MapTurns: mapping the structure, H-bonding and contexts of beta turns in proteins

Abstract

AbstractMotivationBeta turns are the most common type of secondary structure in proteins after alpha helices and beta sheets and play key structural and functional roles. Turn backbone (BB) geometry has been classified at multiple levels of precision, but the current picture of side chain (SC) structure and interaction in turns is incomplete, because the distribution of SC conformations associated each sequence motif has commonly been represented only by a static image of a single, typical structure for each turn BB geometry, and only motifs which specify single amino acids have been systematically investigated. Furthermore, no general evaluation has been made of the SC interactions between turns and the structures in their BB neighborhoods. Finally, the visualization and comparison of the wide range of turn conformations has been hampered by the almost exclusive characterization of turn structure in BB dihedralangle (Ramachandran) space.ResultsThis work introduces MapTurns, a web server for motif maps, which employ a turn-local Euclidean-space coordinate system and a global turn alignment to comprehensively map the distributions of BB structure, SC structure, H-bonding and context associated with sequence motifs in beta turns. Maps characterize many new SC motifs, provide detailed rationalizations of sequence preferences, and support mutational analysis and the general study of SC interactions, and they should prove useful in applications such as protein design.Availability and ImplementationMapTurns is available atwww.betaturn.comalong with a broad, map-based survey of side-chain motifs in beta turns. HTML/Javascript code for a sample map is available at:https://github.com/nenewell/MapTurns/tree/main.Supplementary InformationSupplementary File 1: Methods.