Local energetic frustration conservation in protein families and superfamilies

Abstract

Energetic local frustration offers a biophysical perspective to interpret the effects of sequence variability on protein families. Here we present a methodology to analyze local frustration patterns within protein families and superfamilies that allows us to uncover constraints related to stability and function, and identify differential frustration patterns in families with a common ancestry. We analyze these signals in very well studied protein families such as PDZ, SH3, ɑ and β globins and RAS families. Recent advances in protein structure prediction make it possible to analyze a vast majority of the protein space. An automatic and unsupervised proteome-wide analysis on the SARS-CoV-2 virus demonstrates the potential of our approach to enhance our understanding of the natural phenotypic diversity of protein families beyond single protein instances. We apply our method to modify biophysical properties of natural proteins based on their family properties, as well as perform unsupervised analysis of large datasets to shed light on the physicochemical signatures of poorly characterized proteins such as the ones belonging to emergent pathogens.

Heterogeneous folding landscapes and predetermined breaking points within a protein family

“…Overall, the helices a2-a5 were systematically more frustrated than the rest (Figure 2B). Thus, patterns of frustration across secondary structure elements were conserved even in absence of the conservation of individual contacts, as observed before [38]. Furthermore, the average frustration in some secondary structures varied considerably between proteins (Figure 2B).…”

Interpretable Atomistic Prediction and Functional Analysis of Conformational Ensembles and Allosteric States in Protein Kinases Using AlphaFold2 Adaptation with Randomized Sequence Scanning and Local Frustration Profiling

“…The results of conformational frustration analysis (Supplementary Information, Figure S3A-C) highlighted the prevalence of the neutral frustration which is consistent with previous studies of frustration in proteins showing that protein residues tend display neutral frustration which implies a moderate degree of stabilization/destabilization for the native interactions as compared to the average energetics induced by conformational or mutational changes in the respective positions. 55,56 The local frustration analysis of the ABL states is consistent with a more general frustration analysis of different proteins that revealed the majority of local interactions as neutral (~50-60%) or minimally frustrated ( 30%) with only 10% of the total contacts considered as highly frustrated. 50 A direct comparison of high frustration and minimal frustration local densities is particularly revealing, showing the dominance of minimal frustration densities for the active state (Supplementary Information, Figure S3A,D).…”

“…The results of conformational frustration analysis (Supplementary Information, Figure S3A-C) highlighted the prevalence of the neutral frustration which is consistent with previous studies of frustration in proteins showing that protein residues tend display neutral frustration which implies a moderate degree of stabilization/destabilization for the native interactions as compared to the average energetics induced by conformational or mutational changes in the respective positions. 55,56…”

“…These findings are consistent with recent studies showing that identification of conserved highly frustrated contacts can determine residues involved in conformational transitions. 56…”

“…These findings are consistent with recent studies showing that identification of conserved highly frustrated contacts can determine residues involved in conformational transitions. 56 The emergence of local frustration in these regions could also indicate the "initiation cracking points" of the inactive kinase form, ultimately facilitating global conformational transitions and shifting a dynamic equilibrium between kinase states towards the active form. 58 Local cracking model in protein kinases is often referred to formation of unfavorable residue-residue interactions that can be compensated by increased local entropy in intermediate states during large conformational changes between inactive and active states.…”