An investigation to study the effects of cyclic-AMP to cAMP receptor protein from Mycobacterium tuberculosis by computational approach

Abstract The Cyclic AMP Receptor Protein of Mycobacterium tuberculosis , CRP Mt or Rv3676 is a global transcriptional regulator which shares several structural and functional features with the CRP protein of Escherichia coli . CRP Mt or Mtb CRP is also a homodimeric protein consists of an N terminal cAMP binding domain and C terminal DNA binding domain. In spite of having such high sequence identity with E. coli CRP, M.tuberculosis CRP differs in several aspects from this prototype. Moreover, it has also been reported that binding of cAMP to Mtb CRP induces a relatively small enhancement in specific DNA-binding by this protein. However, the main differences between CRP and CRP Mt become more apparent when comparing their functional dependence on cAMP binding. CRP cannot bind DNA in the absence of cAMP, which causes elaborate conformational changes that position the HTH domains for DNA binding. In contrast, CRP Mt shows specific DNA binding at most sites even in the absence of cAMP, although direct binding of cAMP to CRP Mt enhances its DNA binding affinity ∼2-fold. So, the significance of the presence of cAMP binding pocket in CRP Mt is still somewhat poorly understood. A long-standing question has been whether or not cAMP binding alone can cause CRP Mt to activate its cognate promoter. As an attempt to answer this question, we have done several docking experiments of Apo and ligand bound protein from MTb to its cognate promoter and analyze the results accordingly. We have also compared our docking experiment of Mtb CRP with E. coli CRP to have a wholesome idea about the conformational changes occurred by cAMP to Mtb CRP. Preliminary results from these studies are also included in this work.