David S. Cafiso
- AB, University of California, Berkeley, CA
- PhD, University of California, Berkeley, CA
- Postdoc, University of California, Berkeley, CA
- Postdoc, Stanford University, Stanford, CA
- Professor, Chemistry
Molecular Mechanisms for Membrane Transport and Cell Signaling
Membranes and membrane proteins participate in some of the most important and interesting cellular processes. Energy transduction, cell signaling, membrane excitability, secretion and immune recognition are examples of a few of the processes mediated by membrane proteins. However, the molecular mechanisms by which lipids and membrane proteins accomplish these tasks are largely unknown. Approximately 30 to 40 percent of the proteins in a genome are membrane proteins and 70 percent or more of current pharmaceuticals appear to act on membrane proteins. For these reasons, membrane proteins represent one of the most important challenges in the field of structural biology.
Work in our laboratory is directed at studying membranes and membrane proteins, and there are currently two general areas of research ongoing in our laboratory. One area of investigation involves studies on the mechanisms by which proteins become attached to membrane surfaces.This attachment is critical for cell-signaling because it controls protein-protein interactions and the access of enzymes to lipid substrates. For example the oncogenic form of the src tyrosine kinase is not active and fails to transform cells until it becomes attached to membranes. We are currently studying the structure and electrostatic interactions made by MARCKS (the myristoylated alanine rich C-kinase substrate), which has a highly positively charged domain that attaches to the membrane interface. This protein functions to regulate the levels of highly phosphorylated inositol lipids, such as PIP2, in the cell. We are also studying the membrane binding of protein domains such as C2 and PH (pleckstrin homology) domains, which are found in a wide range of proteins involved in cell-signaling. C2 domains function attach to membranes in a Ca++ dependent fashion, and PH domains translocate to the membrane interface and bind to PIP2.
A second area of investigation involves membrane transport. We are currently investigating the molecular mechanisms that function to transport solutes across lipid bilayers. For example, in gram negative bacteria, such as E. coli, we are examining the molecular mechanisms by which vitamin B-12 and iron are transported across the outer membrane. The outer membrane transport proteins in E. coli are beta-barrel structures, which function to drive the accumulation of iron and vitamin B-12. They represent one of only a few classes of transport proteins for which accurate high-resolution structural models have been obtained.
The primary tools that we use in our work include EPR spectroscopy, high-resolution NMR and solid-state NMR. The application of EPR spectroscopy to membrane protein structure is relatively recent. Using EPR spectroscopy in combination with site-directed mutagenesis and spin-labeling, we are probing the structures and conformational transitions in large membrane proteins that would normally be inaccessible using other structural methods.
- Herrick D, Sterbling S, Rasch K, Hinderliter A, Cafiso D. Position of synaptotagmin I at the membrane interface: cooperative interactions of tandem C2 domains. Biochemistry. 2006;45(32): 9668-74. PMID: 16893168
- Kim M, Xu Q, Murray D, Cafiso D. Solutes alter the conformation of the ligand binding loops in outer membrane transporters. Biochemistry. 2007;47(2): 670-9. PMID: 18092811
- Derewenda U, Tarricone C, Choi W, Cooper D, Lukasik S, Perrina F, Tripathy A, Kim M, Cafiso D, Musacchio A, Derewenda Z. The structure of the coiled-coil domain of Ndel1 and the basis of its interaction with Lis1, the causal protein of Miller-Dieker lissencephaly. Structure (London, England : 1993). 2007;15(11): 1467-81. PMID: 17997972
- Liao H, Ellena J, Liu L, Szabo G, Cafiso D, Castle D. Secretory carrier membrane protein SCAMP2 and phosphatidylinositol 4,5-bisphosphate interactions in the regulation of dense core vesicle exocytosis. Biochemistry. 2007;46(38): 10909-20. PMID: 17713930
- Zhou Y, Cierpicki T, Jimenez R, Lukasik S, Ellena J, Cafiso D, Kadokura H, Beckwith J, Bushweller J. NMR solution structure of the integral membrane enzyme DsbB: functional insights into DsbB-catalyzed disulfide bond formation. Molecular cell. 2008;31(6): 896-908. PMID: 18922471 | PMCID: PMC2622435
- Huang H, Cafiso D. Conformation and membrane position of the region linking the two C2 domains in synaptotagmin 1 by site-directed spin labeling. Biochemistry. 2008;47(47): 12380-8. PMID: 18956883 | PMCID: PMC2661311
- Ellena J, Liang B, Wiktor M, Stein A, Cafiso D, Jahn R, Tamm L. Dynamic structure of lipid-bound synaptobrevin suggests a nucleation-propagation mechanism for trans-SNARE complex formation. Proceedings of the National Academy of Sciences of the United States of America. 2009;106(48): 20306-11. PMID: 19918058 | PMCID: PMC2787132
- Herrick D, Kuo W, Huang H, Schwieters C, Ellena J, Cafiso D. Solution and membrane-bound conformations of the tandem C2A and C2B domains of synaptotagmin 1: Evidence for bilayer bridging. Journal of molecular biology. 2009;390(5): 913-23. PMID: 19501597 | PMCID: PMC2763419
- Kuo W, Herrick D, Ellena J, Cafiso D. The calcium-dependent and calcium-independent membrane binding of synaptotagmin 1: two modes of C2B binding. Journal of molecular biology. 2009;387(2): 284-94. PMID: 19302798 | PMCID: PMC2669496
- Freed D, Horanyi P, Wiener M, Cafiso D. Conformational exchange in a membrane transport protein is altered in protein crystals. Biophysical journal. 2010;99(5): 1604-10. PMID: 20816073 | PMCID: PMC2931748
- Wan C, Kiessling V, Cafiso D, Tamm L. Partitioning of synaptotagmin I C2 domains between liquid-ordered and liquid-disordered inner leaflet lipid phases. Biochemistry. 2011;50(13): 2478-85. PMID: 21322640 | PMCID: PMC3094915
- Jiménez R, Freed D, Cafiso D. Lipid and membrane mimetic environments modulate spin label side chain configuration in the outer membrane protein A. The journal of physical chemistry. B. 2011;115(49): 14822-30. PMID: 22034842 | PMCID: PMC3237940
- Freed D, Khan A, Horanyi P, Cafiso D. Molecular origin of electron paramagnetic resonance line shapes on β-barrel membrane proteins: the local solvation environment modulates spin-label configuration. Biochemistry. 2011;50(41): 8792-803. PMID: 21894979 | PMCID: PMC3199607
- Lai A, Tamm L, Ellena J, Cafiso D. Synaptotagmin 1 modulates lipid acyl chain order in lipid bilayers by demixing phosphatidylserine. The Journal of biological chemistry. 2011;286(28): 25291-300. PMID: 21610074 | PMCID: PMC3137100
- Ellena J, Lackowicz P, Mongomery H, Cafiso D. Membrane thickness varies around the circumference of the transmembrane protein BtuB. Biophysical journal. 2011;100(5): 1280-7. PMID: 21354401 | PMCID: PMC3043205
- Kuo W, Herrick D, Cafiso D. Phosphatidylinositol 4,5-bisphosphate alters synaptotagmin 1 membrane docking and drives opposing bilayers closer together. Biochemistry. 2011;50(13): 2633-41. PMID: 21344950 | PMCID: PMC3071796
- Mokdad A, Herrick D, Kahn A, Andrews E, Kim M, Cafiso D. Ligand-Induced Structural Changes in the Escherichia coli Ferric Citrate Transporter Reveal Modes for Regulating Protein-Protein Interactions. Journal of molecular biology. 2012;423(5): 818-30. PMID: 22982293 | PMCID: PMC3472153
- Flores Jiménez R, Cafiso D. The N-terminal domain of a TonB-dependent transporter undergoes a reversible stepwise denaturation. Biochemistry. 2012;51(17): 3642-50. PMID: 22497281 | PMCID: PMC3362919