Atomic-level description of protein–lipid interactions using an accelerated membrane model
- Authors:
- Publication Date:
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1367694
- Alternate Identifier(s):
- OSTI ID: 1326409
- Resource Type:
- Journal Article: Published Article
- Journal Name:
- Biochimica et Biophysica Acta. Biomembranes
- Additional Journal Information:
- Journal Name: Biochimica et Biophysica Acta. Biomembranes Journal Volume: 1858 Journal Issue: 7 PB; Journal ID: ISSN 0005-2736
- Publisher:
- Elsevier
- Country of Publication:
- Netherlands
- Language:
- English
Citation Formats
Baylon, Javier L., Vermaas, Josh V., Muller, Melanie P., Arcario, Mark J., Pogorelov, Taras V., and Tajkhorshid, Emad. Atomic-level description of protein–lipid interactions using an accelerated membrane model. Netherlands: N. p., 2016.
Web. doi:10.1016/j.bbamem.2016.02.027.
Baylon, Javier L., Vermaas, Josh V., Muller, Melanie P., Arcario, Mark J., Pogorelov, Taras V., & Tajkhorshid, Emad. Atomic-level description of protein–lipid interactions using an accelerated membrane model. Netherlands. https://doi.org/10.1016/j.bbamem.2016.02.027
Baylon, Javier L., Vermaas, Josh V., Muller, Melanie P., Arcario, Mark J., Pogorelov, Taras V., and Tajkhorshid, Emad. 2016.
"Atomic-level description of protein–lipid interactions using an accelerated membrane model". Netherlands. https://doi.org/10.1016/j.bbamem.2016.02.027.
@article{osti_1367694,
title = {Atomic-level description of protein–lipid interactions using an accelerated membrane model},
author = {Baylon, Javier L. and Vermaas, Josh V. and Muller, Melanie P. and Arcario, Mark J. and Pogorelov, Taras V. and Tajkhorshid, Emad},
abstractNote = {},
doi = {10.1016/j.bbamem.2016.02.027},
url = {https://www.osti.gov/biblio/1367694},
journal = {Biochimica et Biophysica Acta. Biomembranes},
issn = {0005-2736},
number = 7 PB,
volume = 1858,
place = {Netherlands},
year = {Fri Jul 01 00:00:00 EDT 2016},
month = {Fri Jul 01 00:00:00 EDT 2016}
}
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Works referenced in this record:
Folding and misfolding of alpha-synuclein on membranes
journal, April 2012
- Dikiy, Igor; Eliezer, David
- Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1818, Issue 4
Structure and Dynamics of Micelle-bound Human -Synuclein
journal, December 2004
- Ulmer, T. S.; Bax, A.; Cole, N. B.
- Journal of Biological Chemistry, Vol. 280, Issue 10
Lipid–protein interactions in blood coagulation
journal, November 1998
- Zwaal, Robert F. A.; Comfurius, Paul; Bevers, Edouard M.
- Biochimica et Biophysica Acta (BBA) - Reviews on Biomembranes, Vol. 1376, Issue 3
Structural Basis of Integrin Activation by Talin
journal, January 2007
- Wegener, Kate L.; Partridge, Anthony W.; Han, Jaewon
- Cell, Vol. 128, Issue 1
Ligand Binding to Cytochrome P450 3A4 in Phospholipid Bilayer Nanodiscs
journal, September 2007
- Nath, Abhinav; Grinkova, Yelena V.; Sligar, Stephen G.
- Journal of Biological Chemistry, Vol. 282, Issue 39
Systematic multiscale simulation of membrane protein systems
journal, April 2009
- Ayton, Gary S.; Voth, Gregory A.
- Current Opinion in Structural Biology, Vol. 19, Issue 2
Mapping intact protein isoforms in discovery mode using top-down proteomics
journal, October 2011
- Tran, John C.; Zamdborg, Leonid; Ahlf, Dorothy R.
- Nature, Vol. 480, Issue 7376
Whole-Body Rocking Motion of a Fusion Peptide in Lipid Bilayers from Size-Dispersed 15 N NMR Relaxation
journal, September 2011
- Lorieau, Justin L.; Louis, John M.; Bax, Ad
- Journal of the American Chemical Society, Vol. 133, Issue 36
Folding is not required for bilayer insertion: Replica exchange simulations of an α-helical peptide with an explicit lipid bilayer
journal, April 2005
- Nymeyer, Hugh; Woolf, Thomas B.; Garcia, Angel E.
- Proteins: Structure, Function, and Bioinformatics, Vol. 59, Issue 4
Antiparallel Arrangement of the Helices of Vesicle-Bound α-Synuclein
journal, June 2008
- Drescher, Malte; Veldhuis, Gertjan; van Rooijen, Bart D.
- Journal of the American Chemical Society, Vol. 130, Issue 25
Enhancement of Vitamin-K-Dependent Protein Function by Modification of the γ-Carboxyglutamic Acid Domain Studies of Protein C and Factor VII
journal, August 1999
- Nelsestuen, G.
- Trends in Cardiovascular Medicine, Vol. 9, Issue 6
Transmembrane and cytoplasmic domains in integrin activation and protein-protein interactions (Review)
journal, January 2008
- Wegener, Kate L.; Campbell, Iain D.
- Molecular Membrane Biology, Vol. 25, Issue 5
Parkinson's disease
journal, June 2009
- Lees, Andrew J.; Hardy, John; Revesz, Tamas
- The Lancet, Vol. 373, Issue 9680
Distribution of Amino Acids in a Lipid Bilayer from Computer Simulations
journal, May 2008
- MacCallum, Justin L.; Bennett, W. F. Drew; Tieleman, D. Peter
- Biophysical Journal, Vol. 94, Issue 9
Effects of Curvature and Composition on α-Synuclein Binding to Lipid Vesicles
journal, October 2010
- Middleton, Elizabeth R.; Rhoades, Elizabeth
- Biophysical Journal, Vol. 99, Issue 7
Dynamic, yet structured: The cell membrane three decades after the Singer–Nicolson model
journal, June 2003
- Vereb, G.; Szöllősi, J.; Matkó, J.
- Proceedings of the National Academy of Sciences, Vol. 100, Issue 14
Mutagenesis of the γ-Carboxyglutamic Acid Domain of Human Factor VII to Generate Maximum Enhancement of the Membrane Contact Site
journal, March 2003
- Harvey, Stephen B.; Stone, Matthew D.; Martinez, Michael B.
- Journal of Biological Chemistry, Vol. 278, Issue 10
-Synuclein Promotes SNARE-Complex Assembly in Vivo and in Vitro
journal, August 2010
- Burre, J.; Sharma, M.; Tsetsenis, T.
- Science, Vol. 329, Issue 5999
The interactions of peripheral membrane proteins with biological membranes
journal, November 2015
- Whited, A. M.; Johs, A.
- Chemistry and Physics of Lipids, Vol. 192
The Cation-π Box Is a Specific Phosphatidylcholine Membrane Targeting Motif
journal, April 2013
- Cheng, Jiongjia; Goldstein, Rebecca; Gershenson, Anne
- Journal of Biological Chemistry, Vol. 288, Issue 21
A host-guest system to study structure-function relationships of membrane fusion peptides
journal, November 2000
- Han, X.; Tamm, L. K.
- Proceedings of the National Academy of Sciences, Vol. 97, Issue 24
Membrane Interaction of the Factor VIIIa Discoidin Domains in Atomistic Detail
journal, September 2015
- Madsen, Jesper J.; Ohkubo, Y. Zenmei; Peters, Günther H.
- Biochemistry, Vol. 54, Issue 39
Membrane lipids: where they are and how they behave
journal, February 2008
- van Meer, Gerrit; Voelker, Dennis R.; Feigenson, Gerald W.
- Nature Reviews Molecular Cell Biology, Vol. 9, Issue 2
Synaptotagmin’s Role in Neurotransmitter Release Likely Involves Ca 2+ -induced Conformational Transition
journal, September 2014
- Wu, Zhe; Schulten, Klaus
- Biophysical Journal, Vol. 107, Issue 5
The Tail of Integrins, Talin, and Kindlins
journal, May 2009
- Moser, M.; Legate, K. R.; Zent, R.
- Science, Vol. 324, Issue 5929
Simulations of Phospholipids Using a Coarse Grain Model
journal, October 2001
- Shelley, John C.; Shelley, Mee Y.; Reeder, Robert C.
- The Journal of Physical Chemistry B, Vol. 105, Issue 40
The MARTINI Coarse-Grained Force Field: Extension to Proteins
journal, April 2008
- Monticelli, Luca; Kandasamy, Senthil K.; Periole, Xavier
- Journal of Chemical Theory and Computation, Vol. 4, Issue 5
Characterizing the Membrane-Bound State of Cytochrome P450 3A4: Structure, Depth of Insertion, and Orientation
journal, May 2013
- Baylon, Javier L.; Lenov, Ivan L.; Sligar, Stephen G.
- Journal of the American Chemical Society, Vol. 135, Issue 23
Structural Determinants of Integrin Recognition by Talin
journal, January 2003
- Garcı́a-Alvarez, Begoña; de Pereda, José M.; Calderwood, David A.
- Molecular Cell, Vol. 11, Issue 1
The Talin Head Domain Binds to Integrin β Subunit Cytoplasmic Tails and Regulates Integrin Activation
journal, October 1999
- Calderwood, David A.; Zent, Roy; Grant, Richard
- Journal of Biological Chemistry, Vol. 274, Issue 40
Platelet integrin ? IIb ? 3 : activation mechanisms
journal, July 2007
- Ma, Y. -Q.; Qin, J.; Plow, E. F.
- Journal of Thrombosis and Haemostasis, Vol. 5, Issue 7
Redox Potential Tuning through Differential Quinone Binding in the Photosynthetic Reaction Center of Rhodobacter sphaeroides
journal, March 2015
- Vermaas, Josh V.; Taguchi, Alexander T.; Dikanov, Sergei A.
- Biochemistry, Vol. 54, Issue 12
High Resolution Structures of p-Aminobenzamidine- and Benzamidine-VIIa/Soluble Tissue Factor
journal, August 2006
- Bajaj, S. Paul; Schmidt, Amy E.; Agah, Sayeh
- Journal of Biological Chemistry, Vol. 281, Issue 34
Replica-exchange molecular dynamics method for protein folding
journal, November 1999
- Sugita, Yuji; Okamoto, Yuko
- Chemical Physics Letters, Vol. 314, Issue 1-2
Integrin activation by talin
journal, August 2005
- Ratnikov, B. I.; Partridge, A. W.; Ginsberg, M. H.
- Journal of Thrombosis and Haemostasis, Vol. 3, Issue 8
Bidirectional Transmembrane Signaling by Cytoplasmic Domain Separation in Integrins
journal, September 2003
- Kim, M.
- Science, Vol. 301, Issue 5640
A Designed Inhibitor of a CLC Antiporter Blocks Function through a Unique Binding Mode
journal, November 2012
- Howery, Andrew E.; Elvington, Shelley; Abraham, Sherwin J.
- Chemistry & Biology, Vol. 19, Issue 11
Peptide-specific antibodies localize the major lipid binding sites of talin dimers to oppositely arranged N-terminal 47 kDa subdomains 1
journal, April 1998
- Isenberg, Gerhard; Goldmann, Wolfgang H.
- FEBS Letters, Vol. 426, Issue 2
Membrane Docking of the Synaptotagmin 7 C2A Domain: Electron Paramagnetic Resonance Measurements Show Contributions from Two Membrane Binding Loops
journal, September 2015
- Osterberg, J. Ryan; Chon, Nara Lee; Boo, Arthur
- Biochemistry, Vol. 54, Issue 37
Membrane recognition by phospholipid-binding domains
journal, February 2008
- Lemmon, Mark A.
- Nature Reviews Molecular Cell Biology, Vol. 9, Issue 2
Directed Self-Assembly of Monodisperse Phospholipid Bilayer Nanodiscs with Controlled Size
journal, March 2004
- Denisov, I. G.; Grinkova, Y. V.; Lazarides, A. A.
- Journal of the American Chemical Society, Vol. 126, Issue 11
Intrinsically Disordered p53 Extreme C-Terminus Binds to S100B(ββ) through “Fly-Casting”
journal, February 2009
- Chen, Jianhan
- Journal of the American Chemical Society, Vol. 131, Issue 6
Predictive energy landscapes for folding membrane protein assemblies
journal, December 2015
- Truong, Ha H.; Kim, Bobby L.; Schafer, Nicholas P.
- The Journal of Chemical Physics, Vol. 143, Issue 24
Multiscale simulations suggest a mechanism for integrin inside-out activation
journal, July 2011
- Kalli, A. C.; Campbell, I. D.; Sansom, M. S. P.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 29
Ca2+-independent Binding of Anionic Phospholipids by Phospholipase C δ1 EF-hand Domain
journal, December 2013
- Cai, Jingfei; Guo, Su; Lomasney, Jon W.
- Journal of Biological Chemistry, Vol. 288, Issue 52
Designs for life: protocell models in the laboratory
journal, January 2012
- Dzieciol, Alicja J.; Mann, Stephen
- Chem. Soc. Rev., Vol. 41, Issue 1
Dynamics in atomistic simulations of phospholipid membranes: Nuclear magnetic resonance relaxation rates and lateral diffusion
journal, November 2006
- Wohlert, Jakob; Edholm, Olle
- The Journal of Chemical Physics, Vol. 125, Issue 20
The Structure of the Talin Head Reveals a Novel Extended Conformation of the FERM Domain
journal, October 2010
- Elliott, Paul R.; Goult, Benjamin T.; Kopp, Petra M.
- Structure, Vol. 18, Issue 10
Accelerating Membrane Insertion of Peripheral Proteins with a Novel Membrane Mimetic Model
journal, May 2012
- Ohkubo, Y. Zenmei; Pogorelov, Taras V.; Arcario, Mark J.
- Biophysical Journal, Vol. 102, Issue 9
Perspective on the Martini model
journal, January 2013
- Marrink, Siewert J.; Tieleman, D. Peter
- Chemical Society Reviews, Vol. 42, Issue 16
Phospholipid Binding of Synthetic Talin Peptides Provides Evidence for an Intrinsic Membrane Anchor of Talin
journal, June 2000
- Seelig, Anna; Blatter, Xiaochun Li; Frentzel, Adrian
- Journal of Biological Chemistry, Vol. 275, Issue 24
The Structure of the Talin/Integrin Complex at a Lipid Bilayer: An NMR and MD Simulation Study
journal, October 2010
- Kalli, Antreas C.; Wegener, Kate L.; Goult, Benjamin T.
- Structure, Vol. 18, Issue 10
Surface-Tension Replica-Exchange Molecular Dynamics Method for Enhanced Sampling of Biological Membrane Systems
journal, November 2013
- Mori, Takaharu; Jung, Jaewoon; Sugita, Yuji
- Journal of Chemical Theory and Computation, Vol. 9, Issue 12
Direct Evidence of Coexisting Horseshoe and Extended Helix Conformations of Membrane-Bound Alpha-Synuclein
journal, December 2010
- Robotta, Marta; Braun, Patrick; van Rooijen, Bart
- ChemPhysChem, Vol. 12, Issue 2
Docking Phospholipase A2 on Membranes Using Electrostatic Potential-Modulated Spin Relaxation Magnetic Resonance
journal, March 1998
- Lin, Y.
- Science, Vol. 279, Issue 5358
Mammalian Microsomal Cytochrome P450 Monooxygenase
journal, January 2000
- Williams, Pamela A.; Cosme, Jose; Sridhar, Vandana
- Molecular Cell, Vol. 5, Issue 1
Structure of membrane-bound -synuclein from site-directed spin labeling and computational refinement
journal, December 2008
- Jao, C. C.; Hegde, B. G.; Chen, J.
- Proceedings of the National Academy of Sciences, Vol. 105, Issue 50
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
Drug—target network
journal, October 2007
- Yıldırım, Muhammed A.; Goh, Kwang-Il; Cusick, Michael E.
- Nature Biotechnology, Vol. 25, Issue 10
Direct in vivo interaction of the antibiotic primycin with the plasma membrane of Candida albicans: An EPR study
journal, January 2012
- Virág, Eszter; Belagyi, Joseph; Gazdag, Zoltán
- Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1818, Issue 1
Sequence-Dependent Interaction of β-Peptides with Membranes
journal, October 2010
- Mondal, Jagannath; Zhu, Xiao; Cui, Qiang
- The Journal of Physical Chemistry B, Vol. 114, Issue 42
Coarse Grained Model for Semiquantitative Lipid Simulations
journal, January 2004
- Marrink, Siewert J.; de Vries, Alex H.; Mark, Alan E.
- The Journal of Physical Chemistry B, Vol. 108, Issue 2
H+-induced Membrane Insertion of Influenza Virus Hemagglutinin Involves the HA2 Amino-terminal Fusion Peptide but Not the Coiled Coil Region
journal, June 1996
- Durrer, Peter; Galli, Carmela; Hoenke, Stefan
- Journal of Biological Chemistry, Vol. 271, Issue 23
Mechanism of Drug–Drug Interactions Mediated by Human Cytochrome P450 CYP3A4 Monomer
journal, March 2015
- Denisov, Ilia G.; Grinkova, Yelena V.; Baylon, Javier L.
- Biochemistry, Vol. 54, Issue 13
The power of coarse graining in biomolecular simulations: The power of coarse graining in biomolecular simulations
journal, August 2013
- Ingólfsson, Helgi I.; Lopez, Cesar A.; Uusitalo, Jaakko J.
- Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 4, Issue 3
α-Synuclein Membrane Interactions and Lipid Specificity
journal, November 2000
- Jo, Euijung; McLaurin, JoAnne; Yip, Christopher M.
- Journal of Biological Chemistry, Vol. 275, Issue 44
The structure of an integrin/talin complex reveals the basis of inside-out signal transduction
journal, October 2009
- Anthis, Nicholas J.; Wegener, Kate L.; Ye, Feng
- The EMBO Journal, Vol. 28, Issue 22
Definition of a Molecular Pathway Mediating -Synuclein Neurotoxicity
journal, April 2015
- Burre, J.; Sharma, M.; Sudhof, T. C.
- Journal of Neuroscience, Vol. 35, Issue 13
Defining Specific Lipid Binding Sites for a Peripheral Membrane Protein in Situ Using Subtesla Field-cycling NMR
journal, August 2010
- Pu, Mingming; Orr, Andrew; Redfield, Alfred G.
- Journal of Biological Chemistry, Vol. 285, Issue 35
A novel membrane-dependent on/off switch mechanism of talin FERM domain at sites of cell adhesion
journal, June 2012
- Song, Xianqiang; Yang, Jun; Hirbawi, Jamila
- Cell Research, Vol. 22, Issue 11
Contribution of Membrane Elastic Energy to Rhodopsin Function
journal, August 2010
- Soubias, Olivier; Teague, Walter E.; Hines, Kirk G.
- Biophysical Journal, Vol. 99, Issue 3
New Insights into the Spring-Loaded Conformational Change of Influenza Virus Hemagglutinin
journal, May 2002
- Gruenke, Jennifer A.; Armstrong, R. Todd; Newcomb, William W.
- Journal of Virology, Vol. 76, Issue 9
The Molecular Biology, Biochemistry, and Physiology of Human Steroidogenesis and Its Disorders
journal, February 2011
- Miller, Walter L.; Auchus, Richard J.
- Endocrine Reviews, Vol. 32, Issue 1
Dynamical motions of lipids and a finite size effect in simulations of bilayers
journal, October 2006
- Klauda, Jeffery B.; Brooks, Bernard R.; Pastor, Richard W.
- The Journal of Chemical Physics, Vol. 125, Issue 14
A Combinatorial NMR and EPR Approach for Evaluating the Structural Ensemble of Partially Folded Proteins
journal, June 2010
- Rao, Jampani Nageswara; Jao, Christine C.; Hegde, Balachandra G.
- Journal of the American Chemical Society, Vol. 132, Issue 25
Prediction of the human membrane proteome
journal, February 2010
- Fagerberg, Linn; Jonasson, Kalle; von Heijne, Gunnar
- PROTEOMICS, Vol. 10, Issue 6
A Highly Tilted Membrane Configuration for the Prefusion State of Synaptobrevin
journal, November 2014
- Blanchard, Andrew E.; Arcario, Mark J.; Schulten, Klaus
- Biophysical Journal, Vol. 107, Issue 9
A Microscopic View of Phospholipid Insertion into Biological Membranes
journal, December 2013
- Vermaas, Josh V.; Tajkhorshid, Emad
- The Journal of Physical Chemistry B, Vol. 118, Issue 7
Molecular Determinants of Phospholipid Synergy in Blood Clotting
journal, May 2011
- Tavoosi, Narjes; Davis-Harrison, Rebecca L.; Pogorelov, Taras V.
- Journal of Biological Chemistry, Vol. 286, Issue 26
Solvation Energies of Amino Acid Side Chains and Backbone in a Family of Host−Guest Pentapeptides †
journal, January 1996
- Wimley, William C.; Creamer, Trevor P.; White, Stephen H.
- Biochemistry, Vol. 35, Issue 16
The Fluid Mosaic Model of the Structure of Cell Membranes
journal, February 1972
- Singer, S. J.; Nicolson, G. L.
- Science, Vol. 175, Issue 4023
CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model
journal, November 2015
- Qi, Yifei; Cheng, Xi; Lee, Jumin
- Biophysical Journal, Vol. 109, Issue 10
Capturing Spontaneous Membrane Insertion of the Influenza Virus Hemagglutinin Fusion Peptide
journal, June 2015
- Baylon, Javier L.; Tajkhorshid, Emad
- The Journal of Physical Chemistry B, Vol. 119, Issue 25
Signalling ballet in space and time
journal, June 2010
- Kholodenko, Boris N.; Hancock, John F.; Kolch, Walter
- Nature Reviews Molecular Cell Biology, Vol. 11, Issue 6
Extensive Small-Angle X-ray Scattering Studies of Blood Coagulation Factor VIIa Reveal Interdomain Flexibility
journal, November 2010
- Mosbæk, Charlotte Rode; Nolan, David; Persson, Egon
- Biochemistry, Vol. 49, Issue 45
Membrane curvature modulation of protein activity determined by NMR
journal, January 2015
- Epand, Richard M.; D'Souza, Kenneth; Berno, Bob
- Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1848, Issue 1
Substrate Routes to the Buried Active Site May Vary among Cytochromes P450: Mutagenesis of the F−G Region in P450 2B1 †
journal, November 2002
- Scott, Emily E.; He, You Qun; Halpert, James R.
- Chemical Research in Toxicology, Vol. 15, Issue 11
Incorporation of charged residues in the CYP2J2 F-G loop disrupts CYP2J2–lipid bilayer interactions
journal, October 2015
- McDougle, Daniel R.; Baylon, Javier L.; Meling, Daryl D.
- Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1848, Issue 10
α-Synuclein Populates Both Elongated and Broken Helix States on Small Unilamellar Vesicles
journal, April 2011
- Lokappa, Sowmya Bekshe; Ulmer, Tobias S.
- Journal of Biological Chemistry, Vol. 286, Issue 24
Effective energy function for proteins in lipid membranes
journal, June 2003
- Lazaridis, Themis
- Proteins: Structure, Function, and Genetics, Vol. 52, Issue 2
Alpha-Synuclein Binds to the Inner Membrane of Mitochondria in an α-Helical Conformation
journal, September 2014
- Robotta, Marta; Gerding, Hanne R.; Vogel, Antonia
- ChemBioChem, Vol. 15, Issue 17
Spectrin Domains Lose Cooperativity in Forced Unfolding
journal, January 2007
- Randles, Lucy G.; Rounsevell, Ross W. S.; Clarke, Jane
- Biophysical Journal, Vol. 92, Issue 2
SLIM: An improved generalized Born implicit membrane model
journal, September 2014
- Setzler, Julia; Seith, Carolin; Brieg, Martin
- Journal of Computational Chemistry, Vol. 35, Issue 28
pH-triggered, activated-state conformations of the influenza hemagglutinin fusion peptide revealed by NMR
journal, November 2012
- Lorieau, J. L.; Louis, J. M.; Schwieters, C. D.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 49
Balancing Solvation and Intramolecular Interactions: Toward a Consistent Generalized Born Force Field
journal, March 2006
- Chen, Jianhan; Im, Wonpil; Brooks, Charles L.
- Journal of the American Chemical Society, Vol. 128, Issue 11
Membrane-Protein Interactions in Cell Signaling and Membrane Trafficking
journal, June 2005
- Cho, Wonhwa; Stahelin, Robert V.
- Annual Review of Biophysics and Biomolecular Structure, Vol. 34, Issue 1
Functional role of cardiolipin in mitochondrial bioenergetics
journal, April 2014
- Paradies, Giuseppe; Paradies, Valeria; De Benedictis, Valentina
- Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1837, Issue 4
Membrane-Induced Structural Rearrangement and Identification of a Novel Membrane Anchor in Talin F2F3
journal, November 2014
- Arcario, Mark J.; Tajkhorshid, Emad
- Biophysical Journal, Vol. 107, Issue 9
C2 Domain of Protein Kinase Cα: Elucidation of the Membrane Docking Surface by Site-Directed Fluorescence and Spin Labeling †
journal, February 2003
- Kohout, Susy C.; Corbalán-García, Senena; Gómez-Fernández, Juan C.
- Biochemistry, Vol. 42, Issue 5
Multiscale coarse graining of liquid-state systems
journal, October 2005
- Izvekov, Sergei; Voth, Gregory A.
- The Journal of Chemical Physics, Vol. 123, Issue 13
Crystal structure of the prothrombinase complex from the venom of Pseudonaja textilis
journal, October 2013
- Lechtenberg, Bernhard C.; Murray-Rust, Thomas A.; Johnson, Daniel J. D.
- Blood, Vol. 122, Issue 16
Neutron Reflectometry Studies Define Prion Protein N-terminal Peptide Membrane Binding
journal, November 2014
- Le Brun, Anton P.; Haigh, Cathryn L.; Drew, Simon C.
- Biophysical Journal, Vol. 107, Issue 10
Hierarchical coarse-graining strategy for protein-membrane systems to access mesoscopic scales
journal, January 2010
- Ayton, Gary S.; Lyman, Edward; Voth, Gregory A.
- Faraday Discuss., Vol. 144
CYTOCHROME P-450 3A4: Regulation and Role in Drug Metabolism
journal, April 1999
- Guengerich, F. Peter
- Annual Review of Pharmacology and Toxicology, Vol. 39, Issue 1
α-Synuclein Induces Both Positive Mean Curvature and Negative Gaussian Curvature in Membranes
journal, January 2012
- Braun, Anthony R.; Sevcsik, Eva; Chin, Pamela
- Journal of the American Chemical Society, Vol. 134, Issue 5
pH-dependent Self-association of Influenza Hemagglutinin Fusion Peptides in Lipid Bilayers
journal, December 2000
- Han, Xing; Tamm, Lukas K.
- Journal of Molecular Biology, Vol. 304, Issue 5
Partitioning of Amino Acids into a Model Membrane: Capturing the Interface
journal, January 2014
- Pogorelov, Taras V.; Vermaas, Josh V.; Arcario, Mark J.
- The Journal of Physical Chemistry B, Vol. 118, Issue 6
Lipids as Universal Biomarkers of Extraterrestrial Life
journal, June 2014
- Georgiou, Christos D.; Deamer, David W.
- Astrobiology, Vol. 14, Issue 6
Membrane topology of the mammalian P450 cytochromes
journal, January 1992
- Black, Shaun D.
- The FASEB Journal, Vol. 6, Issue 2
An Implicit Membrane Generalized Born Theory for the Study of Structure, Stability, and Interactions of Membrane Proteins
journal, November 2003
- Im, Wonpil; Feig, Michael; Brooks, Charles L.
- Biophysical Journal, Vol. 85, Issue 5
Quantifying Transient Interactions between Bacillus Phosphatidylinositol-Specific Phospholipase-C and Phosphatidylcholine-Rich Vesicles
journal, December 2014
- Yang, Boqian; Pu, Mingming; Khan, Hanif M.
- Journal of the American Chemical Society, Vol. 137, Issue 1
Capturing Spontaneous Partitioning of Peripheral Proteins Using a Biphasic Membrane-Mimetic Model
journal, June 2011
- Arcario, Mark J.; Ohkubo, Y. Zenmei; Tajkhorshid, Emad
- The Journal of Physical Chemistry B, Vol. 115, Issue 21
Conditional Peripheral Membrane Proteins: Facing up to Limited Specificity
journal, January 2012
- Moravcevic, Katarina; Oxley, Camilla L.; Lemmon, Mark A.
- Structure, Vol. 20, Issue 1
Structural basis of membrane binding by Gla domains of vitamin K–dependent proteins
journal, August 2003
- Huang, Mingdong; Rigby, Alan C.; Morelli, Xavier
- Nature Structural & Molecular Biology, Vol. 10, Issue 9
Cytochromes P450 and metabolism of xenobiotics
journal, May 2001
- Anzenbacher, P.; Anzenbacherová, E.
- Cellular and Molecular Life Sciences, Vol. 58, Issue 5
The final steps of integrin activation: the end game
journal, April 2010
- Shattil, Sanford J.; Kim, Chungho; Ginsberg, Mark H.
- Nature Reviews Molecular Cell Biology, Vol. 11, Issue 4
The talin–tail interaction places integrin activation on FERM ground
journal, August 2004
- Campbell, Iain D.; Ginsberg, Mark H.
- Trends in Biochemical Sciences, Vol. 29, Issue 8
α-Synuclein Binds Large Unilamellar Vesicles as an Extended Helix †
journal, March 2009
- Trexler, Adam J.; Rhoades, Elizabeth
- Biochemistry, Vol. 48, Issue 11
Integrin structure: heady advances in ligand binding, but activation still makes the knees wobble
journal, June 2003
- Humphries, Martin J.; McEwan, Paul A.; Barton, Stephanie J.
- Trends in Biochemical Sciences, Vol. 28, Issue 6
Conformational heterogeneity of α -synuclein in membrane
journal, December 2014
- Vermaas, Josh V.; Tajkhorshid, Emad
- Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1838, Issue 12
Membrane proteins bind lipids selectively to modulate their structure and function
journal, June 2014
- Laganowsky, Arthur; Reading, Eamonn; Allison, Timothy M.
- Nature, Vol. 510, Issue 7503
Recognition of transmembrane helices by the endoplasmic reticulum translocon
journal, January 2005
- Hessa, Tara; Kim, Hyun; Bihlmaier, Karl
- Nature, Vol. 433, Issue 7024
Fluorescence Correlation Spectroscopy of Phosphatidylinositol-Specific Phospholipase C Monitors the Interplay of Substrate and Activator Lipid Binding
journal, July 2009
- Pu, Mingming; Roberts, Mary F.; Gershenson, Anne
- Biochemistry, Vol. 48, Issue 29
Cytochrome P450 and Chemical Toxicology
journal, January 2008
- Guengerich, F. Peter
- Chemical Research in Toxicology, Vol. 21, Issue 1
New PI(4,5)P2- and membrane proximal integrin–binding motifs in the talin head control β3-integrin clustering
journal, November 2009
- Saltel, Frédéric; Mortier, Eva; Hytönen, Vesa P.
- Journal of Cell Biology, Vol. 187, Issue 5
Dynamical view of membrane binding and complex formation of human factor VIIa and tissue factor
journal, May 2010
- Ohkubo, Y. Z.; Morrissey, J. H.; Tajkhorshid, E.
- Journal of Thrombosis and Haemostasis, Vol. 8, Issue 5
Tissue Factor Positions and Maintains the Factor VIIa Active Site Far above the Membrane Surface Even in the Absence of the Factor VIIa Gla Domain
journal, November 1997
- McCallum, Christine D.; Su, Bixia; Neuenschwander, Pierre F.
- Journal of Biological Chemistry, Vol. 272, Issue 48
Cooperativity in Cytochrome P450 3A4: LINKAGES IN SUBSTRATE BINDING, SPIN STATE, UNCOUPLING, AND PRODUCT FORMATION
journal, January 2007
- Denisov, Ilia G.; Baas, Bradley J.; Grinkova, Yelena V.
- Journal of Biological Chemistry, Vol. 282, Issue 10
Membrane-Bound α-Synuclein Forms an Extended Helix: Long-Distance Pulsed ESR Measurements Using Vesicles, Bicelles, and Rodlike Micelles
journal, October 2008
- Georgieva, Elka R.; Ramlall, Trudy F.; Borbat, Peter P.
- Journal of the American Chemical Society, Vol. 130, Issue 39
Membrane proteins: molecular dynamics simulations
journal, August 2008
- Lindahl, E.; Sansom, M.
- Current Opinion in Structural Biology, Vol. 18, Issue 4
Membrane Assembly of Simple Helix Homo-Oligomers Studied via Molecular Dynamics Simulations
journal, February 2007
- Bu, Lintao; Im, Wonpil; Brooks, Charles L.
- Biophysical Journal, Vol. 92, Issue 3
Phospholipid-binding Sites of Phosphatase and Tensin Homolog (PTEN)
journal, January 2015
- Wei, Yang; Stec, Boguslaw; Redfield, Alfred G.
- Journal of Biological Chemistry, Vol. 290, Issue 3
The crystal structure of the complex of blood coagulation factor VIIa with soluble tissue factor
journal, March 1996
- Banner, David W.; D'Arcy, Allan; Chène, Christiana
- Nature, Vol. 380, Issue 6569
Crystal Structure of Human Factor VIII: Implications for the Formation of the Factor IXa-Factor VIIIa Complex
journal, April 2008
- Ngo, Jacky Chi Ki; Huang, Mingdong; Roth, David A.
- Structure, Vol. 16, Issue 4
Arachidonic Acid-metabolizing Cytochrome P450 Enzymes Are Targets of ω-3 Fatty Acids*
journal, October 2010
- Arnold, Cosima; Markovic, Marija; Blossey, Katrin
- Journal of Biological Chemistry, Vol. 285, Issue 43
Interaction of NBD-talin with lipid monolayers: A film balance study
journal, June 1993
- Dietrich, C.; Goldmann, W. H.; Sackmann, E.
- FEBS Letters, Vol. 324, Issue 1
Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution
journal, March 1988
- Radzicka, Anna; Wolfenden, Richard
- Biochemistry, Vol. 27, Issue 5
From Self-Assembled Vesicles to Protocells
journal, June 2010
- Chen, I. A.; Walde, P.
- Cold Spring Harbor Perspectives in Biology, Vol. 2, Issue 7
The Lipid-binding Domain of Wild Type and Mutant α-Synuclein
journal, September 2010
- Georgieva, Elka R.; Ramlall, Trudy F.; Borbat, Peter P.
- Journal of Biological Chemistry, Vol. 285, Issue 36
Molecular Dynamics Simulations of Large Integral Membrane Proteins with an Implicit Membrane Model
journal, January 2006
- Tanizaki, Seiichiro; Feig, Michael
- The Journal of Physical Chemistry B, Vol. 110, Issue 1
The Structure of an Interdomain Complex That Regulates Talin Activity
journal, May 2009
- Goult, Benjamin T.; Bate, Neil; Anthis, Nicholas J.
- Journal of Biological Chemistry, Vol. 284, Issue 22
Side-chain hydrophobicity scale derived from transmembrane protein folding into lipid bilayers
journal, May 2011
- Moon, C. P.; Fleming, K. G.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 25
Integrin activation takes shape
journal, September 2002
- Liddington, R. C.; Ginsberg, M. H.
- Journal of Cell Biology, Vol. 158, Issue 5
A short amino-terminal segment of microsomal cytochrome P-450 functions both as an insertion signal and as a stop-transfer sequence.
journal, August 1987
- Sakaguchi, M.; Mihara, K.; Sato, R.
- The EMBO Journal, Vol. 6, Issue 8
From The Cover: Structure of membrane-bound -synuclein studied by site-directed spin labeling
journal, May 2004
- Jao, C. C.; Der-Sarkissian, A.; Chen, J.
- Proceedings of the National Academy of Sciences, Vol. 101, Issue 22
Cation−π Interactions As Lipid-Specific Anchors for Phosphatidylinositol-Specific Phospholipase C
journal, April 2013
- Grauffel, Cédric; Yang, Boqian; He, Tao
- Journal of the American Chemical Society, Vol. 135, Issue 15
Molecular Basis for Immune Recognition of Exposed Phosphatidylserine via the Tim Family of Proteins
journal, January 2012
- Tietjen, Gregory T.; Vargas, Ernesto; Chen, Chiu-Hao
- Biophysical Journal, Vol. 102, Issue 3
Biological membranes: the importance of molecular detail
journal, September 2011
- Lee, Anthony G.
- Trends in Biochemical Sciences, Vol. 36, Issue 9
The complete influenza hemagglutinin fusion domain adopts a tight helical hairpin arrangement at the lipid:water interface
journal, June 2010
- Lorieau, J. L.; Louis, J. M.; Bax, A.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 25
Distinct Structural and Adhesive Roles of Ca2+ in Membrane Binding of Blood Coagulation Factors
journal, January 2008
- Ohkubo, Y. Zenmei; Tajkhorshid, Emad
- Structure, Vol. 16, Issue 1
Mechanosensitive Channel MscS in the Open State: Modeling of the Transition, Explicit Simulations, and Experimental Measurements of Conductance
journal, June 2008
- Anishkin, Andriy; Kamaraju, Kishore; Sukharev, Sergei
- Journal of General Physiology, Vol. 132, Issue 1
Amyloid Aggregation: Role of Biological Membranes and the Aggregate–Membrane System
journal, January 2014
- Bucciantini, Monica; Rigacci, Stefania; Stefani, Massimo
- The Journal of Physical Chemistry Letters, Vol. 5, Issue 3
Molecular Model of Hemoglobin N from Mycobacterium tuberculosis Bound to Lipid Bilayers: A Combined Spectroscopic and Computational Study
journal, March 2015
- Rhéault, Jean-François; Gagné, Ève; Guertin, Michel
- Biochemistry, Vol. 54, Issue 11
Insertion of the Ca2+-Independent Phospholipase A2 into a Phospholipid Bilayer via Coarse-Grained and Atomistic Molecular Dynamics Simulations
journal, July 2013
- Bucher, Denis; Hsu, Yuan-Hao; Mouchlis, Varnavas D.
- PLoS Computational Biology, Vol. 9, Issue 7
Integrin regulation
journal, October 2005
- Ginsberg, Mark H.; Partridge, Anthony; Shattil, Sanford J.
- Current Opinion in Cell Biology, Vol. 17, Issue 5
Molecular Details of α-Synuclein Membrane Association Revealed by Neutrons and Photons
journal, March 2015
- Jiang, Zhiping; Hess, Sara K.; Heinrich, Frank
- The Journal of Physical Chemistry B, Vol. 119, Issue 14
Efficient Exploration of Membrane-Associated Phenomena at Atomic Resolution
journal, May 2015
- Vermaas, Josh V.; Baylon, Javier L.; Arcario, Mark J.
- The Journal of Membrane Biology, Vol. 248, Issue 3
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
α-Synuclein Reduces Tension and Increases Undulations in Simulations of Small Unilamellar Vesicles
journal, April 2015
- Braun, Anthony R.; Sachs, Jonathan N.
- Biophysical Journal, Vol. 108, Issue 8
Molecular dynamics simulations of cholesterol-rich membranes using a coarse-grained force field for cyclic alkanes
journal, December 2015
- MacDermaid, Christopher M.; Kashyap, Hemant K.; DeVane, Russell H.
- The Journal of Chemical Physics, Vol. 143, Issue 24
Predictive energy landscapes for folding -helical transmembrane proteins
journal, July 2014
- Kim, B. L.; Schafer, N. P.; Wolynes, P. G.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 30
P450 superfamily: update on new sequences, gene mapping, accession numbers and nomenclature
journal, January 1996
- Nelson, David R.; Koymans, Luc; Kamataki, Tetsuya
- Pharmacogenetics, Vol. 6, Issue 1
The Structure and Function of the Hemagglutinin Membrane Glycoprotein of Influenza Virus
journal, June 1987
- Wiley, D. C.; Skehel, J. J.
- Annual Review of Biochemistry, Vol. 56, Issue 1
Combinatorial antibody libraries from cancer patients yield ligand-mimetic Arg-Gly-Asp-containing immunoglobulins that inhibit breast cancer metastasis
journal, November 2004
- Felding-Habermann, B.; Lerner, R. A.; Lillo, A.
- Proceedings of the National Academy of Sciences, Vol. 101, Issue 49
α-Synuclein-Induced Membrane Remodeling Is Driven by Binding Affinity, Partition Depth, and Interleaflet Order Asymmetry
journal, July 2014
- Braun, Anthony R.; Lacy, Michael M.; Ducas, Vanessa C.
- Journal of the American Chemical Society, Vol. 136, Issue 28
Talin Binding to Integrin Tails: A Final Common Step in Integrin Activation
journal, October 2003
- Tadokoro, S.
- Science, Vol. 302, Issue 5642
A reinterpretation of neutron scattering experiments on a lipidated Ras peptide using replica exchange molecular dynamics
journal, February 2012
- Vogel, Alexander; Roark, Matthew; Feller, Scott E.
- Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1818, Issue 2
Membrane structure and fusion-triggering conformational change of the fusion domain from influenza hemagglutinin
journal, August 2001
- Han, Xing; Bushweller, John H.; Cafiso, David S.
- Nature Structural Biology, Vol. 8, Issue 8, p. 715-720
α-Synuclein in Lewy bodies
journal, August 1997
- Spillantini, Maria Grazia; Schmidt, Marie Luise; Lee, Virginia M. -Y.
- Nature, Vol. 388, Issue 6645
Site-Specific Interaction between α-Synuclein and Membranes Probed by NMR-Observed Methionine Oxidation Rates
journal, February 2013
- Maltsev, Alexander S.; Chen, Jue; Levine, Rodney L.
- Journal of the American Chemical Society, Vol. 135, Issue 8
Membrane Docking Geometry and Target Lipid Stoichiometry of Membrane-Bound PKCα C2 Domain: A Combined Molecular Dynamics and Experimental Study
journal, September 2010
- Lai, Chun-Liang; Landgraf, Kyle E.; Voth, Gregory A.
- Journal of Molecular Biology, Vol. 402, Issue 2
Molecular Mechanism of Membrane Binding of the GRP1 PH Domain
journal, September 2013
- Lai, Chun-Liang; Srivastava, Anand; Pilling, Carissa
- Journal of Molecular Biology, Vol. 425, Issue 17
PSII–LHCII Supercomplex Organizations in Photosynthetic Membrane by Coarse-Grained Simulation
journal, February 2015
- Lee, Cheng-Kuang; Pao, Chun-Wei; Smit, Berend
- The Journal of Physical Chemistry B, Vol. 119, Issue 10
Inter-Helix Distances in Lysophospholipid Micelle-Bound α-Synuclein from Pulsed ESR Measurements
journal, August 2006
- Borbat, Peter; Ramlall, Trudy F.; Freed, Jack H.
- Journal of the American Chemical Society, Vol. 128, Issue 31