|
| 214. Structural insights into the lipid a transport pathway in MsbA.
P. S. Padayatti, S. C. Lee, R. L. Stanfield, P.-C. Wen, E. Tajkhorshid, I. A.
Wilson, and Q. Zhang.
Structure, 2019.
In press.
|
| 213. Serotonin transporter-ibogaine complexes illuminate mechanisms of
inhibition and transport.
Jonathan A. Coleman, Dongxue Yang, Zhiyu Zhao, Po-Chao Wen, Craig Yoshioka,
Emad Tajkhorshid, and Eric Gouaux.
Nature, 569:141-145, 2019.
|
| 212. Characterization of lipid-protein interactions and lipid-mediated
modulation of membrane protein function through molecular simulations.
Melanie P. Muller, Tao Jiang, Chang Sun, Muyun Lihan, Shashank Pant, Paween
Mahinthichaichan, Anda Trifan, and Emad Tajkhorshid.
Chemical Reviews, 119:6086-6161, 2019.
|
| 211. Allosteric interactions in human cytochrome P450 CYP3A4: The role
of phenylalanine 213.
Ilia G. Denisov, Yelena V. Grinkova, Prithviraj Nandigrami, Mrinal S. Shekhar,
Emad Tajkhorshid, and Stephen G. Sligar.
Biochemistry, 58:1411-1422, 2019.
|
| 210. The SERM/SERD bazedoxifene disrupts ESR1 helix 12 to overcome
acquired hormone resistance in breast cancer cells.
Sean W Fanning, Rinath Jeselsohn, Venkatasubramanian Dharmarajan, Christopher G
Mayne, Mostafa Karimi, Gilles Buchwalter, René Houtman, Weiyi Toy,
Colin E Fowler, Ross Han, Muriel Lainé, Kathryn E Carlson, Teresa A
Martin, Jason Nowak, Jerome C Nwachukwu, David J Hosfield, Sarat
Chandarlapaty, Emad Tajkhorshid, Kendall W Nettles, Patrick R Griffin, Yang
Shen, John A Katzenellenbogen, Myles Brown, and Geoffrey L Greene.
eLife, 7:e37161, 2018.
(PMC: PMC6335054) |
| 209. Calcium-induced lipid nanocluster structures: Sculpturing of the
plasma membrane.
Michael J. Hallock, Alexander I. Greenwood, Yan Wang, James H. Morrissey, Emad
Tajkhorshid, Chad M. Rienstra, and Taras V. Pogorelov.
Biochemistry, 57:6897-6905, 2018.
|
| 208. Phosphatidic acid induces conformational changes in Sec18 protomers
that prevent SNARE priming.
Matthew L Starr, Robert P Sparks, Andres S Arango, Logan R Hurst, Zhiyu Zhao,
Muyun Lihan, Jermaine L Jenkins, Emad Tajkhorshid, and Rutilio A Fratti.
Journal of Biological Chemistry, 294:3100-3116, 2019.
(PMC: PMC6398130) |
| 207. Menthol stereoisomers exhibit different effects on α4β2
nAChR upregulation and dopamine neuron spontaneous firing.
Brandon J. Henderson, Stephen Grant, Betty W. Chu, Rezvan Shahoei, Stephanie M.
Huard, Shyam S. M. Saladi, Emad Tajkhorshid, Dennis A. Dougherty, and
Henry A. Lester.
eNeuro, 5:ENEURO.0465, 2018.
(PMC: PMC6325563) |
| 206. Scalable Molecular Dynamics with NAMD on the Summit system.
Bilge Acun, David Hardy, Laxmikant Kale, Ke Li, James C. Phillips, and John E.
Stone.
IBM Journal of Research and Development, 62:4:1-4:9, 2019.
|
| 205. Best practices in running collaborative GPU hackathons: Advancing
scientific applications with a sustained impact.
Sunita Chandrasekaran, Guido Juckeland, Meifeng Lin, Matthew Otten, Dirk
Pleiter, John E Stone, Juan Lucio-Vega, Michael Zingale, and Fernanda
Foertter.
Computing in Science and Engineering, 20:95-106, 2018.
|
| 204. NanoShaper-VMD interface: computing and visualizing surfaces,
pockets and channels in molecular systems.
Sergio Decherchi, Andrea Spitaleri, John Stone, and Walter Rocchia.
Bioinformatics, 2018.
In Press.
|
| 203. Main-chain mutagenesis reveals intrahelical coupling in an ion
channel voltage-sensor.
Daniel T. Infield, Kimberly Matulef, Jason D. Galpin, Kin Lam, Emad
Tajkhorshid, Christopher A. Ahern, and Francis I. Valiyaveetil.
Nature Communications, 9:5055, 2018.
(PMC: PMC6265297) |
| 202. Endocannabinoid virodhamine is an endogenous inhibitor of human
cardiovascular CYP2J2 epoxygenase.
Lauren Carnevale, Andres Arango, William R. Arnold, Emad Tajkhorshid, and Aditi
Das.
Biochemistry, 57:6489-6499, 2018.
(PMC: PMC6262108) |
| 201. Selective permeability of carboxysome shell pores to anionic
molecules.
Paween Mahinthichaichan, Dylan M. Morris, Yi Wang, Grant J. Jensen, and Emad
Tajkhorshid.
Journal of Physical Chemistry B, 122:9110-9118, 2018.
(PMC: PMC6311388) |
| 200. Direct protein-lipid interactions shape the conformational landscape
of secondary transporters.
C. Martens, M. Shekhar, A. Borysik, A. Lau, E. Reading, E. Tajkhorshid, P. J.
Booth, and A. Politis.
Nature Communications, 9:4151, 2018.
(PMC: PMC6175955) |
| 199. Constructing atomic structural models into cryo-EM densities using
molecular dynamics - pros and cons.
Yuhang Wang, Mrinal Shekhar, Darren Thifault, Christopher J Williams, Ryan
Mcgreevy, Jane Richardson, Abhishek Singharoy, and Emad Tajkhorshid.
Journal of Structural Biology, 204:319-328, 2018.
|
| 198. Probing key elements of teixobactin-lipid II interactions in
membrane.
Po-Chao Wen, Juan M Vanegas, Susan B Rempe, and Emad Tajkhorshid.
Chemical Science, 9:6997-7008, 2018.
(PMC: PMC6124899) |
| 197. Reconstitution and substrate specificity for isopentenyl
pyrophosphate of the antiviral radical SAM enzyme viperin.
Arpita Chakravarti, Kiruthika Selvadurai, Rezvan Shahoei, Hugo Lee, Shirin
Fatma, Emad Tajkhorshid, and Raven H. Huang.
Journal of Biological Chemistry, 293:14122-14133, 2018.
(PMC: PMC6130951) |
| 196. Molecular insight into drug exporters within the cellular membrane.
Emad Tajkhorshid.
Pharmacological Research, 133:328, 2018.
|
| 195. Microscopic view of lipids and their diverse biological functions.
Po-Chao Wen, Paween Mahinthichaichan, Noah Trebesch, Tao Jiang, Zhiyu Zhao,
Eric Shinn, Mrinal Shekhar Yuhang Wang, Karan Kapoor, Chun Kit Chan, and Emad
Tajkhorshid.
Current Opinion in Structural Biology, 51:177-186, 2018.
(PMC: PMC6221948) |
| 194. Sensitivity of peripheral membrane proteins to the membrane context:
A case study of phosphatidylserine and the TIM proteins.
Daniel Kerr, Gregory T Tietjen, Zhiliang Gong, Emad Tajkhorshid, Erin J Adams,
and Ka Yee C. Lee.
Biochimica et Biophysica Acta - Biomembranes, 1860:2126-2133,
2018.
(PMC: PMC6290684) |
| 193. Electrostatic lock in the transport cycle of the multi-drug
resistance transporter EmrE.
Josh V Vermaas, Susan B. Rempe, and Emad Tajkhorshid.
Proceedings of the National Academy of Sciences, USA,
115:E7502-E7511, 2018.
(PMC: PMC6094130) |
| 192. Bacterial denitrifying nitric oxide reductases and aerobic
respiratory terminal oxidases use similar delivery pathways for their
molecular substrates.
Paween Mahinthichaichan, Robert B. Gennis, and Emad Tajkhorshid.
Biochimica et Biophysica Acta - Bioenergetics, 1859:712-724,
2018.
(PMC: PMC6078787) |
| 191. Inchworm movement of two rings switching onto a thread by biased
Brownian diffusion represent a three-body problem.
Christopher R. Benson, Christopher Maffeo, Elisabeth M. Fatila, Yun Liu,
Edward G. Sheetz, Aleksei Aksimentiev, Abhishek Singharoy, and Amar H. Flood.
Proceedings of the National Academy of Sciences, USA,
115:9391-9396, 2018.
(PMC: PMC6156619) |
| 190. A "cross-stitched" peptide with improved helicity and proteolytic
stability.
Thomas E. Speltz, Christopher G. Mayne, Sean W. Fanning, Zamia Siddiqui, Emad
Tajkhorshid, Geoffrey L Greene, and Terry W. Moore.
Organic & Biomolecular Chemistry, 16:3702-3706, 2018.
(PMC: PMC5993042) |
| 189. Structural underpinnings of oestrogen receptor mutations in endocrine
therapy resistance.
John A. Katzenellenbogen, Christopher G. Mayne, Benita S. Katzenellenbogen,
Geoffrey L. Greene, and Sarat Chandarlapaty.
Nature Reviews Cancer, 18:377-388, 2018.
(PMC: PMC6252060) |
| 188. Cytochrome aa3 oxygen reductase utilizes the tunnel
observed in the crystal structures to deliver O2 for catalysis.
Paween Mahinthichaichan, Robert B. Gennis, and Emad Tajkhorshid.
Biochemistry, 57:2150-2161, 2018.
(PMC: PMC5936630) |
| 187. Structure of the alternative complex III in a supercomplex with
cytochrome oxidase.
Chang Sun, Samir Benlekbir, Padmaja Venkatakrishnan, Yuhang Wang, Emad
Tajkhorshid, John L. Rubinstein, and Robert B. Gennis.
Nature, 557:123-126, 2018.
(PMC: PMC6004266) |
| 186. In situ structure of neuronal C9orf72 poly-GA
aggregates reveals proteasome recruitment.
Qiang Guo, Carina Lehmer, Antonio Martínez-Sánchez, Till Rudack,
Florian Beck, Hannelore Hartmann, Manuela Pérez-Berlanga,
Frédéric Frottin, Mark S. Hipp, F. Ulrich Hartl, Dieter Edbauer,
Wolfgang Baumeister, and Rubén Fernández-Busnadiego.
Cell, 172:696-705, 2018.
(PMC: PMC6035389) |
| 185. Effects of cytosine modifications on DNA flexibility and nucleosome
mechanical stability.
Thuy TM Ngo, Jejoong Yoo, Qing Dai, Qiucen Zhang, Chuan He, Aleksei
Aksimentiev, and Taekjip Ha.
Nature Communications, 7:10813, 2016.
(PMC: PMC4770088) |
| 184. Simulating biological processes: Stochastic physics from whole cells
to colonies.
Tyler Earnest, John Cole, and Zaida Luthey-Schulten.
Reports on Progress in Physics, 81:052601, 2018.
|
| 183. Population FBA predicts metabolic phenotypes in yeast.
Piyush Labhsetwar, Marcelo C. R. Melo, John A. Cole, and Zaida Luthey-Schulten.
PLoS Computational Biology, 13:e1005728, 2017.
(PMC: PMC5626512) |
| 182. Nanoscale ion pump derived from a biological water channel.
Karl Decker, Martin Page, and Aleksei Aksimentiev.
Journal of Physical Chemistry B, 121:7899-7906, 2017.
(PMC: PMC5570624) |
| 181. Salt bridges gate α-catenin activation at intercellular
junctions.
Samantha Barrick, Jing Li, Xinyu Kong, Alokananda Ray, Emad Tajkhorshid, and
Deborah Leckband.
Molecular Biology of the Cell, 29:111-122, 2018.
(PMC: PMC5909925) |
| 180. Drug-drug interactions between atorvastatin and dronedarone mediated
by monomeric CYP3A4.
Ilia G. Denisov, Javier L. Baylon, Yelena V. Grinkova, Emad Tajkhorshid, and
Stephen G. Sligar.
Biochemistry, 57:805-816, 2017.
(PMC: PMC5800941) |
| 179. Arachidonic acid metabolism by human cardiovascular CYP2J2 is
modulated by doxorubicin.
William R. Arnold, Javier L. Baylon, Emad Tajkhorshid, and Aditi Das.
Biochemistry, 56:6700-6712, 2017.
(PMC: PMC5743546) |
| 178. CryoEM structure refinement by integrating NMR chemical shifts
with molecular dynamics simulations.
Juan R. Perilla, Gongpu Zhao, Manman Lu, Jiying Ning, Guangjin Hou, In-Ja L.
Byeon, Angela M. Gronenborn, Tatyana Polenova, and Peijun Zhang.
Journal of Physical Chemistry B, 121:3853-3863, 2017.
(PMC: PMC5459578) |
| 177. Parametric studies of metabolic cooperativity in escherichia coli
colonies: Strain and geometric confinement effects.
Joseph R. Peterson, John A. Cole, and Zaida Luthey-Schulten.
PLoS One, 12:e0182570, 2017.
(PMC: PMC5562313) |
| 176. Careful accounting of extrinsic noise in protein expression reveals
correlations among its sources.
John A. Cole and Zaida Luthey-Schulten.
Physical Review E, 95:062418, 2017.
(PMC: PMC5669626) |
| 175. Porphyrin-assisted docking of a thermophage portal protein into lipid
bilayers: Nanopore engineering and characterization.
Benjamin Cressiot, Sandra J. Greive, Wei Si, Tomas C. Pascoa, Mehrnaz
Mojtabavi, Maria Chechik, Huw T. Jenkins, Xueguang Lu, Ke Zhang, Aleksei
Aksimentiev, Alfred A. Antson, and Meni Wanunu.
ACS Nano, 11:11931-11945, 2017.
(PMC: PMC5963890) |
| 174. Quantification of membrane protein-detergent complex interactions.
Aaron J. Wolfe, Wei Si, Zhengqi Zhang, Adam R. Blanden, Yi-Ching Hsueh, Jack F.
Gugel, Bach Pham, Min Chen, Stewart N. Loh, Sharon Rozovsky, Aleksei
Aksimentiev, and Liviu Movileanu.
Journal of Physical Chemistry B, 121:10228-10241, 2017.
(PMC: PMC5680101) |
| 173. Dimeric structure of the uracil: proton symporter UraA provides
mechanistic insights into the SLC4/23/26 transporters.
Xinzhe Yu, Guanghui Yang, Chuangye Yan, Javier L Baylon, Jing Jiang, He Fan,
Guifeng Lu, Kazuya Hasegawa, Hideo Okumura, Tingliang Wang, Emad Tajkhorshid,
Shuo Li, and Nieng Yan.
Cell Research, 27:1020-1033, 2017.
(PMC: PMC5539350) |
| 172. Determination of cell doubling times from the return-on-investment
time of photosynthetic vesicles based on atomic detail structural models.
Andrew Hitchcock, C. Neil Hunter, and Melih Sener.
Journal of Physical Chemistry B, 121:3787-3797, 2017.
|
| 171. Q-band electron-nuclear double resonance reveals out-of-plane
hydrogen bonds stabilize an anionic ubisemiquinone in cytochrome bo3 from
Escherichia coli.
Chang Sun, Alexander T. Taguchi, Josh V. Vermaas, Nathan J. Beal, Patrick J.
O'Malley, Emad Tajkhorshid, Robert B. Gennis, and Sergei A. Dikanov.
Biochemistry, 55:5714-5725, 2016.
(PMC: PMC5558440) |
| 170. Atomic-level description of protein-lipid interactions using an
accelerated membrane model.
Javier L. Baylon, Josh V. Vermaas, Melanie P. Muller, Mark J. Arcario, Taras V.
Pogorelov, and Emad Tajkhorshid.
Biochimica et Biophysica Acta - Biomembranes, 1858:1573-1583,
2016.
(PMC: PMC4877275) |
| 169. Ribosome biogenesis in replicating cells: integration of experiment
and theory.
Tyler M. Earnest, John A. Cole, Joseph R. Peterson, Michael J. Hallock,
Thomas E. Kuhlman, and Zaida Luthey-Schulten.
Biopolymers, 105:735-751, 2016.
(PMC: PMC4958520) |
| 168. Conformational dynamics of the human islet amyloid polypeptide in a
membrane environment: Toward the aggregation prone form.
Katrine Kirkeby Skeby, Ole Juul Andersen, Taras V. Pogorelov, Emad Tajkhorshid,
and Birgit Schiott.
Biochemistry, 55:2031-2042, 2016.
|
| 167. TopoGromacs: Automated topology conversion from CHARMM to
GROMACS within VMD.
Josh V. Vermaas, David J. Hardy, John E. Stone, Emad Tajkhorshid, and Axel
Kohlmeyer.
Journal of Chemical Information and Modeling, 56:1112-1116,
2016.
|
| 166. CryoEM-based hybrid modeling approaches for structure
determination.
C Keith Cassidy, Benjamin A Himes, Zaida Luthey-Schulten, and Peijun Zhang.
Current Opinion in Microbiology, 43:14-23, 2018.
(PMC: PMC5934336) |
| 165. Mitochondrial VDAC1: A key gatekeeper as potential therapeutic
target.
Amadou K.S. Camara, Yi Fan Zhou, Po Chao Wen, Emad Tajkhorshid, and Wai Meng
Kwok.
Frontiers in Physiology, 8:640, 2017.
(PMC: PMC5491678) |
| 164. Activation and desensitization mechanism of AMPA receptor-tarp
complex by cryo-EM.
Shanshuang Chen, Yan Zhao, Yuhang Wang, Mrinal Shekhar, Emad Tajkhorshid, and
Eric Gouaux.
Cell, 170:1234-1246, 2017.
(PMC: PMC5621841) |
| 163. Lipids and ions traverse the membrane by the same physical pathway in
the nhTMEM16 scramblase.
Tao Jiang, Kuai Yu, H. Criss Hartzell, and Emad Tajkhorshid.
eLife, 6:e28671, 2017.
(PMC: PMC5628016) |
| 162. Chasing the open-state structure of pentameric ligand-gated ion
channels.
Giovanni Gonzalez-Gutierrez, Yuhang Wang, Gisela Cymes, Emad Tajkhorshid, and
Claudio Grosman.
Journal of General Physiology, 149:1119-1138, 2017.
(PMC: PMC5715906) |
| 161. Combining in Vitro and in Silico single molecule force
spectroscopy to characterize and tune cellulosomal scaffoldin mechanics.
Tobias Verdorfer, Rafael C. Bernardi, Aylin Meinhold, Wolfgang Ott, Zaida
Luthey-Schulten, Michael A. Nash, and Hermann E. Gaub.
Journal of the American Chemical Society, 139:17841-17852,
2017.
(PMC: PMC5737924) |
| 160. Coupling X-ray reflectivity and in silico binding to yield dynamics
of membrane recognition by Tim1.
Gregory T. Tietjen, Javier L. Baylon, Daniel Kerr, Zhiliang Gong, J. Michael
Henderson, Charles T. R. Heffern, Mati Meron, Binhua Lin, Mark L. Schlossman,
Erin J. Adams, Emad Tajkhorshid, and Ka Yee C. Lee.
Biophysical Journal, 113:1505-1519, 2017.
(PMC: PMC5627149) |
| 159. X-ray structures define human P2X3 receptor gating cycle and
antagonist action.
Steven E. Mansoor, Wei Lü, Wout Oosterheert, Mrinal Shekhar, Emad
Tajkhorshid, and Eric Gouaux.
Nature, 538:66-71, 2016.
(PMC: PMC5161641) |
| 158. Lipid specificity of the membrane binding domain of coagulation
factor X.
Melanie P. Muller, Yan Wang, James H. Morrissey, and Emad Tajkhorshid.
Journal of Thrombosis and Haemostasis, 15:2005-2016, 2017.
(PMC: PMC5630516) |
| 157. Critical role of water molecules in proton translocation by the
membrane-bound transhydrogenase.
Pius S. Padayatti, Josephine H. Leung, Paween Mahinthichaichan, Emad
Tajkhorshid, Andrii Ishchenko, Vadim Cherezov, S. Michael Soltis, J. Baz
Jackson, C. David Stout, Robert B. Gennis, and Qinghai Zhang.
Structure, 25:1111-1119, 2017.
(PMC: PMC5524145) |
| 156. Computational characterization of molecular mechanisms of membrane
transporter function.
Noah Trebesch, Josh V. Vermaas, and Emad Tajkhorshid.
In Carmen Domene, editor, Computational Biophysics of Membrane
Proteins, chapter 7, pp. 197-236. Royal Society of Chemistry, Cambridge,
UK, 2017.
|
| 155. Challenges of integrating stochastic dynamics and cryo-electron
tomograms in whole-cell simulations.
Tyler M. Earnest, Reika Watanabe, John E. Stone, Julia Mahamid, Wolfgang
Baumeister, Elizabeth Villa, and Zaida Luthey-Schulten.
Journal of Physical Chemistry B, 121:3871-3881, 2017.
|
| 154. Extension of the highly mobile membrane mimetic to transmembrane
systems through customized in silico solvents.
Josh V. Vermaas, Taras V. Pogorelov, and Emad Tajkhorshid.
Journal of Physical Chemistry B, 121:3764-3776, 2017.
|
| 153. Modulation of molecular flux using a graphene nanopore capacitor.
Manish Shankla and Aleksei Aksimentiev.
Journal of Physical Chemistry B, 121:3724-3733, 2016.
|
| 152. Tribute to Klaus Schulten.
Emad Tajkhorshid and Christophe Chipot.
Journal of Physical Chemistry B, 121:3203-3205, 2017.
|
| 151. A membrane-embedded pathway delivers general anesthetics to two
interacting binding sites in the Gloeobacter violaceus ion channel.
Mark J Arcario, Christopher G Mayne, and Emad Tajkhorshid.
Journal of Biological Chemistry, 9:9480-9492, 2017.
(PMC: PMC5465477) |
| 150. Energy transduction and alternating access of the mammalian ABC
transporter P-glycoprotein.
Brandy Verhalen, Reza Dastvan, Sundarapandian Thangapandian, Yelena Peskova,
Hanane A. Koteiche, Robert K. Nakamoto, Emad Tajkhorshid, and Hassane S.
Mchaourab.
Nature, 543:738-741, 2017.
(PMC: PMC5558441) |
| 149. Mass spectrometry-based cross-linking study shows that the Psb28
protein binds to cytochrome b559 in Photosystem II.
Daniel A. Weisz, Haijun Liu, Hao Zhang, Sundarapandian Thangapandian, Emad
Tajkhorshid, Michael L. Gross, and Himadri B. Pakrasi.
Proceedings of the National Academy of Sciences, USA,
114:2224-2229, 2017.
(PMC: PMC5338524) |
| 148. Structural basis of co-translational quality control by ArfA and
RF2 bound to ribosome.
Fuxing Zeng, Yanbo Chen, Jonathan Remis, Mrinal Shekhar, James C. Phillips,
Emad Tajkhorshid, and Hong Jin.
Nature, 541:554-557, 2017.
(PMC: PMC5679781) |
| 147. Differential membrane binding mechanics of synaptotagmin isoforms
observed at atomic detail.
Josh V. Vermaas and Emad Tajkhorshid.
Biochemistry, 56:281-293, 2017.
(PMC: PMC5557660) |
| 146. Methodology for the simulation of molecular motors at different
scales.
Abhishek Singharoy and Christophe Chipot.
Journal of Physical Chemistry B, 121:3502-3514, 2017.
(PMC: PMC5518690) |
| 145. Genome-wide gene expression and RNA half-life measurements allow
predictions of regulation and metabolic behavior in Methanosarcina
acetivorans.
Joseph R Peterson, ShengShee Thor, Lars Kohler, Petra RA Kohler, William W
Metcalf, and Zaida Luthey-Schulten.
BMC Genomics, 17:924, 2016.
(PMC: PMC5112694) |
| 144. Asymmetric binding and metabolism of polyunsaturated fatty acids
(PUFAs) by CYP2J2 epoxygenase.
William R. Arnold, Javier L. Baylon, Emad Tajkhorshid, and Aditi Das.
Biochemistry, 55:6969-6980, 2016.
(PMC: PMC5558443) |
| 143. Large-conductance transmembrane porin made from DNA origami.
Kerstin Göpfrich, Chen-Yu Li, Maria Ricci, Satya Prathyusha Bhamidimarri,
Jejoong Yoo, Bertalan Gyenes, Alexander Ohmann, Mathias Winterhalter, Aleksei
Aksimentiev, and Ulrich F. Keyser.
ACS Nano, 10:8207-8214, 2016.
|
| 142. Ion channels made from a single membrane-spanning DNA duplex.
Kerstin Göpfrich, Chen-Yu Li, Iwona Mames, Satya Prathyusha Bhamidimarri,
Maria Ricci, Jejoong Yoo, Adam Mames, Alexander Ohmann, Mathias Winterhalter,
Eugen Stulz, Aleksei Aksimentiev, and Ulrich F. Keyser.
Nano Letters, 16:4665-4669, 2016.
(PMC: PMC4948918) |
| 141. Mechanical properties of a complete microtubule revealed through
molecular dynamics simulation.
David B. Wells and Aleksei Aksimentiev.
Biophysical Journal, 99:629-637, 2010.
(PMC: PMC2905083) |
| 140. Microscopic perspective on the adsorption isotherm of a heterogeneous
surface.
Rogan Carr, Jeffrey Comer, Mark D. Ginsberg, and Aleksei Aksimentiev.
Journal of Physical Chemistry Letters, 2:1804-1807, 2011.
(PMC: PMC3353733) |
| 139. Noise contributions in an inducible genetic switch: a whole-cell
simulation study.
Elijah Roberts, Andrew Magis, Julio O Ortiz, Wolfgang Baumeister, and Zaida
Luthey-Schulten.
PLoS Computational Biology, 7:e1002010, 2011.
(PMC: PMC3053318) |
| 138. Dna looping increases the range of bistability in a stochastic model
of the lac genetic switch.
Tyler M Earnest, Elijah Roberts, Michael Assaf, Karin Dahmen, and Zaida
Luthey-Schulten.
Physical Biology, 10:026002, 2013.
|
| 137. Heterogeneity in protein expression induces metabolic variability in
a modeled Escherichia coli population.
Piyush Labhsetwar, John Andrew Cole, Elijah Roberts, Nathan D Price, and
Zaida A Luthey-Schulten.
Proceedings of the National Academy of Sciences, USA,
110:14006-14011, 2013.
(PMC: PMC3752265) |
| 136. Towards a whole-cell model of ribosome biogenesis: Kinetic modeling
of SSU assembly.
Tyler M Earnest, Jonathan Lai, Ke Chen, Michael J Hallock, James R Williamson,
and Zaida Luthey-Schulten.
Biophysical Journal, 109:1117-1135, 2015.
(PMC: PMC4576174) |
| 135. Spatially-resolved metabolic cooperativity within dense bacterial
colonies.
John A Cole, Lars Kohler, Jamila Hedhli, and Zaida Luthey-Schulten.
BMC Systems Biology, 9:15, 2015.
(PMC: PMC4376365) |
| 134. Computational characterization of structural dynamics underlying
function in active membrane transporters.
Jing Li, Po-Chao Wen, Mahmoud Moradi, and Emad Tajkhorshid.
Current Opinion in Structural Biology, 31:96-105, 2015.
(PMC: PMC4476910) |
| 133. Improving reaction kernel performance in Lattice Microbes:
particle-wise propensities and run-time generated code.
Michael J. Hallock and Zaida Luthey-Schulten.
pp. 428-434. IEEE, 2016.
|
| 132. End-to-end attraction of duplex DNA.
Christopher Maffeo, Binquan Luan, and Aleksei Aksimentiev.
Nucleic Acids Research, 40:3812-3821, 2012.
(PMC: PMC3351176) |
| 131. Improved parametrization of Li+, Na+,
K+, and Mg2+.
J. Yoo and A. Aksimentiev.
Journal of Physical Chemistry Letters, 3:45-50, 2012.
|
| 130. A coarse-grained model of unstructured single-stranded DNA derived
from atomistic simulation and single-molecule experiment.
Christopher Maffeo, Thuy T. M. Ngo, Taekjip Ha, and Aleksei Aksimentiev.
Journal of Chemical Theory and Computation, 10:2891-2896,
2014.
(PMC: PMC4132850) |
| 129. DNA-DNA interactions in tight supercoils are described by a small
effective charge density.
Christopher Maffeo, Robert Schöpflin, Hergen Brutzer, René Stehr,
Aleksei Aksimentiev, Gero Wedemann, and Ralf Seidel.
Physical Review Letters, 105:158101, 2010.
(PMC: PMC3170404) |
| 128. Direct evidence for sequence-dependent attraction between
double-stranded DNA controlled by methylation.
Jejoong Yoo, Hajin Kim, Aleksei Aksimentiev, and Taekjip Ha.
Nature Communications, 7:11045, 2016.
(PMC: PMC4804163) |
| 127. The structure and intermolecular forces of DNA condensates.
Jejoong Yoo and Aleksei Aksimentiev.
Nucleic Acids Research, 44:2036-2046, 2016.
(PMC: PMC4797306) |
| 126. Improved parameterization of amine-carboxylate and amine-phosphate
interactions for molecular dynamics simulations using the CHARMM and
AMBER force fields.
Jejoong Yoo and Aleksei Aksimentiev.
Journal of Chemical Theory and Computation, 12:430-443, 2016.
|
| 125. Molecular architecture of the retroviral capsid.
Juan R Perilla and Angela M Gronenborn.
Trends in Biochemical Sciences, 41:410-420, 2016.
(PMC: PMC4879823) |
| 124. Towards a computational model of a methane producing archaeum.
Joseph R Peterson, Piyush Labhsetwar, Jeremy R Ellermeier, Petra R A Kohler,
Ankur Jain, Taekjip Ha, William W Metcalf, and Zaida Luthey-Schulten.
Archaea, 2014, 2014.
(18 pages).
(PMC: PMC3960522) |
| 123. Effects of dna replication on mrna noise.
Joseph R. Peterson, John A. Cole, Jingyi Fei, Taekjip Ha, and Zaida A.
Luthey-Schulten.
Proceedings of the National Academy of Sciences, USA,
112:15886-15891, 2015.
(PMC: PMC4702981) |
| 122. In situ structure and dynamics of DNA origami determined through
molecular dynamics simulations.
Jejoong Yoo and Aleksei Aksimentiev.
Proceedings of the National Academy of Sciences, USA,
110:20099-20104, 2013.
(PMC: PMC3864285) |
| 121. Ionic conductivity, structural deformation, and programmable
anisotropy of DNA origami in electric field.
Chen-Yu Li, Elisa A. Hemmig, Jinglin Kong, Jejoong Yoo, Silvia
Hernández-Ainsa, Ulrich F. Keyser, and Aleksei Aksimentiev.
ACS Nano, 9:1420-1433, 2015.
PMID: 25623807.
(PMC: PMC4469488) |
| 120. Molecular dynamics of membrane-spanning DNA channels: Conductance
mechanism, electro-osmotic transport and mechanical gating.
Jejoong Yoo and Aleksei Aksimentiev.
Journal of Physical Chemistry Letters, 6:4680-4687, 2015.
(NIHMS: PMID26551518) |
| 119. Computational recipe for efficient description of large-scale
conformational changes in biomolecular systems.
Mahmoud Moradi and Emad Tajkhorshid.
Journal of Chemical Theory and Computation, 10:2866-2880,
2014.
(PMC: PMC4089915) |
| 118. Atomic-level characterization of transport cycle thermodynamics in
the glycerol-3-phosphate:phosphate transporter.
Mahmoud Moradi, Giray Enkavi, and Emad Tajkhorshid.
Nature Communications, 6:8393, 2015.
(PMC: PMC4598623) |
| 117. Incorporation of charged residues in the CYP2J2 FG loop disrupts
CYP2J2-lipid bilayer interactions.
Daniel R McDougle, Javier L Baylon, Daryl D Meling, Amogh Kambalyal, Yelena V
Grinkova, Jared Hammernik, Emad Tajkhorshid, and Aditi Das.
Biochimica et Biophysica Acta - Biomembranes, 1848:2460-2470,
2015.
(PMC: PMC4559526) |
| 116. Mechanism of drug-drug interactions mediated by human cytochrome
P450 CYP3A4 monomer.
Ilia G. Denisov, Yelena V. Grinkova, Javier L. Baylon, Emad Tajkhorshid, and
Stephen G. Sligar.
Biochemistry, 54:2227-2239, 2015.
(PMC: PMC4757451) |
| 115. The cellular membrane as a mediator for small molecule interaction
with membrane proteins.
Christopher G. Mayne, Mark J. Arcario, Paween Mahinthichaichan, Javier L.
Baylon, Josh V. Vermaas, Latifeh Navidpour, Po-Chao Wen, Sundarapandian
Thangapandian, and Emad Tajkhorshid.
Biochimica et Biophysica Acta - Biomembranes, 1858:2290-2304,
2016.
(PMC: PMC4983535) |
