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Department of Biochemistry and Molecular Medicine

Department of Biochemistry and Molecular Medicine

 

Madhu Budamagunta, Ph.D.
Project Scientist

530-752-3164
msbudamagunta@ucdavis.edu

Dr. Budamugunta is a nationally and internationally renowned scientist in the area of biological magnetic resonance spectroscopy.  His field of expertise is “Electron Paramagnetic Resonance (EPR) Spectroscopy”, a unique technique and powerful tool in several disciplines starting from Solid-state materials to biological/medical applications.  Electron paramagnetic resonance (EPR, a.k.a ESR) spectroscopy is a technique for studying the chemical species that have one or more unpaired electrons such as organic and inorganic free radicals or inorganic complexes possessing a transition metal ion.  The potential of ESR is exemplified by its high spin sensitivity, its excellent spectral resolution, its high sensitivity to the motion of molecules, its ability to image a probe molecule with micron resolution. All in all, EPR provides a powerful and unique combination features central to molecular science.

With spin labeling reagent, Dr. Budamagunta can introduce a unique and stable species whose unpaired electrons produce a unique EPR signal.  When the spin label is attached to a biological molecule the EPR signal (spectrum) reports on motions and structure within the molecule.  This approach, known as site-directed spin-labeling (SDSL) represents one of the most powerful techniques currently available to investigate structure-function relationships in protein and DNA, the molecules whose activity provides the fundamental processes of life.  In addition, EPR analysis can now be used in vivo, including imaging of structures visible only to EPR, providing a new Magnetic Resonance Imaging tool.   The application of EPR technology is not limited to living systems.  For example, because of its high sensitivity, EPR has recently been used to measure the quantity of energy used locally during a mechano-chemical milling process, semi-conductor doping, archeological dating, and food science. In summary, EPR spectroscopy is striving to bridge the gap between laboratory science and clinical medicine.

At present Dr. Budamagunta is developing new EPR tools to study the structural dynamics and folding of several proteins that are especially important in human health and disease. His research contributions have made a significant impact in several fields, as communicated in more than forty peer-reviewed publications in internationally-reputed journals that span multiple disciplines.

Recent Publications

Acar S, Carlson DB, Budamagunta MS, Yarov-Yarovoy V, Correia JJ, Niñonuevo MR, Jia W, Tao L, Leary JA, Voss JC, Evans JE, Scholey JM., The bipolar assembly domain of the mitotic motor kinesin-5., Nat Commun. 2013 Jan 8;4:1343. doi: 10.1038/ncomms2348.

den Hartigh LJ, Altman R, Hutchinson R, Petrlova J, Budamagunta MS, Tetali SD, Lagerstedt JO, Voss JC, Rutledge JC., Postprandial apoE isoform and conformational changes associated with VLDL lipolysis products modulate monocyte inflammation., PLoS One. 2012;7(11):e50513. doi: 10.1371/journal.pone.0050513. Epub 2012 Nov 28.

Hess JF, Budamagunta MS, Aziz A, FitzGerald PG, Voss JC., Electron paramagnetic resonance analysis of the vimentin tail domain reveals points of order in a largely disordered region and conformational adaptation upon filament assembly., Protein Sci. 2013 Jan;22(1):47-55. doi: 10.1002/pro.2182.

Li Y, Budamagunta MS, Luo J, Xiao W, Voss JC, Lam KS., Probing of the assembly structure and dynamics within nanoparticles during interaction with blood proteins., ACS Nano. 2012 Nov 27;6(11):9485-95. doi: 10.1021/nn302317j. Epub 2012 Oct 30.

Wang L, Shearer GC, Budamagunta MS, Voss JC, Molfino A, Kaysen GA., Proteinuria decreases tissue lipoprotein receptor levels resulting in altered lipoprotein structure and increasing lipid levels., Kidney Int. 2012 Nov;82(9):990-9. doi: 10.1038/ki.2012.244. Epub 2012 Jul 11.

Aziz A, Hess JF, Budamagunta MS, Voss JC, Kuzin AP, Huang YJ, Xiao R, Montelione GT, FitzGerald PG, Hunt JF., The structure of vimentin linker 1 and rod 1B domains characterized by site-directed spin-labeling electron paramagnetic resonance (SDSL-EPR) and X-ray crystallography., J Biol Chem. 2012 Aug 17;287(34):28349-61. doi: 10.1074/jbc.M111.334011. Epub 2012 Jun 26.

Lagerstedt JO, Budamagunta MS, Liu GS, DeValle NC, Voss JC, Oda MN., The "beta-clasp" model of apolipoprotein A-I--a lipid-free solution structure determined by electron paramagnetic resonance spectroscopy., Biochim Biophys Acta. 2012 Mar;1821(3):448-55. doi: 10.1016/j.bbalip.2011.12.010. Epub 2012 Jan 8.

Chen HK, Liu Z, Meyer-Franke A, Brodbeck J, Miranda RD, McGuire JG, Pleiss MA, Ji ZS, Balestra ME, Walker DW, Xu Q, Jeong DE, Budamagunta MS, Voss JC, Freedman SB, Weisgraber KH, Huang Y, Mahley RW., Small molecule structure correctors abolish detrimental effects of apolipoprotein E4 in cultured neurons., J Biol Chem. 2012 Feb 17;287(8):5253-66. doi: 10.1074/jbc.M111.276162. Epub 2011 Dec 12.

Lagerstedt JO, Cavigiolio G, Budamagunta MS, Pagani I, Voss JC, Oda MN., Structure of apolipoprotein A-I N terminus on nascent high density lipoproteins., J Biol Chem. 2011 Jan 28;286(4):2966-75. doi: 10.1074/jbc.M110.163097. Epub 2010 Nov 3.

Nygaard EB, Lagerstedt JO, Bjerre G, Shi B, Budamagunta M, Poulsen KA, Meinild S, Rigor RR, Voss JC, Cala PM, Pedersen SF., Structural modeling and electron paramagnetic resonance spectroscopy of the human Na+/H+ exchanger isoform 1, NHE1., J Biol Chem. 2011 Jan 7;286(1):634-48. doi: 10.1074/jbc.M110.159202. Epub 2010 Oct 25.

For more information regarding the high profile research Dr. Budamagunta is doing please see his List of Publications.

Michael Saxton, Ph.D.
Research Associate

530-752-6163
mjsaxton@ucdavis.edu

Dr. Saxton's research interests include computer modeling of hindered diffusion in cells—plasma membrane, cytoplasm, and nucleus, mostly the plasma membrane.

The basic question he is currently addressing is: How do proteins find their biological targets in a crowded, sticky environment? His current work is based on ideas from the physics of inhomogeneous systems, including anomalous diffusion, percolation theory, and fractals. A major part of his work includes methods of analysis of single-particle tracking experiments.