ProteoVision: web server for advanced visualization of ribosomal proteins

Abstract

ProteoVision is a web server designed to explore protein structure and evolution through simultaneous visualization of multiple sequence alignments, topology diagrams and 3D structures. Starting with a multiple sequence alignment, ProteoVision computes conservation scores and a variety of physicochemical properties and simultaneously maps and visualizes alignments and other data on multiple levels of representation. The web server calculates and displays frequencies of amino acids. ProteoVision is optimized for ribosomal proteins but is applicable to analysis of any protein. ProteoVision handles internally generated and user uploaded alignments and connects them with a selected structure, found in the PDB or uploaded by the user. It can generate de novo topology diagrams from three-dimensional structures. All displayed data is interactive and can be saved in various formats as publication quality images or external datasets or PyMol Scripts. ProteoVision enables detailed study of protein fragments defined by Evolutionary Classification of protein Domains (ECOD) classification. ProteoVision is available at http://proteovision.chemistry.gatech.edu/.

Fold Evolution before LUCA: Common Ancestry of SH3 Domains and OB Domains

“…Our analysis includes 11 ribosomal proteins (rProteins) and four translational GTPases that have SH3 and/or OB domains. Orthologous sequences of proteins of the translation system from a Sparse and Efficient Representation of Extant Biology (SEREB) within Bacteria and Archaea ( Bernier et al 2018 ; Penev et al 2021 ) were retrieved from UniProt ( UniProt Consortium 2019 ) and NCBI RefSeq ( O’Leary et al 2016) databases. This set includes ancient and well-characterized orthologous proteins ( table 1 ).…”

“…The resulting MSAs were manually curated based on structural superimposition. The alignments of rProteins are available in ProteoVision, an in house web server for visualization and data mapping of proteins ( Penev et al 2021 ). The final manually curated MSAs of orthologous proteins were then trimmed to match the domain definitions in ECOD ( Schaeffer et al 2017 ).…”

“…The domain boundaries of rProteins were further adjusted to match the Phase definitions in the Accretion Model schema ( Kovacs et al 2017 ) ( table 1 ). Structural visualizations of protein domains were performed by PyMOL ( Schrödinger LLC 2021 ) and ProteoVision ( Penev et al 2021 ).…”

Untitled

“…TwinCons can be mapped onto three dimensional structures and employs a wide variety of sequence-and structure-informed substitution matrices, as well as sequence weighing based on global similarity measures. Automated visualization of TwinCons has been implemented in ProteoVision [77], an online webserver that enables simultaneous structural visualization and custom data mapping at levels of primary, secondary, and three-dimensional structure of proteins. TwinCons displays signatures and conservation in a single convenient layout and highlights alternative sequences of purple indicates signature regions between bacterial and archaeal sequences; white indicates sequence variable regions.…”

“…Here we probe the ability of TwinCons to detect highly conserved sequence motifs for 27 proteins or protein fragments from the translation and transcription systems with known or suspected ancestry (Table D in S1 Appendix) based on structural similarity or previous literature [75,76] (S5 Dataset). All translation proteins were retrieved from the advanced visualization website ProteoVision [77]. Sequences for transcription systems were retrieved from NCBI and are available at https://apollo2.chemistry.gatech.edu/ TwinConsDatasets/.…”