Poster Presentation 23rd International Society of Magnetic Resonance Conference 2023

A generalised force field for NMR structure calculation: application to peptides containing non-standard amino acids (#205)

Tye Gonzalez 1 , K. Johan Rosengren 1 , Martin Stroet 1
  1. The University of Queensland, St Lucia, QUEENSLAND, Australia

Solution Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful method for determining three-dimensional structures of peptides. Structural information from NMR is combined with a ‘force field’ that describes the general geometries of proteins to compute structures. Although such forcefields have been optimised over a long time to effectively model standard amino acids, they are less capable to deal with modified non-canonical amino acids. In this study, parameters generated by the Automated Topology Builder (ATB) were used to produce a new generalised force field for NMR based peptide structure determination. The performance of this was elucidated using a variety of peptides, including those incorporating post-translational modifications such as disulfide bonds, hydroxyproline, pyroglutamic acid and sulfotyrosine. The results confirm that this general force field perform comparably or better than the established PARALLHDG5.5 force field in most quality indicators, with the exception of a reduction in the percentage of favoured side chain rotamers. The ATB’s ability to provide a force field that results in peptide structures of comparable quality, incorporating both canonical and non-canonical amino acids, validates the ATB as a valuable tool in structural biology. Non-standard amino acids are commonly used in peptide drug design and an ability to determine precise conformational preferences is essential for effective peptide engineering.