Modeling structure/dynamics of fibrin(ogen)

  • Y. F. Zuev, R. I. Litvinov, A. E. Sitnitsky, B. Z. Idiyatullin, D. R. Bakirova, D. K. Galanakis, A. Zhmurov, V. Barsegov, J. W. Weisel, “Non-Enzymatic Self- Association of Fibrinogen,” submitted to Biomacromolecules
  • A. Zhmurov, A. Protopopova, R. I. Litvinov, P. Zhukov, J. W. Weisel, and V. Barsegov, “Structural basis of interfacial flexibility in fibrin oligomers,” accepted to Structure [PDF]
  • A. Zhmurov, А. Е. Alekseenko, V. Barsegov, О. Kononova, Y. А. Kholodov, “Force-induced phase transition from α-helices to β-sheets in fibrous proteins”, (in Russian), Computer Research & Modeling, 5, 705-725 (2013).
  • O. Kononova, R. I. Litvinov, A. Zhmurov, A. Alekseenko, C.-H. Cheng, S. Agarwal, K. A. Marx, J. W. Weisel and V. Barsegov, "Molecular mechanisms, thermodynamics, and dissociation kinetics of knob-hole interactions in fibrin", J. Biol. Chem., 288, 22681-22692 (2013) [PDF]
  • A. Zhmurov, O. Kononova, R. I. Litvinov, R. I. Dima, V. Barsegov and J. W. Weisel, "Mechanical transition from α-helical coiled coils to β-sheets in fibrin(ogen)", J. Am. Chem. Soc., 134, 20396-20402 (2012) [PDF]
  • A. Zhmurov, A. E. X. Brown, R. I. Litvinov, R. I. Dima, J. W. Weisel, and V. Barsegov, "Mechanism of fibrin(ogen) forced unfolding", Structure, 19, 1615-1624 (2011) [PDF]

Biomechanics of biological particles

  • J. Snijder, O. Kononova, I. M. Barbu, C. Uetrecht, W. F. Rurup, R. J. Burnley, M. S. T. Koay, J. J. L. M. Cornelissen, W. H. Roos, V. Barsegov, G. J. L. Wuite, A. J. R. Heck, "Assembly and Mechanical Properties of the Cargo-Free and Cargo-Loaded Bacterial Nanocompartment Encapsulin", Biomacromolecules, 17, 2522-2529 (2016) [PDF]
  • O. Kononova, J. Snijder, Y. Kholodov, K. A. Marx, G. J. L. Wuite, W. H. Roos, V. Barsegov, "Fluctuating Nonlinear Spring Model of Mechanical Deformation of Biological Particles", PLoS Comput. Biol., 12, e1004729 (2016) [PDF]
  • O. Kononova, Y. Kholodov, K. E. Theisen, K. A. Marx, R. I. Dima, F. I. Ataullakhanov, E. L. Grishchuk and V. Barsegov, "Tubulin bond energies and microtubule biomechanics determined from nanoindentation in silico", J. Am. Chem. Soc., 136, 17036-17045 (2014) [PDF]
  • O. Kononova, J. Snijder, M. Brasch, J. Cornelissen, R. I. Dima, K. A Marx, G. J. L. Wuite, W. H. Roos and V. Barsegov, "Structural transitions and energy landscape for cowpea chlorotic mottle virus capsid mechanics from nanomanipulation in vitro and in silico", Biophys. J., 105, 1893-1903 (2013) [PDF]

MD simulations on GPU

  • A. Alekseenko, O. Kononova, Y. Kholodov, K. A. Marx, and V. Barsegov, "SOP‐GPU: influence of solvent‐induced hydrodynamic interactions on dynamic structural transitions in protein assemblies", J. Comput. Chem., 37, 1537-1551 (2016) [PDF]
  • A. Zhmurov, V. Barsegov, S.Trifonov, Y. Kholodov, and A. Kholodov, “Langevin dynamics simulations of micromechanics on graphics processors” (in Russian), Molecular Modeling, 23, 133-156 (2011).
  • A. Zhmurov, V. Barsegov, S. Trifonov, Y. Kholodov, and A. Kholodov, “Efficient pseudorandom number generators for biomolecular simulations on graphics processors” (in Russian), Computer Research & Modeling, 3, 161-171 (2011).
  • A. Zhmurov, K. Rybnikov, Y. Kholodov, and V. Barsegov, "Generation of random numbers on graphics processors: Forced indentation in silico of the bacteriophage HK97", J. Phys. Chem. B, 115, 5278-5288 (2011) [PDF]
  • A. Zhmurov, R. I. Dima, Y. Kholodov, and V. Barsegov, "SOP-GPU: Accelerating biomolecular simulations in the centisecond timescale using graphics processors", Proteins, 78, 2984-2999 (2010) [PDF]

Protein folding/forced unfolidng

  • R. Kumar, R. V. Kukreja, L. Li, A. Zhmurov, O. Kononova, S. Cai, S. A. Ahmed, V. Barsegov, and B. R. Singh, "Botulinum neurotoxin: unique folding of enzyme domain of the most-poisonous poison", J. Biomol. Struct. Dyn., 32, 804-815 (2014) [PDF]
  • K. E. Theisen, A. Zhmurov, M. E. Newberry, V. Barsegov and R. I. Dima, "Multiscale modeling of the nanomechanics of microtubule protofilaments", J. Phys. Chem., 116, 8545-8555 (2012) [PDF]
  • L. Duan, A. Zhmurov, V. Barsegov and R. I. Dima, "Exploring the Mechanical Stability of the C2 Domains in Human Synaptotagmin 1", J. Phys. Chem B, 115, 10133-10146 (2011) [PDF]
  • E. P. Raman, T. Takeda, V. Barsegov and D. K. Klimov , "Mechanical unbinding of Aβ peptides from amyloid fibrils", J. Mol. Biol., 373, 785-800 (2007) [PDF].

Theory/modeling of biomolecules

  • O. Kononova, L. Jones and V. Barsegov, "Order statistics inference for describing topological coupling and mechanical symmetry breaking in multidomain proteins", J. Chem. Phys., 139, 121913 (2013) [PDF]
  • R. I. Litvinov, A. Mekler, H. Shuman, J. S. Bennett, V. Barsegov, and J. W. Weisel, “Resolving two-dimensional kinetics of receptor-ligand interactions using Binding- Unbinding Correlation Spectroscopy”, Journal of Biological Chemistry, 287, 35272-35285 (2012) [PDF]
  • A. Zhmurov, R. I. Dima, and V. Barsegov, "Order Statistics theory of unfolding of multimeric proteins, "Biophys. J., 99, 1959-1268 (2010) [PDF]
  • E Bura, A. Zhmurov, and V. Barsegov, "Nonparametric density estimation and optimal bandwidth selection for protein unfolding and unbinding data, "J. Chem. Phys., 130, 015102 (2009) [PDF]
  • V. Barsegov, G. Morrison, and D. Thirumalai, "Role of internal chain dynamics on the rupture kinetics of adhesive contacts, "Phys. Rev. Lett., 100, 248102 (2008) [PDF]
  • E. Bura, D. K. Klimov and V. Barsegov , "Analyzing forced unfolding of protein tandems by ordered variates: 2. Dependent unfolding times", Biophys. J., 94, 2516-2528 (2008) [PDF].
  • E. Bura, D. K. Klimov and V. Barsegov, "Analyzing forced unfolding of protein tandems by ordered variates: 1. Independent unfolding times", Biophys. J., 93, 1100-1115 (2007) [PDF].
  • V. Barsegov, D. Klimov and D. Thirumalai, "Mapping the energy landscape of biomolecules using single molecule force correlation spectroscopy (FCS): Theory and applications", Biophys. J., 90, 3827-3841 (2006) [PDF].
  • V. Barsegov and D. Thirumalai, "Influence of surface interactions on folding and forced unbinding of semiflexible chains", J. Phys. Chem. B, 109, 21979-21988 (2005) [PDF].

Molecular modeling of protein-protein interactions

  • O. Kononova, R. I. Litvinov, D. S. Blokhin, V. V. Klochkov, J. W. Weisel, J. S. Bennett, V. Barsegov, “Structural and Thermodynamic Basis for Differential Binding of RGD- and AGDV-Peptides to the Platelet Integrin αIIbβ3,” submitted to Journal of Biological Chemistry.
  • R. I. Litvinov, S. V. Yarovoi, L. Rauova, V. Barsegov, B. S. Sachais, A. H. Rux, J. L. Hinds, G. M. Arepally, D. B. Cines and J. W. Weisel, "Distinct specificity and single-molecule kinetics characterize the interaction of pathogenic and non-pathogenic antibodies against platelet factor 4-heparin complexes with platelet factor 4", J. Biol. Chem., 288, 33060-33070 (2013) [PDF]
  • R. A. Toubar, A. Zhmurov, V. Barsegov, and K. A. Marx, "Comparative simulation studies of native and single-site mutant human beta-defensin-1 peptides", J. Biomol. Struct. Dyn., 31, 174-194 (2013) [PDF]
  • R. Litvinov, V. Barsegov, A. Schissler, A. Fisher, J. Bennett, J. Weisel, H. Shuman, "Dissociation of biomolecular αIIβ3-fibrinogen complex under a constant tensile force", Biophys J., 100, 165-173 (2011) [PDF]
  • E. P. Raman, V. Barsegov and D. K. Klimov , "Folding of tandem-linked domains", Proteins: Struct. Func. Bioinform., 67, 795-810 (2007) [PDF]
  • V. Barsegov and D. Thirumalai, "Dynamic competition between catch and slip bonds in selectins bound to ligands", J. Phys. Chem. B, 110, 26403-26412 (2006) [PDF].
  • V. Barsegov and D. Thirumalai, "Probing protein-protein interaction by dynamic force correlation spectroscopy (FCS)", Phys. Rev. Lett., 95, 168302-168305 (2005) [PDF].
  • V. Barsegov and D. Thirumalai, "Dynamics of unbinding of cell adhesion molecules: Transition from catch to slip bonds", Proc. Natl. Acad. Sci. USA, 102, 1835-1839 (2005) [PDF].

Other papers

  • V. Barsegov and P. J. Rossky, "Constructing quantum dynamics from mixed quantum-classical descriptions", Special Issue on the Spin-Boson Model, Chem. Phys., 296, 103-115 (2004) [PDF].
  • V. Barsegov and S. Mukamel, "Multipoint fluorescence quenching-time statistics for single molecules with anomalous diffusion", J. Phys. Chem. A, 108, 15-24 (2004) [PDF].
  • V. Barsegov, Y. Shapir and S. Mukamel, "One-dimensional transport with dynamic disorder, "Phys. Rev. E, 68, 011101-011114 (2003) [PDF].
  • V. Barsegov, V. Chernyak and S. Mukamel, "Quantum quadratic Brownian-oscillator model for absorption lineshapes, " Israel J. Chem., 16, 143-149 (2002) [PDF].
  • V. Barsegov and S. Mukamel, "Multidimensional spectroscopic probes of single molecule fluctuations", J. Chem. Phys., 117, 9465-9477 (2002) [PDF].
  • V. Barsegov and S. Mukamel, "Probing single molecule kinetics by photon arrival trajectories", J. Chem. Phys., 116, 9802-9810 (2002) [PDF].
  • V. Barsegov, V. Chernyak and S. Mukamel, "Multitime correlation functions for single molecule kinetics with fluctuating bottlenecks", J. Chem. Phys., 116, 4240-4251 (2002) [PDF].