Team:EPF-Lausanne/Information & references

 

 

 



References

LOV2 & LOVTAP references

 * 1) Strickland et al. Light-activated DNA binding in a designed allosteric protein. Proceedings of the National Academy of Sciences (2008) vol. 105 (31) pp. 10709 ([[Media:Light-activated.pdf‎ |Article]])
 * 2) Freddolino, P.L., Dittrich M., Schulten K., Dynamic Switching Mechanisms in LOV1 and LOV2 Domains of Plant Phototropins. Biophysical Journal, 91, 3630-3639, 2006 (Article)
 * 3) Atsushi Yamamoto, Tatsuya Iwata, Satoru Tokutomi and Hideki Kandori, Role of Phe1010 in Light-Induced Structural Changes of the neo1-LOV2 Domain of Adiantum Biochemistry, 2008, 47 (3), pp 922–928 (Article)
 * 4) Brian D Zoltowski, Brian Vaccaro & Brian R Crane, Mechanism-based tuning of a LOV domain photoreceptor Published online: 30 August 2009 | doi:10.1038/nchembio.210 (Article)
 * 5) Markus Dittrich, Peter L. Freddolino, and Klaus Schulten,  When Light falls in LOV: A QM/MM Study of Photoexcitation in Phot-LOV1 of C. Reinhardtii, Published in final edited form as: J Phys Chem B. 2005 July 7; 109(26): 13006–13013N (Article)
 * 6) John M. Christie, Stephanie B. Corchnoy, Trevor E. Swartz, Mark Hokenson, In-Seob Han, Winslow R. Briggs, and Roberto A. Bogomolni, Steric Interactions Stabilize the Signaling State of the LOV2 Domain of Phototropin 1, Published in Biochemistry, 2007, 46 (32), pp 9310–9319, July 21, 2007 (Article)
 * 7) Halavaty AS, Moffat K.,  N- and C-terminal flanking regions modulate light-induced signal transduction in the LOV2 domain of the blue light sensor phototropin 1 from Avena sativa, Published in Biochemistry. 2007 Dec 11;46(49):14001-9. Epub 2007 Nov 15. (Article)

Molecular dynamics references

 * 1) Michael P. Allen, Introduction to Molecular Dynamics Simulation published in Computational Soft Matter: From Synthetic Polymers to Proteins, Lecture Notes, Norbert Attig, Kurt Binder, Helmut Grubmüller, Kurt Kremer(Eds.), John von Neumann Institute for Computing, Jülich, NIC Series, Vol. 23, ISBN3-00-012641-4, pp. 1-28, 2004. ([[Media:Introduction_to_molecular_Dynamics_Simulation.pdf |Article]])
 * 2) Introduction to molecular dynamics: website

VMD informations
VMD is used to visualize molecules. It is quite user friendly.
 * A tutorial for VMD can be found here.

NAMD informations
NAMD performs minimization and equilibration.
 * A tutorial is on the same page as for VMD, here.
 * NAMD 2.7b1 User's Guide
 * [[Media: NAMD_set_param.pdf‎|Summary of parameters setting]]

Run a simulation
A simulation is composed of different steps. Here are a few links that deal with heating and stabilization.
 * Building Gramicidin A: Equilibration: protocol uses a single .conf file, heating process is too fast.
 * NAMD notes from Robinson Lab: a really nice heating process, but involves different .conf files, which is really painful.

