The group's papers have been cited so far over 56,000 times (ISI, August 2015), and according to Google Scholar over 160,000 times (as of July 2017). See highly cited publications. Our group's papers have made a few journal covers.

  Recent Publications


M. P. Muller*, T. Jiang*, C. Sun, M. Lihan, S. Pant, P. Mahinthichaichan, A. Trifan, and E. Tajkhorshid (2019) Characterization of Lipid-Protein Interactionsand Lipid-mediated Modulation of MembraneProtein Function Through Molecular Simulation. Chemical Reviews, 119:6086-6161.

J. A. Coleman, D. Yang, Z. Zhao, P. C. Wen, C. Yoshioka , E. Tajkhorshid, and E. Gouaux (2019) Serotonin transporter-ibogaine complexes illuminate mechanisms of inhibition and transport. Nature, 569:141-145.

M. B. Prigozhin, Y. Zhang, K. Schulten, M. Gruebele, and T. V. Pogorelov (2019) Fast pressure-jump all-atom simulations and experiments reveal site-specific protein dehydration-folding dynamics. PNAS, 116(12):5356-5361.

I. G. Denisov ,Y. V. Grinkova,P. Nandigrami, M. S. Shekhar, E. Tajkhorshid, and S. G. Sligar (2019) Allosteric Interactions in Human Cytochrome P450 CYP3A4: The Role of Phenylalanine 213. Biochemistry, 58(10):1411-1422.

M. L. Starr, R. P. Sparks, A. S. Arango, L. R. Hurst, Z. Zhao, M. Lihan, J. L. Jenkins, and E. Tajkhorshid, and R. A. Fratti (2019) Phosphatidic acid induces conformational changes in Sec18 protomers that prevent SNARE priming. Journal of Biological Chemistry, 294(9):3100-3116.


P. Mahinthichaichan, D. M. Morris, Y. Wang, G. J. Jensen, and E. Tajkhorshid. (2018) Selective permeability of carboxysome shell pores to anionic molecules. Journal of Physical Chemistry B (web version; page numbers forthcoming).

C. Martens, M. Shekhar, A. Borysik, A. Lau, E. Reading, E. Tajkhorshid, P. J. Booth, and A. Politis. (2018) Direct protein-lipid interactions shape the conformational landscape of secondary transporters. Nature Communications, 9:4151.

D. T. Infield, K. Matulef, J. D. Galpin, K. Lam, E. Tajkhorshid, C. A. Ahern, and F. I. Valiyaveetil. (2018) Main-chain mutagenesis reveals intrahelical coupling in an ion channel voltage-sensor. Nature Communications, 9:5055.

Y. Wang, M. Shekhar, D. Thifault, C. J Williams, R. Mcgreevy, J. Richardson, A. Singharoy, and E. Tajkhorshid. (2018) Constructing atomic structural models into Cryo-EM densities using molecular dynamics - pros and cons. Journal of Structural Biology, 204:319-328.

A. Chakravarti, K. Selvadurai, R. Shahoei, H. Lee, S. Fatma, E.Tajkhorshid, and R. H. Huang. (2018) Reconstitution and substrate specificity for isopentenyl pyrophosphate of the antiviral radical SAM enzyme viperin. Journal of Biological Chemistry, 293:14122-14133.

P.-C. Wen, J. M. Vanegas, S. B. Rempe, and E. Tajkhorshid. (2018) Probing key elements of teixobactin-lipid II interactions in membrane. Chemical Science, 9:6997-7008.

J. V. Vermaas, S. B. Rempe, and E. Tajkhorshid. (2018) Electrostatic lock in the transport cycle of the multi-drug resistance transporter EmrE. Proceedings of the National Academy of Sciences, USA, 115:E7502-E7511.

E. Tajkhorshid. (2018) Molecular insight into drug exporters within the cellular membrane. Pharmacological Research, 133:328.

P.-C. Wen, P. Mahinthichaichan, N. Trebesch, T. Jiang, Z. Zhao, E.Shinn, M. Shekhar, Y. Wang, K.Kapoor, C. K. Chan, and E. Tajkhorshid. (2018) Microscopic view of lipids and their diverse biological functions. Current Opinion in Structural Biology, 51:177-186.

D. Kerr, G. T. Tietjen, Z. Gong, E. Tajkhorshid, E.J Adams, and K. Y. C. Lee. (2018) Sensitivity of peripheral membrane proteins to the membrane context: A case study of phosphatidylserine and the TIM proteins. Biochimica et Biophysica Acta - Biomembranes, 1860:2126-2133.

P. Mahinthichaichan, R. B. Gennis, and E. Tajkhorshid. (2018) Bacterial denitrifying nitric oxide reductases and aerobic respiratory terminal oxidases use similar delivery pathways for their molecular substrates. Biochimica et Biophysica Acta - Bioenergetics, 1859:712-724.

C K. Cassidy, B. A. Himes, Z.Luthey-Schulten, and P. Zhang. (2018) CryoEM-based hybrid modeling approaches for structure determination. Current Opinion in Microbiology, 43:14-23.

C. R. Benson, C. Maffeo, E. M. Fatila, Y. Liu, E. G. Sheetz, A. Aksimentiev, A. Singharoy, and A. H. Flood. (2018) Inchworm movement of two rings switching onto a thread by biased Brownian diffusion represent a three-body problem. Proceedings of the National Academy of Sciences, USA, 115:9391-9396.

J. A. Hadden, J. R. Perilla, C. J. Schlicksup, B. Venkatakrishnan, A. Zlotnick, and K. Schulten. (2018) All-atom molecular dynamics of the HBV capsid reveals insights into biological function and cryo-EM resolution limits. eLife, 7:e32478.

T. E. Speltz, C. G. Mayne, S. W. Fanning, Z. Siddiqui, E. Tajkhorshid, G. L. Greene, and T. W. Moore. (2018) A "cross-stitched" peptide with improved helicity and proteolytic stability. Organic & Biomolecular Chemistry, 16:3702-3706.

J. A. Katzenellenbogen, C. G. Mayne, B. S. Katzenellenbogen, G. L. Greene, and S. Chandarlapaty. (2018) Structural underpinnings of oestrogen receptor mutations in endocrine therapy resistance. Nature Reviews Cancer, 18:377-388.

L. F. Milles, K. Schulten, H. E. Gaub, and R. C. Bernardi. (2018) Molecular mechanism of extreme mechanostability in a pathogen adhesin. Science, 359:1527-1533.

M. Melo, R. Bernardi, T. Rudack, M. Scheurer, C. Riplinger, J. Phillips, J. Maia, G. Rocha, J. Ribeiro, J. Stone, F. Nesse, K. Schulten, and Z. Luthey-Schulten. (2018) NAMD goes quantum: An integrative suite for QM/MM simulations. Nature Methods, 15:351-354.

C. Sun, S. Benlekbir, P. Venkatakrishnan, Y. Wang, E. Tajkhorshid, J. L. Rubinstein, and R. B. Gennis. (2018) Structure of the alternative complex III in a supercomplex with cytochrome oxidase. Nature, 557:123-126.

P. Mahinthichaichan, R. B. Gennis, and E. Tajkhorshid. (2018) Cytochrome aa3 oxygen reductase utilizes the tunnel observed in the crystal structures to deliver O2 for catalysis. Biochemistry, 57:2150-2161.

Q. Guo, C. Lehmer, A. Martínez-Sánchez, T. Rudack, F. Beck, H. Hartmann, M. Pérez-Berlanga, F. Frottin, M. S. Hipp, F. U. Hartl, D. Edbauer, W. Baumeister, and R. Fernández-Busnadiego. (2018) In situ structure of neuronal C9orf72 poly-GA aggregates reveals proteasome recruitment. Cell, 172:696-705.

T. Earnest, J. Cole, and Z. Luthey-Schulten. (2018) Simulating biological processes: Stochastic physics from whole cells to colonies. Reports on Progress in Physics, 81:052601.

M. Scheurer, P. Rodenkirch, M. Siggel, R. C. Bernardi, K. Schulten, E. Tajkhorshid, and T. Rudack. (2018) PyContact: Rapid, customizable and visual analysis of non-covalent interactions in MD simulations. Biophysical Journal, 114:577-583.

S. Barrick, J. Li, X. Kong, A. Ray, E. Tajkhorshid, and D. Leckband. (2018) Salt bridges gate α-catenin activation at intercellular junction. Molecular Biology of the Cell, 29:111-122.


T. Jiang, K. Yu, H. C. Hartzell, and E. Tajkhorshid (2017) Lipids and Ions Traverse the Membrane by the Same Physical Pathway in the nhTMEM16 Scramblase. eLife, 6: e28671.

T. Verdorfer, R. C. Bernardi, A. Meinhold, W. Ott, Z. Luthey-Schulten, M. A. Nash and H. E. Gaub (2017) Combining in Vitro and in Silico Single-Molecule Force Spectroscopy to Characterize and Tune Cellulosomal Scaffoldin Mechanics. JACS, 139, 17841-17852. (Cover Article)

G. G. Gutierrez*, Y. Wang*, G. Cymes, E. Tajkhorshid, and C. Grosman (2017) Chasing the open-state structure of pentameric ligand-gated ion channels. Journal of General Physiology, 149, 1119-1138. (Cover Article)

M. P. Muller, Y. Wang, J. H. Morrissey, and E. Tajkhorshid (2017) Lipid Specificity of the Membrane Binding Domain of Coagulation Factor X. J. Thromb. Haemost. 15(10), 2005-2016. (Cover Article)

S. Chen, Y, Zhao, Y. Wang, M. Shekhar, E. Tajkhorshid and E. Gouaux (2017) Activation and desensitization mechanism of AMPA receptor-TARP complex by cryo-EM Cell, 170(6), 1234-1246

X. Yu, G. Yang, C. Yan, J. L. Baylon, J. Jiang, H. Fan, G. Lu, K. Hasegawa, H. Okumura, T. Wang, E. Tajkhorshid, S. Li, and N. Yan (2017) Dimeric structure of the uracil:proton symporter UraA provides mechanistic insights into the SLC4/23/26 transporters. Cell Research, 27:1020-1033.

J. H. Leung, P. Mahinthichaichan, E. Tajkhorshid, A. Ishchenko, V. Cherezov, M. Soltis, B. J. Jackson, C. D. Stout, R. B. Gennis, Q. Zhang, and P. S. Padayatti (2017) Critical role of water molecules in proton translocation by the membrane-bound transhydrogenase. Structure, 25(7), 1111-1119.

F. J. D. Alvarez, S. He, J. R. Perilla, S. Jang, K. Schulten, A. N. Engelman, S. H. W. Scheres, and P. Zhang (2017) CryoEM structure of MxB reveals a novel oligomerization interface critical for HIV restriction Science Advances, 3:e1701264

G. T. Tietjen, J. L. Baylon, D. Kerr, Z. Gong, J. M. Henderson, C. T. R. Heffern, M. Meron, B. Lin, M. L. Schlossman, E. J. Adams, E. Tajkhorshid, and Ka Yee C. Lee (2017) Coupling X-ray reflectivity and in silico binding to yield dynamics of membrane recognition by Tim1. Biophysical Journal, 113:1505-1519

J. R. Perilla & K. Schulten (2017) Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations. Nature Communications, 8: 15959

M. J. Arcario, C. G. Mayne, and E. Tajkhorshid (2017) A membrane-embedded pathway delivers general anesthetics to two interacting binding sites in the Gloeobacter violaceus Ion Channel. J. Biol. Chem., 292(23), 9480-9492. (Cover Article)

B. Verhalen, R. Dastvan, S. Thangapandian, Y. Peskova, H. A. Koteiche, R. K. Nakamoto, E. Tajkhorshid, and H. S. Mchaourab (2017) Energy Transduction and Alternating Access of the mammalian ABC Transporter P-glycoprotein. Nature, 543: 738-741.

F. Zeng, Y. Chen, J. Remis, M. S. Shekhar, J. C. Phillips, E. Tajkhorshid, and H. Jin (2017) Structural Basis of Co-translational Quality Control by ArfA and RF2 Binding to Ribosome. Nature, 541, 554-557.

J. V. Vermaas and E. Tajkhorshid (2017) Differential Membrane Binding Mechanics of Synaptotagmin Isoforms Observed at Atomic Detail. Biochemistry, 56: 281-293.

D. A. Weisz, H. Liu, H. Zhang, S. Thangapandian, E. Tajkhorshid, M. L. Gross, and H. B. Pakrasi (2017) Structural analysis of Photosystem II: Mass spectrometry-based cross-linking study show that the Psb28 protein binds to cytochrome b559. Proceedings of the National Academy of Sciences USA, 114: 2224-2229.

L. G. Lippert, T. Dadosh, J. A. Hadden, B. T. Diroll, C. B. Murray, E. L.F. Holzbaur, K. Schulten, S. L. Reck-Peterson, and Y. E. Goldman (2017) Angular measurements of the dynein ring reveal a stepping mechanism dependent on a flexible stalk. Proceedings of the National Academy of Sciences USA, 114(23):E4564-E4573.

J. Seppälä, R. C. Bernardi, T. J. K. Haataja, M. Hellman, O. T. Pentikäinen, K. Schulten, P. Permi, J. Ylänne, and U. Pentikäinen (2017) Skeletal dysplasia mutations effect on human filamins' structure and mechanosensing. Scientific Reports, 7:4218.

E. Tajkhorshid and C. Chipot (2017) Tribute to Klaus Schulten. Journal of Physical Chemistry B, Klaus Schulten Memorial Issue, 121: 3203-5.

H. Qiu, A. Sarathy, K. Schulten, and J. P. Leburton (2017) Detection and mapping of DNA methylation with 2D material nanopores. npj 2D Materials and Applications, 1:3.

S. Maji, R. Shahoei, K. Schulten, and J. Frank (2017) Quantitative characterization of domain motions in molecular machines. Journal of Physical Chemistry B, 121: 3747-3756.

J. V. Vermaas, T. V. Pogorelov, and E. Tajkhorshid (2017) Extension of the Highly Mobile Membrane Mimetic to Transmembrane Systems through Customized in Silico Solvents. Journal of Physical Chemistry B, 121: 3764-3776.

A. K. S. Camara, Y. Zhou, P.-C. Wen, E. Tajkhorshid and W.-M. Kwok (2017) Mitochondrial VDAC1: A Key Gatekeeper as Potential Therapeutic Target. Frontiers in Physiology, 8: 640.

M. Wehmer, T. Rudack, F. Beck, A. Aufderheide, G. Pfeifer, J. M. Plitzko, F. Förster, K. Schulten, W. Baumeister, and E. Sakata (2017) Structural insights into the functional cycle of the ATPase module of the 26S proteasome. Proceedings of the National Academy of Sciences, USA, 114:1305-1310.

V. G. Poosarla, T. Li, B. C. Goh, K. Schulten, T. K. Wood, and C. D. Maranas (2017) Computational de novo design of antibodies binding to a peptide with high affinity. Biotechnology and Bioengineering, 114:1331-1342.

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