Abstract:

Detailed understanding of how conformational dynamics orchestrates function in allosteric regulation of recognition and catalysis at atomic resolution remains ambiguous. The three dimensional structure of protein is not always adequate to provide a complete understanding of protein function. We use atomistic molecular dynamics simulations to complement experiments to understand how protein conformational dynamics are coupled to allosteric function. We analyze multi-dimensional simulation trajectories by mapping key dynamical features within individual macrostates as residue-residue contacts. In this talk, we will discuss computational studies on members of a ubiquitous family of enzymes that regulate many sub-cellular processes. The effects of distal mutations and substrate binding are observed at locations far beyond the mutation and binding sites, implying their importance in allostery. The results provide insights into the general interplay between enzyme conformational dynamics and catalysis from an atomistic perspective that have implications for structure based drug design and protein engineering.

Abstract:

Polymerizing monomers into periodic two-dimensional (2D) networks provides structurally precise, layered macromolecular sheets that exhibit desirable mechanical, optoelectrotronic, and molecular transport properties. 2D covalent organic frameworks (COFs) offer broad monomer scope but are generally isolated as powders comprised of aggregated nanometer-scale crystallites. I will discuss 2D COF formation using a two-step procedure, in which monomers are added slowly to pre-formed nanoparticle seeds. The resulting 2D COFs are isolated as single-crystalline, micron-sized particles. Transient absorption spectroscopy of the dispersed COF nanoparticles provides two to three orders of magnitude improvement in signal quality relative to polycrystalline powder samples and suggests exciton diffusion over longer length scales than those obtained through previous approaches. These findings will enable a broad exploration of synthetic 2D polymer structures and properties.

ABSTRACT: What are the thermodynamic driving forces that influence the free energy of membrane protein folding and association in lipid bilayers? For soluble proteins, the burial of hydrophobic groups away from aqueous interfaces is a major driving force, but membrane-embedded proteins cannot experience hydrophobic forces, as the lipid bilayer lacks water. A fundamental conundrum thus arises: how does a greasy protein surface find its greasy protein partner in the greasy lipid bilayer to fold faithfully into its native structure? Recently, a structurally stable and functional monomeric form of the normally homodimeric Cl^-/H⁺ antiporter CLC-ec1 was designed by introducing tryptophan mutations at the dimer interface. We have used this to develop a new model system for studying reversible dimerization in membranes for free energy measurements, which encompasses the thermodynamic properties of protein interactions in the membrane environment. To quantify monomer vs. dimer populations across a wide range of protein densities, we developed a method that quantifies the capture of subunits into liposomes from large equilibrium membranes single-molecule photobleaching by total internal reflection microscopy.  With this, we are able to determine that CLC-ec1 has a free energy of dimerization of -11 kcal/mole in 2:1 POPE/POPG membranes.  We are now investigating why this complex is so stable, dissecting the changes in enthalpy and entropy while varying protein interactions or the composition of the lipid solvent.  The results from this study will provide a physical foundation for the development of informed strategies aimed at correcting protein mis-folding or regulating protein interactions in membranes in physiologically and pathological situations.