Dear valued researchers,
I am working on a protein consisted of 461 amino acids. My colleagues and I are focusing on a 14 amino acids-based well-conserved motif. We have developed a model (E.coli) with point mutation of each amino acids and we were also working on double mutant for that model. The objective of this study is to identify molecular active site(s) that is/are responsible for the protein enzymatic activity. We did find some amino acid residue plays important role in regulating the protein enzymatic activity.
Therefore, I am trying to develop different hypothesis or plausible explanation underlying such activity including using bioinformatic approach. I tried to simulate theoretical properties of the mutant using Pepdraw (http://pepdraw.com/) and ProtParam (https://web.expasy.org/protparam/) but I am unsure if my approach is appropriate. PepDraw is for peptide, but I am using this to see any changes on the motif properties (isoelectric, hydrophobicity and etc). And then I compared with the result from ProtParam which give me bigger picture on protein level. Currently I am looking for software/website that can help me to predict structural conformation and functional in three dimension.
I am hoping someone can give an opinion on this matter.
p/s: provided are some information I obtained regarding my protein from PepDraw and ProtParam
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