Relating circular dichroism to atomic structure by means of MD simulations and computed CD spectra with α-peptoids as an example

Bhattacharjee, Nicholus; Perrin, Lionel; Jolibois, Franck

doi:10.1039/d0cp01336f

Cited by 2 publications

(1 citation statement)

References 32 publications

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“…It is worth noting that multiple force fields are available in the protein space, but that field is significantly more developed and studied. Despite this higher bar to entry, peptoid simulation papers include at least 19 GAFF-based, ,,− 13 MFTOID-, ,− 11 CHARMM-, or CGenFF-based, − 3 PEPDROID-based, − and other computational studies. − One particularly noteworthy effort was the development of a peptoid rotamer library containing over 50 side chains in the structural prediction tool ROSETTA based on CHARMM peptide parameters. , …”

Section: Introductionmentioning

confidence: 99%

Development of a Systematic and Extensible Force Field for Peptoids (STEPs)

2023

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Peptoids (N-substituted glycines) are a class of biomimetic polymers that have attracted significant attention due to their accessible synthesis and enzymatic and thermal stability relative to their naturally occurring counterparts (polypeptides). While these polymers provide the promise of more robust functional materials via hierarchical approaches, they present a new challenge for computational structure prediction for material design. The reliability of calculations hinges on the accuracy of interactions represented in the force field used to model peptoids. For proteins, structure prediction based on sequence and de novo design has made dramatic progress in recent years; however, these models are not readily transferable for peptoids. Current efforts to develop and implement peptoid-specific force fields are spread out, leading to replicated efforts and a fragmented collection of parameterized sidechains. Here, we developed a peptoid-specific force field containing 70 different side chains, using GAFF2 as starting point. The new model is validated based on the generation of Ramachandran-like plots from DFT optimization compared against force field reproduced potential energy and free energy surfaces as well as the reproduction of equilibrium cis/trans values for some residues experimentally known to form helical structures. Equilibrium cis/trans distributions (Kct) are estimated for all parameterized residues to identify which residues have an intrinsic propensity for cis or trans states in the monomeric state.

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