A simple contact mapping algorithm form identifying potential peptide mimetics in protein-protein interaction partners.

作者：Krall Alex; Brunn Jonathan; Kank****a Spandana; Peters Michael H^*

来源：Proteins: Structure, Function, and Genetics , 2014, 82(9): 2253-2262.

DOI：10.1002/prot.24592

• protein-protein interaction
• peptide mimetics
• static mapping

A simple, static contact mapping algorithm has been developed as a first step at identifying potential peptide biomimetics from protein interaction partner structure files. This rapid and simple mapping algorithm, %26quot;OpenContact%26quot; provides potential interactions. The algorithm, which uses all-atom Amber03 force field models, was blindly tested on several unrelated cases from the literature where potential peptide mime-tics have been experimentally developed to varying degrees of success. In all cases, the screening algorithm efficiently predicted proposed or potential peptide biomimetics, or close variations thereof, and provided complete atom-atom interaction data necessary for further detailed analysis and drug development. In addition, we used the static parsing/mapping method to develop a peptide mimetic to the cancer protein target, epidermal growth factor receptor. In this case, secondary, loop structure for the peptide was indicated from the intmprotein mapping, and the peptide was subsequently synthesized and shown to exhibit successful binding to the target protein. The case studies, which all involved experimental peptide drug advancement, illustrate ma

• 出版日期2014-9