kyama@umich.edu

Biophysics

930 N. University Ave.

Ann Arbor, MI, 48109

(734) 763-9318

Research Projects

• Development of Nuclear Magnetic Resonance (NMR) methods to study membrane proteins and material chemistry
• The sensitivity enhancement and faster data acquisition of NMR spectroscopy
• Solid-state NMR characterization of materials, such as liquid crystals, lipid bilayers, antimicrobial peptides and nanoparticles containing hydrophobic drugs.
• Structure and dynamics investigation of rhodopsin and bacteriorhodopsin by NMR Spectroscopy
• Structure and dynamics investigation of Cytochrome b₅-Cytochrome P450-Cytochrome P450 reductase membrane protein complex by solid-state NMR Spectroscopy
• Development of novel methods to stabilize the native structure of membrane proteins for structural biology
• Cryogenic temperature and Dynamic Nuclear Polarization (DNP) NMR experiments on biomolecules at high magnetic fields

Publications

34. “High-resolution NMR characterization of low abundance oligomers of amyloid-b without purification” S.A. Kotler, J.R. Brender, S. Vivekanandan, Y. Suzuki, K. Yamamoto, M. Monette, J. Krishnamoorthy, P. Walsh, M. Cauble, M. M. Holl, E.N. Marsh, and A. Ramamoorthy., Sci. Rep.(Nature), 5(2015)11811.

33. “Temperature-Resistant Bicelles for Structural Studies by Solid-State NMR Spectroscopy” K. Yamamoto, P. Pearcy, S.C. Im, L. Waskell, and A. Ramamoorthy., Langmuir, 31(2015)1496-1504.

32. “Cellular Solid-State NMR Investigation of a Membrane Protein Using Dynamic Nuclear Polarization” K. Yamamoto, M.A. Caporini, S.C. Im, L. Waskell, and A. Ramamoorthy., Biochim. Biophys. Acta., 1848 (2015)342-349.

31. “Proton-detected 2D radio frequency driven recoupling solid-state NMR studies on micelle-associated cytochrome-b5” M.K. Pandey, S. Vivekanandan, K. Yamamoto, S.C. Im, L. Waskell and A. Ramamoorthy., J. Magn. Reson., 242(2014)169-179.

30. “Bicelles Exhibiting Magnetically-Alignment for a Broad Range of Temperatures - A Solid-State NMR Study” K. Yamamoto, P. Peracy and A. Ramamoorthy. Langmuir, 30(2014)1622-1629.

29. “Probing the Transmembrane Structure and Dynamics of Microsomal Cytochrome P450 Reductase by Solid-state NMR” R. Huang, K. Yamamoto, M. Zhang, N. Popovych, I. Hung, S.C. Im, Z. Gan, L. Waskell and A. Ramamoorthy., 106(2014)2126-2133.

28. “High-Resolution Insights into Interaction between Mefenamic Acid and Eudragit® EPO in Supersaturated Solution by Magic Angle Spinning Solid-State NMR Spectroscopy” K. Higashi, K. Yamamoto, M. Pandey, K. Mroue, K. Moribe, K. Yamamoto and A. Ramamoorthy., Mol. Pharm., 11(2014)351-357.

27. “Shortening Spin-lattice Relaxation Using a Copper-Chelated lipid at Low-Temperatures - A Magic Angle Spinning Solid-sState NMR study on a Membrane-Bound Protein” K. Yamamoto, M. Caporini, S.C. Im, L. Waskell and A. Ramamoorthy., J. Magn. Reson., 237(2013)175-181.

26. “Probing the Transmembrane Structure and Topology of Microsomal Cytochrome-P450 by Solid-State NMR on Temperature-Resistant Bicelles” K. Yamamoto, M. Gildenberg, S. Ahuja, S.C. Im, P. Peracy, L. Waskell and A. Ramamoorthy., Sci. Rep. (Nature), 3(2013)2556.

25. “Dynamic Interactions Between Membrane-Bound Full-Length Cytochrome b5 and Cytochrome P450 Observed by Solid-State NMR Spectroscopy” K. Yamamoto, U.H.N. Durr, J. Xu, S.C. Im, L. Waskell and A. Ramamoorthy., Sci. Rep. (Nature), 3(2013)2538.

24. “A Model of the Membrane-bound Cytochrome b5-Cytochrome P450 Complex from NMR and Mutagenesis Data” S. Ahuja, N. Jahr, S.C. Im, S. Vivekanandan, N. Popovych, S.V. Le Clair, R. Huang, R. Soong, J. Xu, K. Yamamoto, R.P.R. Nanga, A. Bridges, L. Waskell and A. Ramamoorthy., J. Bio. Chem., 288(2013)22080-22095.

23. “Fast NMR Data Acquisition From Bicelles Containing a Membrane-Associated Peptide at Natural-Abundance” K. Yamamoto, S. Vivekanandan and A. Ramamoorthy., J. Phys. Chem. B., 115(2011)12448-12455.

22. “Use of a Copper-Chelated-Lipid Speeds Up NMR Measurements From Membrane Proteins” K. Yamamoto, J. Xu, K.E. Kawulka, J.C. Vederas and A. Ramamoorthy., J. Am. Chem. Soc.(Communication), 132(2010)6929-6931.

21. “Proton-Evolved Local-Field Imaging of Membrane Proteins in Aligned Bicelles – Revealing both Structures and Dynamics” R. Soong, J. Xu, P.E.S. Smith, K. Yamamoto, S.C. Im, L. Waskell and A. Ramamoorthy, J. Am. Chem. Soc., 132(2010)5779-5788.

20. “Homogeneous nanoparticles to enhance the efficiency of a hydrophobic drug, anti-hyperlipidemic Probucol, characterized by solid-state NMR” T. Io, T. Fukami, K. Yamamoto, T. Suzuki, J. Xu, K. Tomono and A. Ramamoorthy., Mol. Pharm. 7(2010)299-305.

19. “A comprehensive analysis of lipid dynamics variation with lipid composition and hydration of bicelles using Nuclear Magnetic Resonance (NMR) spectroscopy” K. Yamamoto, R. Soong and A. Ramamoorthy., Langmuir, 25(2009)7010-7018.

18. “Nanoparticle Processing in the Solid State Dramatically Increases the Cell Membrane Permeation of a Cholesterol-Lowering Drug, Probucol” T. Fukami, T. Ishii, T. Io, N. Suzuki, T. Suzuki, K. Yamamoto, J. Xu, A. Ramamoorthy and K. Tomono., Mol. Pharm., 6(2009)1029-1035.

17. “High-resolution characterization of liquid-crystalline [60]fullerenes using solid-state nuclear magnetic resonance spectroscopy ” S.V. Dvinskikh, K. Yamamoto, D. Scanu, R. Deschenaux and A. Ramamoorthy, J. Phys. Chem. B., 112(2008)12347-12353.

16. “The structure and dynamics of membrane-bound cytochrome b₅ – cytochrome P450 complex by means of solid-state NMR spectroscopy” K. Yamamoto, J. Xu S.C. Im, L. Waskell and A. Ramamoorthy, Mag. Lab. Reports., 14(2008)7-8.

15. “Solid-State NMR Reveals Structural and Dynamical Properties of a Membrane-Anchored Electron-Carrier Protein, Cytochrome b₅” U.H.N. Durr, K. Yamamoto, S.C. Im, L. Waskell and A. Ramamoorthy, J. Am. Chem. Soc.(Communication), 129(2007)794-802.

14. “Surface and Dynamic Structures of Bacteriorhodopsin in 2D Crystal, Distorted or Disrupted Lattice, Revealed by Site-directed Solid-state ¹³C NMR.” H. Saito, Y. Kawase, A. Kira, K. Yamamoto, M. Tanio, S. Yamaguchi, S. Tuzi and A. Naito, Photochem. Photobiol., 83(2007)253-262.

13. “Sensitivity and resolution enhancement in solid-state NMR spectroscopy of bicelles” S.V. Dvinskikh, K. Yamamoto, U.H.N. Durr and A. Ramamoorthy, J. Magn. Reson., 184(2007)228-235.

12. “High-Resolution 2D NMR spectroscopy of bicelles to measure the membrane interaction of ligands” S.V. Dvinskikh, U.H.N. Durr, K. Yamamoto, and A. Ramamoorthy, J. Am. Chem. Soc., 129(2007)794-802.

11. “Measurement of heteronuclear dipolar couplings using the heteronuclear isotropic mixing leading to spin exchange via the local field solid-state NMR experiment” S.V. Dvinskikh, K. Yamamoto and A. Ramamoorthy., J. Chem. Phys., 125(2006) 034507.

10. “A High-Resolution Solid-state NMR Approach for the Structural Studies of Bicelles” S.V. Dvinskikh, U.H.N. Durr, K. Yamamoto, and A. Ramamoorthy, J. Am. Chem. Soc.(Communication), 128(2006)6326-6327.

9. “Conformation and dynamics changes of bacteriorhodopsin and its D85N mutant in the absence of 2D crystalline lattice as revealed by site-directed ¹³C NMR” K. Yamamoto, S. Tuzi, H. Saito, I. Kawamura and A. Naito. Biochim. Biophys.Acta., 1758(2)(2006)181-189.

8. “Measurement of heteronuclear dipolar couplings using a rotating frame solid-state NMR experiment” K. Yamamoto, S.V. Dvinskikh and A. Ramamoorthy., Chem. Phys. Lett., 419(2006)533-536.

7. “Separated local field NMR spectroscopy by windowless isotropic mixing” S.V. Dvinskikh, K. Yamamoto and A. Ramamoorthy., Chem. Phys. Lett., 419(2006)167-173.

6. “A Family of PISEMA Experiments for Structural Studies of Biological Solids” A. Ramamoorthy, K. Yamamoto, Handbook of Modern Magnetic Resonance (Chemistry section) edit by Graham Webb, (2006).

5. “A 2D Solid-State NMR Experiment to Resolve Overlapping Aromatic Resonances of Thiophene Nematogens” T. Narasimhaswamy, D. K. Lee, N. Somanathan, K. Yamamoto, A. Ramamoorthy, J. Am. Chem. Soc.(Communication), 127(2005)6958-6959.

4. “PITANSEMA-MAS, a Solid-State NMR Method to Measure Heteronuclear Dipolar Couplings Under MAS” K. Yamamoto, V. L. Ermakov, D. K. Lee, and A. Ramamoorthy, Chem. Phys. Lett. 408 (2005)118-122.

3. “Broadband-PISEMA solid-state NMR spectroscopy” K. Yamamoto, D.K. Lee and A. Ramamoorthy, Chem. Phys. Lett., 407 (2005) 289-293.

2. “Backbone Dynamics of Membrane Proteins in Lipid Bilayers: The Effect of Two Dimensional Array Formation as Revealed by Site-Directed Solid-State ¹³CNMR Studies on [3-¹³C]Ala-and [1-¹³C]Val-labeled Bacteriorhodopsin” H. Saito, K. Yamamoto, S. Tuzi, and S. Yamaguchi. Biochim. Biophys.Acta. 1616 (2) (2003) 127-36.

1. “Site-Directed ¹³C Solid-State NMR Studies on Membrane Proteins: Strategy and Goals toward Revealing Conformation and Dynamics as Illustrated for Bacteriorhodopsin Labeled with [1-¹³C] Amino-Acid Residues” H. Saito, J. Mikami, S. Yamaguchi, M. Tanio, A. Kira, T. Arakawa, K. Yamamoto and S. Tuzi. Magn. Reson. Chem. 42(2)(2004)218-30.

Oral Presentations

• [The Ritchey Award-Winning Research] “Fast Data Acquisition Enables Multidimensional NMR Experiments on Bicelles Containing Membrane Proteins at Natural-Abundance” K. Yamamoto, S. Vivekanandan, M. Gildenberg, J. Xu and A. Ramamoorthy, at 52^th Experimental Nuclear Magnetic Resonance Conference, April 10-15, 2011 California, U.S.A. (Invited speaker, the travel stipend supported by an organizer)
• “Dynamic structure of a 73 kDa cytochrome b₅-cytochrome P450 complex determined by solid-state NMR spectroscopy” K. Yamamoto at The Vaughan Symposium (PECRUM), August 1st, 2008 Ann Arbor, U.S.A.
• “Solid-State NMR Investigation of the Structure and Dynamics Bicelles” K. Yamamoto, J. Brender, U.H.N. Dürr and A. Ramamoorthy, at 49^th Experimental Nuclear Magnetic Resonance Conference, March 9-14, 2008 California, U.S.A. (Invited speaker, the travel stipend supported by an organizer)
• “A family of PISEMA-type pulse sequences” K. Yamamoto, at Chicago area NMR discussion group 2005 meeting, November 5, 2005 Illinois, U.S.A. (Invited speaker)

Academic Awards

• The Ritchey Award at 52^nd Experimental Nuclear Magnetic Resonance Conference (April 2011)
• Rackham Dissertation Fellowships, The University of Michigan (September 2010)
• The travel award at 51^st Experimental Nuclear Magnetic Resonance Conference (April 2010)
• Excellence in research fellowships, The University of Michigan (January 2009)
• Margaret & Herman Sokol Graduate Summer Research Fellowship, The University of Michigan (May 2008)
• The travel award at 49^th Experimental Nuclear Magnetic Resonance Conference (March 2008)
• The travel award at 48^th Experimental Nuclear Magnetic Resonance Conference (April 2007)
• The travel award at 47^th Rocky mountain conference on analytical chemistry (August 2005)