I am looking for some tools for disulfide bonds prediction and energy/structure estimation. What I have: patch-clamp results of WT, single and double cysteine mutant of the ionotropic receptor that are indicating the possibility of the disulfide bond formation. In addition, there are some pdbs of the receptor structure available, importantly, they are in different functional (apo, resting etc.) states. Also, I prepared homology models of single and double cysteine mutants based on respective templates. I would like to somehow asses the impact of this double mutantion and probability of the bond formation and differences between given structures/homology models. By far I found MAESTROweb and Disulfide by Desing web servers that allow for estimation of the bond energies and probability of the bond formation at all. Of course, it would be best to use some MD to simulate WT/double CYS/double CYS with disulfide ff patch receptor systems and compare them, but I am looking for some less time consuming approaches. I there anything you would suggest? Could be something like mentioned webserves but I would be also interested in some robust and coarse molecular modeling approaches.
There are some online tools* offering disulfide connectivity prediction from amino-acid sequence. Without a clear indication which tool is the most reliable i would use them all and try to arrive to a consensual conclusion.
*For example: http://www.csbio.sjtu.edu.cn/bioinf/Cyscon/
Thanks for the answers! So, indeed, there is a lot of tools for disulfide prediction form sequence. The problem is, that my disulfide is formed between two subunits and as far as I recall, none of the sequence based prediction methods will work in this case. This is not surprising, given the general idea behind the sequence-based prediction. And, what is most important, the sequence based methods are rather for initial scan of disulfide propensity rather for more detailed analysis in specific cases, what is my goal.
Michał Adam Michałowski, the particulars can be inferred from the universals, and vice versa. That the disulfide bond is formed between two subunits is not necessarily a problem: let the prediction algorithms assume that the two subunits form a unit by providing them with a continuous sequence of the two subunits. If the results are still unsatisfactory, there is no avoiding of building a three-dimensional model.
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