Travers, T. | Search bioRxiv

bioRxiv2019

A Graph-Directed Approach for Creation of a Homology Modeling Library: Application to Venom Structure Prediction

Many toxins are short, cysteine-rich peptides that are of great interest as novel therapeutic leads and of great concern as lethal biological agents due to their high affinity and specificity for various receptors involved in neuromuscular transmission. To perform initial candidate identification for design of a drug impacting a particular receptor or for threat assessment as a harmful toxin, one requires a set of candidate structures of reasonable accuracy with potential for interaction with the target receptor. In this article, we introduce a graph-based algorithm for identifying good extant template structures from a library of evolutionarily-related cysteine-containing sequences for structural determination of target sequences by homology modeling. We employ this approach to study the conotoxins, a set of toxin peptides produced by the family of aquatic cone snails. Currently, of the approximately six thousand known conotoxin sequences, only about three percent have experimentally characterized three-dimensional structures, leading to a serious bottleneck in identifying potential drug candidates. We demonstrate that the conotoxin template library generated by our approach may be employed to perform homology modeling and greatly increase the number of characterized conotoxin structures. We also show how our approach can guide experimental design by identifying and ranking sequences for structural characterization in a similar manner. Overall, we present and validate an approach for venom structure modeling and employ it to expand the library of extant conotoxin structures by almost 300% through homology modeling employing the template library determined in our approach.

bioinformatics↗

bioRxiv2018

Molecular aspects of multivalent engagement between Syk and FcϵRIγ

Syk/Zap70 family kinases are essential for signaling via multichain immune-recognition receptors such as the tetrameric ({beta}{gamma}2) Fc{varepsilon}RI The simplest model assumes that Syk activation occurs through cis binding of its tandem SH2 domains to dual phosphotyrosines within immunoreceptor tyrosine-based activation motifs of individual {gamma} chains. In this model, Syk activity is modulated by phosphorylation occurring between adjacent Syk molecules docked on {gamma} homodimers and by Lyn molecules bound to Fc{varepsilon}RI{beta}. However, the mechanistic details of Syk docking on {gamma} homodimers are not fully resolved, particularly the possibility of trans binding orientations and the impact of Y130 autophosphorylation within Syk interdomain A. Analytical modeling shows that multivalent interactions lead to increased WT Syk cis-oriented binding by three orders of magnitude. Molecular dynamics (MD) simulations show increased inter-SH2 flexibility in a Y130E phosphomimetic form of Syk, associated with reduced overall helicity of interdomain A. Hybrid MD/worm-like chain polymer models show that the Y130E substitution reduces cis binding of Syk. We report computational models and estimates of relative binding for all possible cis and trans 2:2 Syk:Fc{varepsilon}RI{gamma} complexes. Calcium imaging experiments confirm model predictions that cis binding of WT Syk is strongly preferred for efficient signaling, while trans conformations trigger weak but measurable responses.

biophysics↗