UC Irvine

Local interactions within and between proteins (or interacting objects in general) inherently determine the resulting global structure, whether that be a monomeric protein structure, a dimer or multimer, or a larger aggregate consisting of tens to thousands of proteins. For proteins, structure is canonically partitioned into four levels: primary, which describes the sequence of residues that make up the protein; secondary, the α-helices and β-sheets that result from hydrogen-bonding interactions between residues; tertiary, which describes (somewhat arbitrarily defined) domains of clustered secondary structures that are typically held together with salt-bridges; and finally, quaternary structures composed of multiple proteins interacting via hydrogen-bonding or other polar interactions. Variants are proteins with point mutations, or mutations occurring to a small number (typically one) of the amino acids in the primary structure. Point mutations can alter the higher-order structure and dynamics of the protein, and thus how it responds to its environment, making it susceptible to evolutionary forces that dampen or put emphasis on a given variant. Such changes in structure and dynamics can range from subtle deformations to changes in the way the protein folds, inhibiting function. Mutations that are favored by evolution provide information about how the protein’s relationship with its environment affects its function and applies pressure to the adaptative evolution of the protein. The effects of mutations on protein structure, function, and interactions are explored in chapters two and three of this text. To contrast, the fourth chapter takes a generalized approach by delving into the range of emergent multi-body structures that can arise from slight changes in environmental or structural parameters while remaining agnostic to any specific features of a single protein sequence.