A CGenFF‐based force field for simulations of peptoids with both cis and trans peptide bonds. Issue 22 (6th May 2019)

• Record Type: Journal Article
• Authors: Weiser, Laura J.; Santiso, Erik E.
• Is Part Of: Journal of computational chemistry. Volume 40:Issue 22(2019)
• Page Start: 1946
• Page End: 1956
• Publication Date: 2019-05-06
• Subjects: peptoids -- CGenFF -- CHARMM; Chemistry -- Data processing -- Periodicals; 542.85
• DOI: 10.1002/jcc.25850
• Languages: English
• ISSNs: 0192-8651

Abstract

Abstract : Peptoids, or poly‐n‐substituted glycines, are peptide‐like polymers composed of a flexible backbone decorated with diverse chemical side chains. Peptoids can form a variety of self‐assembling structures based on the type and sequence of the side chains attached to their backbones. All‐atom molecular dynamics simulations have been useful in predicting the conformational structures of proteins and will be valuable tools for identifying combinations of peptoid side chains that may form interesting folded structures. However, peptoid models must address a major degree of freedom not common in proteins – the cis/trans isomerization of the peptide bond. This work presents CHARMM general force field (CGenFF) parameters developed to accurately represent peptoid conformational behavior, with an emphasis on a correct representation of both the cis and trans isomers of the peptoid backbone. These parameters are validated against experimental and quantum mechanics data and used to simulate three peptoid side chains in explicitly solvated systems. © 2019 Wiley Periodicals, Inc. Abstract : CHARMM general force field parameters (CGenFF) are presented for the simulation of peptoid polymers. Peptoids are protein‐like polymers that have two major isomers, cis and trans . CGenFF parameters are developed to reproduce peptoid conformational energies for both isomers. Potential energy and free energy conformational plots are calculated for a simple peptoid and are validated against quantum and experimental data. Parameters are then developed for common peptoid side chains and solvated simulations are performed in TIP3P water.