Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server

Abstract

BackgroundProtein variability can now be studied by measuring high-resolution tolerance-to-substitution maps and fitness landscapes in saturated mutational libraries. But these rich and expensive datasets are typically interpreted coarsely, restricting detailed analyses to positions of extremely high or low variability or dubbed important beforehand based on existing knowledge about active sites, interaction surfaces, (de)stabilizing mutations, etc.ResultsOur new webserver PsychoProt (freely available without registration at http://psychoprot.epfl.ch or at http://lucianoabriata.altervista.org/psychoprot/index.html) helps to detect, quantify, and sequence/structure map the biophysical and biochemical traits that shape amino acid preferences throughout a protein as determined by deep-sequencing of saturated mutational libraries or from large alignments of naturally occurring variants.DiscussionWe exemplify how PsychoProt helps to (i) unveil protein structure-function relationships from experiments and from alignments that are consistent with structures according to coevolution analysis, (ii) recall global information about structural and functional features and identify hitherto unknown constraints to variation in alignments, and (iii) point at different sources of variation among related experimental datasets or between experimental and alignment-based data. Remarkably, metabolic costs of the amino acids pose strong constraints to variability at protein surfaces in nature but not in the laboratory. This and other differences call for caution when extrapolating results from in vitro experiments to natural scenarios in, for example, studies of protein evolution.ConclusionWe show through examples how PsychoProt can be a useful tool for the broad communities of structural biology and molecular evolution, particularly for studies about protein modeling, evolution and design.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1124-4) contains supplementary material, which is available to authorized users.

Web Apps Come of Age for Molecular Sciences

“…Specific to biomolecular sciences, examples of full web apps include the very complete molecular visualization libraries and web apps discussed above, the very successful Sequence Manipulation Suite for analyzing and editing nucleic acid and protein sequences [17] and an upcoming PDB manipulation suite to analyze and edit PDB files (available from the author's website), the PsychoProt server for analysis of amino acid variability and tolerance to substitutions in proteins [16,44], the Wikipedia Chemical Structure Explorer [19], and PDB-Explorer [18], among others.…”

“…Since computational models are not available in standard databases like the Protein Data Bank for experimental structures, they remain as no more than mere static pictures, hence the importance of resources for easily sharing 3D views, such as JavaScript molecular viewers; (B) Two JSmol applets embedded side to side in the same webpage and synchronized such that rotating any of them produces the same rotation on the other, thus facilitating comparison of two related structures, in this case two X-ray structures of a histidine kinase in different conformational states [41] (https://lucianoabriata.altervista.org/papersdata/accounts2017.html). See also the works by Mwalongo et al about more complex setups for remote and concurrent visualizations [42,43]; (C) Example of JSmol being used to display results from online analyses, in this case data about amino acid variability in proteins by the PsychoProt server [16,44]; (D) JSME and JSmol coupled inside the Hack-a-mol web app together with JavaScript queries to external web services to achieve a complete molecular editor, molecular data search facility, and molecular format converter (https://chemapps.stolaf.edu/jmol/jsmol/hackamol.htm); (E) Proof-of-concept augmented reality web app that displays lysine and glutamate side chains which the user can move in space with two physical markers. The example uses atomic coordinates for real-time computations of the distance and electrostatic potential between lysine's side chain N atom and glutamate's side chain O atoms.…”

“…altervista.org/papersdata/accounts2017.html). See also the works by Mwalongo et al about more complex setups for remote and concurrent visualizations [42,43]; (C) Example of JSmol being used to display results from online analyses, in this case data about amino acid variability in proteins by the PsychoProt server [16,44]; (D) JSME and JSmol coupled inside the Hack-a-mol web app together with JavaScript queries to external web services to achieve a complete molecular editor, molecular data search facility, and molecular format converter (https://chemapps.stolaf.edu/jmol/jsmol/hackamol.htm); (E) Proof-of-concept augmented reality web app that displays lysine and glutamate side chains which the user can move in space with two physical markers. The example uses atomic coordinates for real-time computations of the distance and electrostatic potential between lysine's side chain N atom and glutamate's side chain O atoms.…”

“…Thus, it is widely used for visualization in multiple websites for displaying structures retrieved from databases [48], as well as for calculations and for extracting information from files with molecular data in web applications such as protein sequences from PDB files ( Figure 3C,D) [16]. Also, JSmol is often used for building molecules and submitting them to servers for calculations through third-party programs, as in the MolCalc [49] web app for fast quantum mechanics-based estimation of molecular properties using GAMESS [50], whose results are displayed back through JSmol-a very interesting tool for education, outreach, and simple research questions.…”

“…PsychoProt [16] A tool to analyze amino acid variation in proteins in terms of protein physical chemistry, to aid in the analysis of sequence alignments and deepsequencing-based tolerance to substitutions maps. Sequence Manipulation Suite [17] A collection of tools to handle, build, and analyze DNA and protein sequences.…”