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Di Xia, Ph.D.
Structural Study of Biological Membrane Proteins
Recent advances in genome research revealed that over one-third of open reading frames in yeast (S. cerevisiae) are predicted to be integral membrane proteins with 1 to 14 transmembrane segments, reflecting the importance of membrane proteins in the life cycle of this unicellular eukaryotic organism. In multicellular organisms, cellular communication and interaction require increased biological complexity and likely an increased fraction of membrane proteins. Membrane proteins provide vital cellular functions involved in cell-cell communication, recognition, adhesion, and membrane fusion; in material exchange, transportation and detoxication; and in processes of cellular energy conservation. Structural studies on a limited number of membrane proteins have contributed to our understanding of the function of these biological macromolecules. In the light of the increased number of membrane proteins being studied, the paucity of structural data of membrane proteins at atomic resolution creates a vacuum in our knowledge which is only being filled rather slowly. To date, only a few families of membrane protein structures have been determined; most of them are of bacterial origin. The situation arises mainly due to tremendous difficulty in purifying sufficient quantity of most membrane proteins, especially those of eukaryotic origin, needed for structural analysis and in producing diffraction quality crystals; and failure in overexpressing membrane proteins only makes the situation worse. In collaboration with both intramural and extramural laboratories, we try to explore the structure and function relations of polytopic membrane proteins crystallographically by examining a few carefully selected membrane proteins such as those involved in cellular multidrug resistance (human P-glycoprotein) and respiration (cytochrome bc1 complex of both mitochondria and bacteria). We hope that these studies will result in deep understanding of membrane protein architecture in general, the mechanism of function of these important biological membrane proteins, and in potential development of therapeutics for the benefit of mankind.
Protein degradation is a major posttranslational mechanism for modulating the amounts of specific regulatory proteins and is involved in processes as diverse as timing of the cell cycle, the heat shock response, developmental changes, cell signaling pathways, metabolic adaptation to nutrient availability, response to DNA damage, and oncogenesis. Moreover, protein degradation is an important mechanism of protein quality control, removing damaged or misfolded proteins as well as improperly synthesized peptides from cells. Almost all important cytosolic and nuclear protein degradations are carried out by ATP-dependent proteases that have been found in all organisms; loss of function mutations is usually lethal. Despite sequence divergence among them, there is a remarkable conservation in basic architecture and biochemical mechanisms in ATP-dependent proteases, such as prokaryotic ClpAP and Lon and eukaryotic proteasomes. The ClpAP protease, which we propose to study, is especially important for a number of reasons. First, ClpAP or its close homolog, ClpXP, are essential in many microorganisms. Second, ClpAP and ClpXP are highly conserved: ClpAP is found in the chloroplast of all plants and in photosynthetic bacteria, and ClpXP is found in the mitochondria of eukaryotes, including humans. Third, ClpA is the prototype of the Hsp100 molecular chaperones, which include yeast Hsp104, a chaperone shown to be involved in prion formation. Fourth, ClpA has significant sequence and structural similarity to AAA proteins, a broad class of protein conformation-transducing ATPases involved in a plethora of vital cellular functions. Last, Clp and other ATP-dependent proteases are structurally and mechanistically complex proteins, whose structure/function relationships reflect important biochemical principles that need to be understood at the submolecular level. Structural investigations have been conducted extensively on ClpA, ClpP, and ClpAP complexes, mostly by electron microscopic methods, and the structure of ClpP at atomic resolution is available. While the EM studies have provided rich information with respect to the subunit composition and molecular morphology, they are insufficient in elucidating the atomic details of these complexes. Atomic level structural information of ClpA would provide a high-resolution basis upon which models for function of this enzyme could be formulated, especially the binding of substrates and coupling of ATP hydrolysis to substrate folding/unfolding, about which very little is known. The structural solution would also provide an opportunity to explore the interaction between ClpA and ClpP and perhaps help to explain the functional implication of the symmetry mismatch at the interface of hexameric ClpA and heptameric ClpP rings in the ClpAP complex. We have initiated the project of structural investigation of ClpA by crystallographic method.
This page was last updated on 6/7/2013.