Lehman College, City University of New York NY, Chemistry, B.S., 1996
State University of New York at Stony Brook , Chemistry, Ph. D., 2001
Title of thesis: Studies in protein folding and dynamics using magnetic resonance spectroscopy.
Thesis supervisors: Prof. Daniel P. Raleigh, SUNY at Stony Brook,
Prof. Arthur G. Palmer, Columbia University.
Postdoctoral and other appointments
Visiting Scientist, Laboratory of Prof. James McKnight Boston University
School of Medicine, Boston, MA, 2006
Postdoctoral, Laboratory of Prof. Judith Herzfeld, Brandeis University,
Waltham MA, 2005
Postdoctoral, Laboratory of Prof. Geoffrey Bodenhausen, Ecole Polytechnique
Fédérale de Lausanne, Switzerland, 2002-2004
Visiting Scientist, Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge MA 2004-2005
Main Current Collaborators
- Robert L. Vold, Dept. of Applied Science, College of William and Mary
- Birgit Hagedorn, University of Alaska Anchorage
- Dmitry Ostrovsky, University of Alaska Anchorage
- Gina L. Hoatson, Dept. of Physics, College of William and Mary
- Riqiang Fu, National High Field Magnetic Laboratory at Tallahassee
- C. James McKnight, Dept. of Physiology and Biophysics, Boston University School of Medicine
- Andrew S. Lipton, Pacific Northwest National Laboratory
- Ying Li and Arthur G. Palmer, Columbia University
- Joseph Ford, Sarah Burton, Pacific Northwest National Laboratory
UNDERGRADUATE STUDENT TRAINING
Janelle Sharp, Toni Villafranca, Matthew Clark
Tien Do, Kirsten Penland, Michael Hamman, Anastasia Khadjinova, Brody Bessire, Mark Moses, Derek Clark, Philip Hayes.
Summary of student Training
|Computational modeling techniques
||Kirsten Penland, Tien Do, Michael Hamman, Janelle Sharp, Toni Villafranca
|Experimental NMR techniques via travel to external laboratories
||Derek Clark, Anastasia Khadjinova, Tien Do, Kirsten Penland, Matthew Clark
|Structure modeling via basic molecular dynamics
||Brody Bessire, Anastasia Khadjinova, Mark Moses
|Sample preparation techniques
||Anastasia Khadjinova, Tien Do, Kirsten Penland, Matthew Clark
|Chemical potentials measurements of soil samples
||Tien Do, Mathew Clark
|Quantum mechanical calculations (WEBMO)
|Chemical equilibria calculations (FREEZECHEM)
||Tien Do, Mathew Clark
Students Honors and Awards:
- Janelle Sharp and Toni Villafrance: UAA Honor’s College Group Project OURS award, Spring 2014
- Mathew Clark: Alaska Space Grant Student Award Fall 2013; UAA Honor’s College OURS award, Spring 2014
- Kirsten Penland: NIH INBRE-Alaska Undergraduate Student Award, Spring 2012 and Summer 2012.
Discovery Grant from UAA Honor’s College, Spring 2012.
- Tien Do: NIH INBRE-Alaska Undergraduate Student Award, Spring 2013 and Summer 2013.
Discovery Grant from UAA Honor’s College, Summer 2011. Alaska Space Grant Student Award Spring 2012.
- Anastasia Khadjinova: NIH INBRE-Alaska award summer 2011. UAA Honor’s College Discovery travel grant December 2010.
Student co-authors in peer-reviewed papers:
Mark Moses, Anastasia Khadjinova, Kirsten Penland, Tien Do.
General Chemistry I and II, Contemporary Chemistry, Survey of Chemistry I, Survey of Chemistry Laboratory, Physical Chemistry I and II, Physical Chemistry for Life Sciences, Physical Chemistry Laboratory. Please see Appendix I for a full list of classes taught each semester.
a wide combination of traditional lecturing techniques, active learning approaches, and problem solving. Examples include traditional lecturing, workshops with students outside of class time, Team-Based Learning, Mazur teaching methods, and Process-Oriented Guided Inquiry.
Blackboard on-line tools, OWL and Web-Assign homework, in-class and on-line video presentations, optional e-live sessions, MasteringChemistry (Pearson) online shells. Online hybrid class: CHEM A105, Spring 2014.
I have conducted two research projects within the framework of the Scholarship of Teaching and Learning. The overall goal is to look for techniques that can have a direct positive impact on my teaching.
- Team-Based Learning Technique in General Chemistry Classroom – Catalyst or Anticatalyst?
Uploaded as a teaching portfolio on CAFE website.
- The Role of Enhanced Instructor-Student Interactions in Performance and Retention of Students in General Chemistry Classes.
Dynamics and folding of proteins using solution and solid-state nuclear magnetic resonance techniques and theoretical/computational approaches.
One of the proteins I look at is a classic model system of protein folding studies: chicken villin headpiece subdomain (HP35). It is a small protein consisting of 35 amino acids which span three helices. The ribbon diagram is shown in the figure below.
Three-dimensional molecular shapes of proteins have been long recognized to play an important role in their biological functions. Many structural studies have been performed that aim at finding exact structures of proteins. In the past decade it became clear that protein molecules “breathe” and their structures fluctuate. It turned out that this breathing has important consequences for specific functions and characteristics of proteins.
My studies investigate the dynamics of proteins on various time scales and at various conditions: in solution and solids phases, at temperatures from 4K to 300K by experimental and computational approaches.
Nuclear Magnetic Resonance (NMR) techniques are particularly suitable for the investigation of protein dynamics, since they allow measurements at many sites on a protein molecule, thus providing us with the picture of what’s going on in various parts of the protein. Further, these techniques can be sensitive to motions over a very broad range of time scales, from picoseconds (10-9sec) to seconds. I use NMR as a major experimental tool to probe protein dynamics. In addition, I use a number of theoretical and computation approaches for data analysis and interpretation.
Determination of Unfrozen Water Content and Mechanisms of its Survival in Soils of the Dry Valleys of Antarctica by Nuclear Magnetic Resonance
Subsurface ice and salt are very common in soils of the Dry Valleys, Antarctica. Evidence based on chemical analysis points to the existence of unfrozen water. Reasons for the considerable interest in the formation and stability of subsurface ice and water stem from their crucial role in the genesis of landscapes and formation and survival of life. Ice is critical to the development of polygonal patterned ground surfaces in Antarctic Dry Valleys that serve as an analogue to Martian surfaces where subsurface ice has recently been confirmed by the Phoenix Mars Lander. Antarctic soils serve as a testing ground to develop models for ice and water formation and their survival mechanisms. We will conduct a preliminary study of the content of the unfrozen water in frozen ground of the Dry Valleys, the dependence of the amount of water on salt concentration and composition, as well as factors contributing to the mechanisms of its formation and survival.
LIST OF PUBLICATIONS
J. Chem. Phys. accepted (2014)
Restricted Diffusion of Methyl Groups in Proteins Revealed by Deuteron NMR: Manifestation of Intra-well Dynamic
Protein Science 23, 145-156 (2014)
Effect of Subdomain Interactions on Methyl Group Dynamics in the Hydrophobic Core of Villin Headpiece Protein
J. Phys. Chem. B 117 (20), 6129–6137 (2013)
Origin of Abrupt Rise in Deuteron NMR Longitudinal Relaxation Times of Protein Methyl Groups Below 90 K
J. Phys. Chem. B, 117 (4), 1051–1061 (2013)
Glassy Dynamics of Methyl groups in Chicken Villin Headpiece Subdomain Protein Revealed by Deuteron NMR
Solid State NMR, 45-46, 11-15 (2012)
Characterization of Water Dynamics in Frozen Soils by Solid-State Deuteron NMR
Biochemistry (2011), 50 (49), 110637-10646
Slow motions in the hydrophobic core of chicken villin headpiece subdomain and their contributions to configurational entropy and heat capacity from solid-state deuteron NMR measurements
J. Biomol. NMR, 50(2), 119-127 (2011)
Temperature Dependence of Fast Carbonyl Backbone Dynamics in Chicken Villin Headpiece Subdomain.
J. Phys. Chem. 114 (48), 15799–15807 (2010)
Comparative Dynamics of Leucine Methyl Groups in FMOC-Leucine and in a Protein
Hydrophobic Core Probed by Solid-State Deuteron NMR over 7-324K Temperature Range.
J. Biomol. NMR 47 (2), 155-162 (2010)
Comparison of fast backbone dynamics at amide nitrogen and carbonyl sites In dematin headpiece C-terminal domain and Its S74E mutant.
J. Am. Chem. Soc. 132 (12), 4038–4039 (2010)
Freezing of dynamics of a methyl group in a protein hydrophobic core at cryogenic temperatures by deuteron NMR spectroscopy.
J. Am. Chem. Soc. 131 (38), 13651–13658 (2009)
Probing the dynamics of a protein hydrophobic core by deuteron solid-state nuclear magnetic resonance spectroscopy.
Phys. Chem. Chem. Phys. 11, 7008-7012 (2009)
Solid State Deuteron Relaxation Time Anisotropy Measured With Multiple Echo Acquisition.
Magn. Reson. Chem. 47, 746-751 (2009)
Slow Backbone Dynamics of Chicken Villin Headpiece Subdomain Probed by NMR C′-N Cross-Correlated Relaxation.
J Biomol NMR 43, 39-50 (2009) Phosphorylation-induced changes in backbone dynamics of dematin headpiece C-terminal subdomain.
Biophys J 95, 5941-5960 (2008) Slow Motions in Chicken Villin Headpiece Subdomain Probed by Cross-correlated NMR Relaxation of Amide NH Bonds in Successive Residues.
Appl Magn Reson 28, 147-163 (2005) Temperature dependent protein backbone dynamics from auto- and cross-correlated NMR relaxation rates.
J Biomol NMR 28, (2), 173-177 (2004) Evidence of slow motions by cross-correlated chemical shift modulation in deuterated and protonated proteins.
Comptes Rendus de l'Académie des Sciences (section de Physique) 5 (3), 377-386 (2004) Cross-correlated relaxation in NMR of macromolecules in the presence of fast and slow dynamics.
J Am Chem Soc 125 (20), 6032-6033 (2003) Dynamic NMR lineshape analysis demonstrates that the Villin Headpiece Domain folds on the microsecond time scale.
J Am Chem Soc 125 (27), 8400-8404 (2003) Beyond the decoupling approximation in the model free approach for the interpretation of NMR relaxation of macromolecules in solution.
J Mol Biol, 320 (4), 841-854 (2002) Temperature-dependent dynamics of the villin headpiece helical subdomain, an unusually small thermostable protein.
J Am Chem Soc , 122 (22), 5387-5388 (2000) N15 R1rho measurements allow the determination of ultrafast protein folding rates.
Protein Science, 7 (9), 1994-1997 (1998) Amide proton exchange measurements as a probe of the stability and dynamics of the N-terminal domain of the ribosomal protein L9: Comparison with the intact protein.
External Research Grants
- National Science Foundation –Research at Undergraduate Institutions (RUI): “Probing the Free Energy Landscape of Hydrophobic Cores by Solid-State NMR.” 9/1/2011-8/31/2014 Role: PI $201,000
Research Corporation Cottrell College Award “Dynamics of Protein Hydrophobic Cores by Deuteron Solid-State NMR Spectroscopy” 01/2010-12/2012. Role: PI. $48,000
National Science Foundation-Research Opportunity Award (ROA) through the supplement to the grant of Prof. Robert L. Vold, College of William and Mary “Quantitative Studies of Molecular Dynamics in Solids by Nuclear Magnetic Resonance of Quadrupolar Nuclei” 06/09-07/10. Role: Investigator $20,000
Instrumentation Time Awards at National Labs
National High Field Magnetic Laboratory at Tallahassee, FL instrumentation time awards, 7/2012 – 8/2014 and 6/2011-6/2012 Role: PI
Pacific Northwest National Laboratory, 06/2007-06/2008; 06/2009-06/2010, 10/2011-8/2012 Role: PI.
Internal Grants through UA and UAA
- Faculty Seed Grant , Environmental and Natural Resources Institute , seed grant “Mechanisms of survival of unfrozen water in Antarctic soils and the effect of antifreeze proteins” 1/2014-6/2014 Role: PI $10,000
- Innovate Award “Computational Modeling of Protein Flexibility via Bridging Polymer and Protein Sciences”, University of Alaska Anchorage, 1/01/2013-12/31/2013 Role: PI $10,000
- NIH IDEA INBRE-Alaska faculty affiliate grant “Dynamics of Actin-binding Chicken Villin Headpiece Domain: The role of a buried salt bridge” 3/2012-2/2013 Role: PI $25,000
- NIH IDEA INBRE-Alaska “Investigations of Dynamics of Actin-binding Chicken Villin Headpiece Subdomain” 3/2011-2/2012 Role: PI $25,000
- Alaska Space Grant Program “Follow the water. Unfrozen Water Content and Dynamics in Dry Valleys of Antarctica” 06/01/2011- 05/31/2012, role PI. $16,000
- Environmental and Natural Resources Institute, seed grant, “Determination Of Unfrozen Water Content and Mechanisms Of Its Survival In Soils Of the Dry Valleys Of Antarctica By Nuclear Magnetic Resonance” 2/ 2011-6/2011. Role: PI $8,000
- UAA Faculty Development grants, 2008, 2009, 2010 Role: PI $4500 each