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Zhongyu Yang

Electron Paramagnetic Resonance (EPR) Spectroscopy and Bioanalytical Chemistry.

We are interested in probing the structure-function relationship of proteins upon conjugation with synthetic materials using bioanalytical chemistry and EPR spectroscopy. The ultimate goals are to understand how the synthetic materials influence the structure and function of proteins and guide the rational design of materials to prepare for novel biocatalysts and biomaterials. Our key to probe protein structural information is EPR spectroscopy, which overcomes the challenges and complexities caused by large size, high heterogeneity, and molecular interaction between proteins and synthetic materials. We have three major directions: the nano-bio interface, the protein-polymer conjugates, and the enzyme-metal organic framework (MOF) composites.

A. Nano-bio interface.

The rapid development of nanoparticles (NPs) has improved many areas including energy efficiency, material science, biosensing, and medical therapeutics. Recently, NPs have been utilized to immobilize enzymes in order to enhance enzyme stability and reusability. In most applications, the contact of NPs with biomacromolecules, especially enzymes is either necessary or inevitable, leading to alterations in the structure and function of the enzyme. In biocatalysis, NPs often reduce the desired catalytic activity; in living organisms NPs can even cause adverse effects, raising concerns about public health and “nanotoxicity”. Therefore, understanding the correlation of structure and activity of enzymes upon contact with NPs is essential for enhancing catalytic efficiency and reducing nanotoxicity. We are particularly interested in an important pathway of nanotoxicity, NPs suppressing the activity of antioxidant enzymes (AOEs) and inducing the accumulation of reactive oxygen species (ROS). The involved NPs include but not limited to carbon nanotubes, metallic NPs, and silica NPs. We use EPR to determine the structural basis of AOE dysfunction caused by NPs in order to 1) deepen the understanding of nanotoxicity mechanism, 2) develop NPs with antioxidant functions or reduced toxicity, and 3) design treatments for damages caused by ROS accumulation.

B. Protein-polymer conjugates.

Protein-polymer conjugates have shown promising potential to improve biocatalysis, protein storage/delivery, and biomaterials. These conjugates can retain the functions and characteristics of both proteins and polymers, resulting in hybrids with enhanced protein stability and reusability. It is also possible to control protein function by tuning polymer conformation. The current hurdle preventing further development of these conjugates is the protein activity loss upon polymer conjugation. Although such loss is believed to be originated from the structure perturbation caused by the polymer, details such as the location and structure of the disturbed areas are mostly unclear. In cases where polymers are used to control protein function, the details of the changes in protein structure, polymer conformation, and the relative position of the polymer on the host protein are mostly unclear and challenging to obtain. We are interested in determining the structural details of hybrids formed between representative polymers and three model proteins, the antimicrobial T4 lysozyme (T4L), the antioxidant Cu-Zn Superoxide Dismutase (SOD1), and Insulin. This information will help design polymers to prepare for conjugates with desired stability and function.

C. Protein encapsulated in metal organic frameworks (MOFs).

Protein-MOF nanocomposites have shown enhanced protein stability and reusability, reduced leaching, unique substrate (size) selectivity, and even enhanced biocatalytic efficiency in certain cases. In general, there are two ways to prepare the composites, de novo co-precipitation of proteins and the MOF building blocks and post-synthetic encapsulation where proteins diffuse into MOFs. While exciting progress has been made in both approaches, the current focus was mainly on adjusting MOF building blocks. The current knowledge gaps are the detailed structural changes and relative orientations of proteins upon the assembly of protein and MOF, the structural basis and driving force of how proteins diffuse into MOFs in the post-synthetic encapsulation, and the correlation of protein structure with the choice of MOF. We are interested in monitoring protein structural changes upon formation of the composites using EPR. We select three model proteins, T4 lysozyme (T4L), cytochrome c (CytC), and Cu-Zn superoxide dismutase (SOD1), for our investigation. Several MOFs with varied aperture and cage sizes are involved in our studies.

Publications

(Corresponding Author: *).
31. Y. Pan, S. Neupane, J. Farmakes, M. Oh, K. Bentz, Y. Choi, Z. Yang,* “Insights on the Structure, Molecular Weight, and Activity of an Antibacterial Protein‐Polymer Hybrid”, ChemPhysChem, (2018), 19, 651-658.
30. Y. Pan, S. Neupane, J. Farmakes, M. Bridges, K. Bentz, J. Rao, S.Y. Qian, G. Liu, Z. Yang,* “Probing the Structural Basis and Adsorption Mechanism of an Enzyme on Nano-sized Protein Carriers”, Nanoscale, (2017), 9, 3512-3523.
29. Y. Pan, S. Neupane, B. Liu, J. Farmakes, W. Sun, Z. Yang,* “Revealing the conformational changes of polymeric micelles using electron paramagnetic resonance spectroscopy”, Journal of Polymer Science, Part B: Polymer Physics, (2017), 55, 1770-1782.
28. S. Neupane, Y. Pan, S. Takalkar, K. Bentz, J. Farmakes, Y. Xu, B. Chen, G. Liu, S.Y. Qian, Z. Yang,* “Probing the aggregation mechanism of gold nanoparticles triggered by a globular protein”, The Journal of Physical Chemistry C, (2017), 121, 1377-1386.
27. Y. Xu, X. Yang, P. Zhao, Z. Yang, C. Yan, B. Guo, and S. Y. Qian, “Knockdown of delta-5-desaturase promotes the anti-cancer activity of dihomo-γ-linolenic acid and enhances the efficacy of chemotherapy in colon cancer cells expressing COX-2”, Molecular Cancer Therapeutics, (2016), 96, 67-77.
26. S. Sinha, Y. Mei, A. Ramanathan, K. Glover, Z. Yang, C. L Colbert, “Conformational Flexibility Enables the Function of a BECN1 Region Essential for Starvation-Mediated Autophagy”, The FASEB Journal, (2016), 1062.6-1062.6.
25. Y. Mei, A. Ramanathan, K. Glover, C. Stanley, R. Sanishvili, S. Chakravarthy, Z. Yang, C. L Colbert, S. C Sinha “Conformational Flexibility Enables the Function of a BECN1 Region Essential for Starvation-Mediated Autophagy”, Biochemistry, (2016), 55, 1945-1958.      

24. M. Bridges, Z. Yang, C. Altenbach, and W. L. Hubbell, “Analysis of Saturation Recovery Amplitudes to Characterize Conformational Exchange in Spin Labeled Proteins”, Applied Magnetic Resonance, (2017), 48, 1315-1340.
23. B. M. Stadtmueller, Z. Yang, K. E. Huey-Tubman, H. Roberts-Mataric, W. L. Hubbell, and P. J. Bjorkman, “Biophysical and biochemical characterization of avian secretory component provides structural insights into the evolution of the polymeric Ig receptor”, Journal of Immunology, (2016), 197, 1408-1414.
22. Z. Yang, M. D. Bridges, C. J. López, O. Yu. Rogozhnikova, D. V. Trukhin, E. K. Brooks, V. Tormyshev, H. J. Halpern, W. L. Hubbell, “A Triarylmethyl Spin Label for Long-Range Distance Measurement at Physiological Temperatures Using T1 Relaxation Enhancement”, Journal of Magnetic Resonance, (2016), 269, 50-54.
21. R. Guo, K. Gaffney, Z. Yang, M. Kim, S. Sungsuwan, X. Huang, W. L. Hubbell and H. Hong, “General steric trapping strategy reveals an intricate cooperativity network in the intramembrane protease GlpG under native condition”, Nature Chemical Biology. (2016), 12, 353-360.
20. D. Davydov, Z. Yang, N. Davydova, J. Halpert, and W. L. Hubbell, “Cytochrome P450 3A4 transitions revealed in a pressure perturbation study by LRET and EPR spectroscopy”, Biophysical Journal. (2016), 110, 1485-1498.
19. B. M. Stadtmueller, K. Huey-Tubman1, C. Lopez, Z. Yang, W. L. Hubbell, and P. J. Bjorkman, “The structure and dynamics of secretory component and its interactions with polymeric immunoglobulins”, Elife. (2016), 5, e10640.
18. R. O. Dror, T. J. Mildorf, D. Hilger, A. Manglik, D. W. Borhani, D. H. Arlow, A. Philippsen, Z. Yang, M. T. Lerch, W. L. Hubbell, B. K. Kobilka, R. K. Sunahara, and D. E. Shaw, “Structural basis for nucleotide exchange in heterotrimeric G proteins”, Science. (2015), 348, 1361-1365.
17. M. Lerch, Z. Yang, C. Altenbach and W.L. Hubbell, “Measuring structure and dynamics of proteins using high pressure EPR spectroscopy”, Methods in Enzymology. (2015), 564, 29-57.
16. Z. Yang, M. Bridges, M. Lerch, C. Altenbach and W.L. Hubbell, “Saturation recovery EPR spectroscopy in protein structure and dynamics determination”, Methods in Enzymology. (2015), 564, 3-27.
15. Z. Yang, M. Ji, T. Cunningham and S. Saxena, “Cu2+ as an ESR probe of protein structure and function”, Methods in Enzymology. (2015), 563, 459-481.

14. C. J. Lopez, M. Lerch, Z. Yang, J. Horwitz, M. Kreitman and W. L. Hubbell, “A structure-relaxation mechanism for the response of proteins to hydrostatic pressure”, Proc. Natl. Acad. Sci. USA. (2015), 112, E2437-E2446.
13. A. Manglik, T. H. Kim, M. Masureel, C. Altenbach, Z. Yang, D. Hilger, T. S. Kobilka, F. S. Thian, W. L. Hubbell, R. S. Prosser, and B. K. Kobilka, “Structural insights into the dynamic process of β2-adrenergic receptor signaling”, Cell, (2015), 161, 1101-1110.
12. Z. Yang, G. Jimenez, C. Lopez, M. bridges, K. Houk, and W.L. Hubbell, “Long range distance measurement in proteins at physiological temperatures using Saturation-Recovery EPR”, J. Am. Chem. Soc. (2014), 136, 15356−15365 (JACS spotlights).
11. M. C. Thompson, N. M. Wheatley, J. Jorda, M. R. Sawaya, S. D. Gidaniyan, H. Ahmed, Z. Yang, K. N. McCarty, J. P. Whitelegge, and T. O. Yeates, “Identification of a Unique Fe-S Cluster Binding Site in a Glycyl-Radical Type Microcompartment Shell Protein”, J. Mol. Biol. (2014), 426, 3287-3304.
10. J. Vendome, K. Felsovalyi, H. Song, Z. Yang, X. Jin, J. Brasch, O. Harrison, G. Ahlsen, F. Bahna, A Kaczynska, P. Katsamba, D. Edmond, W. L. Hubbell, L. Shapiro, and B. Honig, “Structural and energetic determinants of adhesive binding specificity in type I cadherins”, Proc. Natl. Acad. Sci. USA., (2014), 111, E4175-E4184.
9. D. Davydov, Z. Yang, J. Halpert, and W. L. Hubbell, “Exploring enzyme conformational landscape with pressure-perturbation: allosteric rearrangements in P450 3A4 revealed with FRET and SDSL-EPR", The FASEB journal, (2014), Vol 28, n.1, Supplement, 796.16
8. M. Lerch, Z. Yang, C. J. Lopez, C. Altenbach, and W. L. Hubbell, “Determination of the conformational states of myoglobin trapped at high pressure using double electron-electron resonance spectroscopy”, Proc. Natl. Acad. Sci. USA, (2014), 111,  E1201–E1210.
7. C. J. Lopez, Z. Yang, C. Altenbach and W. L. Hubbell,  “Conformational selection and adaption in ligand binding to T4 lysozyme cavity mutants”, Proc. Natl. Acad. Sci. USA., (2013), 110, E4306–E4315.
6. W. L. Hubbell, C. J. Lopez, C. Altenbach, and Z. Yang, “New frontiers in site directed spin labeling of proteins”, Curr. Opin. Struct. Biol. (2013), 23, 725-733.
5. Z. Yang, Y. Liu, P. Borbat, J. Zweier, J. Freed and W. L. Hubbell, “Pulsed dipolar spectroscopy for distance measurements in spin labeled proteins near physiological temperature”, J. Am. Chem. Soc. (2012), 134, 9950-9952.
4. Z. Yang, M.R. Kurpiewski, M. Ji, J.E. Townsend, P. Mehta, L. Jen-Jacobson and S. Saxena, “ESR spectroscopy reveals a novel allosteric mechanism of Cu2+ inhibition of magnesium-dependent nuclease catalysis”, Proc. Natl. Acad. Sci. USA., (2012), 109, E993-E1000.
3. Z. Yang, M. Ji and S. Saxena, “Practical aspects of copper ion-based double electron electron resonance distance measurements”, Appl. Magn. Reson., (2011), 39, 487-500.
2. Z. Yang, D. Kise and S. Saxena, “An approach towards the measurement of nanometer range distances based on Cu(II) ions and ESR”, J. Phys. Chem. B. (2010), 114, 6165–6174.
1. Z. Yang, J. S. Becker and S. Saxena, “On Cu(II)-Cu(II) distance measurements using pulsed electron electron double resonance", J. Magn. Reson.(2007), 188, 337-343.

Zhongyu Yang

Assistant Professor

BS, University of Science and Technology of China 2004
PhD, University of Pittsburgh 2010
Post-doctoral Fellow, University of California, Los Angeles 2010-2015

Office: Dunbar 61
tel: 701-231-8639
fax: 701-231-8831

zhongyu.yang@ndsu.edu