Team:EPF-Lausanne/Information & references
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# 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]) | # 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]) | ||
# 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]) | # 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]) | ||
- | # 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 | + | # 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 |
+ | # 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]) | ||
===Molecular dynamics references=== | ===Molecular dynamics references=== |
Revision as of 16:49, 19 October 2009
Contents |
LOV2 & LOVTAP references
- 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)
- 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])
- 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])
- 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])
- 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
- 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])
Molecular dynamics references
- 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)
- 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.