All-atom molecular dynamic simulations for peptoids: a procedure and implementation

Peptoids (poly-N-substituted glycines) are a special class of synthetic biopolymer. Peptoids have the same backbone structure as peptides, but have sidechains attached to backbone Nitrogens as opposed to α-carbons. This conformational change gives peptoids useful properties that make them candidates for practical application, but work is needed to determine how the sidechain composition and sidechain sequence of a peptoid infleunces its overall behavior. Molecular Dynamics (MD) simulations are a promising tool that can be used to learn how a peptoid’s structure determines its behavior. MD simulations can be used to determine how a peptoid’s secondary structure influences its three-dimensional structure in solvated environments, as well as a peptoid’s ability to aggregate with other peptoids in solvated environments. The ability to understand aggregation behavior of peptoid’s has large implications for understanding the practical application of peptoids. Therefore, there is significant interest surrounding the development of MD simulations to simulate the aggregation behavior of peptoids. This work aims to develop a specific process for performing all-atom MD simulations on peptoids, and use the developed approach to explore the three-dimensional conformation and aggregation behavior of a 12-monomer peptoid unit. This work demonstrates how changes and additions can be made to already existing simulation forcefields to adapt them to peptoid simulations. This work will outline specifically how to set up a peptoid MD simulation by making specific changes to commonly used forcefields. After developing the process for creating a peptoid MD simulation, this work will use the process to simulate the molecular dynamics of a 12-monomer peptoid. It will show that the peptoid attains a helical three-dimensional conformation, and that the peptoid forms aggregates in solvated environments.M.S.Includes bibliographical reference