Assessing the Strength of Weak Ties - Even though the paradigm shift in structure biology, heralded by AlphaFold2 of the deep-learning era, has transformed biological sciences, the true physics of the protein folding problem remains unresolved. For example, predicting the effects of mutations on protein stability remains an outstanding challenge, even though structure prediction is highly accurate. The lack of an understanding of the forces, especially the weak interactions (e.g., p-interactions), for a proper description of protein biophysics, has continued leading to a lack of comprehension of the impacts of disease-causing mutations, post-translational modifications (PTMs), interactions contributing to protein aggregation, phase separation, etc. The continued existence of this knowledge gap represents an important problem because, until it is filled, manipulations of weak interactions for beneficial interventions will not be possible. An important step towards addressing this problem is correctly identifying weak interactions in protein structures so that perturbations of such interactions through experiments would facilitate a complete comprehension of their roles. To identify weak interactions, we recently developed a web service, AQcalc, that correctly identifies a few weak interactions. Even with limited capabilities, AQcalc revealed several novel interaction mechanisms in aggregation, disease mutants, PTMs, etc. Our long-term goal is to understand the mechanisms of how weak interactions regulate macromolecular structure and function. The scientific objective for this R15 application is to develop a comprehensive web utility (AQcalc upgrade) that anyone can accurately and conveniently identify various weak interactions in the structures of proteins and their complexes (DNA/RNA/lipid-bilayer/small-molecules) in the limitless structures of the deep-learning era. The utility, for thoroughness, will identify weak interactions in the context of conservation, sequence designability, and dynamics (CDD) that no other services provide. Furthermore, convenient rapid experimental assay systems are also developed to facilitate hypothesis testing of the roles of the identified weak interactions. Our rationale is that (a) accurate and comprehensive identification of various weak interactions, as shown with strong preliminary results, will provide new insights by enabling subsequent studies on proteins or other biomolecules by manipulating weak interactions, (b) the availability of convenient rapid experimental assay systems will facilitate probing molecular mechanism of weak interaction. The two specific aims are: 1) Upgrade the functional utility of AQcalc. 2) Experimentally investigate the perturbations of weak interactions through rapid assays. The approach is innovative for integrating various important elements (comprehensive identification, CDD thoroughness, and experimental probing) into a one-stop-shop platform unavailable elsewhere. The research is significant because it is expected to vertically expand the understanding of how weak interactions contribute to macromolecular structure and function. Comprehensive knowledge of weak interactions will ultimately facilitate preventative manipulations of the human proteome.
