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.
|
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
(Image Size: 5.8MB ) |
|
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.
(Image Size: 3.2MB ) |
|
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.
(Image Size: 3.9MB ) |
|
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.
(Image Size: 9.1MB ) |
|
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.
(Image Size: 5.7MB ) |
|
Assembly and analysis of cell-scale membrane envelopes.
Josh Vermaas, Chris Mayne, Eric Shinn, and Emad Tajkhorshid. Journal of Chemical Information and Modeling, 2021.
(Image Size: 10.1MB ) |
|
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.
(Image Size: 596.3KB ) |
|
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.
(Image Size: 547.8KB ) |
|
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.
(Image Size: 752.4KB ) |
|
Active participation of membrane lipids in inhibition of multidrug transporter P-glycoprotein.
Karan Kapoor, Shashank Pant, and Emad Tajkhorshid. Chemical Science, 2021.
(Image Size: 598.3KB ) |
|
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.
(Image Size: 1.4MB ) |
|
Twisting of a mechanosensitive molecular probe detects order in membranes.
Giuseppe Licari, Karolina Strakova, Stefan Matile, and Emad Tajkhorshid. Chemical Science.
(Image Size: 467.1KB ) |
|
Microscopic characterization of GRP1 PH domain interaction with anionic membranes.
Shashank Pant and Emad Tajkhorshid. Journal of Computational Chemistry.
(Image Size: 413.9KB ) |
|
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.
(Image Size: 3.9MB ) |
|
Probing cholesterol binding and translocation in P-glycoprotein.
Sundar Thangapandian, Karan Kapoor, and Emad Tajkhorshid. Biochimica et Biophysica Acta - Biomembranes, 2019. In press.
(Image Size: 663.4KB ) |
|
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.
(Image Size: 2.3MB ) |
|
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
(Image Size: 207.4KB ) |
|
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.
(Image Size: 635.4KB ) |
|
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
(Image Size: 279.4KB ) |
|
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.
(Image Size: 81.8KB ) |
|
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)
(Image Size: 1.9MB ) |
|
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.
(Image Size: 249.1KB ) |
|
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
(Image Size: 4.4MB ) |
|
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.
(Image Size: 2.6MB ) |
|
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.
(Image Size: 3.1MB ) |
|
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.
(Image Size: 3.0MB ) |
|
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)
(Image Size: 6.7MB ) |
|
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.
(Image Size: 327.9KB ) |
|
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)
(Image Size: 297.8KB ) |
|
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.
(Image Size: 327.9KB ) |
|
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)
(Image Size: 9.2MB ) |
|
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.
(Image Size: 327.9KB ) |
|
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.
(Image Size: 376.3KB ) |
|
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.
(Image Size: 1.9MB ) |
|
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.
(Image Size: 636.6KB ) |
|
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.
(Image Size: 252.4KB ) |
|
Excited state dynamics in photosynthetic reaction center and light harvesting complex 1. Johan Strümpfer and Klaus Schulten. Journal of Chemical Physics, 137:065101, 2012.
(Image Size: 296.6KB ) |
|
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)
(Image Size: 289.7KB ) |
|
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.
(Image Size: 306.4KB ) |
|
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.
(Image Size: 305.7KB ) |
|
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.
(Image Size: 407.1KB ) |
|
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.
(Image Size: 417.7KB ) |
|
Common structural transitions in explicit-solvent simulations of villin headpiece folding. Peter L. Freddolino and Klaus Schulten. Biophysical Journal, 97:2337-2346, 2009.
(Image Size: 329.2KB ) |
|
Magnetoreception through cryptochrome may involve superoxide.. Ilia A. Solov'yov and Klaus Schulten. Biophysical Journal, 96:4804-4813, 2009.
(Image Size: 203.3KB ) |
|
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.
(Image Size: 9.4KB ) |
|
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.
(Image Size: 119.2KB ) |
|
Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF. Jerome Henin, Emad Tajkhorshid, Klaus Schulten, and Christophe Chipot. Biophysical Journal, 94:832-839, 2008.
(Image Size: 140.0KB ) |
|
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).
(Image Size: 11.3MB ) |
|
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.
(Image Size: 280.6KB ) |
|
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.
(Image Size: 94.1KB ) |
|
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.
(Image Size: 86.2KB ) |
|
Stability and dynamics of virus capsids
described by coarse-grained modeling.
Anton Arkhipov, Peter L. Freddolino, and Klaus Schulten. Structure, 14:1767–1777, 2006.
(Image Size: 230.9KB ) |
|
Molecular mechanisms of cellular mechanics.
Mu Gao, Marcos Sotomayor, Elizabeth Villa, Eric Lee, and Klaus Schulten. Physical Chemistry - Chemical Physics, 8:3692-3706, 2006.
(Image Size: 146.1KB ) |
|
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.
(Image Size: 110.3KB ) |
|
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.
(Image Size: 144.8KB ) |
|
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.
(Image Size: 194.6KB ) |
|
Cover of: Japanese edition of the textbook "The Physical Basis of Biochemistry". (Image Size: 82.4KB ) |
|
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.
(Image Size: 86.0KB ) |
|
Gating of MscL studied by steered molecular dynamics.
Justin Gullingsrud and Klaus Schulten.
Biophysical Journal, 85:2087-2099, 2003.
(Image Size: 84.6KB ) |
|
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. (Image Size: 105.0KB ) |
|
The Mechanism
of Glycerol Conduction in Aquaglyceroporins. Morten O. Jensen, Emad
Tajkhorshid, and Klaus Schulten. Structure, Vol. 9, November 2001,
1083-1093.
(Image Size: 67.7KB ) |
|
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.
(Image Size: 105.3KB ) |
|
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.
(Image Size: 103.4KB ) |
|
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. (Image Size: 69.6KB ) |
|
Structural
determinants of MscL gating studied by molecular dynamics
simulations. Justin Gullingsrud, Dorina Kosztin, and Klaus Schulten.
Biophysical Journal, 80:2074-2081, 2001.
(Image Size: 45.6KB ) |
|
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. |
|
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.
(Image Size: 65.1KB ) |
|
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.) (Image Size: 103.1KB ) |
|
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.
(Image Size: 86.4KB ) |
|
Structure and
dynamics of calmodulin in solution. Willy Wriggers, Ernest Mehler,
Felicia Pitici, Harel Weinstein, and Klaus Schulten. Biophysical Journal,
74:1622-1639, 1998.
(Image Size: 92.3KB ) |
|
How nature
harvests sunlight. Xiche Hu and Klaus Schulten. Physics Today,
50:28-34, 1997.
(Image Size: 197.2KB ) |
|
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.
(Image Size: 65.2KB ) |
|
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.
(Image Size: 98.5KB ) |
|
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.
(Image Size: 44.5KB ) |
