Molecular analyses of the C-terminal CRAF variants associated with cardiomyopathy reveal their opposing impacts on the active conformation of the kinase domain.

The germline mutations in the C-terminus of CRAF kinase, particularly L603, and S612T/L613V, are associated with congenital heart disorders, for example, dilated cardiomyopathy (DCM) and hypertrophic cardiomyopathy (HCM). The experimental data suggest that genetic alternation at position 603 impairs, while those at positions 612/613 enhance the CRAF kinase activity. However, the underlying mechanistic details by which these mutations increase or decrease kinase activity remain elusive. Therefore, we applied molecular dynamic simulation to investigate the impacts of these point mutations on the conformation of the CRAF kinase domain. The results revealed that the substitution of Leucine 603 for proline transits the kinase domain to a state that exhibits the molecular hallmarks of an inactive kinase, for example, a closed activation loop, 'αC-helix out' conformation and a distorted regulatory hydrophobic spine. However, two HCM-associated variants (S612T and L613V) show features of an active conformation, such as an open activation loop conformation, 'αC-helix in', the assembly of the hydrophobic spine, and more surface-exposed catalytic residues of phosphoryl transfer reaction. Overall, our study provides a mechanistic basis for the contradictory effects of the CRAF variants associated with HCM and DCM.

Recent advances in computational methods for biosensor design.

Biosensors are analytical tools with a great application in healthcare, food quality control, and environmental monitoring. They are of considerable interest to be designed by using cost-effective and efficient approaches. Designing biosensors with improved functionality or application in new target detection has been converted to a fast-growing field of biomedicine and biotechnology branches. Experimental efforts have led to valuable successes in the field of biosensor design; however, some deficiencies restrict their utilization for this purpose. Computational design of biosensors is introduced as a promising key to eliminate the gap. A set of reliable structure prediction of the biosensor segments, their stability, and accurate descriptors of molecular interactions are required to computationally design biosensors. In this review, we provide a comprehensive insight into the progress of computational methods to guide the design and development of biosensors, including molecular dynamics simulation, quantum mechanics calculations, molecular docking, virtual screening, and a combination of them as the hybrid methodologies. By relying on the recent advances in the computational methods, an opportunity emerged for them to be complementary or an alternative to the experimental methods in the field of biosensor design.

How a multimeric macromolecule is affected by divalent salts? Experimental and simulation study.

Salts exist in any cell and living organism in contact with biological macromolecules. How these salts affect biomolecules such as enzyme is important from both basic sciences and practical technologies. It was observed that divalent salts can change structure and function of protein at higher concentrations. Here, we investigated the effect of divalent salt on the behavior of a multimeric enzyme. We treated glucose oxidase as dimer-active enzyme in different CaCl2 concentration and seen that the enzyme become inactive at high concentration of salt. These experimental results are in agreement with recently published researches. To find a possible mechanism, a series of molecular dynamics simulation of the enzyme were performed at different salt concentration. According to the MD simulation, the conformational changes at the active site and FAD-binding site support the hypothesis of enzyme inactivation at high CaCl2 concentration. MD simulations also showed that enzyme has an unstable conformation at higher salt concentration which is in agreement with our experimental data. Detailed structural properties of the enzyme have been analyzed under different conditions. To the best of our knowledge, this is the first study that bears detailed structural mechanism about the salt effects on multimeric macromolecules.

Self-Assembly of a Structurally Defined Chiro-Optical Peptide-Oligothiophene Hybrid Material.

Conducting polymers are routinely used in optoelectronic biomaterials, but large polymer polydispersity and poor aqueous compatibility complicate integration with biomolecular templates and development of discrete and defined supramolecular complexes. Herein, we report on a chiro-optical hybrid material generated by the self-assembly of an anionic peptide and a chemically defined cationic pentameric thiophene in aqueous environment. The peptide acts as a stereochemical template for the thiophene and adopts an α-helical conformation upon association, inducing optical activity in the thiophene π-π* transition region. Theoretical calculations confirm the experimentally observed induced structural changes and indicate the importance of electrostatic interactions in the complex. The association process is also probed at the substrate-solvent interface using peptide-functionalized gold nanoparticles, indicating that the peptide can also act as a scaffold when immobilized, resulting in structurally well-defined supramolecular complexes. The hybrid complex could rapidly be assembled, and the kinetics of the formation could be monitored by utilizing the local surface plasmon resonance originating from the gold nanoparticles. We foresee that these findings will aid in designing novel hybrid materials and provide a possible route for the development of functional optoelectronic interfaces for both biomaterials and energy harvesting applications.

Structure-activity relationship for Fe(III)-salen-like complexes as potent anticancer agents.

Quantitative structure activity relationship (QSAR) for the anticancer activity of Fe(III)-salen and salen-like complexes was studied. The methods of density function theory (B3LYP/LANL2DZ) were used to optimize the structures. A pool of descriptors was calculated: 1497 theoretical descriptors and quantum-chemical parameters, shielding NMR, and electronic descriptors. The study of structure and activity relationship was performed with multiple linear regression (MLR) and artificial neural network (ANN). In nonlinear method, the adaptive neuro-fuzzy inference system (ANFIS) was applied in order to choose the most effective descriptors. The ANN-ANFIS model with high statistical significance (R (2) train = 0.99, RMSE = 0.138, and Q (2) LOO = 0.82) has better capability to predict the anticancer activity of the new compounds series of this family. Based on this study, anticancer activity of this compound is mainly dependent on the geometrical parameters, position, and the nature of the substituent of salen ligand.

Synthesis, experimental and theoretical characterization of N,N'-dipyridoxyl (1,4-butanediamine) Schiff-base ligand and its Cu(II) complex.

A new N,N'-dipyridoxyl(1,4-butanediamine) [=H(2)BS] Schiff-base ligand and its Cu(II) salen complex, [Cu(BS)(H(2)O)(CH(3)OH)], were synthesized and characterized by IR, UV-vis, (1)H NMR, mass spectrometry and elemental analysis. Also, full optimization of the geometries, (1)H NMR chemical shifts (for the H(2)BS) and vibrational frequencies were calculated by using density functional theory (DFT) method. Structure of the H(2)BS ligand is not planar, i.e. two pyridine rings are not in the same plane. In the structure of the Cu complex, the Schiff-base ligand acts as a dianionic tetradentate ligand in N, N, O(-), O(-) manner. The coordinating atoms of BS(2-) occupy equatorial positions of the octahedral complex, where the H(2)O and CH(3)OH ligands locate at axial positions. The calculated results are in good agreement with the experimental data, confirming the suitability of the proposed and optimized structures for the H(2)BS ligand and its Cu complex.

Synthesis, experimental and theoretical characterization of tetra dentate N,N'-dipyridoxyl (1,3-propylenediamine) salen ligand and its Co(III) complex.

The new tetra dentate dianionic H2PS (N,N'-dipyridoxyl (1,3-propylenediamine)) Schiff-base ligand and its octahedral Co(III) salen complex [Co(PS)(H2O)(CH3OH)]+CH3COO(-) were synthesized, where coordinating atoms of H2PS (N,N,O(-),O(-)) occupied equatorial positions with H2O and CH3OH as axial ligands. The nature of the H2PS and its complex were determined by elemental and spectrochemical (IR, UV-vis, 1H NMR and Mass) analysis. Also, the fully optimized geometries and vibrational frequencies of them together with the 1H NMR chemical shifts of H2PS have been calculated using density functional theory (B3LYP) method. Obtained structural parameters are in good agreement with the experimental data reported for similar compounds. The calculated and experimental results confirmed the suggested structures for the ligand and complex.

An approach based on diffusion to study ligand-macromolecule interaction.

A new approach has been developed to study binding of a ligand to a macromolecule based on the diffusion process. In terms of the Fick's first law, the concentration of free ligand in the presence of a protein can be determined by the measurement of those ligands which are diffused out. This method is applied to the study of binding of methyl-orange to lysozyme in phosphate buffer of pH 6.2, at 30 degrees C. The binding isotherm was determined initially, followed by application of the Hill equation to the data obtained, then binding constant and binding capacity were estimated.