Team:EPF-Lausanne/Information & references

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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 (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 ([http://www.ncbi.nlm.nih.gov/sites/entrez?db=pmc&cmd=search&term=PMC1630464 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 ([http://pubs.acs.org/doi/full/10.1021/bi701851v 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 ([http://www.nature.com/nchembio/journal/vaop/ncurrent/full/nchembio.210.html 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 ([http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2453334/ 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 ([http://pubs.acs.org/doi/full/10.1021/bi700852w 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. ([http://www.ncbi.nlm.nih.gov/pubmed/18001137 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. (Article)
2. Introduction to molecular dynamics: [http://chsfpc5.chem.ncsu.edu/~franzen/CH795N/lecture/IV/IV.html website]

VMD informations

VMD is used to visualize molecules. It is quite user friendly.

• A tutorial for VMD can be found [http://www.ks.uiuc.edu/Training/Tutorials/ here].

NAMD informations

NAMD performs minimization and equilibration.

• A tutorial is on the same page as for VMD, [http://www.ks.uiuc.edu/Training/Tutorials/ here].
• [http://www.ks.uiuc.edu/Research/namd/2.7b1/ug/ NAMD 2.7b1 User's Guide]
• 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.

• [http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/ Building Gramicidin A: Equilibration]: protocol uses a single .conf file, heating process is too fast.
• [http://www.biochemistry.uab.edu/robinson/documents/howto/modeling/NAMD_notes.htm NAMD notes from Robinson Lab]: a really nice heating process, but involves different .conf files, which is really painful.