Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins

Theory of protein folding

Protein folding should be complex. Proteins organize themselves into specific three-dimensional structures, through a myriad of conformational changes. The classical view of protein folding describes this process as a nearly sequential series of discrete intermediates. In contrast, the energy landscape theory of folding considers folding as the progressive organization of an ensemble of partially folded structures through which the protein passes on its way to the natively folded structure. As a result of evolution, proteins have a rugged funnel-like landscape biased toward the native structure. Connecting theory and simulations of minimalist models with experiments has completely revolutionized our understanding of the underlying mechanisms that control protein folding.

Dynamical transition and proteinquake in photoactive yellow protein

Conformational dynamics in protein functioning covers a wide range of time scales from nanosecond fluctuations around a conformation to the large-amplitude conformational changes of milliseconds or longer. We illustrate a picture of cooperative coupling among such motions of different time scales in a model protein, photoactive yellow protein, by proposing a model that can consistently explain the experimental results on the photocycle of photoactive yellow protein. The model provides a scenario in which the global collective motion induced by the unfolding of the N-terminal domain promotes the loosening of the atomistic packing around the chromophore, which produces the favorable molecular environment for the photoexcited chromophore, thereby stabilizing the partially unfolded intermediate in the photocycle. The proteinquake, the large conformational change triggered by the local structural disturbance, plays a decisive role in controlling the kinetics of functioning.

Relationship of Leffler (Bronsted) alpha values and protein folding Phi values to position of transition-state structures on reaction coordinates

The positions of transition states along reaction coordinates (r++) for simple chemical reactions are often estimated from Leffler alpha values, the slope of plots of DeltaG++ (activation energy) versus DeltaG(0) (equilibrium free energy) for a series of structural variants. Protein folding is more complex than simple chemical reactions and has a multitude of reaction coordinates. Phi-Value analysis measures degree of structure formation at individual residues in folding transition states from the ratio DeltaDeltaG++/DeltaDeltaG(0) for mutations. alpha values are now being used to analyze protein folding by lumping series of Phi values into single plots. But, there are discrepancies in the values of alpha for folding with more classical measures of the extent of structure formation, which I rationalize here. I show for chemical reactions with just a single reaction coordinate that alpha = r++ only for limiting cases, such as for reactants and products being in parabolic energy wells of identical curvature. Otherwise, alpha can differ radically from r++, with alpha being determined just by the angles of intersection of reactant and product energy surfaces. Phi is an index of the progress of a local, energy-based reaction coordinate at the global transition state: Phi <0.5 corresponds to <50% progress of the local coordinate at the global transition state and Phi >0.5 means >50%. Protein Leffler plots can force different local indexes to a single fit and give skewed underestimates of the extent of global structure formation in transition states that differ from other measures of structure formation.

Dynamic coupling between the SH2 domain and active site of the COOH terminal Src kinase, Csk

The SH2 domain is required for high catalytic activity in the COOH-terminal Src kinase (Csk). Previous solution studies suggest that a short peptide sequence, the SH2-kinase linker, provides a functional connection between the active site and the distal SH2 domain that could underlie this catalytic phenomenon. Substitutions in Phe183 (tyrosine, alanine, and glycine), a critical hydrophobic residue in the linker, result in large decreases in substrate turnover and large increases in the K(m) for ATP. Indeed, F183G possesses kinetic parameters that are similar to that for a truncated form of Csk lacking the SH2 domain, suggesting that a single mutation disrupts communication between this domain and the active site. Based on equilibrium and stopped-flow fluorescence experiments, the elevated K(m) values for the mutants are due to changes in the rates of phosphoryl transfer and not to reduced ATP-binding affinities. Based on hydrogen-deuterium exchange experiments, glycine substitution reduces flexibility in several polypeptide regions in Csk, tyrosine substitution increases flexibility, and alanine substitution leads to mixed effects compared to wild-type. Normal mode analysis indicates that Phe183 and its environment are under strain, a theoretical finding that supports the results of mutations. Overall, the data indicate that domain-domain interactions, controlled through the SH2-kinase linker, provide a dynamic balance within the Csk framework that is ideal for efficient phosphoryl transfer in the active site.