Shakhnovich Research

Shakhnovich Research

A recent finding in the Shakhnovich Lab demonstrates how components belonging to opposite branches of Protein Quality Control – chaperonins (GroEL) and ATP-dependent proteases (Lon) – shape fitness landscape of living cells by acting on equilibrium Molten Globule folding intermediate of an essential protein (DHFR) in E. coli cytoplasm.

Shakhnovich Research

In molecular biophysics, the view that properties of proteins can be determined from first principles of physics and chemistry is almost a canon law. Advances in molecular dynamics, protein folding, ab initio structure prediction, and design of novel protein folds and function all support this view.  Notwithstanding these developments, proteins in the context of the cellular milieu, which impose selection for function and/or against the toxic effects of protein misfolding. Cells likewise evolve as a population, thus demography and population history could scale the stringency of selection. Indeed, to what extent can physics and chemistry account for the diversity of biophysical and biochemical properties of proteins in nature?  If protein evolution must reckon with the stochastic processes of mutation and purifying selection, what is the contribution of effective population size? Through the systematic synthesis of biophysics, molecular biology, and population dynamics, our goal is to arrive at unified understanding of protein evolution

Shakhnovich Research

Rate of evolution of a protein (the rate of nonsynymous substitutions per nonsynonymous sites) as a function of its intracellular abundance (A) and folding stability ΔG. Because fixation of a mutation changes ΔG, the evolution of a gene is essentially a walk on the molecular clock surface, and this walk is slowest in the neighborhood of the gully (red line). In analogy to energy landscapes in physics, the minimum of the evolutionary surface defines the location of genes over evolutionary timescales. This minimum defines the average relationship between the folding stability, abundance, and population size (Equation). The specific relationship between abundance and folding stability manifests on the 3D structures of Yeast proteins (panels A to D).

The Shakhnovich lab develops dynamic multiscale models that predict evolutionary dynamics from first principles of physical chemistry and tests their implications experimentally by introducing mutations in essential genes directly on E.Coli chromosome and evaluating their fitness effects and longer term consequences for evolution and adaptation. Given that the effect of mutations on chemical properties of a protein is evaluated in vitro, these studies close the genotype-phenotype gap in a consistent and rigorous manner.