Is it possible to study the effect of denaturants on the structure of the proteins through molecular dynamics simulations? Experiments using fluorescence and circular dichroism are showing prominent changes in the secondary structure. Is there any way to get a detailed information about the changes by carrying out molecular dynamics simulations? Maybe seeing the change in the secondary structure by placing denaturant molecules while carrying MD simulations?
Thanks Stephane. Thanks for the paper. It is very informative. I looked up for the ENCAD software(used in the paper). But I could not find it. Any info regarding similar studies with contemporary softwares like Gromacs, Schrodinger etc. would be great.
You may use GROMACS package. Following papers may be helpful:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2711416/
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000221
http://pubs.acs.org/doi/abs/10.1021/ja076216j
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