Ligand binding site identification by higher dimension molecular dynamics.

We propose a new molecular dynamics (MD) protocol to identify the binding site of a guest within a host. The method utilizes a four spatial (4D) dimension representation of the ligand allowing for rapid and efficient sampling within the receptor. We applied the method to two different model receptors characterized by diverse structural features of the binding site and different ligand binding affinities.

Structural analysis of the human cannabinoid receptor one carboxyl-terminus identifies two amphipathic helices.

Recent research has implicated the C-terminus of G-protein coupled receptors in key events such as receptor activation and subsequent intracellular sorting, yet obtaining structural information of the entire C-tail has proven a formidable task. Here, a peptide corresponding to the full-length C-tail of the human CB1 receptor (residues 400-472) was expressed in E.coli and purified in a soluble form.

Carbohydrate surface attachment characterized by sum frequency generation spectroscopy.

Covalent surface attachment of carbohydrate moieties using maleimide-sulfhydril reaction was characterized by surface-selective vibrational sum-frequency generation (VSFG) spectroscopy. The comparative VSFG spectra of the precursor maleimide-terminated SAM and the product glucose adlayer reveal the high efficiency of the surface coupling reaction (>90%) and the details of the molecular organization of the formed carbohydrate adlayer. The glucose groups are orientationally well ordered, as judged by their sharp C-H stretch bands.

Molecular organization in SAMs used for neuronal cell growth.

The attachment of cells onto solid supports is fundamental in the development of advanced biosensors or biochips. In this work, we characterize cortical neuron adhesion, growth, and distribution of an adhesive layer, depending on the molecular structure and composition . Neuronal networks are successfully grown on amino-terminated alkanethiol self-assembled monolayer (SAM) on a gold substrate without adhesion protein interfaces.

Effect of nanoscale geometry on molecular conformation: vibrational sum-frequency generation of alkanethiols on gold nanoparticles.

Vibrational sum frequency generation (VSFG) spectroscopy was used to study the nanoscale geometric effects on molecular conformation of dodecanethiol ligand on gold nanoparticles of varying size between 1.8 and 23 nm. By analyzing the CH3 and CH2 stretch transitions of dodecanethiol using the spectroscopic propensity rules for the SFG process, we observe the increase of the gauche defects in the alkyl chain of the ligand on the nanoparticle surface when the curvature approaches the size of the molecule ( approximately 1.