Calmodulin-Calcineurin Interaction beyond the Calmodulin-Binding Region Contributes to Calcineurin Activation.

Calcineurin (CaN) is a calcium-dependent phosphatase involved in numerous signaling pathways. Its activation is in part driven by the binding of calmodulin (CaM) to a CaM recognition region (CaMBR) within CaN's regulatory domain (RD). However, secondary interactions between CaM and the CaN RD may be necessary to fully activate CaN. Specifically, it is established that the CaN RD folds upon CaM binding and a region C-terminal to CaMBR, the "distal helix", assumes an α-helix fold and contributes to activation [Dunlap, T. B., et al. (2013) Biochemistry 52, 8643-8651]. We hypothesized in that previous study that this distal helix can bind CaM in a region distinct from the canonical CaMBR. To test this hypothesis, we utilized molecular simulations, including replica-exchange molecular dynamics, protein-protein docking, and computational mutagenesis, to determine potential distal helix-binding sites on CaM's surface. We isolated a potential binding site on CaM (site D) that facilitates moderate-affinity interprotein interactions and predicted that mutation of site D residues K30 and G40 on CaM would weaken CaN distal helix binding. We experimentally confirmed that two variants (K30E and G40D) indicate weaker binding of a phosphate substrate p-nitrophenyl phosphate to the CaN catalytic site by a phosphatase assay. This weakened substrate affinity is consistent with competitive binding of the CaN autoinhibition domain to the catalytic site, which we suggest is due to the weakened distal helix-CaM interactions. This study therefore suggests a novel mechanism for CaM regulation of CaN that may extend to other CaM targets.

Predicting the influence of long-range molecular interactions on macroscopic-scale diffusion by homogenization of the Smoluchowski equation.

The macroscopic diffusion constant for a charged diffuser is in part dependent on (1) the volume excluded by solute "obstacles" and (2) long-range interactions between those obstacles and the diffuser. Increasing excluded volume reduces transport of the diffuser, while long-range interactions can either increase or decrease diffusivity, depending on the nature of the potential. We previously demonstrated [P. M. Kekenes-Huskey et al., Biophys. J. 105, 2130 (2013)] using homogenization theory that the configuration of molecular-scale obstacles can both hinder diffusion and induce diffusional anisotropy for small ions. As the density of molecular obstacles increases, van der Waals (vdW) and electrostatic interactions between obstacle and a diffuser become significant and can strongly influence the latter's diffusivity, which was neglected in our original model. Here, we extend this methodology to include a fixed (time-independent) potential of mean force, through homogenization of the Smoluchowski equation. We consider the diffusion of ions in crowded, hydrophilic environments at physiological ionic strengths and find that electrostatic and vdW interactions can enhance or depress effective diffusion rates for attractive or repulsive forces, respectively. Additionally, we show that the observed diffusion rate may be reduced independent of non-specific electrostatic and vdW interactions by treating obstacles that exhibit specific binding interactions as "buffers" that absorb free diffusers. Finally, we demonstrate that effective diffusion rates are sensitive to distribution of surface charge on a globular protein, Troponin C, suggesting that the use of molecular structures with atomistic-scale resolution can account for electrostatic influences on substrate transport. This approach offers new insight into the influence of molecular-scale, long-range interactions on transport of charged species, particularly for diffusion-influenced signaling events occurring in crowded cellular environments.

Finite Element Estimation of Protein-Ligand Association Rates with Post-Encounter Effects: Applications to Calcium binding in Troponin C and SERCA.

We introduce a computational pipeline and suite of software tools for the approximation of diffusion-limited binding based on a recently developed theoretical framework. Our approach handles molecular geometries generated from high-resolution structural data and can account for active sites buried within the protein or behind gating mechanisms. Using tools from the FEniCS library and the APBS solver, we implement a numerical code for our method and study two Ca(2+)-binding proteins: Troponin C and the Sarcoplasmic Reticulum Ca(2+) ATPase (SERCA). We find that a combination of diffusional encounter and internal 'buried channel' descriptions provide superior descriptions of association rates, improving estimates by orders of magnitude.

Unimolecular rate constants for HX or DX elimination (X = F, Cl) from chemically activated CF3CH2CH2Cl, C2H5CH2Cl, and C2D5CH2Cl: threshold energies for HF and HCl elimination.

Vibrationally activated CF(3)CH(2)CH(2)Cl molecules were prepared with 94 kcal mol(-1) of vibrational energy by the combination of CF(3)CH(2) and CH(2)Cl radicals and with 101 kcal mol(-1) of energy by the combination of CF(3) and CH(2)CH(2)Cl radicals at room temperature. The unimolecular rate constants for elimination of HCl from CF(3)CH(2)CH(2)Cl were 1.2 x 10(7) and 0.24 x 10(7) s(-1) with 101 and 94 kcal mol(-1), respectively. The product branching ratio, k(HCl)/k(HF), was 80 +/- 25. Activated CH(3)CH(2)CH(2)Cl and CD(3)CD(2)CH(2)Cl molecules with 90 kcal mol(-1) of energy were prepared by recombination of C(2)H(5) (or C(2)D(5)) radicals with CH(2)Cl radicals. The unimolecular rate constant for HCl elimination was 8.7 x 10(7) s(-1), and the kinetic isotope effect was 4.0. Unified transition-state models obtained from density-functional theory calculations, with treatment of torsions as hindered internal rotors for the molecules and the transition states, were employed in the calculation of the RRKM rate constants for CF(3)CH(2)CH(2)Cl and CH(3)CH(2)CH(2)Cl. Fitting the calculated rate constants from RRKM theory to the experimental values provided threshold energies, E(0), of 58 and 71 kcal mol(-1) for the elimination of HCl or HF, respectively, from CF(3)CH(2)CH(2)Cl and 54 kcal mol(-1) for HCl elimination from CH(3)CH(2)CH(2)Cl. Using the hindered-rotor model, threshold energies for HF elimination also were reassigned from previously published chemical activation data for CF(3)CH(2)CH(3,) CF(3)CH(2)CF(3), CH(3)CH(2)CH(2)F, CH(3)CHFCH(3), and CH(3)CF(2)CH(3). In an appendix, the method used to assign threshold energies was tested and verified using the combined thermal and chemical activation data for C(2)H(5)Cl, C(2)H(5)F, and CH(3)CF(3).