A backbone‐dependent rotamer library with high (ϕ, ψ) coverage using metadynamics simulations

• Published in: Protein science 2022-12, Vol.31 (12), p.e4491-n/a
• Main Authors: Mortensen, Jennifer C., Damjanovic, Jovan, Miao, Jiayuan, Hui, Tiffani, Lin, Yu‐Shan
• Format: Article
• Language: English
• Subjects: Accuracy; Amino acids; Amino Acids - chemistry; Chains; Crystal structure; cyclic peptides; Dipeptides; Libraries; metadynamics simulations; Modelling; Molecular conformation; Peptides; Peptides, Cyclic; protein; Protein Conformation; Protein structure; Proteins; Proteins - chemistry; rotamer library; side chain rotamers; Tools for Protein Science
• ISSN: 0961-8368; 1469-896X
• DOI: 10.1002/pro.4491

Backbone‐dependent rotamer libraries are commonly used to assign the side chain dihedral angles of amino acids when modeling protein structures. Most rotamer libraries are created by curating protein crystal structure data and using various methods to extrapolate the existing data to cover all possible backbone conformations. However, these rotamer libraries may not be suitable for modeling the structures of cyclic peptides and other constrained peptides because these molecules frequently sample backbone conformations rarely seen in the crystal structures of linear proteins. To provide backbone‐dependent side chain information beyond the α‐helix, β‐sheet, and PPII regions, we used explicit‐solvent metadynamics simulations of model dipeptides to create a new rotamer library that has high coverage in the (ϕ, ψ) space. Furthermore, this approach can be applied to build high‐coverage rotamer libraries for noncanonical amino acids. The resulting Metadynamics of Dipeptides for Rotamer Distribution (MEDFORD) rotamer library predicts the side chain conformations of high‐resolution protein crystal structures with similar accuracy (~80%) to a state‐of‐the‐art rotamer library. Our ability to test the accuracy of MEDFORD at predicting the side chain dihedral angles of amino acids in noncanonical backbone conformation is restricted by the limited structural data available for cyclic peptides. For the cyclic peptide data that are currently available, MEDFORD and the state‐of‐the‐art rotamer library perform comparably. However, the two rotamer libraries indeed make different rotamer predictions in noncanonical (ϕ, ψ) regions. For noncanonical amino acids, the MEDFORD rotamer library predicts the χ1 values with approximately 75% accuracy.