Mechanism of Substrate Translocation in an Alternating Access Transporter
- Authors:
- Publication Date:
- Research Org.:
- Carnegie Inst. of Science, Stanford, CA (United States)
- Sponsoring Org.:
- USDOE; National Institutes of Health (NIH); National Science Foundation (NSF); Alfred P. Sloan Foundation; Harold and Leila Y. Mathers Charitable Foundation; Stanford University
- OSTI Identifier:
- 1429555
- Alternate Identifier(s):
- OSTI ID: 1398626; OSTI ID: 1473844
- Grant/Contract Number:
- FG02-04ER15542
- Resource Type:
- Published Article
- Journal Name:
- Cell
- Additional Journal Information:
- Journal Name: Cell Journal Volume: 169 Journal Issue: 1; Journal ID: ISSN 0092-8674
- Publisher:
- Elsevier
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; molecular dynamics (MD) simulation; membrane protein; transporter; sugar transporter; SemiSWEET; structure
Citation Formats
Latorraca, Naomi R., Fastman, Nathan M., Venkatakrishnan, A. J., Frommer, Wolf B., Dror, Ron O., and Feng, Liang. Mechanism of Substrate Translocation in an Alternating Access Transporter. United States: N. p., 2017.
Web. doi:10.1016/j.cell.2017.03.010.
Latorraca, Naomi R., Fastman, Nathan M., Venkatakrishnan, A. J., Frommer, Wolf B., Dror, Ron O., & Feng, Liang. Mechanism of Substrate Translocation in an Alternating Access Transporter. United States. https://doi.org/10.1016/j.cell.2017.03.010
Latorraca, Naomi R., Fastman, Nathan M., Venkatakrishnan, A. J., Frommer, Wolf B., Dror, Ron O., and Feng, Liang. Wed .
"Mechanism of Substrate Translocation in an Alternating Access Transporter". United States. https://doi.org/10.1016/j.cell.2017.03.010.
@article{osti_1429555,
title = {Mechanism of Substrate Translocation in an Alternating Access Transporter},
author = {Latorraca, Naomi R. and Fastman, Nathan M. and Venkatakrishnan, A. J. and Frommer, Wolf B. and Dror, Ron O. and Feng, Liang},
abstractNote = {},
doi = {10.1016/j.cell.2017.03.010},
journal = {Cell},
number = 1,
volume = 169,
place = {United States},
year = {Wed Mar 01 00:00:00 EST 2017},
month = {Wed Mar 01 00:00:00 EST 2017}
}
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1016/j.cell.2017.03.010
https://doi.org/10.1016/j.cell.2017.03.010
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 60 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
SPFP: Speed without compromise—A mixed precision model for GPU accelerated molecular dynamics simulations
journal, February 2013
- Le Grand, Scott; Götz, Andreas W.; Walker, Ross C.
- Computer Physics Communications, Vol. 184, Issue 2
A chemiosmotic mechanism of symport
journal, January 2015
- Kaback, H. Ronald
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 5
Solving structures of protein complexes by molecular replacement with Phaser
journal, December 2006
- McCoy, Airlie J.
- Acta Crystallographica Section D Biological Crystallography, Vol. 63, Issue 1
The Crystal Structure of a Sodium Galactose Transporter Reveals Mechanistic Insights into Na+/Sugar Symport
journal, August 2008
- Faham, S.; Watanabe, A.; Besserer, G. M.
- Science, Vol. 321, Issue 5890
Simple Allosteric Model for Membrane Pumps
journal, August 1966
- Jardetzky, Oleg
- Nature, Vol. 211, Issue 5052
Mechanistic diversity in ATP-binding cassette (ABC) transporters
journal, June 2016
- Locher, Kaspar P.
- Nature Structural & Molecular Biology, Vol. 23, Issue 6
Functional role of oligomerization for bacterial and plant SWEET sugar transporter family
journal, September 2013
- Xuan, Y. H.; Hu, Y. B.; Chen, L. -Q.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 39
CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data
journal, July 2013
- Huang, Jing; MacKerell, Alexander D.
- Journal of Computational Chemistry, Vol. 34, Issue 25
Crystal structure of a eukaryotic phosphate transporter
journal, March 2013
- Pedersen, Bjørn P.; Kumar, Hemant; Waight, Andrew B.
- Nature, Vol. 496, Issue 7446
Protonation drives the conformational switch in the multidrug transporter LmrP
journal, December 2013
- Masureel, Matthieu; Martens, Chloé; Stein, Richard A.
- Nature Chemical Biology, Vol. 10, Issue 2
Visualizing Functional Motions of Membrane Transporters with Molecular Dynamics Simulations
journal, January 2013
- Shaikh, Saher A.; Li, Jing; Enkavi, Giray
- Biochemistry, Vol. 52, Issue 4
Structure of sugar-bound LacY
journal, January 2014
- Kumar, Hemant; Kasho, Vladimir; Smirnova, Irina
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 5
Structural Biology of the Major Facilitator Superfamily Transporters
journal, June 2015
- Yan, Nieng
- Annual Review of Biophysics, Vol. 44, Issue 1
Structure of a eukaryotic SWEET transporter in a homotrimeric complex
journal, October 2015
- Tao, Yuyong; Cheung, Lily S.; Li, Shuo
- Nature, Vol. 527, Issue 7577
Simulations of the Alternating Access Mechanism of the Sodium Symporter Mhp1
journal, November 2011
- Adelman, Joshua L.; Dale, Amy L.; Zwier, Matthew C.
- Biophysical Journal, Vol. 101, Issue 10
Structural basis for the facilitative diffusion mechanism by SemiSWEET transporter
journal, January 2015
- Lee, Yongchan; Nishizawa, Tomohiro; Yamashita, Keitaro
- Nature Communications, Vol. 6, Issue 1
Atomic-level characterization of transport cycle thermodynamics in the glycerol-3-phosphate:phosphate antiporter
journal, September 2015
- Moradi, Mahmoud; Enkavi, Giray; Tajkhorshid, Emad
- Nature Communications, Vol. 6, Issue 1
Modeling and simulation of ion-coupled and ATP-driven membrane proteins
journal, April 2011
- Faraldo-Gómez, José D.; Forrest, Lucy R.
- Current Opinion in Structural Biology, Vol. 21, Issue 2
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald
journal, August 2013
- Salomon-Ferrer, Romelia; Götz, Andreas W.; Poole, Duncan
- Journal of Chemical Theory and Computation, Vol. 9, Issue 9
Understanding transport by the major facilitator superfamily (MFS): structures pave the way
journal, January 2016
- Quistgaard, Esben M.; Löw, Christian; Guettou, Fatma
- Nature Reviews Molecular Cell Biology, Vol. 17, Issue 2
A General Theory of Membrane Transport From Studies of Bacteria
journal, July 1957
- Mitchell, Peter
- Nature, Vol. 180, Issue 4577
Substrate Recognition at the Cytoplasmic and Extracellular Binding Site of the Lactose Transport Protein of Streptococcus thermophilus
journal, November 1999
- Veenhoff, Liesbeth M.; Poolman, Bert
- Journal of Biological Chemistry, Vol. 274, Issue 47
Unbiased Simulations Reveal the Inward-Facing Conformation of the Human Serotonin Transporter and Na+ Ion Release
journal, October 2011
- Koldsø, Heidi; Noer, Pernille; Grouleff, Julie
- PLoS Computational Biology, Vol. 7, Issue 10
Hydrophilicity of cavities in proteins
journal, April 1996
- Zhang, Li; Hermans, Jan
- Proteins: Structure, Function, and Genetics, Vol. 24, Issue 4
Inclusion of Many-Body Effects in the Additive CHARMM Protein CMAP Potential Results in Enhanced Cooperativity of α-Helix and β-Hairpin Formation
journal, September 2012
- Best, Robert B.; Mittal, Jeetain; Feig, Michael
- Biophysical Journal, Vol. 103, Issue 5
Crystal structure of a bacterial homologue of Na+/Cl--dependent neurotransmitter transporters
journal, July 2005
- Yamashita, Atsuko; Singh, Satinder K.; Kawate, Toshimitsu
- Nature, Vol. 437, Issue 7056
Structure of the Multidrug Transporter EmrD from Escherichia coli
journal, May 2006
- Yin, Y.
- Science, Vol. 312, Issue 5774
Ion-Controlled Conformational Dynamics in the Outward-Open Transition from an Occluded State of LeuT
journal, September 2012
- Zhao, Chunfeng; Stolzenberg, Sebastian; Gracia, Luis
- Biophysical Journal, Vol. 103, Issue 5
Conformational Change in an MFS Protein: MD Simulations of LacY
journal, July 2007
- Holyoake, John; Sansom, Mark S. P.
- Structure, Vol. 15, Issue 7
Conformational dynamics of ligand-dependent alternating access in LeuT
journal, April 2014
- Kazmier, Kelli; Sharma, Shruti; Quick, Matthias
- Nature Structural & Molecular Biology, Vol. 21, Issue 5
Integration, scaling, space-group assignment and post-refinement
journal, January 2010
- Kabsch, Wolfgang
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 133-144
Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types
journal, June 2010
- Klauda, Jeffery B.; Venable, Richard M.; Freites, J. Alfredo
- The Journal of Physical Chemistry B, Vol. 114, Issue 23
Biomolecular Simulation: A Computational Microscope for Molecular Biology
journal, June 2012
- Dror, Ron O.; Dirks, Robert M.; Grossman, J. P.
- Annual Review of Biophysics, Vol. 41, Issue 1
Allosteric Mechanisms of Molecular Machines at the Membrane: Transport by Sodium-Coupled Symporters
journal, February 2016
- LeVine, Michael V.; Cuendet, Michel A.; Khelashvili, George
- Chemical Reviews, Vol. 116, Issue 11
Molecular simulations elucidate the substrate translocation pathway in a glutamate transporter
journal, February 2009
- Gu, Yan; Shrivastava, Indira H.; Amara, Susan G.
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 8
Glucose transport families SLC5 and SLC50
journal, April 2013
- Wright, Ernest M.
- Molecular Aspects of Medicine, Vol. 34, Issue 2-3
Induced fit substrate binding to an archeal glutamate transporter homologue
journal, July 2013
- Ewers, D.; Becher, T.; Machtens, J. -P.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 30
Apo-intermediate in the transport cycle of lactose permease (LacY)
journal, September 2012
- Madej, M. G.; Soro, S. N.; Kaback, H. R.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 44
Sugar transporters for intercellular exchange and nutrition of pathogens
journal, November 2010
- Chen, Li-Qing; Hou, Bi-Huei; Lalonde, Sylvie
- Nature, Vol. 468, Issue 7323
Multiscale Simulations Reveal Key Aspects of the Proton Transport Mechanism in the ClC-ec1 Antiporter
journal, March 2016
- Lee, Sangyun; Swanson, Jessica M. J.; Voth, Gregory A.
- Biophysical Journal, Vol. 110, Issue 6
Crystal structure of the human glucose transporter GLUT1
journal, May 2014
- Deng, Dong; Xu, Chao; Sun, Pengcheng
- Nature, Vol. 510, Issue 7503
Crystal structure of a bacterial homologue of glucose transporters GLUT1–4
journal, October 2012
- Sun, Linfeng; Zeng, Xin; Yan, Chuangye
- Nature, Vol. 490, Issue 7420
Computational characterization of structural dynamics underlying function in active membrane transporters
journal, April 2015
- Li, Jing; Wen, Po-Chao; Moradi, Mahmoud
- Current Opinion in Structural Biology, Vol. 31
Coupled ion binding and structural transitions along the transport cycle of glutamate transporters
journal, May 2014
- Verdon, Grégory; Oh, SeCheol; Serio, Ryan N.
- eLife, Vol. 3
Transport domain unlocking sets the uptake rate of an aspartate transporter
journal, February 2015
- Akyuz, Nurunisa; Georgieva, Elka R.; Zhou, Zhou
- Nature, Vol. 518, Issue 7537
P-Type ATPases
journal, June 2011
- Palmgren, Michael G.; Nissen, Poul
- Annual Review of Biophysics, Vol. 40, Issue 1
Coot model-building tools for molecular graphics
journal, November 2004
- Emsley, Paul; Cowtan, Kevin
- Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
Structures of bacterial homologues of SWEET transporters in two distinct conformations
journal, September 2014
- Xu, Yan; Tao, Yuyong; Cheung, Lily S.
- Nature, Vol. 515, Issue 7527
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ 1 and χ 2 Dihedral Angles
journal, August 2012
- Best, Robert B.; Zhu, Xiao; Shim, Jihyun
- Journal of Chemical Theory and Computation, Vol. 8, Issue 9
Mechanistic picture for conformational transition of a membrane transporter at atomic resolution
journal, November 2013
- Moradi, M.; Tajkhorshid, E.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 47
Crystal structure of a catalytic intermediate of the maltose transporter
journal, November 2007
- Oldham, Michael L.; Khare, Dheeraj; Quiocho, Florante A.
- Nature, Vol. 450, Issue 7169
PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010
- Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
Protonation of Glu 135 Facilitates the Outward-to-Inward Structural Transition of Fucose Transporter
journal, August 2015
- Liu, Yufeng; Ke, Meng; Gong, Haipeng
- Biophysical Journal, Vol. 109, Issue 3
The structural basis of secondary active transport mechanisms
journal, February 2011
- Forrest, Lucy R.; Krämer, Reinhard; Ziegler, Christine
- Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1807, Issue 2
Molecular Basis of Alternating Access Membrane Transport by the Sodium-Hydantoin Transporter Mhp1
journal, April 2010
- Shimamura, T.; Weyand, S.; Beckstein, O.
- Science, Vol. 328, Issue 5977
Gating Topology of the Proton-Coupled Oligopeptide Symporters
journal, February 2015
- Fowler, Philip W.; Orwick-Rydmark, Marcella; Radestock, Sebastian
- Structure, Vol. 23, Issue 2
Crystal structure of a phosphorylation-coupled saccharide transporter
journal, April 2011
- Cao, Yu; Jin, Xiangshu; Levin, Elena J.
- Nature, Vol. 473, Issue 7345
Shared Molecular Mechanisms of Membrane Transporters
journal, June 2016
- Drew, David; Boudker, Olga
- Annual Review of Biochemistry, Vol. 85, Issue 1
CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses
journal, August 2009
- Guvench, Olgun; Hatcher, Elizabeth; Venable, Richard M.
- Journal of Chemical Theory and Computation, Vol. 5, Issue 9
Matplotlib: A 2D Graphics Environment
journal, January 2007
- Hunter, John D.
- Computing in Science & Engineering, Vol. 9, Issue 3
Transport of Sugars
journal, June 2015
- Chen, Li-Qing; Cheung, Lily S.; Feng, Liang
- Annual Review of Biochemistry, Vol. 84, Issue 1
Towards an understanding of the structural basis of ‘forbidden’ transport pathways in the Escherichia coli lactose carrier: mutations probing the energy barriers to uncoupled transport
journal, September 1990
- King, S. C.; Wilson, T. H.
- Molecular Microbiology, Vol. 4, Issue 9
OPM: Orientations of Proteins in Membranes database
journal, January 2006
- Lomize, M. A.; Lomize, A. L.; Pogozheva, I. D.
- Bioinformatics, Vol. 22, Issue 5
The mechanism of sodium and substrate release from the binding pocket of vSGLT
journal, December 2010
- Watanabe, Akira; Choe, Seungho; Chaptal, Vincent
- Nature, Vol. 468, Issue 7326
Complete Mapping of Substrate Translocation Highlights the Role of LeuT N-terminal Segment in Regulating Transport Cycle
journal, October 2014
- Cheng, Mary Hongying; Bahar, Ivet
- PLoS Computational Biology, Vol. 10, Issue 10
[20] Processing of X-ray diffraction data collected in oscillation mode
book, January 1997
- Otwinowski, Zbyszek; Minor, Wladek
- Macromolecular Crystallography Part A, 307-326
Stochastic steps in secondary active sugar transport
journal, June 2016
- Adelman, Joshua L.; Ghezzi, Chiara; Bisignano, Paola
- Proceedings of the National Academy of Sciences, Vol. 113, Issue 27
Super-resolution biomolecular crystallography with low-resolution data
journal, April 2010
- Schröder, Gunnar F.; Levitt, Michael; Brunger, Axel T.
- Nature, Vol. 464, Issue 7292
Flexible Gates Generate Occluded Intermediates in the Transport Cycle of LacY
journal, February 2014
- Stelzl, Lukas S.; Fowler, Philip W.; Sansom, Mark S. P.
- Journal of Molecular Biology, Vol. 426, Issue 3
VMD: Visual molecular dynamics
journal, February 1996
- Humphrey, William; Dalke, Andrew; Schulten, Klaus
- Journal of Molecular Graphics, Vol. 14, Issue 1
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
journal, June 2013
- Roe, Daniel R.; Cheatham, Thomas E.
- Journal of Chemical Theory and Computation, Vol. 9, Issue 7
Crystal structure of a bacterial homologue of SWEET transporters
journal, November 2014
- Wang, Jing; Yan, Chuangye; Li, Yini
- Cell Research, Vol. 24, Issue 12
Structural basis for dynamic mechanism of nitrate/nitrite antiport by NarK
journal, May 2015
- Fukuda, Masahiro; Takeda, Hironori; Kato, Hideaki E.
- Nature Communications, Vol. 6, Issue 1