Computational Force Microscopy
Applications of Steered Molecular Dynamics (1997-2005)
Stretching fibronectin.
What makes an aquaporin a glycerol channel: A comparative study of AqpZ and GlpF. Yi Wang, Klaus Schulten, and Emad Tajkhorshid. Structure, 13:1107-1118, 2005.
In search of the hair-cell gating spring: Elastic properties of ankyrin and cadherin repeats. Marcos Sotomayor, David P. Corey, and Klaus Schulten. Structure, 13:669-682, 2005.
Structural dynamics of the Lac repressor-DNA complex revealed by a multiscale simulation. Elizabeth Villa, Alexander Balaeff, and Klaus Schulten. Proceedings of the National Academy of Sciences, USA, 102:6783-6788, 2005.
Role of water in transient cytochrome c2 docking. Felix Autenrieth, Emad Tajkhorshid, Klaus Schulten, and Zaida Luthey-Schulten. Journal of Physical Chemistry B, 108:20376-20387, 2004.
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.
Molecular dynamics study of gating in the mechanosensitive channel of small conductance MscS. Marcos Sotomayor and Klaus Schulten. Biophysical Journal, 87:3050-3065, 2004.
Forced dissociation of the strand dimer interface between C-cadherin ectodomains. M. V. Bayas, K. Schulten, and D. Leckband. Mechanics and Chemistry of Biosystems, 1:101-111, 2004.
Calculating potentials of mean force from steered molecular dynamics simulations. Sanghyun Park and Klaus Schulten. Journal of Chemical Physics, 120:5946-5961, 2004.
The mechanism of proton exclusion in aquaporin channels. Boaz Ilan, Emad Tajkhorshid, Klaus Schulten, and Gregory A. Voth. PROTEINS: Structure, Function, and Bioinformatics, 55:223-228, 2004.
Mechanism of anionic conduction across ClC. Jordi Cohen and Klaus Schulten. Biophysical Journal, 86:836-845, 2004.
Insights into the molecular mechanism of rotation in the Fo sector of ATP synthase. Aleksij Aksimentiev, Ilya A. Balabin, Robert H. Fillingame, and Klaus Schulten. Biophysical Journal, 86:1332-1344, 2004.
Tuning the mechanical stability of fibronectin type III modules through sequence variation. David Craig, Mu Gao, Klaus Schulten, and Viola Vogel. Structure, 12:21-30, 2004.
Theory and simulation of water permeation in aquaporin-1. Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 86:50-57, 2004.
Structure and functional significance of mechanically unfolded fibronectin type III1 intermediates. Mu Gao, David Craig, Olivier Lequin, Iain D. Campbell, Viola Vogel, and Klaus Schulten. Proceedings of the National Academy of Sciences, USA, 100:14784-14789, 2003.
Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality. Sanghyun Park, Fatemeh Khalili-Araghi, Emad Tajkhorshid, and Klaus Schulten. Journal of Chemical Physics, 119:3559-3566, 2003.
Water and proton conduction through carbon nanotubes as models for biological channels. Fangqiang Zhu and Klaus Schulten. Biophysical Journal, 85:236-244, 2003.
Mechanisms of selectivity in channels and enzymes studied with interactive molecular dynamics. Paul Grayson, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 85:36-48, 2003.
Forced detachment of the CD2-CD58 complex. M. V. Bayas, Klaus Schulten, and D. Leckband. Biophysical Journal, 84:2223-2233, 2003.
Constant velocity SMD simulation. Identifying unfolding intermediates of FN-III10 by steered molecular dynamics. Mu Gao, David Craig, Viola Vogel, and Klaus Schulten. Journal of Molecular Biology, 323:939-950, 2002.
Steered molecular dynamics studies of titin I1 domain unfolding. Mu Gao, Matthias Wilmanns, and Klaus Schulten. Biophysical Journal, 83:3435-3445, 2002.
Energetics of glycerol conduction through aquaglyceroporin GlpF. Morten Ø. Jensen, Sanghyun Park, Emad Tajkhorshid, and Klaus Schulten. Proceedings of the National Academy of Sciences, USA, 99:6731-6736, 2002.
Pressure-induced water transport in membrane channels studied by molecular dynamics. Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 83:154-160, 2002.
Mechanical force generation by G-proteins. Ioan Kosztin, Robijn Bruinsma, Paul O'Lague, and Klaus Schulten. Proceedings of the National Academy of Sciences, USA, 99:3575-3580, 2002.
A structural model for force regulated integrin binding to fibronectin's RGD-synergy site. André Krammer, David Craig, Wendy E. Thomas, Klaus Schulten, and Viola Vogel. Matrix Biology, 21:139-147, 2002.
Simulated refolding of stretched titin immunoglobulin domains. Mu Gao, Hui Lu, and Klaus Schulten. Biophysical Journal, 81:2268-2277, 2001.
Comparison of the early stages of forced unfolding of fibronectin type III modules. David Craig, André Krammer, Klaus Schulten, and Viola Vogel. Proceedings of the National Academy of Sciences, USA, 98:5590-5595, 2001.
Structural determinants of MscL gating studied by molecular dynamics simulations. Justin Gullingsrud, Dorina Kosztin, and Klaus Schulten. Biophysical Journal, 80:2074-2081, 2001.
A system for interactive molecular dynamics simulation. John Stone, Justin Gullingsrud, Paul Grayson, and Klaus Schulten. In John F. Hughes and Carlo H. Séquin, editors, 2001 ACM Symposium on Interactive 3D Graphics, pp. 191-194, New York, 2001. ACM SIGGRAPH.
The key event in force-induced unfolding of titin's immunoglobulin domains. Hui Lu and Klaus Schulten. Biophysical Journal, 79:51-65, 2000.
Simulated unbinding and binding of fatty acid substrates in the cyclooxygenase site of prostaglandin H2 synthase-1. Ferenc Molnar, Lawrence S. Norris, and Klaus Schulten. Progress in Reaction Kinetics and Mechanism, 25:263-298, 2000.
Mechanical unfolding intermediates in titin modules. Piotr E. Marszalek, Hui Lu, Hongbin Li, Mariano Carrion-Vazquez, Andres F. Oberhauser, Klaus Schulten, and Julio M. Fernandez. Nature, 402:100-103, 1999.
Computer modeling of force-induced titin domain unfolding. Hui Lu, André Krammer, Barry Isralewitz, Viola Vogel, and Klaus Schulten. In Jerry Pollack and Henk Granzier, editors, Elastic Filaments of the Cell, chapter 1, pp. 143-162. Kluwer Academic/Plenum Publishers, New York, NY, 2000.
Steered molecular dynamics simulation of the Rieske subunit motion in the cytochrome bc1 complex. Sergei Izrailev, Antony R. Crofts, Edward A. Berry, and Klaus Schulten. Biophysical Journal, 77:1753-1768, 1999.
Steered molecular dynamics simulation of conformational changes of immunoglobulin domain I27 interpret atomic force microscopy observations. Hui Lu and Klaus Schulten. Chemical Physics, 247:141-153, 1999.
Steered molecular dynamics simulations of force-induced protein domain unfolding. Hui Lu and Klaus Schulten. PROTEINS: Structure, Function, and Genetics, 35:453-463, 1999.
Forced unfolding of the fibronectin type III module reveals a tensile molecular recognition switch. André Krammer, Hui Lu, Barry Isralewitz, Klaus Schulten, and Viola Vogel. Proceedings of the National Academy of Sciences, USA, 96:1351-1356, 1999.
Reconstructing potentials of mean force through time series analysis of steered molecular dynamics simulations. Justin Gullingsrud, Rosemary Braun, and Klaus Schulten. Journal of Computational Physics, 151:190-211, 1999.
Investigating a back door mechanism of actin phosphate release by steered molecular dynamics. Willy Wriggers and Klaus Schulten. PROTEINS: Structure, Function, and Genetics, 35:262-273, 1999.
Unbinding of retinoic acid from its receptor studied by steered molecular dynamics. Dorina Kosztin, Sergei Izrailev, and Klaus Schulten. Biophysical Journal, 76:188-197, 1999.
Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation. Hui Lu, Barry Isralewitz, André Krammer, Viola Vogel, and Klaus Schulten. Biophysical Journal, 75:662-671, 1998.
Extraction of lipids from phospholipid membranes by steered molecular dynamics. Sergey Stepaniants, Sergei Izrailev, and Klaus Schulten. Journal of Molecular Modeling, 3:473-475, 1997.
Binding pathway of retinal to bacterio-opsin: A prediction by molecular dynamics simulations. Barry Isralewitz, Sergei Izrailev, and Klaus Schulten. Biophysical Journal, 73:2972-2979, 1997.
Reconstructing potential energy functions from simulated force-induced unbinding processes. Manel Balsera, Sergey Stepaniants, Sergei Izrailev, Yoshitsugu Oono, and Klaus Schulten. Biophysical Journal, 73:1281-1287, 1997.
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.
Related TCB Group Projects
- Mechanical Proteins
- Molecular Basis of Hearing
- Multiscale Modeling of Gene Repression
- Mechanical Strength of the Titin/Telethonin Complex
- Fibronectin and Integrin
- Unfolding Titin Immunoglobulin Domains
- Molecular Motor Scooting along DNA
- Bacteria Swim and Tumble
- IMD and the Glycerol Channel
- Unbinding of Retinoic Acid from its Receptor
- Molecular Basis for Anthrax Intoxication
- Mechanosensitive Channel MscS
- Mechanosensitive Channel MscL
Page created and maintained by Marcos Sotomayor.