Comparing allosteric transitions in the domains of calmodulin through coarse-grained simulations.

Calmodulin (CaM) is a ubiquitous Ca(2+)-binding protein consisting of two structurally similar domains with distinct stabilities, binding affinities, and flexibilities. We present coarse grained simulations that suggest that the mechanism for the domain's allosteric transitions between the open and closed conformations depends on subtle differences in the folded state topology of the two domains. Throughout a wide temperature range, the simulated transition mechanism of the N-terminal domain (nCaM) follows a two-state transition mechanism while domain opening in the C-terminal domain (cCaM) involves unfolding and refolding of the tertiary structure.

Coarse-grained molecular simulations of allosteric cooperativity.

Interactions between a protein and a ligand are often accompanied by a redistribution of the population of thermally accessible conformations. This dynamic response of the protein's functional energy landscape enables a protein to modulate binding affinities and control binding sensitivity to ligand concentration. In this paper, we investigate the structural origins of binding affinity and allosteric cooperativity of binding two Ca(2+) ions to each domain of Calmodulin (CaM) through simulations of a simple coarse-grained model.

Allostery and folding of the N-terminal receiver domain of protein NtrC.

The N-terminal receiver domain of protein NtrC (NtrC(r)) exhibits allosteric transitions between the inactive (unphosphorylated) and active (phosphorylated) state on the microsecond time scale. Using a coarse-grained variational model with coupled energy basins, we illustrate that significant loss of conformational flexibility is the key determinant of the inactive (I) → active (A) state transition mechanism of NtrC(r). In particular, our results reveal that the rearrangements of the native contacts involving the regulatory helix-α4 and the flexible β3-α3 loop upon activation play a crucial role in the activation mechanism.

Conformational flexibility and the mechanisms of allosteric transitions in topologically similar proteins.

Conformational flexibility plays a central role in allosteric transition of proteins. In this paper, we extend the analysis of our previous study [S. Tripathi and J.

Cooperativity and protein folding rates.

Despite the large and complex conformational space available to an unfolded protein, many small globular proteins fold with simple two-state cooperative kinetics. Understanding what determines folding rates beyond simple rules summarizing kinetic trends has proved to be more elusive than predicting folding mechanism. Topology-based models with smooth energy landscapes give reasonable predictions of the structure of the transition state ensemble, but do not have the kinetic or thermodynamic cooperativity exhibited by two-state proteins.

Inherent flexibility determines the transition mechanisms of the EF-hands of calmodulin.

We explore how inherent flexibility of a protein molecule influences the mechanism controlling allosteric transitions by using a variational model inspired from work in protein folding. The striking differences in the predicted transition mechanism for the opening of the two domains of calmodulin (CaM) emphasize that inherent flexibility is key to understanding the complex conformational changes that occur in proteins. In particular, the C-terminal domain of CaM (cCaM), which is inherently less flexible than its N-terminal domain (nCaM), reveals "cracking" or local partial unfolding during the open/closed transition.

Capillarity-like growth of protein folding nuclei.

A full structural description of transition state ensembles in protein folding includes the specificity of the ordered residues composing the folding nucleus as well as spatial density. To our knowledge, the spatial properties of the folding nucleus and interface of specific nuclei have yet to receive significant attention. We analyze folding routes predicted by a variational model in terms of a generalized formalism of the capillarity scaling theory that assumes the volume of the folded core of the nucleus grows with chain length as V(f) approximately N(3nu).

Inherent flexibility and protein function: The open/closed conformational transition in the N-terminal domain of calmodulin.

The key to understand a protein's function often lies in its conformational dynamics. We develop a coarse-grained variational model to investigate the interplay between structural transitions, conformational flexibility, and function of the N-terminal calmodulin domain (nCaM). In this model, two energy basins corresponding to the "closed" apo conformation and "open" holo conformation of nCaM are coupled by a uniform interpolation parameter.

Variationally determined free energy profiles for structural models of proteins: characteristic temperatures for folding and trapping.

Characterizing the phase diagram for proteins is important both for laboratory studies and for the development of structure prediction algorithms. Using a variational scheme, we calculated the generic features of the protein thermostability over a large range of temperatures for a set of more than 50 different proteins using a model based on native structure alone. Focusing on a specific system, protein G, we further examined, using a more realistic model that includes the nonnative interaction, the thermostability of both the native state and a collection of trap structures.

Excluded volume, local structural cooperativity, and the polymer physics of protein folding rates.

A coarse-grained variational model is used to investigate the polymer dynamics of barrier crossing for a diverse set of two-state folding proteins. The model gives reliable folding rate predictions provided excluded volume terms that induce minor structural cooperativity are included in the interaction potential. In general, the cooperative folding routes have sharper interfaces between folded and unfolded regions of the folding nucleus and higher free energy barriers.