The Effect of Macromolecular Crowding, Ionic Strength and Calcium Binding on Calmodulin Dynamics

The flexibility in the structure of calmodulin (CaM) allows its binding to over 300 target proteins in the cell. To investigate the structure-function relationship of CaM, we combined methods of computer simulation and experiments based on circular dichroism (CD) to investigate the structural characteristics of CaM that influence its target recognition in crowded cell-like conditions. We developed a unique multiscale solution of charges computed from quantum chemistry, together with protein reconstruction, coarse-grained molecular simulations, and statistical physics, to represent the charge distribution in the transition from apoCaM to holoCaM upon calcium binding. Computationally, we found that increased levels of macromolecular crowding, in addition to calcium binding and ionic strength typical of that found inside cells, can impact the conformation, helicity and the EF hand orientation of CaM. Because EF hand orientation impacts the affinity of calcium binding and the specificity of CaM's target selection, our results may provide unique insight into understanding the promiscuous behavior of calmodulin in target selection inside cells.Comment: Accepted to PLoS Comp Biol, 201

Gas sensing mechanisms in chemiresistive metal phthalocyanine nanofilms

Chemiresistive films of metallophthalocyanines (MPcs; M = Fe, Co, Ni, Cu, Zn, and H₂) are shown to be sensitive to gas phase electron donors and acceptors. The mechanism of sensing occurs through coordination of the analyte molecule to metal center of the phthalocyanine; electron donors cause film current losses by trapping of charge carriers, while electron acceptors causes current gains by generation of charge carriers within the film. Vapor phase peroxides may cause gains or losses of film current by electrocatalytic processes dependent on the metal center. MPcs featuring varied metal centers and peripheral substituents are prepared via literature procedures. A novel route is devised for synthesis of a copper phthalocyanine incorporating the 1,1,1,3,3,3- hexafluoropropan-2-ol (HFIP) group. MPc films are deposited by organic molecular beam epitaxy (OMBE) and spin-coating; film morphologies are examined by atomic force microscopy (AFM). It is demonstrated that substrate temperature during OMBE deposition can significantly alter grain morphology. Spin-coating offers a cost-effective alternative to OMBE, with soluble, functionalized phthalocyanines. The roles of solvent and functional group are explored and procedures for preparing uniform amorphous films are described. The differing mechanisms of sensing in metal-free phthalocyanine (H₂Pc) and metalated phthalocyanines (MPc) are examined with respect to electron-donating (basic) analytes. MPc sensitivities to vapor phase electron donors are correlated exponentially with analyte basicity as described by binding enthalpy, consistent with the van't Hoff equation and the standard free energy of reaction. Coordination of analytes to the phthalocyanine metal center (MPc) or inner protons (H₂Pc) is the dominant mechanism of chemical sensing for basic analytes. Sensor recovery times t'₉₀ are demonstrated to depend exponentially on binding enthalpy. Linear discriminant analysis is used to identify analytes. Single sensor normalization of analyte concentration leads to excellent discrimination and identification of analytes. MPc sensing arrays are shown to be redox-selective vapor sensors of hydrogen peroxide and di-t-butyl peroxide. These peroxides cause unique current losses in CoPc sensors and current gains in FePc, NiPc, CuPc, ZnPc, and H₂Pc sensors. Detection limits of 50 ppb and 250 ppb are achieved for hydrogen peroxide and di-t-butyl peroxide, respectively. Oxidation and reduction of peroxides via catalysis at the phthalocyanine surface is consistent with the pattern of sensor responses. Differential analysis by redox contrast of a small array of sensors thus uniquely identifies peroxide vapors. Chemically sensitive field- effect transistors (ChemFETs) of ZnPc are evaluated for use as vapor sensors. The average carrier mobility is 1.3x10⁻⁴ cm² V⁻¹ s⁻¹, comparable to previously reported phthalocyanine mobility values. ZnPc ChemFETs display persistent photoconductivity, lasting up to 1.5 months, which induces significant baseline drift. Persistent photoconductivity and sensor instability require improvements to the ZnPc ChemFET architecture before its implementation as vapor sensor