|
| 10075. Functional interplay between acetylation and methylation of the
RelA subunit of NF-kB.
X.-D. Yang, E. Tajkhorshid, and L.-F. Chen.
Molecular and Cellular Biology, 30:2170-2180, 2010.
|
| 10074. The binding interface of cytochrome c and cytochrome c1 in the
bc1 complex: rationalizing the role of key residues.
A. Kokhan, C. Wraight, and E. Tajkhorshid.
Biophysical Journal, 99:2647-2656, 2010.
|
| 10070. Accelerating membrane insertion of peripheral proteins with a novel
membrane mimetic model.
Y. Zenmei Ohkubo, Taras V. Pogorelov, Mark J. Arcario, Geoff A. Christensen,
and Emad Tajkhorshid.
Biophysical Journal, 102:2130-2139, 2012.
|
| 10065. A gate-free pathway for substrate release from the inward-facing
state of the Na+-galactose transporter.
Jing Li and Emad Tajkhorshid.
Biochimica et Biophysica Acta - Biomembranes, 1818:263-271,
2012.
|
| 10064. Membrane transporters: Molecular machines coupling cellular energy to
vectorial transport across the membrane.
Zhijian Huang, Saher A. Shaikh, Po-Chao Wen, Giray Enkavi, Jing Li, and Emad
Tajkhorshid.
In Benoit Roux, editor, Molecular Machines, chapter 9, pp.
151-182. World Scientific Publishing, Singapore, 2011.
|
| 10063. Capturing spontaneous partitioning of peripheral proteins using a
biphasic membrane-mimetic model.
Mark J. Arcario, Y. Zenmei Ohkubo, and Emad Tajkhorshid.
Journal of Physical Chemistry B, 115:7029-7037, 2011.
|
| 10062. Nanoscale studies of protein-membrane interactions in blood clotting.
James H. Morrissey, Emad Tajkhorshid, and Chad M. Rienstra.
Journal of Thrombosis and Haemostasis, 9 (Suppl. 1):167-167,
2011.
|
| 10061. Atomic view of calcium-induced clustering of phosphatidylserine in
mixed lipid bilayers.
John M. Boettcher, Rebecca L. Davis-Harrison, Mary C. Clay, Andrew J.
Nieuwkoop, Y. Zenmei Ohkubo, Emad Tajkhorshid, James H. Morrissey, and
Chad M. Rienstra.
Biochemistry, 50:2264-2273, 2011.
|
| 10060. Molecular determinants of phospholipid synergy in blood clotting.
Narjes Tavoosi, Rebecca L. Davis-Harrison, Taras V. Pogorelov, Y. Zenmei
Ohkubo, Mark J. Arcario, Mary C. Clay, Chad M. Rienstra, Emad Tajkhorshid,
and James H. Morrissey.
Journal of Biological Chemistry, 286:23247-23253, 2011.
|
| 10052. Modeling and dynamics of the inward-facing state of a
Na+/Cl- dependent neurotransmitter transporter homologue.
Saher Afshan Shaikh and Emad Tajkhorshid.
PLoS Computational Biology, 6(8):e1000905, 2010.
|
| 10051. Protein membrane interactions: blood clotting on nanoscale bilayer.
J. H. Morrissey, V. Pureza, R. L. Davis-Harrison, S. G. Sligar, C. M. Rienstra,
A. Z. Kijac, Y. Z. Ohkubo, and E. Tajkhorshid.
Journal of Thrombosis and Haemostasis, 7:169-172, 2009.
|
| 10050. Tyrosine phosphorylation by Src within the cavity of the adenine
nucleotide translocase 1 regulates ADP/ATP exchange in mitochondria.
Jianhua Feng, Eliana Lucchinetti, Giray Enkavi, Yi Wang, Peter Gehrig, Bernd
Roschitzki, Marcus C. Schaub, Emad Tajkhorshid, Kathrin Zaugg, and Michael
Zaugg.
2010.
In press.
|
| 10049. Structural basis of substrate selectivity in the
glycerol-3-phosphate:phosphate antiporter GlpT.
Christopher J. Law, Giray Enkavi, Da-Neng Wang, and Emad Tajkhorshid.
Biophysical Journal, 97:1346-1353, 2009.
|
| 10048. Identification of the third Na+ site and the sequence of
extracellular binding events in the glutamate transporter.
Zhijian Huang and Emad Tajkhorshid.
Biophysical Journal, 99:1416-1425, 2010.
|
| 10046. Capturing functional motions of membrane channels and transporters
with molecular dynamics simulation.
Saher A. Shaikh, Po-Chao Wen, Giray Enkavi, Zhijian Huang, and Emad
Tajkhorshid.
Journal of Computational and Theoretical Nanosciences,
7:2481-2500, 2010.
|
| 10045. Exploring transmembrane diffusion pathways with molecular dynamics.
Yi Wang, Saher A. Shaikh, and Emad Tajkhorshid.
Physiology, 25:142-154, 2010.
|
| 10044. Ion-releasing state of a secondary membrane transporter.
Jing Li and Emad Tajkhorshid.
Biophysical Journal, 97:L29-L31, 2009.
|
| 10043. Nitric oxide conduction by the brain aquaporin AQP4.
Yi Wang and Emad Tajkhorshid.
PROTEINS: Structure, Function, and Bioinformatics, 78:661-670,
2010.
|
| 10042. Dynamical view of membrane binding and complex formation of human
factor VIIa and tissue factor.
Y. Zenmei Ohkubo, James H. Morrissey, and Emad Tajkhorshid.
Journal of Thrombosis and Haemostasis, 8:1044-1053, 2010.
|
| 10041. Interplay of mechanical and binding properties of Fibronectin type
I.
Jiankuai Diao, Andrew J. Maniotis, Robert Folberg, and Emad Tajkhorshid.
Theoretica Chimica Acta, 125:397-405, 2010.
|
| 10040. Protein-phospholipid interactions in blood clotting.
James H. Morrissey, Rebecca L. Davis-Harrison, Narjes Tavoosi, Ke Ke, Vincent
Pureza, John M. Boettcher, Mary C. Clay, Chad M. Rienstra, Y. Zenmei Ohkubo,
Taras V. Pogorelov, and Emad Tajkhorshid.
Thrombosis Research, 125(Suppl. 1):S23-S25, 2010.
|
| 10038. Simulation of spontaneous substrate binding revealing the binding
pathway and mechanism and initial conformational response of GlpT.
Giray Enkavi and Emad Tajkhorshid.
Biochemistry, 49:1105-1114, 2010.
|
| 10037. Coupling of calcium and substrate binding through loop alignment in
the outer membrane transporter BtuB.
James Gumbart, Michael C. Wiener, and Emad Tajkhorshid.
Journal of Molecular Biology, 393:1129-1142, 2009.
|
| 10036. Molecular mechanisms of active transport across the cellular
membrane.
Po-Chao Wen, Zhijian Huang, Giray Enkavi, Yi Wang, James Gumbart, and Emad
Tajkhorshid.
In Philip Biggin and Mark Sansom, editors, Molecular Simulations
and Biomembranes: From Biophysics to Function, chapter 10, pp. 248-286.
Royal Society of Chemistry, 2010.
|
| 10035. Structural and functional analysis of SoPIP2;1 mutants add insight
into plant aquaporin gating.
Maria Nyblom, Anna Frick, Yi Wang, Mikael Ekvall, Karin Hallgren, Kristina
Hedfalk, Richard Neutze, Emad Tajkhorshid, and Susanna
Törnroth-Horsefield.
Journal of Molecular Biology, 387:653-668, 2009.
|
| 10034. Dimer opening of the nucleotide binding domains of ABC transporters
after ATP hydrolysis.
P.-C. Wen and E. Tajkhorshid.
Biophysical Journal, 95:5100-5110, 2008.
|
| 10033. Potential cation and H+ binding sites in acid sensing ion
channel-1.
S. A. Shaikh and E. Tajkhorshid.
Biophysical Journal, 95:5153-5164, 2008.
|
| |
| 10027. Dynamics of the extracellular gate and ion-substrate coupling in the
glutamate transporter.
Zhijian Huang and Emad Tajkhorshid.
Biophysical Journal, 95:2292-2300, 2008.
|
| 10026. Electrostatic funneling of substrate in mitochondrial inner membrane
carriers.
Yi Wang and Emad Tajkhorshid.
Proceedings of the National Academy of Sciences, USA,
105:9598-9603, 2008.
|
| 10025. Resolution enhancement in solid-state NMR spectra of oriented
membrane proteins by anisotropic differential linebroadening.
T. Vosegaard, K. Bertelsen, J. M. Pedresen, L. Thøgersen, B. Schiøtt,
E. Tajkhorshid, T Skrydstrup, and N. Chr. Nielsen.
Journal of the American Chemical Society, 130:5028-5029, 2008.
|
| 10024. Blood clotting reactions on nanoscale phospholipid bilayers.
J. H. Morrissey, V. Pureza, R. L. Davis-Harrison, S. G. Sligar, Y. Z. Ohkubo,
and E. Tajkhorshid.
Thrombosis Research, 122:S23-S26, 2008.
|
| 10023. Indirect role of Ca2+ in the assembly of extracelluar matrix
proteins.
Jiankuai Diao and Emad Tajkhorshid.
Biophysical Journal, 95:120-127, 2008.
|
| 10022. Gas conduction of lipid bilayers and membrane channels.
Y. Wang, Y. Zenmei Ohkubo, and E. Tajkhorshid.
In Scott Feller, editor, Current Topics in Membranes:
Computational Modeling of Membrane Bilayers, volume 60, chapter 12, pp.
343-367. Elsevier, 2008.
|
| 10014. Substrate binding and formation of an occluded state in the leucine
transporter.
L. Celik, B. Schiott, and E. Tajkhorshid.
Biophysical Journal, 94:1600-1612, 2008.
|
| 10013. Distinct structural and adhesive roles of Ca2+ in membrane
binding of blood coagulation factors.
Y. Zenmei Ohkubo and Emad Tajkhorshid.
Structure, 16:72-81, 2008.
|
| 10012. Molecular mechanisms of conduction and selectivity in aquaporin water
channels.
Yi Wang and Emad Tajkhorshid.
Journal of Nutrition, 137:1509S-1515S, 2007.
|
| 10010. Mechanics of force propagation in TonB-dependent outer membrane
transport.
James Gumbart, Michael C. Wiener, and Emad Tajkhorshid.
Biophysical Journal, 93:496-504, 2007.
|
| 10008. Structural mechanism of plant aquaporin gating.
S. Törnroth-Horsefield, Y. Wang, K. Hedfalk, U. Johanson, M. Karlsson,
E. Tajkhorshid, R. Neutze, and P. Kjellbom.
Nature, 439:688-694, 2006.
|
| 10007. Towards theoretical analysis of long-range proton transfer kinetics
in biomolecular pumps.
P. H. Koenig, N. Ghosh, M. Hoffmann, M. Elstner, E. Tajkhorshid, Th.
Frauenheim, and Q. Cui.
Journal of Physical Chemistry A, 110:548-563, 2006.
|
| 10004. Classical force field parameters for the heme prosthetic group of
cytochrome c.
F. Autenrieth, E. Tajkhorshid, J. Baudry, and Z. Luthey-Schulten.
Journal of Computational Chemistry, 25:1613-1622, 2004.
|
| 10003. Molecular basis of proton blockage in aquaporins.
N. Chakrabarti, E. Tajkhorshid, B. Roux, and R. Pomes.
Structure, 12:65-74, 2004.
|
| |
| 575. Molecular dynamics investigation of the w current in the
Kv1.2 voltage sensor domains.
Fatemeh Khalili-Araghi, Emad Tajkhorshid, Benoit Roux, and Klaus Schulten.
Biophysical Journal, 102:258-267, 2012.
|
| 521. Calculation of the gating charge for the Kv1.2 voltage-activated
potassium channel.
Fatemeh Khalili-Araghi, Vishwanath Jogini, Vladimir Yarov-Yarovoy, Emad
Tajkhorshid, Benoit Roux, and Klaus Schulten.
Biophysical Journal, 98:2189-2198, 2010.
|
| 495. Molecular dynamics simulations of membrane channels and transporters.
Fatemeh Khalili-Araghi, James Gumbart, Po-Chao Wen, Marcos Sotomayor, Emad
Tajkhorshid, and Klaus Schulten.
Current Opinion in Structural Biology, 19:128-137, 2009.
|
| 483. Photochemical reaction dynamics of the primary event of vision
studied by a hybrid molecular simulation.
Shigehiko Hayashi, Emad Tajkhorshid, and Klaus Schulten.
Biophysical Journal, 96:403-416, 2009.
|
| 470. Mechanism of signal propagation upon retinal isomerization: Insights
from molecular dynamics simulations of rhodopsin restrained by normal modes.
Basak Isin, Klaus Schulten, Emad Tajkhorshid, and Ivet Bahar.
Biophysical Journal, 95:789-803, 2008.
|
| 458. Diffusion of glycerol through Escherichia coli
aquaglyceroporin GlpF.
Jerome Henin, Emad Tajkhorshid, Klaus Schulten, and Christophe Chipot.
Biophysical Journal, 94:832-839, 2008.
|
| 441. Sugar transport across lactose permease probed by steered molecular
dynamics.
Morten Ø. Jensen, Ying Yin, Emad Tajkhorshid, and Klaus Schulten.
Biophysical Journal, 93:92-102, 2007.
|
| 436. Exploring gas permeability of cellular membranes and membrane
channels with molecular dynamics.
Yi Wang, Jordi Cohen, Walter F. Boron, Klaus Schulten, and Emad Tajkhorshid.
Journal of Structural Biology, 157:534-544, 2007.
|
| 431. Sugar binding and protein conformational changes in lactose permease.
Ying Yin, Morten Ø. Jensen, Emad Tajkhorshid, and Klaus Schulten.
Biophysical Journal, 91:3972-3985, 2006.
|
| 425. Mechanism of gating and ion conductivity of a possible tetrameric
pore in Aquaporin-1.
Jin Yu, Andrea J. Yool, Klaus Schulten, and Emad Tajkhorshid.
Structure, 14:1411-1423, 2006.
|
| 424. Dynamics of K+ ion conduction through Kv1.2.
Fatemeh Khalili-Araghi, Emad Tajkhorshid, and Klaus Schulten.
Biophysical Journal, 91:L72-L74, 2006.
|
| 421. Color tuning in rhodopsins: the mechanism for the spectral shift
between bacteriorhodopsin and sensory rhodopsin II.
Michael Hoffmann, Marius Wanko, Paul Strodel, Peter H. Koenig, Thomas
Frauenheim, Klaus Schulten, Walter Thiel, Emad Tajkhorshid, and Marcus
Elstner.
Journal of the American Chemical Society, 128:10808-10818,
2006.
|
| 400. Scalable molecular dynamics with NAMD.
James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid,
Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kale, and
Klaus Schulten.
Journal of Computational Chemistry, 26:1781-1802, 2005.
|
| 397. Molecular dynamics simulations of proteins in lipid bilayers.
James Gumbart, Yi Wang, Alekseij Aksimentiev, Emad Tajkhorshid, and Klaus
Schulten.
Current Opinion in Structural Biology, 15:423-431, 2005.
|
| 392. What makes an aquaporin a glycerol channel: A comparative study of
AqpZ and GlpF.
Yi Wang, Klaus Schulten, and Emad Tajkhorshid.
Structure, 13:1107-1118, 2005.
|
| 384. Kinetic theory and simulation of single-channel water transport.
Emad Tajkhorshid, Fangqiang Zhu, and Klaus Schulten.
In S. Yip, editor, Handbook of Materials Modeling, Vol. I:
Methods and Models, pp. 1797-1822. Springer, Netherlands, 2005.
|
| 381. Towards understanding membrane channels.
Emad Tajkhorshid, Jordi Cohen, Aleksij Aksimentiev, Marcos Sotomayor, and Klaus
Schulten.
In Boris Martinac and Andrzej Kubalski, editors, Bacterial ion
channels and their eukaryotic homologues, pp. 153-190. ASM Press,
Washington, DC, 2005.
|
| 378. Collective diffusion model for water permeation through microscopic
channels.
Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten.
Physical Review Letters, 93:224501, 2004.
(4 pages).
|
| 375. Role of water in transient cytochrome c2 docking.
Felix Autenrieth, Emad Tajkhorshid, Klaus Schulten, and Zaida Luthey-Schulten.
Journal of Physical Chemistry B, 108:20376-20387, 2004.
|
| 369. Role of hydrogen-bond network in energy storage of
bacteriorhodopsin's light-driven proton pump revealed by ab initio
normal mode analysis.
Shigehiko Hayashi, Emad Tajkhorshid, Hideki Kandori, and Klaus Schulten.
Journal of the American Chemical Society, 126:10516-10517,
2004.
|
| 365. Complementarities and convergence of results in bacteriorhodopsin
trimer simulations.
Jerome Baudry, Emad Tajkhorshid, and Klaus Schulten.
Biophysical Journal, 87:1394-1395, 2004.
|
| 355. The mechanism of proton exclusion in aquaporin channels.
Boaz Ilan, Emad Tajkhorshid, Klaus Schulten, and Gregory A. Voth.
PROTEINS: Structure, Function, and Bioinformatics, 55:223-228,
2004.
|
| 350. Theory and simulation of water permeation in aquaporin-1.
Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten.
Biophysical Journal, 86:50-57, 2004.
|
| 344. Electrostatic tuning of permeation and selectivity in aquaporin water
channels.
Morten Ø. Jensen, Emad Tajkhorshid, and Klaus Schulten.
Biophysical Journal, 85:2884-2899, 2003.
|
| 342. Free energy calculation from steered molecular dynamics simulations
using Jarzynski's equality.
Sanghyun Park, Fatemeh Khalili-Araghi, Emad Tajkhorshid, and Klaus Schulten.
Journal of Chemical Physics, 119:3559-3566, 2003.
|
| 341. Molecular dynamics simulation of bacteriorhodopsin's
photoisomerization using ab initio forces for the excited chromophore.
Shigehiko Hayashi, Emad Tajkhorshid, and Klaus Schulten.
Biophysical Journal, 85:1440-1449, 2003.
|
| 340. Large scale simulation of protein mechanics and function.
Emad Tajkhorshid, Aleksij Aksimentiev, Ilya Balabin, Mu Gao, Barry Isralewitz,
James C. Phillips, Fangqiang Zhu, and Klaus Schulten.
In Frederic M. Richards, David S. Eisenberg, and John Kuriyan,
editors, Advances in Protein Chemistry, volume 66, pp. 195-247.
Elsevier Academic Press, New York, 2003.
|
| 337. Mechanisms of selectivity in channels and enzymes studied with
interactive molecular dynamics.
Paul Grayson, Emad Tajkhorshid, and Klaus Schulten.
Biophysical Journal, 85:36-48, 2003.
|
| 333. Molecular dynamics investigation of primary photoinduced events in
the activation of rhodopsin.
Jan Saam, Emad Tajkhorshid, Shigehiko Hayashi, and Klaus Schulten.
Biophysical Journal, 83:3097-3112, 2002.
|
| 329. Control of the selectivity of the aquaporin water channel family by
global orientational tuning.
Emad Tajkhorshid, Peter Nollert, Morten Ø. Jensen, Larry J. W. Miercke,
Joseph O'Connell, Robert M. Stroud, and Klaus Schulten.
Science, 296:525-530, 2002.
|
| 328. Energetics of glycerol conduction through aquaglyceroporin GlpF.
Morten Ø. Jensen, Sanghyun Park, Emad Tajkhorshid, and Klaus Schulten.
Proceedings of the National Academy of Sciences, USA,
99:6731-6736, 2002.
|
| 327. Pressure-induced water transport in membrane channels studied by
molecular dynamics.
Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten.
Biophysical Journal, 83:154-160, 2002.
|
| 325. Structural changes during the formation of early intermediates in the
bacteriorhodopsin photocycle.
Shigehiko Hayashi, Emad Tajkhorshid, and Klaus Schulten.
Biophysical Journal, 83:1281-1297, 2002.
|
| 318. The mechanism of glycerol conduction in aquaglyceroporins.
Morten Ø. Jensen, Emad Tajkhorshid, and Klaus Schulten.
Structure, 9:1083-1093, 2001.
|
| 313. Molecular dynamics study of aquaporin-1 water channel in a lipid
bilayer.
Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten.
FEBS Letters, 504:212-218, 2001.
|
| 312. Structural determinants of spectral tuning in retinal proteins -
bacteriorhodopsin vs sensory rhodopsin II.
Shigehiko Hayashi, Emad Tajkhorshid, Eva Pebay-Peyroula, Antoine Royant,
Ehud M. Landau, Javier Navarro, and Klaus Schulten.
Journal of Physical Chemistry B, 105:10124-10131, 2001.
|
| 302. Molecular dynamics study of bacteriorhodopsin and the purple
membrane.
Jerome Baudry, Emad Tajkhorshid, Ferenc Molnar, James Phillips, and Klaus
Schulten.
Journal of Physical Chemistry B, 105:905-918, 2001.
|
| 285. Molecular dynamics study of the nature and origin of retinal's
twisted structure in bacteriorhodopsin.
Emad Tajkhorshid, Jerome Baudry, Klaus Schulten, and Sandor Suhai.
Biophysical Journal, 78:683-693, 2000.
|
