Physical Biology
Physical Biology
5 years ago

Automated design evolution of stereo- chemically randomized protein foldamers.

Vibin Ramakrishnan, Susheel Durani, Ranjit Ranbhor, Anil Kumar, Kirti Patel
Diversification of chain stereochemistry opens up the possibilities of 'in principle' increase in the design space of proteins. This huge increase in the sequence and consequent structural variation is aimed at the generation of smart materials of biological origin. For diversifying protein structure stereochemically, we introduced L- and D--amino acids as the design alphabet. With an inverse design algorithm, we now explore the usage of specific variables such as stereochemistry and sequence of this alphabet in independent steps. With molecular dynamics, we fold stereochemically diverse homo-polypeptides and evaluate their 'fitness' for possible design as protein-like foldamers. We formulated a fitness function to prune the most optimal fold among 1000 structures simulated with Automated Repetitive Simulated Annealing Molecular Dynamics (AR-SAMD) approach. The highly scored poly-leucine fold of sequence length 24 and 30 amino-acids, were later sequence optimized using a Dead End Elimination cum Monte Carlo based optimization tool. This paper demonstrates a novel approach for the de novo design of protein-like foldamers with tailor made applications.

Publisher URL: http://doi.org/10.1088/1478-3975/aaac9a

DOI: 10.1088/1478-3975/aaac9a

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