Using evolutionary data to make sense of macromolecules with a “face‐lifted” ConSurf

Abstract

The ConSurf web‐sever for the analysis of proteins, RNA, and DNA provides a quick and accurate estimate of the per‐site evolutionary rate among homologues. The analysis reveals functionally important regions, such as catalytic and ligand‐binding sites, which often evolve slowly. Since the last report in 2016, ConSurf has been improved in multiple ways. It now has a user‐friendly interface that makes it easier to perform the analysis and to visualize the results. Evolutionary rates are calculated based on a set of homologous sequences, collected using hidden Markov model‐based search tools, recently embedded in the pipeline. Using these, and following the removal of redundancy, ConSurf assembles a representative set of effective homologues for protein and nucleic acid queries to enable informative analysis of the evolutionary patterns. The analysis is particularly insightful when the evolutionary rates are mapped on the macromolecule structure. In this respect, the availability of AlphaFold model structures of essentially all UniProt proteins makes ConSurf particularly relevant to the research community. The UniProt ID of a query protein with an available AlphaFold model can now be used to start a calculation. Another important improvement is the Python re‐implementation of the entire computational pipeline, making it easier to maintain. This Python pipeline is now available for download as a standalone version. We demonstrate some of ConSurf's key capabilities by the analysis of caveolin‐1, the main protein of membrane invaginations called caveolae.

Enzymatic Hydroxylation of Aliphatic C–H Bonds by a Mn/Fe Cofactor

“…Sequences lacking one or more of the aligned amino acid residues found to coordinate the Mn/Fe cofactor (25D, 27H, 211H, 265E, 337D, and 340H in AibH2) were removed, leaving 555 unique proteins. The genome neighborhoods (Figure b) of these proteins were downloaded and evaluated using the Enzyme Function Initiative suite of online tools and visualized using Gene Graphics. , To correlate the amino acid conservation with predicted 3D structures, 255 sequences were randomly eliminated, and the resultant 300 sequences were used to generate Figure d using the default algorithm parameters on the ConSurf Web site …”

“…60,61 To correlate the amino acid conservation with predicted 3D structures, 255 sequences were randomly eliminated, and the resultant 300 sequences were used to generate Figure 5d using the default algorithm parameters on the ConSurf Web site. 62 All resultant 555 amino acid sequences (and AibH2) are classified to the protein family (Pfam) PF04909. To evaluate their evolutionary relatedness to other biochemically characterized enzymes within this family, these sequences were aligned alongside the 30 SwissProtannotated PF04909 sequences and the sequence for PtmU3.…”

Structure and mechanism of a eukaryotic ceramide synthase complex

“…The predicted catalytic histidine and aspartate residues in the Lag1p motif are shown in sticks. A conserved hydrophilic cavity within the TLC domain of Lac1. Lac1 is colored by the amino acid conservation scores calculated by ConSurf (Yariv et al , 2023) analysis of the yeast and human CerS members presented in Fig EV1. The conserved charged and polar residues within the hydrophilic cavity are shown in sticks.…”

Structural study of UFL1‐UFC1 interaction uncovers the role of UFL1 N‐terminal helix in ufmylation

“…Conservation of UFL1 was calculated with the ConSurf server (Yariv et al , 2023), using default parameters. Alignment of the human and model animal sequences of UFL1 was performed using ClustalOmega (Sievers et al , 2011) on the UniProt server (UniProt Consortium, 2021).…”