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

Abstract

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.

The relevance of short peptides for an understanding of unfolded and intrinsically disordered proteins

“…Analyses of coil libraries and MD simulations have clearly revealed that different amino acid side chains differ in terms of the population of these rotamers and that these populations depends on the backbone conformation. 155,[174][175][176][177] Experimental work exploring the rotamer populations of residues in short peptide is practically non existing. The only exception I am aware of is the paper of Rybka et al, who measured 3 J(H Ca H Cb ) coupling constant of the two C b -protons to determine the rotamer distributions of GNG, protonated and ionized GDG and of the protonated blocked tetrapeptide Ac-GDG.…”