The Structural Properties of Adaptation and Allostery in Proteins: A Case Study in a PDZ Domain

Complex systems are present at all scales of biology spanning amino acid interactions in proteins to inter-species interactions in ecosystems. Despite their ubiquity, an understanding of how to study complex systems methodically is lacking. Fundamentally, this is because a procedure to discover the appropriate parametrization of such systems into relevant parts is absent. The Ranganathan Lab developed an evolutionary approach, Statistical Coupling Analysis (SCA), to understand how amino acid interactions within proteins give rise to basic protein characteristics such as fold and function. The result of this approach was a structural decomposition of proteins into units of coevolving residues termed protein 'sectors'.
Is the transformation from amino acids to protein sectors a useful and relevant representation of the essence of proteins? Previous work has demonstrated that specifying co-evolution is sufficient to design synthetic natural-like proteins and encodes the information needed to execute a primary function. As evolved biological systems however, proteins must also also adapt quickly to new functions. In addition, a fundamental characteristic of many proteins is the ability to transmit information over a significant distance in the protein structure, a phenomenon known as allostery. Where in the protein do these characteristics lie? Here, we address the sequence origins and structural properties of a) the adaptive capacity of proteins and b) allosteric communication within proteins. Understanding how proteins can adapt quickly to new function is an outstanding question in biology, marked by failed attempts at engineering new or altered function guided by structural approaches focused on the importance of active site or binding pocket positions. It is often the case that mutations located distal to the active site harbor adaptive potential, a non-obvious observation given the crystal structure of a protein. To more fundamentally understand the adaptive process in proteins, here we examine a two-step mutational path to new specificity in a model protein PSD95pdz3 where one intermediate, a Glycine (G) to Threonine (T) mutation at position 330, removed from the binding site of the protein, maintains native function while simultaneously adapting the protein to an alternate function (termed a 'conditionally neutral' mutation) whereas the other intermediate, a Histidine (H) to Alanine (A) mutation at position 372, promotes a direct specificity switch, abrogating native function. Through a stochastic population dynamics simulation, we find the conditionally neutral intermediate promotes adaptation over a wide range of mutation rates and rates of environmental fluctuation while the direct specificity switching mutation facilitates adaptation only within a special regime of population dynamics parameters. We comprehensively identify the spatial distribution of all adaptive mutations in PSD95pdz3, finding that direct specificity switching mutations are found exclusively at sector positions directly at the binding site whereas conditionally neutral mutations are generally found distal to the binding site but connected to it through the protein sector. Crystal structures reveal how a mutation at position 330 creates plasticity at the binding site to create a dual function protein. Overall, these results illustrate the importance of a spatially distributed network of coupled residues for adapting in a fluctuating environment. Revealing paths of allostery in protein structures has been a central goal of structural biology. In PSD95pdz3, we find that the G330T mutation causes local backbone remodeling and structurally affects solely a distant conserved helix. Detecting structurally coupled residues in the protein reveals a network of connected residues spanning the 330 position to the distant helix propagating through the core of the protein sector. As a check of this allosteric path, we are able to abrogate the allosteric transmission through a mutation in the middle of the protein sector. Both the ability to adapt to new function and the property of allostery are found almost exclusively within the protein sector. The work highlighted here in addition to previous studies in the lab thus appear to suggest that the sector is a good descriptor and model for understanding how proteins work. It will therefore be important for future studies to determine if other methods of protein design such as Direct Coupling Analysis and Rosetta provide equivalently sufficient descriptions of proteins and what additional information, if any, these approaches reveal.