Joint ChBE/Chem-Biochem Seminar: Klauda and Nie
Tuesday, May 10, 2011
Marker Seminar Room, Chemistry Building
Professor Ray Adomaitis
Department of Chemical and Biomolecular Engineering
University of Maryland, College Park
Molecular Modeling of Cellular Membranes and Associated Proteins
Cellular biomembranes are essential to life by preventing unwanted molecules into a cell and allowing others to traverse the membrane (typically via transport or peripheral membrane proteins). Our research involves atomic-level molecular dynamics (MD) simulations of membranes with lipids and bilayers with lipids and proteins. Accurate lipid force fields used to describe atomic-level interactions are essential to this work. Therefore, ab initio quantum mechanical methods have been used to improve the existing force field to allow for accurate simulations of mixed lipid membranes. Our recent focus has been to go beyond standard studies of simple membrane models of three or less lipid types and develop realistic models of certain organelles in bacteria and yeast. For example, lipid bilayers with branched acyl-chains result in an increase in area elastic moduli and lateral surface area. These branched lipids are common in certain bacterial membranes and influence, along with cholesterol, properties of Chlamydia membranes.
Lipids play an important structural role for cellular membranes but transmembrane and peripheral membrane proteins are the main vehicles for substrate transport. Oxysterol-binding protein homologues (Osh), specifically Osh4, are important peripheral membrane proteins in the sterol transport pathway from the endoplasmic reticulum (ER) to the plasma membrane (PM). Our docking studies have been used to discover lipid binding sites for this protein and possible regions for ER/PM membrane attachment. Our initial MD simulations of Osh4 with donor/acceptor membranes will also be presented. In addition to peripheral membrane proteins, a method is being developed to enhance conformational sampling of secondary active transport membrane proteins. Initial studies on lactose permease demonstrate that this method can, in an unbiased manner, probe the periplasmic-open state starting from the known crystal structure of the cytoplasmic-open state. The periplasmic-open conformations are in compliance with various experimental studies, i.e., substrate accessibility/reactivity, double electronelectron resonance, fluorescence resonance energy transfer, and varying sized cross-linkers. Since most of these transmembrane proteins are crystallized in a single conformation, our new method may be able to probe protein conformations that have not been experimentally determined.
Chemistry and Biochemistry
University of Maryland, College Park
Supracolloidal Physics and Chemistry: Assembly of 3D Nanostructures
The organization of nanoscale objects relative to one another and to larger structures is crucial to the advancement of nanoscience and nanotechnology. For example, the assembly of inorganic nanoparticles allows the best exploration of the collective optical, electronic, and magnetic properties of their individuals, and is vital for their utilization in energy, optoelectronics, sensing, and biomedical applications. So far, significant progress has been achieved in the self-assembly of nanoparticles, yet the precise control over the structural characteristics of nanoparticles ensembles remains a challenge. In this talk, I will present our efforts to develop original assembly rules to facilitate the design of new functional 3-D nanostructures, and to achieve new understanding on the physical and chemical interactions underlying the self-assembly of colloidal nanoparticles.