Research Projects - Other

The nature of modern science is that it is ever-changing, energetically crossing boundaries heretofore defined by traditional areas of inquiry. Research at the Theoretical and Computational Biophysics group reflects this dynamic, with studies employing theoretical perspectives and methodological approaches or addressing topics that don't fall easily into one of the above categories. Included in this broad category are studies of a four-way DNA junction, the nuclear pore complex, gas transport in hydrogenase that may provide a source of renewable fuel, and other topics.

Spotlight - Kinetic Diffusion
Ion Diffusion on a Grid near MscS

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Traffic flow in a city is affected by large-scale features, like the layout of road networks, as much as it is by small-scale ones, like traffic lights at a road junction. Likewise, the transport of small molecules in cells occur on multiple scales. For example, ions diffusing through the mechanosensitive channel of small conductance (MscS) (see highlights from Jul 2011, "Smart Bacterial Safety Valve", Mar 2008, "Observation and Simulation depict Cell's Safety Valve", Feb 2007, "Observing and Modeling a crucial Membrane Channel", May 2006, "Electrical Safety Valve", and Nov 2004, "Japanese Lantern Protein") must navigate the intricate geometry of the MscS, which varies by the Ångstrom. At the same time, the distribution of ions within hundreds of Ångstroms of the MscS fluctuate as ions escape through the channel, thus changing the electrostatic landscape seen by other ions as they approach the MscS. In order to model both the fine and bulk aspects of diffusion in systems like that of the MscS, scientists have proposed, in a recent report, a method that marries the high spatial resolution of molecular dynamics to long range diffusion. In the new description, biomolecules "diffuse" by hopping through a grid under the influence of Coulomb and other forces. More on our Kinetic Diffusion web site.

All Spotlights

Papers

Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations. David J. Hardy, Matthew A. Wolff, Jianlin Xia, Klaus Schulten, and Robert D. Skeel. Journal of Chemical Physics, 144:114112, 2016. (16 pages).

Multilevel summation method for electrostatic force evaluation. David J. Hardy, Zhe Wu, James C. Phillips, John E. Stone, Robert D. Skeel, and Klaus Schulten. Journal of Chemical Theory and Computation, 11:766-779, 2015.

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, and Peijun Zhang. Nature, 497:643-646, 2013.

A computational kinetic model of diffusion for molecular systems. Ivan Teo and Klaus Schulten. Journal of Chemical Physics, 139:121929, 2013. (15 pages).

Effects of cytosine hydroxymethylation on DNA strand separation. Philip M.D. Severin, Xueqing Zou, Klaus Schulten, and Hermann E. Gaub. Biophysical Journal, 104:208-215, 2013.

DNA target sequence identification mechanism for dimer-active protein complexes. Markita P. Landry, Xueqing Zou, Lei Wang, Wai Mun Huang, Klaus Schulten, and Yann R. Chemla. Nucleic Acids Research, 41:2416-2427, 2013.

A computational kinetic model of diffusion for molecular systems. Ivan Teo and Klaus Schulten. Journal of Chemical Physics, 139:121929, 2013. (15 pages).

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.

Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: Improved backbone hydration and interactions between charged side chains. Wei Han and Klaus Schulten. Journal of Chemical Theory and Computation, 8:4413-4424, 2012.

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. (DNA P41).

Unique sugar-binding site mediates the distinct anti-influenza activity of pig surfactant protein D. Martin van Eijk, Michael J. Rynkiewicz, Mitchell R. White, Kevan L. Hartshorn, Xueqing Zou, Klaus Schulten, Dong Luo, Erika C. Crouch, Tanya M. Cafarella, James F. Head, Henk P. Haagsman, and Barbara A. Seaton. Journal of Biological Chemistry, 287:26666-26677, 2012.

High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD. Wei Jiang, David Hardy, James Phillips, Alex MacKerell, Klaus Schulten, and Benoit Roux. Journal of Physical Chemistry Letters, 2:87-92, 2011.

Probing a structural model of the nuclear pore complex channel through molecular dynamics. Lingling Miao and Klaus Schulten. Biophysical Journal, 98:1658-1667, 2010.

Flow-induced b-hairpin folding of the glycoprotein Iba b-switch. Xueqing Zou, Yanxin Liu, Zhongzhou Chen, Gloria Ines Cárdenas-Jirón, and Klaus Schulten. Biophysical Journal, 99:1182-1191, 2010.

Challenges in protein folding simulations. Peter L. Freddolino, Christopher B. Harrison, Yanxin Liu, and Klaus Schulten. Nature Physics, 6:751-758, 2010.

O2-reactivity of flavoproteins: Dynamic access of dioxygen to the active site and role of a H+ relay system in D-amino acid oxidase. Jan Saam, Elena Rosini, Gianluca Molla, Klaus Schulten, Loredano Pollegioni, and Sandro Ghisla. Journal of Biological Chemistry, 285:24439-24446, 2010.

Molecular dynamics simulations suggest that electrostatic funnel directs binding of Tamiflu to influenza N1 neuraminidases. Ly Le, Eric H. Lee, David J. Hardy, Thanh N. Truong, and Klaus Schulten. PLoS Computational Biology, 6:e1000939, 2010. (13 pages).

Limits for reduction of effective focal volume in multiple-beam light microscopy. Anton Arkhipov and Klaus Schulten. Optics Express, 17:2861-2870, 2009.

Transport-related structures and processes of the nuclear pore complex studied through molecular dynamics. Lingling Miao and Klaus Schulten. Structure, 17:449-459, 2009.

Double stranded DNA dissociates into single strands when dragged into a poor solvent. Shuxun Cui, Jin Yu, Ferdinand Kühner, Klaus Schulten, and Hermann E. Gaub. Journal of the American Chemical Society, 129:14710-14716, 2007.

Molecular dynamics simulations of the complete satellite tobacco mosaic virus. Peter L. Freddolino, Anton S. Arkhipov, Steven B. Larson, Alexander McPherson, and Klaus Schulten. Structure, 14:437-449, 2006.

Finding gas diffusion pathways in proteins: Application to O2 and H2 transport in CpI [FeFe]-hydrogenase and the role of packing defects. Jordi Cohen, Kwiseon Kim, Paul King, Michael Seibert, and Klaus Schulten. Structure, 13:1321-1329, 2005.

Binding dynamics of isolated nucleoporin repeat regions to importin-b. Timothy A. Isgro and Klaus Schulten. Structure, 13:1869-1879, 2005.

Conformational model of the Holliday junction transition deduced from molecular dynamics simulations. Jin Yu, Taekjip Ha, and Klaus Schulten. Nucleic Acids Research, 32:6683-6695, 2004.

Genetically engineered gold-binding polypeptides: Structure prediction and molecular dynamics. Rosemary Braun, Mehmet Sarikaya, and Klaus Schulten. Journal of Biomaterials Science, 13:747-758, 2002.