Investigation of protein self-assembly processes is important for understanding the growth processes of functional proteins as well as disease-causing amyloids. We tested KFC-E on four benchmark sets of unbound examples and two benchmark sets of bound examples, with the results demonstrating a clear improvement over scores that examine conservation and coevolution across the entire interface. In this study, we propose a scoring function, KFC-E, that accounts for both conservation and coevolution of putative binding hotspot residues at protein–protein interfaces. However, high-scoring modes often match poorly with the true bound form, suggesting a need for improvement of the scoring function. Current protein docking approaches address this problem by sampling multiple binding modes in proteins and scoring each mode, with the lowest-energy (or highest scoring) binding mode being regarded as a near-native complex.
#Capto mmc pi cation interaction free
Protein subunits that form oligomers minimize the free energy of the complex, but exhaustive computational search-based docking methods have not comprehensively addressed the challenge of distinguishing a natively bound complex from non-native forms. Protein–protein interactions play a key role in mediating numerous biological functions, with more than half the proteins in living organisms existing as either homo- or hetero-oligomeric assemblies. The promising beginning and future of nanoscale protein–polymer research endeavors are presented in this article. They include protein self-assembly/packing characteristics, protein–polymer interaction mechanisms/kinetics, and various protein functionalities on polymer nanoconstructs.
Spearheading research efforts so far has led to inspiring initial discoveries of protein interaction mechanisms and kinetics that are entirely unique to nanoscale polymer systems. Therefore, such single biomolecule level approaches taken to examine protein–polymer interaction mark a big departure from the mainstream approaches of collecting indirectly observed, ensemble-averaged protein signals on chemically simple substrates. Spatial and temporal tracking of particular proteins at specific polymer interfaces was made possible by resolving individual proteins simultaneously with those polymer nanodomains responsible for the protein interactions. Being able to discern discrete protein interaction events via simple visualization was crucial to attaining the much needed, direct experimental evidence of protein–polymer interactions at the single biomolecule level. In this Perspective, novel protein interaction phenomena driven by the presence of nanoscale polymer interfaces are discussed. Existing knowledge built from studying the interaction of macroscopic, chemically alike surfaces with an ensemble of protein molecules cannot be simply carried over to nanoscale protein–polymer interactions. With the advancement of nanoscience and nanotechnology, the nature of polymer materials interfacing proteins has evolved to exhibit greater chemical intricacy and smaller physical dimensions.
Protein interactions at polymer interfaces represent a complex but ubiquitous phenomenon that demands an entirely different focus of investigation than what has been attempted before.
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