Nate Traaseth Lab

Research

Overview:

Our research is focused on revealing the transport mechanism of membrane proteins through determination of their structure by nuclear magnetic resonance (NMR) spectroscopy. Membrane transport proteins regulate cellular events by acting as gatekeepers of ions, drugs and other essential molecules. Since more than half of the drugs on the market target membrane embedded proteins, knowledge of how and why these molecules bind and cause biological activation (or inactivation) is of paramount importance. Due to the difficulties in studying these systems, it is advantageous to use multiple approaches such as crystallography, fluorescence, EPR and NMR spectroscopy. While crystallography continues to make enormous strides in revealing large membrane protein structures including GPCRs and ion channels, NMR and other spectroscopies can be highly complementary, revealing structural and dynamic insights of the proteins under nativelike conditions.

Objectives:

The impact of this research will be to contribute a basic understanding toward how multidrug resistance is conferred to pathogenic organisms on a molecular level. The long-term goal of this project is to predict how drug binding might be altered in mutated strains of bacteria, so as to design new and better antibiotics in the event of multidrug resistance.

Major Projects:

(1) Structure Determination of Membrane Proteins within the Small Multidrug Resistance (SMR) Family.

Multidrug resistance is a serious problem in the treatment of infectious diseases. The Institute of Allergy and Infectious Diseases indicates that many diseases are now becoming difficult to treat due to antimicrobial-resistant organisms. Some of these infectious diseases include HIV, tuberculosis, meningitis, staphylococcal infection, influenza, gonorrhea, Candida, and malaria (http://www.cdc.gov/drugresistance/about.html). Members of the small multidrug resistance (SMR) protein family confer resistance to several quaternary ammonium compounds and other lipophilic cations that are commonly used in spray-fogging procedures for hospital rooms to reduce the number of airborne and surface bacteria.

Nate Traaseth Lab multidrug resistance

Bacteria gain resistance to drugs by a number of mechanisms including: efflux of antibiotics, mutation, permeability of the cell wall, alterations to the antibiotic, changes to the binding sites of antibiotics, or deactivation of the drug molecules. One efficient way is through a rather simple mechanism: sending the drug out of the cell. This is the mode of function for a subclass of proteins within the small multidrug resistance (SMR) family called the small multidrug pumps (SMPs). These ion-transporter proteins consist of four transmembrane domains and ~110 residues. While it is believed that most members within the SMP subclass are composed of helical transmembrane domains, these proteins differ in the tertiary, quaternary, and topological assembly, giving rise to different biological functions.


(2) NMR Methodology

Challenging projects require methodological developments. Due to the difficulty in studying membrane proteins, improvements in both solid-state and solution NMR experiments will make studying membrane proteins in detergent micelles, lipid nanodisks, and lipid bilayers more feasible. Additionally, improvements in the sample preparation for large membrane proteins is needed to allow for stable samples that give reproducible results. For example, the ability to directly detect sensitive nuclei (e.g., 1H or 13C) in aligned membrane protein samples would give significantly improved sensitivity over the 15N detected experiment currently relied upon.

Nate Traaseth Lab NMR development and methodology