289)
journal, October 2013
- Friedman, Ran; Caflisch, Amedeo
- Proteins: Structure, Function, and Bioinformatics, Vol. 82, Issue 3
Evolutionary imprint of activation: The design principles of VSDs
journal, January 2014
- Palovcak, Eugene; Delemotte, Lucie; Klein, Michael L.
- The Journal of General Physiology, Vol. 143, Issue 2
Open-cap conformation of intramembrane protease GlpG
journal, February 2007
- Wang, Y.; Ha, Y.
- Proceedings of the National Academy of Sciences, Vol. 104, Issue 7
Quantitative Modeling of Membrane Deformations by Multihelical Membrane Proteins: Application to G-Protein Coupled Receptors
journal, November 2011
- Mondal, Sayan; Khelashvili, George; Shan, Jufang
- Biophysical Journal, Vol. 101, Issue 9
Mechanism and Kinetics of Peptide Partitioning into Membranes from All-Atom Simulations of Thermostable Peptides
journal, March 2010
- Ulmschneider, Martin B.; Doux, Jacques P. F.; Killian, J. Antoinette
- Journal of the American Chemical Society, Vol. 132, Issue 10
Rearrangements of the water trimer
journal, January 1996
- Walsh, Tiffany R.; Wales, David J.
- Journal of the Chemical Society, Faraday Transactions, Vol. 92, Issue 14
Ensemble theory for force networks in hyperstatic granular matter
journal, December 2004
- Snoeijer, Jacco H.; Vlugt, Thijs J. H.; Ellenbroek, Wouter G.
- Physical Review E, Vol. 70, Issue 6
Atomistic Visualization of Mesoscopic Whole-Cell Simulations Using Ray-Casted Instancing: Visualization of Mesoscopic Whole-Cell Simulations
journal, August 2013
- Falk, Martin; Krone, Michael; Ertl, Thomas
- Computer Graphics Forum, Vol. 32, Issue 8
Domain Swapping in the Cytoplasmic Domain of the Escherichia coli Rhomboid Protease
journal, April 2013
- Lazareno-Saez, Christelle; Arutyunova, Elena; Coquelle, Nicolas
- Journal of Molecular Biology, Vol. 425, Issue 7
The structural basis for catalysis and substrate specificity of a rhomboid protease
journal, October 2010
- Vinothkumar, Kutti R.; Strisovsky, Kvido; Andreeva, Antonina
- The EMBO Journal, Vol. 29, Issue 22
Topography of Nicotinic Acetylcholine Receptor Membrane-embedded Domains
journal, August 2000
- Barrantes, Francisco J.; Antollini, Silvia S.; Blanton, Michael P.
- Journal of Biological Chemistry, Vol. 275, Issue 48
Voronoi-Based Extraction and Visualization of Molecular Paths
journal, December 2011
- Lindow, N.; Baum, D.; Hege, H-C
- IEEE Transactions on Visualization and Computer Graphics, Vol. 17, Issue 12
Aggregation of amyloids in a cellular context: modelling and experiment
journal, August 2011
- Friedman, Ran
- Biochemical Journal, Vol. 438, Issue 3
Identification of subunits of acetylcholine receptor that interact with a cholesterol photoaffinity probe
journal, March 1987
- Middlemas, David S.; Raftery, Michael A.
- Biochemistry, Vol. 26, Issue 5
Structure of Staphylococcal alpha -Hemolysin, a Heptameric Transmembrane Pore
journal, December 1996
- Song, L.; Hobaugh, M. R.; Shustak, C.
- Science, Vol. 274, Issue 5294
Phospholipids and the origin of cationic gating charges in voltage sensors
journal, November 2006
- Schmidt, Daniel; Jiang, Qiu-Xing; MacKinnon, Roderick
- Nature, Vol. 444, Issue 7120
Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands
journal, October 2004
- Noskov, Sergei Yu.; Bernèche, Simon; Roux, Benoît
- Nature, Vol. 431, Issue 7010
Omega Currents in Voltage-Gated Ion Channels: What Can We Learn from Uncovering the Voltage-Sensing Mechanism Using MD Simulations?
journal, January 2013
- Tarek, Mounir; Delemotte, Lucie
- Accounts of Chemical Research, Vol. 46, Issue 12
Embedded cholesterol in the nicotinic acetylcholine receptor
journal, September 2008
- Brannigan, G.; Henin, J.; Law, R.
- Proceedings of the National Academy of Sciences, Vol. 105, Issue 38
Ionic Current Blockades from DNA and RNA Molecules in the α-Hemolysin Nanopore
journal, November 2007
- Butler, Tom Z.; Gundlach, Jens H.; Troll, Mark
- Biophysical Journal, Vol. 93, Issue 9
A role for direct interactions in the modulation of rhodopsin by -3 polyunsaturated lipids
journal, March 2006
- Grossfield, A.; Feller, S. E.; Pitman, M. C.
- Proceedings of the National Academy of Sciences, Vol. 103, Issue 13
The calculation of the potential of mean force using computer simulations
journal, September 1995
- Roux, Benoît
- Computer Physics Communications, Vol. 91, Issue 1-3
Influence of membrane cholesterol on modulation of the GABA A receptor by neuroactive steroids and other potentiators
journal, November 2001
- Sooksawate, T.; Simmonds, M. A.
- British Journal of Pharmacology, Vol. 134, Issue 6
Specific Binding of Adamantane Drugs and Direction of Their Polar Amines in the Pore of the Influenza M2 Transmembrane Domain in Lipid Bilayers and Dodecylphosphocholine Micelles Determined by NMR Spectroscopy
journal, March 2011
- Cady, Sarah D.; Wang, Jun; Wu, Yibing
- Journal of the American Chemical Society, Vol. 133, Issue 12
Modeling and simulations of a bacterial outer membrane protein: OprF from Pseudomonas aeruginosa
journal, January 2006
- Khalid, Syma; Bond, Peter J.; Deol, Sundeep S.
- Proteins: Structure, Function, and Bioinformatics, Vol. 63, Issue 1
Predictions for Cholesterol Interaction Sites on the A2A Adenosine Receptor
journal, January 2013
- Lee, Ji Young; Lyman, Edward
- Biophysical Journal, Vol. 104, Issue 2
Force distributions in a triangular lattice of rigid bars
journal, September 2005
- Tighe, Brian P.; Socolar, Joshua E. S.; Schaeffer, David G.
- Physical Review E, Vol. 72, Issue 3
Energy landscapes: some new horizons
journal, February 2010
- Wales, David J.
- Current Opinion in Structural Biology, Vol. 20, Issue 1
Insights into Substrate Gating in H. influenzae Rhomboid
journal, April 2011
- Brooks, Cory L.; Lazareno-Saez, Christelle; Lamoureux, Jason S.
- Journal of Molecular Biology, Vol. 407, Issue 5
Energy landscapes of model polyalanines
journal, July 2002
- Mortenson, Paul N.; Evans, David A.; Wales, David J.
- The Journal of Chemical Physics, Vol. 117, Issue 3
Membrane fusion and vesicular transformation induced by Alzheimer's amyloid beta
journal, April 2013
- Vestergaard, Mun'delanji C.; Morita, Masamune; Hamada, Tsutomu
- Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1828, Issue 4
Intermediate states of the Kv1.2 voltage sensor from atomistic molecular dynamics simulations
journal, March 2011
- Delemotte, L.; Tarek, M.; Klein, M. L.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 15
Ion Channels as Therapeutic Targets: A Drug Discovery Perspective
journal, November 2012
- Bagal, Sharan K.; Brown, Alan D.; Cox, Peter J.
- Journal of Medicinal Chemistry, Vol. 56, Issue 3
Pore architecture and ion sites in acid-sensing ion channels and P2X receptors
journal, July 2009
- Gonzales, Eric B.; Kawate, Toshimitsu; Gouaux, Eric
- Nature, Vol. 460, Issue 7255
Binding Hot Spots and Amantadine Orientation in the Influenza A Virus M2 Proton Channel
journal, November 2009
- Chuang, Gwo-Yu; Kozakov, Dima; Brenke, Ryan
- Biophysical Journal, Vol. 97, Issue 10
Amantadine-induced conformational and dynamical changes of the influenza M2 transmembrane proton channel
journal, January 2008
- Cady, S. D.; Hong, M.
- Proceedings of the National Academy of Sciences, Vol. 105, Issue 5
Anomalous dynamics of forced translocation
journal, February 2004
- Kantor, Yacov; Kardar, Mehran
- Physical Review E, Vol. 69, Issue 2
Electroporation of the E. coli and S. Aureus Membranes: Molecular Dynamics Simulations of Complex Bacterial Membranes
journal, November 2011
- Piggot, Thomas J.; Holdbrook, Daniel A.; Khalid, Syma
- The Journal of Physical Chemistry B, Vol. 115, Issue 45
Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study
journal, September 2012
- Piggot, Thomas J.; Piñeiro, Ángel; Khalid, Syma
- Journal of Chemical Theory and Computation, Vol. 8, Issue 11
X-ray structures of AMPA receptor-cone snail toxin complexes illuminate activation mechanism
journal, August 2014
- Chen, L.; Durr, K. L.; Gouaux, E.
- Science, Vol. 345, Issue 6200
Modulation of rhodopsin function by properties of the membrane bilayer
journal, September 1994
- Brown, Michael F.
- Chemistry and Physics of Lipids, Vol. 73, Issue 1-2
Coexistence of two adamantane binding sites in the influenza A M2 ion channel
journal, July 2010
- Rosenberg, M. R.; Casarotto, M. G.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 31
Catalytic Mechanism of Rhomboid Protease GlpG Probed by 3,4-Dichloroisocoumarin and Diisopropyl Fluorophosphonate
journal, November 2011
- Xue, Yi; Ha, Ya
- Journal of Biological Chemistry, Vol. 287, Issue 5
Detecting protein analytes that modulate transmembrane movement of a polymer chain within a single protein pore
journal, October 2000
- Movileanu, Liviu; Howorka, Stefan; Braha, Orit
- Nature Biotechnology, Vol. 18, Issue 10
Oligomeric state study of prokaryotic rhomboid proteases
journal, December 2012
- Sampathkumar, Padmapriya; Mak, Michelle W.; Fischer-Witholt, Sarah J.
- Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1818, Issue 12
Membrane-Sensitive Conformational States of Helix 8 in the Metabotropic Glu2 Receptor, a Class C GPCR
journal, August 2012
- Bruno, Agostino; Costantino, Gabriele; de Fabritiis, Gianni
- PLoS ONE, Vol. 7, Issue 8
Environment of the Gating Charges in the Kv1.2 Shaker Potassium Channel
journal, May 2006
- Treptow, Werner; Tarek, Mounir
- Biophysical Journal, Vol. 90, Issue 9
Structures of KcsA in Complex with Symmetrical Quaternary Ammonium Compounds Reveal a Hydrophobic Binding Site
journal, August 2014
- Lenaeus, Michael J.; Burdette, Dylan; Wagner, Tobias
- Biochemistry, Vol. 53, Issue 32
Structural Basis for Allosteric Regulation of GPCRs by Sodium Ions
journal, July 2012
- Liu, W.; Chun, E.; Thompson, A. A.
- Science, Vol. 337, Issue 6091
Phosphoinositides regulate ion channels
journal, June 2015
- Hille, Bertil; Dickson, Eamonn J.; Kruse, Martin
- Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids, Vol. 1851, Issue 6
Interactions between Sec Complex and Prepro-α-Factor during Posttranslational Protein Transport into the Endoplasmic Reticulum
journal, January 2004
- Plath, Kathrin; Wilkinson, Barrie M.; Stirling, Colin J.
- Molecular Biology of the Cell, Vol. 15, Issue 1
Crystal structure of a voltage-gated sodium channel in two potentially inactivated states
journal, May 2012
- Payandeh, Jian; Gamal El-Din, Tamer M.; Scheuer, Todd
- Nature, Vol. 486, Issue 7401
Structural basis for intramembrane proteolysis by rhomboid serine proteases
journal, December 2006
- Ben-Shem, A.; Fass, D.; Bibi, E.
- Proceedings of the National Academy of Sciences, Vol. 104, Issue 2
The Structure of the Potassium Channel: Molecular Basis of K+ Conduction and Selectivity
journal, April 1998
- Doyle, D. A.
- Science, Vol. 280, Issue 5360
Amphipathic Lipid Packing Sensor Motifs: Probing Bilayer Defects with Hydrophobic Residues
journal, February 2013
- Vanni, Stefano; Vamparys, Lydie; Gautier, Romain
- Biophysical Journal, Vol. 104, Issue 3
Conical Lipids in Flat Bilayers Induce Packing Defects Similar to that Induced by Positive Curvature
journal, February 2013
- Vamparys, Lydie; Gautier, Romain; Vanni, Stefano
- Biophysical Journal, Vol. 104, Issue 3
Refined Structure of the Nicotinic Acetylcholine Receptor at 4Å Resolution
journal, March 2005
- Unwin, Nigel
- Journal of Molecular Biology, Vol. 346, Issue 4
Structural Characterization and Computer-Aided Optimization of a Small-Molecule Inhibitor of the Arp2/3 Complex, a Key Regulator of the Actin Cytoskeleton
journal, May 2012
- Baggett, Andrew W.; Cournia, Zoe; Han, Min Suk
- ChemMedChem, Vol. 7, Issue 7
Similarities between protein folding and granular jamming
journal, January 2012
- Jose, Prasanth P.; Andricioaei, Ioan
- Nature Communications, Vol. 3, Issue 1
On the Importance of Atomic Fluctuations, Protein Flexibility, and Solvent in Ion Permeation
journal, November 2004
- Allen, Toby W.; Andersen, O. S.; Roux, Benoit
- The Journal of General Physiology, Vol. 124, Issue 6
Theoretical study of the water tetramer
journal, May 1997
- Wales, David J.; Walsh, Tiffany R.
- The Journal of Chemical Physics, Vol. 106, Issue 17
Crystal structure of a heterotetrameric NMDA receptor ion channel
journal, May 2014
- Karakas, E.; Furukawa, H.
- Science, Vol. 344, Issue 6187
Acceleration of oligomerization, not fibrillization, is a shared property of both alpha -synuclein mutations linked to early-onset Parkinson's disease: Implications for pathogenesis and therapy
journal, January 2000
- Conway, K. A.; Lee, S. -J.; Rochet, J. -C.
- Proceedings of the National Academy of Sciences, Vol. 97, Issue 2
Protein Nanopore-Based, Single-Molecule Exploration of Copper Binding to an Antimicrobial-Derived, Histidine-Containing Chimera Peptide
journal, October 2012
- Mereuta, Loredana; Schiopu, Irina; Asandei, Alina
- Langmuir, Vol. 28, Issue 49
The Morphology of Decorated Amyloid Fibers is Controlled by the Conformation and Position of the Displayed Protein
journal, January 2012
- Forman, Christopher J.; Nickson, Adrian A.; Anthony-Cahill, Spencer J.
- ACS Nano, Vol. 6, Issue 2
X-ray structure of a protein-conducting channel
journal, December 2003
- Berg, Bert van den; Clemons, William M.; Collinson, Ian
- Nature, Vol. 427, Issue 6969
A partially folded structure of amyloid-beta(1–40) in an aqueous environment
journal, July 2011
- Vivekanandan, Subramanian; Brender, Jeffrey R.; Lee, Shirley Y.
- Biochemical and Biophysical Research Communications, Vol. 411, Issue 2
The Role of Lipids in the Function of the Acetylcholine Receptor
journal, January 1985
- Zabrecky, James R.; Raftery, Michael A.
- Journal of Receptor Research, Vol. 5, Issue 5-6
Crystal structure of the channelrhodopsin light-gated cation channel
journal, January 2012
- Kato, Hideaki E.; Zhang, Feng; Yizhar, Ofer
- Nature, Vol. 482, Issue 7385
A sub-nanometre view of how membrane curvature and composition modulate lipid packing and protein recruitment
journal, September 2014
- Vanni, Stefano; Hirose, Hisaaki; Barelli, Hélène
- Nature Communications, Vol. 5, Issue 1
Local Frustration Determines Molecular and Macroscopic Helix Structures
journal, May 2013
- Forman, Christopher J.; Fejer, Szilard N.; Chakrabarti, Dwaipayan
- The Journal of Physical Chemistry B, Vol. 117, Issue 26
Molecular Dynamics Simulations of Lipid Membrane Electroporation
journal, May 2012
- Delemotte, Lucie; Tarek, Mounir
- The Journal of Membrane Biology, Vol. 245, Issue 9
THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method
journal, October 1992
- Kumar, Shankar; Rosenberg, John M.; Bouzida, Djamal
- Journal of Computational Chemistry, Vol. 13, Issue 8
Functional reconstitution of the bovine brain GABAA receptor from solubilized components
journal, March 1989
- Dunn, Susan M. J.; Martin, Colleen R.; Agey, Michael W.
- Biochemistry, Vol. 28, Issue 6
Surfactant Effects on Amyloid Aggregation Kinetics
journal, November 2011
- Friedman, Ran; Caflisch, Amedeo
- Journal of Molecular Biology, Vol. 414, Issue 2
Finite-size scaling at the jamming transition: Corrections to scaling and the correlation-length critical exponent
journal, March 2011
- Vågberg, Daniel; Valdez-Balderas, Daniel; Moore, M. A.
- Physical Review E, Vol. 83, Issue 3
Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes
journal, November 2007
- Rapoport, Tom A.
- Nature, Vol. 450, Issue 7170
Conformational Change in Rhomboid Protease GlpG Induced by Inhibitor Binding to Its S′ Subsites
journal, April 2012
- Xue, Yi; Chowdhury, Somenath; Liu, Xuying
- Biochemistry, Vol. 51, Issue 18
Molecular Dynamics Simulations of Voltage-Gated Cation Channels: Insights on Voltage-Sensor Domain Function and Modulation
journal, January 2012
- Delemotte, Lucie; Klein, Michael L.; Tarek, Mounir
- Frontiers in Pharmacology, Vol. 3
Enzymatic activation of voltage-gated potassium channels
journal, June 2006
- Ramu, Yajamana; Xu, Yanping; Lu, Zhe
- Nature, Vol. 442, Issue 7103
Neurosteroid binding sites on GABAA receptors
journal, October 2007
- Hosie, Alastair M.; Wilkins, Megan E.; Smart, Trevor G.
- Pharmacology & Therapeutics, Vol. 116, Issue 1
Conformational dynamics and membrane interactions of the E. coli outer membrane protein FecA: A molecular dynamics simulation study
journal, February 2013
- Piggot, Thomas J.; Holdbrook, Daniel A.; Khalid, Syma
- Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1828, Issue 2
Nanopore Analysis of a Small 86-Residue Protein
journal, January 2008
- Stefureac, Radu; Waldner, Landon; Howard, Peter
- Small, Vol. 4, Issue 1
Regulation of voltage-gated potassium channels by PI(4,5)P2
journal, July 2012
- Kruse, Martin; Hammond, Gerald R. V.; Hille, Bertil
- The Journal of General Physiology, Vol. 140, Issue 2
E. coli Outer Membrane and Interactions with OmpLA
journal, June 2014
- Wu, Emilia L.; Fleming, Patrick J.; Yeom, Min Sun
- Biophysical Journal, Vol. 106, Issue 11
Evaluations of the Absolute and Relative Free Energies for Antidepressant Binding to the Amino Acid Membrane Transporter LeuT with Free Energy Simulations
journal, April 2010
- Zhao, Chunfeng; Caplan, David A.; Noskov, Sergei Yu.
- Journal of Chemical Theory and Computation, Vol. 6, Issue 6
Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms
journal, July 1997
- Wales, David J.; Doye, Jonathan P. K.
- The Journal of Physical Chemistry A, Vol. 101, Issue 28
Cholesterol depletion activates rapid internalization of submicron-sized acetylcholine receptor domains at the cell membrane
journal, January 2007
- Borroni, V.; Borroni, V.; Baier, C. J.
- Molecular Membrane Biology, Vol. 24, Issue 1
Structure and Dynamics of Parallel β-Sheets, Hydrophobic Core, and Loops in Alzheimer’s Aβ Fibrils
journal, May 2007
- Buchete, Nicolae-Viorel; Hummer, Gerhard
- Biophysical Journal, Vol. 92, Issue 9
How Does a Voltage Sensor Interact with a Lipid Bilayer? Simulations of a Potassium Channel Domain
journal, February 2007
- Sands, Zara A.; Sansom, Mark S. P.
- Structure, Vol. 15, Issue 2
Investigation of Single-Molecule Kinetics Mediated by Weak Hydrogen Bonds within a Biological Nanopore
journal, January 2011
- Asandei, Alina; Apetrei, Aurelia; Park, Yoonkyung
- Langmuir, Vol. 27, Issue 1
Protein Translocation Across the Bacterial Cytoplasmic Membrane
journal, June 2008
- Driessen, Arnold J. M.; Nouwen, Nico
- Annual Review of Biochemistry, Vol. 77, Issue 1
Immobilized lipid in acetylcholine receptor-rich membranes from Torpedo marmorata.
journal, September 1978
- Marsh, D.; Barrantes, F. J.
- Proceedings of the National Academy of Sciences, Vol. 75, Issue 9
Interpreting the Aggregation Kinetics of Amyloid Peptides
journal, July 2006
- Pellarin, Riccardo; Caflisch, Amedeo
- Journal of Molecular Biology, Vol. 360, Issue 4
Predictions for Cholesterol Interaction Sites on the A 2A Adenosine Receptor
journal, September 2012
- Lee, Ji Young; Lyman, Edward
- Journal of the American Chemical Society, Vol. 134, Issue 40
Forcing independent velocity distributions in an experimental granular fluid
journal, May 2007
- Reis, P. M.; Ingale, R. A.; Shattuck, M. D.
- Physical Review E, Vol. 75, Issue 5
Molecular Modeling and Simulation of Membrane Lipid-Mediated Effects on GPCRs
journal, December 2012
- Sadiq, S. K.; Guixa-Gonzalez, R.; Dainese, E.
- Current Medicinal Chemistry, Vol. 20, Issue 1
Metastability and Markov State Models in Molecular Dynamics
book, January 2013
- Schütte, Christof; Sarich, Marco
Effect of salt bridges on the energy landscape of a model protein
journal, November 2004
- Wales, David J.; Dewsbury, Peter E. J.
- The Journal of Chemical Physics, Vol. 121, Issue 20
Stationary points and dynamics in high-dimensional systems
journal, December 2003
- Wales, David J.; Doye, Jonathan P. K.
- The Journal of Chemical Physics, Vol. 119, Issue 23, p. 12409-12416
Visualization of Molecules with Positional Uncertainty
book, January 1999
- Rheingans, Penny; Joshi, Shrikant
- Eurographics
Jamming of frictional spheres and random loose packing
journal, January 2010
- Silbert, Leonardo E.
- Soft Matter, Vol. 6, Issue 13
Potential Energy and Free Energy Landscapes
journal, October 2006
- Wales, David J.; Bogdan, Tetyana V.
- The Journal of Physical Chemistry B, Vol. 110, Issue 42
Interaction of the Acetylcholine (Nicotinic) Receptor Protein from Torpedo marmorata Electric Organ with Monolayers of Pure Lipids
journal, April 1978
- Popot, Jean-Luc; Demel, Rudy A.; Sobel, Andre
- European Journal of Biochemistry, Vol. 85, Issue 1
Effects of membrane cholesterol on the sensitivity of the GABAA receptor to GABA in acutely dissociated rat hippocampal neurones
journal, January 2001
- Sooksawate, T.; Simmonds, M. A.
- Neuropharmacology, Vol. 40, Issue 2
Reconstitution of intramembrane proteolysis in vitro reveals that pure rhomboid is sufficient for catalysis and specificity
journal, January 2005
- Urban, S.; Wolfe, M. S.
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 6
Surveying a complex potential energy landscape: Overcoming broken ergodicity using basin-sampling
journal, October 2013
- Wales, David J.
- Chemical Physics Letters, Vol. 584
Naturally secreted oligomers of amyloid β protein potently inhibit hippocampal long-term potentiation in vivo
journal, April 2002
- Walsh, Dominic M.; Klyubin, Igor; Fadeeva, Julia V.
- Nature, Vol. 416, Issue 6880
Globular amyloid beta-peptide1-42 oligomer - a homogenous and stable neuropathological protein in Alzheimer's disease
journal, November 2005
- Barghorn, Stefan; Nimmrich, Volker; Striebinger, Andreas
- Journal of Neurochemistry, Vol. 95, Issue 3
Works referencing / citing this record:
19F NMR as a versatile tool to study membrane protein structure and dynamics
journal, October 2019
- Rose-Sperling, Dania; Tran, Mai Anh; Lauth, Luca M.
- Biological Chemistry, Vol. 400, Issue 10
Demonstration of the Protein Involvement in Cell Electropermeabilization using Confocal Raman Microspectroscopy
journal, January 2017
- Azan, Antoine; Untereiner, Valérie; Gobinet, Cyril
- Scientific Reports, Vol. 7, Issue 1
Optical imaging of single protein size, charge, mobility, binding and conformational change
preprint, March 2019
- Ma, Guanzhong; Zhu, Hao; Wan, Zijian
Interfacing the Cell with “Biomimetic Membrane Proteins”
journal, December 2019
- Grupi, Asaf; Ashur, Idan; Degani‐Katzav, Nurit
- Small, Vol. 15, Issue 52
Self-assembly of anionic, ligand-coated nanoparticles in lipid membranes
journal, January 2017
- Angelikopoulos, Panagiotis; Sarkisov, Lev; Cournia, Zoe
- Nanoscale, Vol. 9, Issue 3
Effect of 5- trans isomer of arachidonic acid on model liposomal membranes studied by a combined simulation and experimental approach
posted_content, March 2018
- Tremi, Ioanna; Anagnostopoulos, Dimitrios; Spyratou, Ellas
- Journal of Membrane Biology
Cell Membrane Electropulsation: Chemical Analysis of Cell Membrane Modifications and Associated Transport Mechanisms
book, June 2017
- Azan, Antoine; Gailliègue, Florian; Mir, Lluis M.
- Transport Across Natural and Modified Biological Membranes and its Implications in Physiology and Therapy
Ubiquitination and the Regulation of Membrane Proteins
journal, January 2017
- Foot, Natalie; Henshall, Tanya; Kumar, Sharad
- Physiological Reviews, Vol. 97, Issue 1
Nanomaterial–microbe cross-talk: physicochemical principles and (patho)biological consequences
journal, January 2018
- Westmeier, D.; Hahlbrock, A.; Reinhardt, C.
- Chemical Society Reviews, Vol. 47, Issue 14
The outer membrane phospholipase A is essential for membrane integrity and type III secretion in Shigella flexneri
journal, September 2016
- Wang, Xia; Jiang, Feng; Zheng, Jianhua
- Open Biology, Vol. 6, Issue 9
Conformational analysis of replica exchange MD: Temperature-dependent Markov networks for FF amyloid peptides
journal, August 2018
- Narayan, Brajesh; Herbert, Colm; Yuan, Ye
- The Journal of Chemical Physics, Vol. 149, Issue 7
REDOR NMR Reveals Multiple Conformers for a Protein Kinase C Ligand in a Membrane Environment
journal, January 2018
- Yang, Hao; Staveness, Daryl; Ryckbosch, Steven M.
- ACS Central Science, Vol. 4, Issue 1
The outer membrane phospholipase A is essential for membrane integrity and type III secretion in Shigella flexneri
journal, September 2016
- Wang, Xia; Jiang, Feng; Zheng, Jianhua
- Open Biology, Vol. 6, Issue 9
Expressing Biologically Active Membrane Proteins in a Cell-Free Transcription-Translation Platform
preprint, January 2017
- Guo, Shaobin; Vaish, Amit; Chen, Qing
Biological Membranes in Extreme Conditions: Simulations of Anionic Archaeal Tetraether Lipid Membranes
journal, May 2016
- Pineda De Castro, Luis Felipe; Dopson, Mark; Friedman, Ran
- PLOS ONE, Vol. 11, Issue 5
Assembly of Spinach Chloroplast ATP Synthase Rotor Ring Protein-Lipid Complex
journal, November 2019
- Novitskaia, Olga; Buslaev, Pavel; Gushchin, Ivan
- Frontiers in Molecular Biosciences, Vol. 6
Recent Insights from Molecular Dynamics Simulations for G Protein-Coupled Receptor Drug Discovery
journal, August 2019
- Zou,
- International Journal of Molecular Sciences, Vol. 20, Issue 17