Robert K. Nakamoto, PhD

Robert K. Nakamoto, PhD

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P-glycoprotein; Structural biology of membrane proteins (Drug resistance)

There are four main projects in the Nakamoto laboratory:

  1. Linking functions of the FOF1 ATP synthase. The long term goal is to understand the mechanism of active transport in the multi-subunit FOF1 ATP synthase. This enzyme complex which is responsible for the vast majority of ATP synthesis. The primary focus has been the elucidation of the mechanism that couples the rotation to the chemical reaction of ATP synthesis or the rotation to the electrochemical gradient of protons. These studies seek to understand the molecular mechanisms which determine the efficiency of energy metabolism which is critical to all life processes and often appear as neurodegenerative disorders.
  2. Mechanism of drug transport by P-glycoprotein. In contrast to the multiple subunit FOF1 ATP synthase, the P-glycoprotein consists of a single large subunit and belongs to an ever growing class of proteins known as the ABC (ATP-Binding Cassette) transporters. Amplification of the P-glycoprotein results in the multiple drug resistance phenotype which is the major cause of failure in chemotherapeutic treatment of cancer. Again, the lab uses genetics and mutagenesis similar to that used for the FOF1 to probe structure-function relationships by genetic, protein chemistry, kinetic and thermodynamic approaches to analyze function-altering mutations, or chemical compounds, which have obvious potential for pharmaceutical applications.
  3. Structural biology of cardiovascular proteins. In the third project, the lab is collaborating with the laboratories of Drs. Avril Somlyo, John Bushweller, Zygmunt Derewenda, Masumi Eto, Barry Gumbiner, and Zhifeng Shao in studying the mechanisms and structures of the small GTP-binding protein RhoA and its effector proteins, and their roles in the regulation of mammalian smooth muscle. RhoA, a member of the ras super family, regulates vascular smooth muscle contraction, cardiac hypertrophy and formation of stress fibers, and its downstream effector, Rho-kinase, is implicated in hypertension and cell motility including metastasis. They intend to generate the structural and biophysical information required for the development of specific drugs to block or enhance angiogenic and metastatic processes.
  4. Structure genomics of membrane proteins from Mycobacterium tuberculosis. The lab is part of a consortium made up of 15 investigators from around the United States, including Dr. Michael Wiener from the U.Va. Department of Molecular Physiology & Biological Physics.  The long-term goal is to develop a genomics approach to the structure biology of membrane proteins, which are the targets of the vast majority of pharmaceutical agents. Despite the importance of these proteins, relatively little is known about their structural biology.  The Consortium is carrying out a highly integrated project to development new methods and approaches to increase the structural knowledge of these critically important proteins, which include channels, transporters, receptors, pathogenicity factors and multiple drug resistance transporters. Each of these classes of proteins plays important roles in the biology of cancer. The lab's role in the project is to develop methods to break through the critical bottleneck of membrane protein expression and sample preparation for either crystallography or NMR spectroscopy approaches.