In this study, we investigate interactions of extended conformations of homodimeric peptides made of small (glycine or alanine) and large hydrophobic (valine or leucine) sidechains using all-atom molecular dynamics simulations to decipher driving forces for β-sheet formation. We make use of a periodic boundary condition setup in which individual peptides are infinitely long and stretched. Dimer...

We establish and quantify correlations among the molecular structures, interaction forces, and physical processes associated with light-responsive self-assembled surfactant monolayers or bilayers at interfaces. Using the surface forces apparatus (SFA), the interaction forces between adsorbed monolayers and bilayers of an azobenzene-functionalized surfactant can be drastically and controllably a...

Combinatorial library screens based on binding affinity may preferentially select ligands with ability for ionic interactions and miss the biologically relevant ligands that bind more weakly with predominantly hydrophobic interactions.

Hydrophobicity underpins self-assembly in many natural and synthetic molecular and nanoscale systems. A signature of hydrophobicity is its temperature dependence. The first experimental evaluation of the temperature and size dependence of hydration free energy in a single hydrophobic polymer is reported, which tests key assumptions in models of hydrophobic interactions in protein folding. Herei...

The formation of structured hydrogen bond networks in the solvation shells immediate to hydrophobic solutes is crucial for a large number of water mediated processes. A long lasting debate in this context regards the mutual influence of the hydrophobic solute into the bulk water and the role of the hydrogen bond network of the bulk in supporting the solvation structure around a hydrophobic mole...

The physicochemical properties (surface tension, dynamic viscosity, crystallization and melting temperatures) of polyvinyl alcohol solutions molecular weight 9, 31 72 kDa have been studied. surface tension the critical concentration micelle formation were determined by method stalogometry, viscosity was using an Oswald viscometer. temperatures in a cooled modified chamber UOP-6 software freezer...

Human serum albumin (HSA) is the most abundant protein in the blood plasma. Molecular dynamics simulations of subdomain IIA of HSA and its complex with salicylic acid (SAL) were performed to investigate structural changes induced by the ligand binding. To estimate the binding affinity of SAL molecule to subdomains IB and IIA in HSA protein, binding free energies were calculated using the Molecu...

The EGFR/ErbB/HER family of kinases contains four homologous receptor tyrosine kinases that are important regulatory elements in key signaling pathways. To elucidate the atomistic mechanisms of dimerization-dependent activation in the ErbB family, we have performed molecular dynamics simulations of the intracellular kinase domains of the four members of the ErbB family (those with known kinase ...

We ran and analyzed a total of eighteen, 10 ns molecular dynamics simulations of two C-terminal beta-hairpins from the B1 domain of Protein G: twelve runs for the last 16 residues and six runs for the last 15 residues, G41-E56 and E42-E56, respectively. Based on their CalphaRMS deviation from the starting structure and the pattern of stabilizing interactions (hydrogen bonds, hydrophobic contact...

Poly(N-isopropylacrylamide) (PNIPAM) is the premier example of a macromolecule that undergoes a hydrophobic collapse when heated above its lower critical solution temperature (LCST). Here we utilize dynamic light scattering, H-NMR, and steady-state and time-resolved UVRR measurements to determine the molecular mechanism of PNIPAM's hydrophobic collapse. Our steady-state results indicate that in...