Zhongyu Yang
Associate Professor
Research Interest(s):
We are a highly active and productive research team focused on researching proteins under spatial confinement at the nanoscale. We have created advanced hybrid synthetic platforms based on Metal-Organic Frameworks (MOFs) and polymeric materials as protein hosts and developed biophysical tools based on various analytical methods especially Electron Paramagnetic Resonance (EPR) spectroscopy to probe the needed structure and dynamics information. Our ultimate goals are to utilize confinement to improve fundamental protein biophysics by mimicking protein behaviors in the physiological conditions and host/deliver functional proteins for biocatalysis and biomedical applications. Three kinds of confinement environment, “rigid with regular shapes”, “rigid with irregular shapes”, and “flexible chambers”, based on MOFs, protein-MOF co-crystallization, and polymeric materials, respectively, have been explored.
Direction A. Protein biophysics under rigid artificial compartment with finely-tunable shape, size, and hydrophobicity.
Proteins are essential for cellular functions. The folding, structure, dynamics, function, translocation, and misfolding /aggregation of proteins is among the most important research topics for decades. Most of the current knowledge, however, is based on studies in dilute solutions, a much different environment from the highly complicated and dynamic cellular environment. In vivo/in-cell protein studies have become possible recently, confirming the importance of studying proteins under or near their physiological conditions. Meanwhile, the complex cellular environments limit fundamental principles on how cellular conditions impact all aspects of proteins to be generated.
We are overcoming these drawbacks by employing Metal-Organic Frameworks (MOFs) and Covalent-Organic Frameworks (COFs), by far the most advanced platforms to create artificial spatial confinement with uniform and tunable compartment size (nanoscale), shape, and wall property (hydrophobicity), perfect for determining how each confinement factor influences proteins. We then combine various analytical tools especially site-directed spin labeling (SDSL) and EPR to probe protein structural and dynamic information in the presence of the complexities caused by MOF/COF or chaperonins/protein-conducting channels. These efforts will enhance our understanding on proteins in nature, eventually leading to potential therapeutic approaches to treat protein malfunctions in cells.
Direction B. Co-crystallization of proteins with MOFs to create rigid but irregular confinement environments.
In nature, a common confinement condition is that proteins are “wrapped” up tightly with rigid boundaries when co-precipitated with metals and organic compounds (biomineralization). Inspired by nature, we also confined proteins in this way in the aqueous phase to form protein@MOF co-crystals. An advantage of this strategy is to remove the size limitation of the proteins that can be encapsulated in MOFs, as most of the current enzyme@MOF/COF biocatalysts are limited to enzymes smaller than MOF/COF pores. We also found it possible to remove the size limitation on enzyme substrates, because a portion of enzymes immobilized this way can be implanted on the surface of the co-crystals, so that a portion of enzymes are partially exposed to contact large substrates such as starch or cellulose, while the partial burying/ protection prevents protein damage under harsh conditions to a certain extent. In addition, we have developed enzyme@ MOF platforms stable under both acidic and basic pHs, which allow for biocatalytic reactions to be carried out under the optimal condition of the immobilized enzymes. Lastly, we have developed MOF systems which can co-crystalize proteins with more choices of metal ions and ligands, leading to custom immobilization of proteins.
Direction C. Functional polypeptides confinement under flexible restriction based on polymeric materials.
“Soft” confinement is also often encountered in nature, which can be mimicked using polymeric materials via crosslinking or self-assembling. Probing the structure and dynamics of proteins under this confinement environment is also challenging due to the complexity caused by the dynamic polymeric compositions. We are combining various analytical tools to overcome this challenge and reveal the structural basis of protein performance under “soft” restrictions, leading to future delivery platforms of protein-based therapeutics."
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