Cover Pages

The members of the Theoretical and Computational Biophysics Group, an NIH Center for Macromolecular Modeling and Bioinformatics, have produced numerous images using our locally developed software. The images have appeared in a variety of publications, from leading journals to reports and books. Here is a sample of covers showcasing several of our images.

Journal of Medicinal Chemistry Quinoline thiourea-based zinc ionophores with antibacterial activity Subhasis Dey, Anjali Patel, Nandan Haloi, Soumya Srimayee, Suman Paul, Ganesh Kumar Barik, Nasim Akhtar, Dipanjan Shaw, Gunanka Hazarika, Biswa Mohan Prusty, Mohit Kumar, Manas Kumar Santra, Emad Tajkhorshid, Surajit Bhattacharjee, and Debasis Manna. Journal of Medicinal Chemistry, 2023

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 Journal of Chemical Theory and Computation Simulations of cortical networks using spatially extended conductance-based neuronal models. Darrell Haufler and Shinya Ito and Christof Koch and Anton Arkhipov. (Cover image: Barry Isralewitz; made with VND.) Journal of Physiology, 2023.

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ACS Chem. Neurosci Microscopic characterization of the chloride permeation pathway in the human excitatory amino acid transporter 1 (EAAT1) Shashank Pant, Qianyi Wu, Renae Ryan, and Emad Tajkhorshid. ACS Chemical Neuroscience.

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Biochemistry Anionic lipids confine cytochrome c2 to the surface of bioenergetic membranes without compromising its interaction with redox partners. Chun Kit Chan, Abhishek Singharoy, and Emad Tajkhorshid. Biochemistry, 2022.

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Journal of Chemical Information and Modeling Membrane Mixer: a toolkit for efficient shuffling of lipids in heterogeneous biological membranes. G. Licari, S. Dehghani-Ghahnavieh, and E. Tajkhorshid. Journal of Chemical Information and Modeling, 2022.

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Journal of Chemical Information and Modeling Assembly and analysis of cell-scale membrane envelopes. Josh Vermaas, Chris Mayne, Eric Shinn, and Emad Tajkhorshid. Journal of Chemical Information and Modeling, 2021.

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Biophysical Journal Rationalizing generation of broad spectrum antibiotics with the addition of a positive charge. Nandan Haloi, Archit Kumar Vasan, Emily Jane Geddes, Arjun Prasanna, Po-Chao Wen, William W. Metcalf, Paul J Hergenrother, and Emad Tajkhorshid. Chemical Science, 2021.

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Matter CryoFold: Determining protein structures and data-guided ensembles from cryo-EM density maps. M. Shekhar, G. Terashi, C. Gupta, D. Sarkar, J. Nguyn, N. J. Sisco, A. Mondal, J. Vant, P. Fromme, W. D. Van Horn, Emad Tajkhorshid, D. Kihara, K. Dill, A. Perez, and A. Singharoy.

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Molecular Cancer Research Defining the energetic basis for a conformational switch mediating ligand-independent activation of mutant estrogen receptors in breast cancer. Chris Mayne, W. Toy, K. Carlson, T. Bhatt, S. W. Fanning, G. L. Greene, B. S. Katzenellenbogen, S. Chandarlapaty, J. A. Katzenellenbogen, and Emad Tajkhorshid.

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Chemical Science, 2021. Active participation of membrane lipids in inhibition of multidrug transporter P-glycoprotein. Karan Kapoor, Shashank Pant, and Emad Tajkhorshid. Chemical Science, 2021.

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Journal of Chemical Physics Confronting pitfalls of AI-augmented molecular dynamics using statistical physics. Shashank Pant, Zachary Smith, Yihang Wang, Emad Tajkhorshid, and Pratyush Tiwarya. Journal of Chemical Physics.

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Chemical Science Twisting of a mechanosensitive molecular probe detects order in membranes. Giuseppe Licari, Karolina Strakova, Stefan Matile, and Emad Tajkhorshid. Chemical Science.

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Journal of Computational Chemistry Microscopic characterization of GRP1 PH domain interaction with anionic membranes. Shashank Pant and Emad Tajkhorshid. Journal of Computational Chemistry.

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ACS Applied Materials and Interfaces Polymer-peptide conjugates convert amyloid into protein nanobundles through fragmentation and lateral association. John W. Smith, Xing Jiang, Hyosung An, Alexander M. Barclay, Giuseppe Licari, Emad Tajkhorshid, Edwin G. Moore, Chad M. Rienstra, Jeffrey S. Moore, and Qian Shen. ACS Applied Materials and Interfaces.

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Biochimica et Biophysica Acta Probing cholesterol binding and translocation in P-glycoprotein. Sundar Thangapandian, Karan Kapoor, and Emad Tajkhorshid. Biochimica et Biophysica Acta - Biomembranes, 2019. In press.

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JOURNAL NAME Direction Matters: Monovalent Streptavidin/Biotin Complex under Load. S. M. Sedlak, L. C. Schendel, M. C. R. Melo, D. A. Pippig, Z. Luthey-Schulten, H. E. Gaub, and R. C. Bernardi. Nano Letters, 19:3415-3421.

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

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Biophysical Journal 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.

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Journal of the American Chemical Society 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, 2017

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Biophysical Journal Lipid specificity of the membrane binding domain of coagulation factor X. Muller MP, Wang Y, Morrissey JH, Tajkhorshid E. Journal Thromb Haemost 2017; 15: 2005~V2016.

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JOURNAL NAME 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)

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Angewandte Chemie Stapled peptides with g-methylated hydrocarbon chains for the estrogen receptor/coactivator interaction. Thomas E. Speltz, Sean W. Fanning, Christopher G. Mayne, Colin Fowler, Emad Tajkhorshid, Geoffrey L. Greene, and Terry W. Moore. Angewandte Chemie - International Edition in English, 55:4252-4255, 2016.

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JOURNAL NAME Mechanism of the primary charge transfer reaction in the cytochrome bc1 complex. Angela M. Barragan, Klaus Schulten, and Ilia A. Solov'yov. Journal of Physical Chemistry B, 2016. DOI:10.1021/acs.jpcb.6b07394

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JOURNAL NAME Contributions of charged residues in structurally dynamic capsid surface loops to Rous sarcoma virus assembly.. Katrina Heyrana, Boon Chong Goh, Juan Roberto Perilla, Tam-Linh N. Nguyen, Matthew R. England, Maria C. Bewley, Klaus Schulten, and Rebecca Craven. Journal of Virology, pp. (52 pages), 2016. In Press.

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Biophysical Journal Disulfide bridges: bringing together frustrated structure in a bioactive peptide. Yi Zhang, Klaus Schulten, Martin Gruebele, Paramjit S. Bansal, David Wilson, and Norelle L. Daly. Biophysical Journal, 110:1744-1752, 2016.

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JOURNAL NAME Mapping mechanical force propaga tion through biomolecular complexes. Constantin Schoeler, Rafael C. Bernardi, Klara H. Malinowska, Ellis Du rner, Wolfgang Ott, Edward A. Bayer, Klaus Schulten, Michael A. Nash, and Hermann E. Gaub. Nano Letters, 15:737 0-7376, 2015.

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JOURNAL NAME All-atom molecular dynamics of virus capsids as drug targets. Juan R. Perilla, Jodi A. Hadden, Boon Chong Goh, Christopher G. Mayne, and Klaus Schulten. Journal of Physical Chemistry Letters, 7:1836-1844, 2016. (PMC: PMC4876486)

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Journal of Physical Chemistry B Identification of ubiquinol binding motifs at the Qo-site of the cytochrome bc1 complex. Angela M. Barragan-Diaz, Antony R. Crofts, Klaus Schulten, and Ilia A. Solov'yov. Journal of Physical Chemistry B, 119:433-447, 2015.

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Journal of Physical Chemistry B A microscopic view of phospholipid insertion into biological membranes. Josh V. Vermaas and Emad Tajkhorshid. Journal of Physical Chemistry B, 118:1754-1764, 2014. (PMC: PMC3933253)

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JACS Observation of complete pressure-jump protein refolding in molecular dynamics simulation and experiment. Yanxin Liu, Maxim B. Prigozhin, Klaus Schulten, and Martin Gruebele. Journal of the American Chemical Society, 136:4265-4272, 2014.

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Journal of Computational Chemistry Rapid parameterization of small molecules using the Force Field Toolkit. Christopher G. Mayne, Jan Saam, Klaus Schulten, Emad Tajkhorshid, and James C. Gumbart. Journal of Computational Chemistry, 34:2757-2770, 2013. (PMC: 3874408)

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Nature Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Gongpu Zhao, Juan R. Perilla, Ernest L. Yufenyuy, Xin Meng, Bo Chen, Jiying Ning, Jinwoo Ahn, Angela M. Gronenborn, Klaus Schulten, Christopher Aiken & Peijun Zhang. Nature, 497:643-646, 2013.

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Journal of the American Chemical Society Decrypting cryptochrome: Revealing the molecular identity of the photoactivation reaction. Ilia A. Solov'yov, Tatiana Domratcheva, Abdul R. M. Shahi, and Klaus Schulten. Journal of the American Chemical Society, 134:18046-18052, 2012.

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Biophysical Journal 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.

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Journal of Chemical Information and Modeling Molecular basis of drug resistance in A/H1N1 virus. Ariela Vergara-Jaque, Horacio Poblete, Eric Lee, Klaus Schulten, Fernando González-Nilo, and Christophe Chipot. Journal of Chemical Information and Modeling, 52:2650-2656, 2012.

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Physical Chemistry - Chemical Physics Vibrationally assisted electron transfer mechanism of olfaction: Myth or reality?. Ilia A. Solov'yov, Po-Yao Chang, and Klaus Schulten. Physical Chemistry - Chemical Physics, 14:13861-13871, 2012.

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Journal of Chemical Physics Excited state dynamics in photosynthetic reaction center and light harvesting complex 1. Johan Strümpfer and Klaus Schulten. Journal of Chemical Physics, 137:065101, 2012.

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Journal of Biological Chemistry 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. (PMC: 3123091)

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Biophysical Journal Extension of a three-helix bundle domain of myosin VI and key role of calmodulins. Yanxin Liu, Jen Hsin, HyeongJun Kim, Paul R Selvin, and Klaus Schulten. Biophysical Journal, 100:2964-2973, 2011.

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Physik Journal How birds and other animals orient in the Earth magnetic field. Ilia A. Solov'yov, Klaus Schulten, and Walter Greiner. Physik Journal, 9:23-28, 2010.

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Biophysical Journal Photosynthetic vesicle architecture and constraints on efficient energy harvesting. Melih Sener, Johan Strumpfer, John A. Timney, Arvi Freiberg, C. Neil Hunter, and Klaus Schulten. Biophysical Journal, 99:67-75, 2010.

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Biophysical Journal Tertiary and secondary structure elasticity of a six-Ig titin chain. Eric H. Lee, Jen Hsin, Eleonore von Castelmur, Olga Mayans, and Klaus Schulten. Biophysical Journal, 98:2337-2346, 2010.

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Biophysical Journal Common structural transitions in explicit-solvent simulations of villin headpiece folding. Peter L. Freddolino and Klaus Schulten. Biophysical Journal, 97:2337-2346, 2009.

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Biophysical Journal Magnetoreception through cryptochrome may involve superoxide.. Ilia A. Solov'yov and Klaus Schulten. Biophysical Journal, 96:4804-4813, 2009.

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IEEE Nanotechnology Magazine Modeling transport through synthetic nanopores. Aleksei Aksimentiev, Robert K. Brunner, Eduardo Cruz-Chu, Jeffrey Comer, and Klaus Schulten. IEEE Nanotechnology Magazine, 3:20-28, 2009.

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Journal of General Physiology The roles of pore ring and plug in the SecY protein-conducting channel. James Gumbart and Klaus Schulten. Journal of General Physiology, 132:709-719, 2008.

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Biophysical Journal Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF. Jerome Henin, Emad Tajkhorshid, Klaus Schulten, and Christophe Chipot. Biophysical Journal, 94:832-839, 2008.

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Biophysical Journal Mechanics of force propagation in TonB-dependent outer membrane transport. James Gumbart, Michael C. Wiener, and Emad Tajkhorshid.Biophysical Journal, 93:496-504, 2007. (PMC: 1896255).

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Journal of Computational Chemistry Accelerating molecular modeling applications with graphics processors. John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, and Klaus Schulten. Journal of Computational Chemistry, 28:2618-2640, 2007.

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Journal of Physical Chemistry B Assembly of lipids and proteins into lipoprotein particles. Amy Y. Shih, Anton Arkhipov, Peter L. Freddolino, Stephen G. Sligar, and Klaus Schulten. Journal of Physical Chemistry B, 111:11095-11104, 2007.

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Journal of Structural Biology Assembly of lipoprotein particles revealed by coarse-grained molecular dynamics simulations. Amy Y. Shih, Peter L. Freddolino, Anton Arkhipov, and Klaus Schulten. Journal of Structural Biology, 157:579-592, 2007.

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Structure Stability and dynamics of virus capsids described by coarse-grained modeling. Anton Arkhipov, Peter L. Freddolino, and Klaus Schulten. Structure, 14:1767–1777, 2006.

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Physical Chemistry - Chemical Physics Molecular mechanisms of cellular mechanics. Mu Gao, Marcos Sotomayor, Elizabeth Villa, Eric Lee, and Klaus Schulten. Physical Chemistry - Chemical Physics, 8:3692-3706, 2006.

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Physical Biology The role of molecular modeling in bionanotechnology. Deyu Lu, Aleksei Aksimentiev, Amy Y. Shih, Eduardo Cruz-Chu, Peter L. Freddolino, Anton Arkhipov, and Klaus Schulten. Physical Biology, 3:S40-S53, 2006.

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Journal of Computational Chemistry 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.

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Biochemical Society Transactions Molecular dynamics and experimental investigation of H2 and O2 diffusion in [Fe]-hydrogenase. Jordi Cohen, Kwiseon Kim, Matthew Posewitz, Maria L. Ghirardi, Klaus Schulten, Michael Seibert, and Paul King, 2005. Biochemical Society Transactions, 33:80-82, 2005.

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The Physical Basis of Biochemistry

Cover of: Japanese edition of the textbook "The Physical Basis of Biochemistry".

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Structure Structural insights into how the MIDAS ion stabilizes integrin binding to an RGD peptide under force. David Craig, Mu Gao, Klaus Schulten, and Viola Vogel. Structure, 12:2049-2058, 2004.

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Biophysical Journal Gating of MscL studied by steered molecular dynamics. Justin Gullingsrud and Klaus Schulten. Biophysical Journal, 85:2087-2099, 2003.

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Molecular Mechanisms of Photosynthesis From simplicity to complexity and back: Function, architecture and mechanism of light harvesting systems in photosynthetic bacteria. Klaus Schulten. In H. Frauenfelder, J. Deisenhofer, and P. G. Wolynes, editors, Simplicity and Complexity in Proteins and Nucleic Acids, pages 227-253, Berlin, 1999. Dahlem University Press.

Cover of: Molecular Mechanisms of Photosynthesis. Blankenship, Robert E., Blackwell Science: 2002.

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Structure The Mechanism of Glycerol Conduction in Aquaglyceroporins. Morten O. Jensen, Emad Tajkhorshid, and Klaus Schulten. Structure, Vol. 9, November 2001, 1083-1093.

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J Phys Chem B 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.

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J Phys Chem B Kinetics of excitation migration and trapping in the photosynthetic unit of purple bacteria. Thorsten Ritz, Sanghyun Park, and Klaus Schulten. Journal of Physical Chemistry B, 105:8259-8267, 2001.

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Physics Today Binding of the estrogen receptor to DNA: The role of waters. Dorina Kosztin, Thomas C. Bishop, and Klaus Schulten. Biophysical Journal, 73:557-570, 1997.

Cover of: Pure Antagonists and Downregulators of the Estrogen Receptor as Therapy for Breast Cancer. C. K. Osborne and R. W. Carlson, Eds. A CME Monograph sponsored by Discovery Intl., Div of Continuing Med. Ed. June 15, 2001.

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Biophysical Journal Structural determinants of MscL gating studied by molecular dynamics simulations. Justin Gullingsrud, Dorina Kosztin, and Klaus Schulten. Biophysical Journal, 80:2074-2081, 2001.

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Current Opinion in Pharmacology Predicting the structure of apolipoprotein A-I in reconstituted high density lipoprotein disks. James C. Phillips, Willy Wriggers, Zhigang Li, Ana Jonas, and Klaus Schulten. Biophysical Journal, 73:2337-2346, 1997.

Cover of: Current Opinion in Pharmacology, Vol. 1, No. 2, April 2001.

J Phys Chem B 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.

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JOURNAL NAME Architecture and function of the light harvesting apparatus of purple bacteria. Xiche Hu, Ana Damjanovic, Thorsten Ritz, and Klaus Schulten. Proceedings of the National Academy of Sciences, USA, 95:5935-5941, 1998.

Cover of: Alliance/NCSA Access Magazine, Vol. 13 No 1, Spring 2000. (Issue on Enabling Research Using Computing, Grid, and Web Technologies.)

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Biophysical Journal Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation. Hui Lu, Barry Isralewitz, Andre Krammer, Viola Vogel, and Klaus Schulten. Biophysical Journal, 75:662-671, 1998.

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Biophysical Journal Structure and dynamics of calmodulin in solution. Willy Wriggers, Ernest Mehler, Felicia Pitici, Harel Weinstein, and Klaus Schulten. Biophysical Journal, 74:1622-1639, 1998.

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Physics Today How nature harvests sunlight. Xiche Hu and Klaus Schulten. Physics Today, 50:28-34, 1997.

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PROTEINS Molecular dynamics study of unbinding of the avidin-biotin complex. Sergei Izrailev, Sergey Stepaniants, Manel Balsera, Yoshi Oono, and Klaus Schulten. Biophysical Journal, 72:1568-1581, 1997.

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PROTEINS Molecular dynamics study of the activation of phospholipase A2 on a membrane surface. Feng Zhou and Klaus Schulten. PROTEINS: Structure, Function, and Genetics, 25:12-27, 1996.

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Israel Journal of Chemistry Molecular dynamics studies of bacteriorhodopsin's photocycles. Klaus Schulten, William Humphrey, Ilya Logunov, Mordechai Sheves, and Dong Xu. Israel Journal of Chemistry, 35:447-464, 1995.

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