Department of Biochemistry
4-403 BSB
Iowa City, IA 52242-1109 USA phone: 877-846-8569
or 319-335-7932
fax: (319) 335-9570
biochem@uiowa.edu
Department of Biochemistry
Assistant Professor of Biochemistry
51 Newton Rd
Biochemistry/Univ. of Iowa
Iowa City, IA 52242
Research Interests
Ammonia Channel
A research focus in the Khademi laboratory is structure and mechanism of ammonia channels. Ammonia transport across biological cell membranes is a critical physiological process in all domains of life. Although simple ammonia diffusion could occur through the lipids of cell membranes and can support growth, at low concentrations of ammonia other regulatable mechanisms of ammonia transport are usually required. The family of AMT/MEP/Rh membrane proteins transports ammonia across cell membrane. While AMT/MEP proteins are found in plant, bacteria and yeast; Rh proteins are expressed mainly in mammalian cells.
There is a fascinating detective story as to which molecular species (NH4+ vs. NH3) is transported by AMT/MEP/Rh proteins, and whether it is driven by a proton gradient (Fig. 1). The X-ray structure of AmtB from E. coli at 1.35? resolution made it possible to specify the most probable mechanism of conduction by this family of membrane proteins (Fig. 2).
Figure 1. Structure and mechanism of ammonia channel, the Cover story of Science Sept. 10, 2004.
Figure 2. The deduced mechanism of conductance is summarized. The green and purple spheres are nitrogen atoms of NH4+ and NH3, respectively. The mechanism involves an extracellular vestibule attracting NH4+/NH3, a recruitment site for NH4+, and a hydrophobic channel that strips the proton (orange spheres) off the NH4+ and conducts NH3. NH3 is reprotonated at the cytoplasmic site at physiologic pH and forms NH4+.
The Khademi laboratory takes three different approaches to understand the atomic mechanism of ammonia conduction by ammonia channels; (1) determination of X-ray structure of the protein in the presence of detergent, (2) fluorescence-based assay to measure the influx of ammonia into vesicles (liposomes or proteoliposomes) by monitoring the pH-sensitive fluorescence of 5-carboxy fluorescein (CF), (3) computer-aided molecular dynamics simulation of ammonia conduction in AmtB embedded into 1-palmitoyl-2-oleoyl-phosphatidyl ethanolamine (POPE) lipid bilayer (Fig. 3).
Figure 3. A snap shot of dynamics simulation of trimeric Amtb in POPE lipid bilayer viewed from the extracellular side. Orange spheres represent phosphorus atoms of phosphatidyl groups in POPE.
Sialic acid Transporter
The study of the structure and mechanism of sialic acid transporter from Haemophilus influenzae is another focus of the Khademi laboratory. Sialic acid (N?acetylneuraminic acid or Neu5Ac) is incorporated into lipooligosaccharides which are the major component of H. influenzae outer membrane and are important in microbial virulence and pathogenicity. Sialic acid can also be utilized as a carbon and nitrogen source. The gene HI0147 (siaT) has been identified by Dr. Michael Apicella to encode a sialic acid transporter in H. influenzae. Sialic acid transporter in H. influenzae belongs to the class of TRAP , tripartite ATP-independent periplasmic, transporters. This is a novel class of transporters with unkown structure and mechanism. In collaboration with Dr. Apicella laboratory, we are working on the structural and mechanism of sialic acid transporter from H. influenzae (SiaT).
Recent Publications
Khademi, S., and Stroud, R. M. (2006) The Amt/MEP/Rh family: Structure of AmtB and the mechanism of ammonia gas conduction. Physiology 21:419-429.
S. Khademi, J. O?Connell, J. Remis, Y. R. Colmenares, L. Miercke and R. M. Stroud.Mechanism of ammonia transport by proteins of the amt/mep/rh family: Structure of amtb at 1.35?. Science 305:1587-1594 (2004) (Cover Article, with Perspective by Knepper and Agre. P1573-1574).
W. E. C. Harries, D. Akhavan, L. J. W. Miercke, S. Khademi, and R. M. Stroud. The channel architecture of aquaporin 0 at a 2.2-? resolution. PNAS 101:14045-50 (2004).
J. K. Lee, S. Khademi, W. Harries, D. Savage, L. Miercke and R. M. Stroud. The Glycerol Channel GlpF and the Aquaporin Family of Membrane Channels. J. Synchrotron Rad. 11:86-88 (2004).
R. M. Stroud, D. Savage, L. J.W. Miercke, J. K. Lee, S. Khademi and W. Harries. Selectivity and conductance among the glycerol and water conducting aquaporin family of channels. FEBS Letters 555:79-84 (2003).
R. M. Stroud, L. J.W. Miercke, J. O?Connell, S. Khademi, J. K. Lee, J. Remis, W. Harries, Y. Robles and D. Akhavan. Glycerol facilitator GlpF and the associated aquaporin family of channels. Current Opinion in Structural Biology 13: 424-431 (2004).
Affiliations
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