David S. Cafiso

Professor, Chemistry

Primary Location

PO Box 400319
McCormick Road

Primary Phone Number

434.924.3067

[email protected]

Website

http://people.virginia.edu/~dsc0b/home.html

Bio & Overview

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.

Academic Information

Department: Chemistry

Academic Title: Professor

Primary Education

AB, Biophysics, University of California, Berkeley, CA, 1974
PhD, Biophysics, University of California, Berkeley, CA, 1979
Postdoc, undefinedUniversity of California, Berkeley, CA, 1980
Postdoc, undefinedStanford University, 1981

Other Appointments

Professor, Molecular Physiology and Biological Physics
Professor, SCBB

Other Affiliations

Cancer Center
Professor and Chair, Arts & Sciences
Member, Chemical and Structural Biology Program
Chemistry
Biophysics
Molecular Physiology
MSTP
Professor, BIMS

Research Interests

Molecular Mechanisms for Membrane Transport and Cell Signaling

Research Disciplines

Biochemistry
Biophysics
Biophysics & Structural Biology
Microbiology
Neuroscience
Structural Biology

Research Opportunities

Biophysics & Structural Biology
Chemistry and Physics of Living Systems
Microbiology
Molecular and Systems Neuroscience
Neuroscience

PhD Programs

Biophysics

Selected Publications

2022

Liang, Q., Ofosuhene, A. P., Kiessling, V., Liang, B., Kreutzberger, A. J. B., Tamm, L. K., & Cafiso, D. S. (2022). Complexin-1 and synaptotagmin-1 compete for binding sites on membranes containing PtdInsP₂. BIOPHYSICAL JOURNAL, 121(18), 3370-3380. doi:10.1016/j.bpj.2022.08.023

2020

Katti, S., Nyenhuis, S. B., Her, B., Cafiso, D. S., & Igumenova, T. I. (2020). Partial Metal Ion Saturation of C2 Domains Primes Synaptotagmin 1-Membrane Interactions. BIOPHYSICAL JOURNAL, 118(6), 1409-1423. doi:10.1016/j.bpj.2020.01.032

2019

Nilaweera, T. D., Nyenhuis, D. A., Nakamoto, R. K., & Cafiso, D. S. (2019). Disulfide Chaperone Knockouts Enable In Vivo Double Spin Labeling of an Outer Membrane Transporter. BIOPHYSICAL JOURNAL, 117(8), 1476-1484. doi:10.1016/j.bpj.2019.09.002

Joseph, B., Jaumann, E. A., Sikora, A., Barth, K., Prisner, T. F., & Cafiso, D. S. (2019). In situ observation of conformational dynamics and protein ligand-substrate interactions in outer-membrane proteins with DEER/PELDOR spectroscopy. NATURE PROTOCOLS, 14(8), 2344-2369. doi:10.1038/s41596-019-0182-2

Nyenhuis, S. B., Thapa, A., & Cafiso, D. S. (2019). Phosphatidylinositol 4,5 Bisphosphate Controls the cis and trans Interactions of Synaptotagmin 1. BIOPHYSICAL JOURNAL, 117(2), 247-257. doi:10.1016/j.bpj.2019.06.016

Hays, J. M., Cafiso, D. S., & Kasson, P. M. (2019). Hybrid Refinement of Heterogeneous Conformational Ensembles Using Spectroscopic Data. JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 10(12), 3410-3414. doi:10.1021/acs.jpclett.9b01407

Stevens, M., Franke, B., Skorupka, K. A., Cafiso, D. S., Pornillos, O., Mayans, O., & Norman, D. G. (2019). Exploration of the TRIM Fold of MuRF1 Using EPR Reveals a Canonical Antiparallel Structure and Extended COS-Box. JOURNAL OF MOLECULAR BIOLOGY, 431(15), 2900-2909. doi:10.1016/j.jmb.2019.05.025

2018

Kiessling, V., Kreutzberger, A. B., Liang, B., Nyenhuis, S. B., Seelheim, P., Castle, J. D., . . . Tamm, L. K. (2018). A molecular mechanism for calcium-mediated synaptotagmin-triggered exocytosis. NATURE STRUCTURAL & MOLECULAR BIOLOGY, 25(10), 911-+. doi:10.1038/s41594-018-0130-9

Nyenhuis, S. B., & Cafiso, D. S. (2018). Choice of reconstitution protocol modulates the aggregation state of full-length membrane-reconstituted synaptotagmin-1. PROTEIN SCIENCE, 27(5), 1008-1012. doi:10.1002/pro.3398

Sarver, J. L., Zhang, M., Liu, L., Nyenhuis, D., & Cafiso, D. S. (2018). A Dynamic Protein-Protein Coupling between the TonB-Dependent Transporter FhuA and TonB. BIOCHEMISTRY, 57(6), 1045-1053. doi:10.1021/acs.biochem.7b01223

2017

Roganowicz, M. D., Komurlu, S., Mukherjee, S., Plewka, J., Alam, S. L., Skorupka, K. A., . . . Pornillos, O. (2017). TRIM5α SPRY/coiled-coil interactions optimize avid retroviral capsid recognition. PLOS PATHOGENS, 13(10). doi:10.1371/journal.ppat.1006686

Katti, S., Nyenhuis, S. B., Her, B., Srivastava, A. K., Taylor, A. B., Hart, P. J., . . . Igumenova, T. I. (2017). Non-Native Metal Ion Reveals the Role of Electrostatics in Synaptotagmin 1-Membrane Interactions. BIOCHEMISTRY, 56(25), 3283-3295. doi:10.1021/acs.biochem.7b00188

Zdanowicz, R., Kreutzberger, A., Liang, B., Kiessling, V., Tamm, L. K., & Cafiso, D. S. (2017). Complexin Binding to Membranes and Acceptor t-SNAREs Explains Its Clamping Effect on Fusion. BIOPHYSICAL JOURNAL, 113(6), 1235-1250. doi:10.1016/j.bpj.2017.04.002

Liu, L., & Cafiso, D. (2017). Determine the Substrate-Regulated TonB-Dependent Transporter and TonB Interactions. Biophysical Journal, 112(3), 358a. doi:10.1016/j.bpj.2016.11.1943

Lee, J., Nyenhuis, D. A., Nelson, E. A., Cafiso, D. S., White, J. M., & Tamm, L. K. (2017). Structure of the Ebola virus envelope protein MPER/TM domain and its interaction with the fusion loop explains their fusion activity. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 114(38), E7987-E7996. doi:10.1073/pnas.1708052114

2016

Sikora, A., Joseph, B., Matson, M., Staley, J. R., & Cafiso, D. S. (2016). Allosteric Signaling Is Bidirectional in an Outer-Membrane Transport Protein. BIOPHYSICAL JOURNAL, 111(9), 1908-1918. doi:10.1016/j.bpj.2016.09.038

Perez-Lara, A., Thapa, A., Nyenhuis, S. B., Nyenhuis, D. A., Halder, P., Tietzel, M., . . . Jahn, R. (2016). PtdInsP₂ and PtdSer cooperate to trap synaptotagmin-1 to the plasma membrane in the presence of calcium. ELIFE, 5. doi:10.7554/eLife.15886

Dawidowski, D., & Cafiso, D. S. (2016). Munc18-1 and the Syntaxin-1 N Terminus Regulate Open-Closed States in a t-SNARE Complex. STRUCTURE, 24(3), 392-400. doi:10.1016/j.str.2016.01.005

Joseph, B., Sikora, A., & Cafiso, D. S. (2016). Ligand Induced Conformational Changes of a Membrane Transporter in E-coli Cells Observed with DEER/PELDOR. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 138(6), 1844-1847. doi:10.1021/jacs.5b13382

Tsui, L. -K., Xu, Y., Dawidowski, D., Cafiso, D., & Zangari, G. (2016). Efficient water oxidation kinetics and enhanced electron transport in Li-doped TiO₂ nanotube photoanodes. JOURNAL OF MATERIALS CHEMISTRY A, 4(48), 19070-19077. doi:10.1039/c6ta08834a

2015

Park, Y., Seo, J. B., Fraind, A., Perez-Lara, A., Yavuz, H., Han, K., . . . Jahn, R. (2015). Synaptotagmin-1 binds to PIP₂-containing membrane but not to SNAREs at physiological ionic strength. NATURE STRUCTURAL & MOLECULAR BIOLOGY, 22(10), 815-823. doi:10.1038/nsmb.3097

Joseph, B., Sikora, A., Bordignon, E., Jeschke, G., Cafiso, D. S., & Prisner, T. F. (2015). Distance Measurement on an Endogenous Membrane Transporter in E. coli Cells and Native Membranes Using EPR Spectroscopy. Angewandte Chemie, 127(21), 6294-6297. doi:10.1002/ange.201501086

Joseph, B., Sikora, A., Bordignon, E., Jeschke, G., Cafiso, D. S., & Prisner, T. F. (2015). Distance Measurement on an Endogenous Membrane Transporter in E-coli Cells and Native Membranes Using EPR Spectroscopy. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 54(21), 6196-6199. doi:10.1002/anie.201501086

2014

Iyalomhe, O., Herrick, D. Z., Cafiso, D. S., & Maloney, P. C. (2014). Closure of the Cytoplasmic Gate Formed by TM5 and TM11 during Transport in the Oxalate/Formate Exchanger from Oxalobacter formigenes. BIOCHEMISTRY, 53(49), 7735-7744. doi:10.1021/bi5012173

Cafiso, D. S. (2014). Identifying and Quantitating Conformational Exchange in Membrane Proteins Using Site-Directed Spin Labeling. ACCOUNTS OF CHEMICAL RESEARCH, 47(10), 3102-3109. doi:10.1021/ar500228s

Lu, B., Kiessling, V., Tamm, L. K., & Cafiso, D. S. (2014). The Juxtamembrane Linker of Full-length Synaptotagmin 1 Controls Oligomerization and Calcium-dependent Membrane Binding. JOURNAL OF BIOLOGICAL CHEMISTRY, 289(32), 22161-22171. doi:10.1074/jbc.M114.569327

Liang, B., Dawidowski, D., Ellena, J. F., Tamm, L. K., & Cafiso, D. S. (2014). The SNARE Motif of Synaptobrevin Exhibits an Aqueous-Interfacial Partitioning That Is Modulated by Membrane Curvature. BIOCHEMISTRY, 53(9), 1485-1494. doi:10.1021/bi401638u

2013

Regan, M. C., Horanyi, P. S., Pryor, E. E. J., Sarver, J. L., Cafiso, D. S., & Bushweller, J. H. (2013). Structural and dynamic studies of the transcription factor ERG reveal DNA binding is allosterically autoinhibited. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 110(33), 13374-13379. doi:10.1073/pnas.1301726110

Freed, D. M., Lukasik, S. M., Sikora, A., Mokdad, A., & Cafiso, D. S. (2013). Monomeric TonB and the Ton Box Are Required for the Formation of a High-Affinity Transporter-TonB Complex. BIOCHEMISTRY, 52(15), 2638-2648. doi:10.1021/bi3016108

Dawidowski, D., & Cafiso, D. S. (2013). Allosteric Control of Syntaxin 1a by Munc18-1: Characterization of the Open and Closed Conformations of Syntaxin. BIOPHYSICAL JOURNAL, 104(7), 1585-1594. doi:10.1016/j.bpj.2013.02.004

2012

Cafiso, D. S. (2012). Taking the Pulse of Protein Interactions by EPR Spectroscopy. BIOPHYSICAL JOURNAL, 103(10), 2047-2048. doi:10.1016/j.bpj.2012.10.005

Mokdad, A., Herrick, D. Z., Kahn, A. K., Andrews, E., Kim, M., & Cafiso, D. S. (2012). Ligand-Induced Structural Changes in the Escherichia coli Ferric Citrate Transporter Reveal Modes for Regulating Protein-Protein Interactions. JOURNAL OF MOLECULAR BIOLOGY, 423(5), 818-830. doi:10.1016/j.jmb.2012.09.003

Boura, E., Rozycki, B., Chung, H. S., Herrick, D. Z., Canagarajah, B., Cafiso, D. S., . . . Hurley, J. H. (2012). Solution Structure of the ESCRT-I and -II Supercomplex: Implications for Membrane Budding and Scission. STRUCTURE, 20(5), 874-886. doi:10.1016/j.str.2012.03.008

Jimenez, R. H. F., & Cafiso, D. S. (2012). The N-Terminal Domain of a TonB-Dependent Transporter Undergoes a Reversible Stepwise Denaturation. BIOCHEMISTRY, 51(17), 3642-3650. doi:10.1021/bi300118a

2011

Jimenez, R. H. F., Freed, D. M., & Cafiso, D. S. (2011). Lipid and Membrane Mimetic Environments Modulate Spin Label Side Chain Configuration in the Outer Membrane Protein A. JOURNAL OF PHYSICAL CHEMISTRY B, 115(49), 14822-14830. doi:10.1021/jp207420d

Freed, D. M., Khan, A. K., Horanyi, P. S., & Cafiso, D. S. (2011). Molecular Origin of Electron Paramagnetic Resonance Line Shapes on β-Barrel Membrane Proteins: The Local Solvation Environment Modulates Spin-Label Configuration. BIOCHEMISTRY, 50(41), 8792-8803. doi:10.1021/bi200971x

Lai, A. L., Tamm, L. K., Ellena, J. F., & Cafiso, D. S. (2011). Synaptotagmin 1 Modulates Lipid Acyl Chain Order in Lipid Bilayers by Demixing Phosphatidylserine. JOURNAL OF BIOLOGICAL CHEMISTRY, 286(28), 25291-25300. doi:10.1074/jbc.M111.258848

Boura, E., Rozycki, B., Herrick, D. Z., Chung, H. S., Vecer, J., Eaton, W. A., . . . Hurley, J. H. (2011). Solution structure of the ESCRT-I complex by small-angle X-ray scattering, EPR, and FRET spectroscopy. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108(23), 9437-9442. doi:10.1073/pnas.1101763108

Kuo, W., Herrick, D. Z., & Cafiso, D. S. (2011). Phosphatidylinositol 4,5-Bisphosphate Alters Synaptotagmin 1 Membrane Docking and Drives Opposing Bilayers Closer Together. BIOCHEMISTRY, 50(13), 2633-2641. doi:10.1021/bi200049c

Wan, C., Kiessling, V., Cafiso, D. S., & Tamm, L. K. (2011). Partitioning of Synaptotagmin I C2 Domains between Liquid-Ordered and Liquid-Disordered Inner Leaflet Lipid Phases. BIOCHEMISTRY, 50(13), 2478-2485. doi:10.1021/bi101864k

Ellena, J. F., Lackowicz, P., Mongomery, H., & Cafiso, D. S. (2011). Membrane Thickness Varies Around the Circumference of the Transmembrane Protein BtuB. BIOPHYSICAL JOURNAL, 100(5), 1280-1287. doi:10.1016/j.bpj.2011.01.055

2010

Lai, A. L., Huang, H., Herrick, D. Z., Epp, N., & Cafiso, D. S. (2011). Synaptotagmin 1 and SNAREs Form a Complex That Is Structurally Heterogeneous. JOURNAL OF MOLECULAR BIOLOGY, 405(3), 696-706. doi:10.1016/j.jmb.2010.11.015

Freed, D. M., Horanyi, P. S., Wiener, M. C., & Cafiso, D. S. (2010). Conformational Exchange in a Membrane Transport Protein Is Altered in Protein Crystals. BIOPHYSICAL JOURNAL, 99(5), 1604-1610. doi:10.1016/j.bpj.2010.06.026

Jimenez, R. H. F., Do Cao, M. -A., Kim, M., & Cafiso, D. S. (2010). Osmolytes modulate conformational exchange in solvent-exposed regions of membrane proteins. PROTEIN SCIENCE, 19(2), 269-278. doi:10.1002/pro.305

Freed, D. M., & Cafiso, D. S. (2010). Structural Origins of Nitroxide EPR Spectra in a β-Barrel Membrane Protein. Biophysical Journal, 98(3), 400a. doi:10.1016/j.bpj.2009.12.2156