Author(s): Bilkiss B Issack

While it has long been known that cholesterol reduces the permeability of biological membranes to water, the exact mechanism by which cholesterol influences transmembrane permeation is still unclear. The thermodynamic and kinetic contributions to the transport of water across mixed DPPC/cholesterol bilayers of different composition are thus examined by mo ...

Article GUID: 25679811

Author(s): Jean-François Rhéault

A singular aspect of the 2-on-2 hemoglobin structures of groups I and II is the presence of tunnels linking the protein surface to the distal heme pocket, supporting the storage and the diffusion of small apolar ligands to/from the buried active site. As the solubility of apolar ligands is greater in biological membranes than in solution, the association ...

Article GUID: 25723781

Author(s): Sefer Baday

In human cells, membrane proteins of the rhesus (Rh) family excrete ammonium and play a role in pH regulation. Based on high-resolution structures, Rh proteins are generally understood to act as NH3 channels. Given that cell membranes are permeable to gases like NH3, the role of such proteins remains a paradox. Using molecular and quantum mechanical calcu ...

Article GUID: 26190573

Author(s): Maria S Shadrina

Atomistic molecular dynamics simulations of diffusion of O2 from the hemes to the external solvent in the a- and ß-subunits of the human hemoglobin (HbA) tetramer reveal transient gas tunnels that are not seen in crystal structures. We find here that the tunnel topology, which encompasses the reported experimental Xe binding cavities, is identical in HbA& ...

Article GUID: 26226318

Author(s): Maria S Shadrina

Hemoglobin transports O2 by binding the gas at its four hemes. Hydrogen bonding between the distal histidine (HisE7) and heme-bound O2 significantly increases the affinity of human hemoglobin (HbA) for this ligand. HisE7 is also proposed to regulate the release of O2 to the solvent via a transient E7 channel. To reveal the O2 escape routes controlled by H ...

Article GUID: 26226401

Author(s): Sandrine Moreira

CONCLUSION: Homology modeling and molecular dynamics simulations strongly suggest that DpRNL is an RNA ligase 2. The predicted innovative reshaping of DpRNL's catalytic pocket is worthwhile to be tested experimentally.

Article GUID: 26449279

Author(s): Esam A Orabi

A polarizable model for ammonia is optimized based on the ab initio properties of the NH3 molecule and the NH3-NH3 and NH3-H2O dimers calculated at the MP2 level. For larger (NH3)m, NH3(H2O)n, and H2O(NH3)n clusters (m = 2-7 and n = 1-4), the model yields structural and binding energies in good agreement with ab initio calculations without further adjustm ...

Article GUID: 26583551

Author(s): Esam A Orabi

A polarizable potential model for M(+)-NH3 interactions (M(+) = Li(+), Na(+), K(+), Rb(+), Cs(+)) is optimized based on the ab initio properties of the ion-ammonia dimers calculated at the MP2 level of theory. The optimized model reproduces the ab initio binding energies of M(+)(NH3)n (n = 2-4) and M(+)(NH3)n(H2O)m (n, m = 1-3 and n + m = 4) clusters and ...

Article GUID: 26583725

Author(s): Soran Jahangiri

Parameter sets of the self-consistent-charge density-functional tight-binding model with and without its third-order extension have been developed to describe the interatomic interactions of halogen elements (X = Cl, Br, I) with hydrogen and oxygen, with the ultimate goal of investigating halide hydration with this approach. The reliability and accuracy o ...

Article GUID: 26584090

Author(s): Esam A Orabi

A polarizable model for hydrogen sulfide (H2S) is optimized based on the experimental properties of the monomer and of the bulk liquid. The model is characterized by rigid SH bonds but flexible HSH angle and the polarizability is based on the Drude oscillator model. Bonded parameters and atomic charges are based on the experimental properties of the gaseo ...

Article GUID: 26588292

Author(s): Esam A Orabi

Polarizable potential models for the interaction of Li(+), Na(+), K(+), and NH4(+) ions with benzene are parametrized based on ab initio quantum mechanical calculations. The models reproduce the ab initio complexation energies and potential energy surfaces of the cation-p dimers. They also reproduce the cooperative behavior of "stacked", cation-p-p trimer ...

Article GUID: 26592880

Author(s): Maria S Shadrina

Standard molecular dynamics (MD) simulations of gas diffusion consume considerable computational time and resources even for small proteins. To combat this, temperature-controlled locally enhanced sampling (TLES) examines multiple diffusion trajectories per simulation by accommodating multiple noninteracting copies of a gas molecule that diffuse independe ...

Article GUID: 26938707