The energetics and structural characteristics of several model proteins stretched at opposing ends are used to examine their sensitivity to the underlying choice of CHARMM potential. Specifically two very different α-helical peptides, 1PEF and our model system Ala10 , serve as benchmark proteins because the incorporation of helicity has been a critical drive in the C22, C27 and C36 versions of CHARMM. Adaptive steered molecular dynamics (ASMD) has been used to measure the potential of mean force, hydrogen-bonding profiles and characteristic residue pair contacts within each peptide along the stretching coordinate.This provides quantitative insight into the specific characteristics arising from each of the CHARMM potentials. Our results also show a baseline similarity in that the transition between α-helical and random coil configurations for the benchmarked linear peptides follow similar pathways of mechanical unfolding across the family of potentials; despite their sequence differences.

Benchmarking adaptive steered molecular dynamics (ASMD) across the family of CHARMM potentials

251st National Meeting (2016)

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