title: Divalent Ion Parameterization Strongly Affects Conformation and Interactions of an Anionic Biomimetic Polymer.
abstract: The description of peptides and the use of molecular dynamics simulations to refine structures and investigate the dynamics on an atomistic scale are well developed. Through a consensus in this community over multiple decades, parameters were developed for molecular interactions that only require the sequence of amino-acids and an initial guess for the three-dimensional structure. The recent discovery of peptoids will require a retooling of the currently available interaction potentials in order to have the same level of confidence in the predicted structures and pathways as there is presently in the peptide counterparts. Here we present modeling of peptoids using a combination of ab initio molecular dynamics (AIMD) and atomistic resolution classical force field (FF) to span the relevant time and length scales. To properly account for the dominant forces that stabilize ordered structures of peptoids, namely steric-, electrostatic, and hydrophobic interactions mediated through side chain-side chain interactions in the FF model, those have to be first mapped out using high fidelity atomistic representations. A key feature here is not only to use gas phase quantum chemistry tools, but also account for solvation effects in the condensed phase through AIMD. One major challenge is to elucidate ion binding to charged or polar regions of the peptoid and its concomitant role in the creation of local order. Here, similar to proteins, a specific ion effect is observed suggesting that both the net charge and the precise chemical nature of the ion will need to be described.
authors.affiliation: Physical Science Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States.|Department of Biochemistry and Molecular Biology, University of Texas Medical Branch , Galveston, Texas 77555, United States.
authors.forename: Michael D
authors.initials: MD
authors.lastname: Daily
authors.affiliation: Physical Science Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States.
authors.forename: Marcel D
authors.initials: MD
authors.lastname: Baer
authors.affiliation: Physical Science Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Mundy
mesh_terms: D000838:Anions / Q000737:chemistry*; D032701:Biomimetics; D057927:Hydrophobic and Hydrophilic Interactions; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry; D011108:Polymers / Q000737:chemistry*
chemical_list: D000838:Anions; D010455:Peptides; D011108:Polymers