Investigation of the mechanical properties of immunoglobulinbinding domains of proteins L and G using the molecular dynamics simulations

 pdf (495K)  / Annotation

List of references:

  1. E. Paci, M. Karplus. Unfolding Proteins by External Forces and Temperature: The Importance of Topology and Energetics // Proc. Natl. Acad. Sci. USA. — 2000. — V. 97. — P. 6521–6526. — DOI: 10.1073/pnas.100124597. — ads: 2000PNAS...97.6521P.
  2. D. K. West, D. J. Brockwell, P. D. Olmsted, Sh. E. Radford, E. Paci. Mechanical Resistance of Proteins Explained Using Simple Molecular Models // Biophysical Journal. — 2006. — V. 90. — P. 287–297. — DOI: 10.1529/biophysj.105.071035. — ads: 2006BpJ....90..287W.
  3. D. K. West, P. D. Olmsted, E. Paci. Free Energy for Protein Folding from Nonequilibrium Simulations Using the Jarzynski Equality // The Journal of Chemical Physics. — 2006. — V. 125. — P. 204910–7. — DOI: 10.1063/1.2393232. — ads: 2006JChPh.125t4910W.
  4. J. Wang, А. Cieplak, P. A. Kollman. How Well a Restrained Electrostatic Potential (RESP) Model Perform in Calculating Conformational Energies of Organic and Biological Molecules? // J. Comp. Chem. — 2000. — V. 21. — P. 1049–1074. — DOI: 10.1002/1096-987X(200009)21:12<1049::AID-JCC3>3.0.CO;2-F.
  5. A. S. Lemak, N. K. Balabaev. A Comparison Between Collisional Dynamics and Brownian Dynamics // Mol. Simul. — 1995. — V. 15. — P. 223–231. — DOI: 10.1080/08927029508022336.
  6. A. S. Lemak, N. K. Balabaev. Molecular Dynamics Simulation of Polymer Chain in Solution by Collisional Dynamics Method // J. Comp. Chem. — 1996. — V. 17. — P. 1685–1695. — DOI: 10.1002/(SICI)1096-987X(19961130)17:15<1685::AID-JCC1>3.0.CO;2-L.
  7. M. P. Allen, D. J. Tildesley. Computer Simulation of Liquids. — Oxford: Clarendon, 1987. — MathSciNet: MR0932966.
  8. D. J. Brockwell, G. S. Beddard, E. Paci, D. K. West, P. D. Olmsted, D. A. Smith, S. E. Radford. Mechanically unfolding the small, topologically simple protein L // Biophys. J. — 2005. — V. 89, no. 1. — P. 506–519. — DOI: 10.1529/biophysj.105.061465.
  9. Y. Cao, H. Li. Polyprotein of GB1 is an ideal artificial elastomeric protein // Nature Mater. — 2007. — V. 6. — P. 109–114. — DOI: 10.1038/nmat1825. — ads: 2007NatMa...6..109C.
  10. Y. Cao, H. Li. How Do Chemical Denaturants Affect the Mechanical Folding and Unfolding of Proteins? // J. Mol. Biol. — 2008. — V. 375. — P. 316–324. — DOI: 10.1016/j.jmb.2007.10.024.
  11. J. Shimada, E. I. Shakhnovich. The Ensemble Folding Kinetics of Protein G from an All-Atom Monte Carlo Simulation // Proc. Natl. Acad. Sci. USA. — 2002. — V. 99. — P. 11175–11180. — DOI: 10.1073/pnas.162268099. — ads: 2002PNAS...9911175S.
  12. Waldauer S. A., O. Bakajin, T. Ball, Y. Chen, S. J. Decamp, M. Kopka, M. Jäger, V. R. Singh, W. J. Wedemeyer, S. Weiss, S. Yao, L. J. Lapidus. Ruggedness in the folding landscape of protein L // HFSP Journal. — 2008. — V. 2. — P. 388–395. — DOI: 10.2976/1.3013702.

Indexed in Scopus

Full-text version of the journal is also available on the web site of the scientific electronic library eLIBRARY.RU

The journal is included in the Russian Science Citation Index

The journal is included in the RSCI

International Interdisciplinary Conference "Mathematics. Computing. Education"