Jonathan R. Lai, Ph.D.
Peptide and protein chemistry
Our lab combines biochemistry, biophysics, organic chemistry, virology, and cell biology to study and engineer proteins and peptides for biomedical applications. We are currently engaged in several active lines of research:
1. Engineering of Novel Virus Immunotherapeutics
There has been much recent interest in the use of monoclonal antibodies (mAbs), or cocktails thereof, for treatment of viral diseases. We are using state-of-the-art protein engineering technologies to develop novel immunotherapeutics against several viruses. A recent example is the use of "synthetic antibody technology" to develop the first humanized protective mAbs against the Sudan ebolavirus species (see below and ACS Chem. Biol., 2014, 9, 2263), the result of a large multi-institution collaborative effort. Synthetic antibody technology is a phage-based approach that allows the production and screening of very large (> 1010) protein libraries. There are five species of ebolavirus and, while many potential mAbs are available for the Zaire ebolavirus species, few are available for Sudan ebolavirus despite its high pathogenicity and increasing prevalence. Subsequent efforts are focused on using nascent protein engineering technologies to address unmet immunotherapeutic needs for this and other viruses.
Figure - Protein engineering of novel, human, protective Sudan ebolavirus antibodies.
2. Mechanisms of Viral Membrane Fusion
Membrane-bound viruses require fusion between the host and viral membranes for infection. Although the details of the mechanism for membrane fusion differ among viruses, a common conformational state is the "extended" or "prehairpin" intermediate, in which the viral fusion subunit spans both the host and viral membranes. Collapse of this extended intermediate into a stable hairpin-like structure provides the energetic driving force for membrane fusion. We are using biophysical and structural methods to dissect fine details of the fusion process (below and: Biochemistry, 2015, 54, 1589; J. Mol. Biol., 2014, 426, 1452; Structure, 2013, 21, 1085 as examples).
Figure - Structural alignment of "post-fusion" hairpin structures of CAS Virus, Marburg virus, Moloney murine leukemia virus, and lymphocytic choriomeningitis virus fusion subunits.
3. Protein Structure and Molecular Recognition
We use combinatorial biochemistry, and traditional biophysical approaches to decipher determinants for protein structure and molecular recognition. These studies illuminate the requirements for specificity and affinity at intermolecular interfaces and provide new tools and potential therapeutics.
Selected Recent Publications
- Frei, J. C.+; Nyakatura, E. K.+; Zak, S. E.+; Bakken, R. R.; Chandran, K.; Dye, J. M.*; Lai, J. R.* Bispecific Antibody Affords Complete Post-Exposure Protection of Mice from Both Ebola (Zaire) and Sudan Viruses. Sci. Rep., 2016, 6, 19193. [[Journal link]] (+Equal contributors)
- Uchime, O.+; Dai, Z.+; Biris, N.; Lee, D., Sidhu, S. S., Li, S., Lai, J. R.*, Gavathiotis, E.* Synthetic Antibodies Inhibit Bcl-2-associated X Protein (BAX) through Blockade of the N-terminal Activation Site. J. Biol. Chem., 2016, 291, 89-102. [[Journal link]]
- Holtsberg FW, Shulenin S, Vu H, Howell KA, Patel SJ, Gunn B, Karim M, Lai JR, Frei JC, Nyakatura EK, Zeitlin L, Douglas R, Fusco ML, Froude JW, Saphire EO, Herbert AS, Wirchnianski AS, Lear-Rooney CM, Alter G, Dye JM, Glass PJ, Warfield KL, Aman MJ. Pan-ebolavirus and Pan-filovirus Mouse Monoclonal Antibodies: Protection against Ebola and Sudan Viruses. J. Virol., 2015, 90, 266-289. [[Journal link]]
- Frei, J. C.; Kielian, M., Lai, J. R.* Comprehensive Mapping of Functional Epitopes on Dengue Virus Glycoprotein E DIII for Binding to Broadly Neutralizing Antibodies 4E11 and 4E5A by Phage Display. Virology, 2015,485, 371-382. [[Journal link]]
- Malashkevich, V. N.; Higgins, C. D.+; Almo, S. C.*; Lai, J. R.* A Switch from Parallel to Antiparallel Strand Orientation in a Coiled-Coil X-Ray Structure via Two Hydrophobic Mutations. Biopolymers: Peptide Science, 2015, 104, 178-185. [[Journal link]]
- Liu, N.; Tao, Y.; Brenowitz, M. D.; Girvin, M. E.; Lai, J. R.* Structural and Functional Studies on the Marburg Virus GP2 Fusion Loop. In press at J. Infect. Dis. [[Journal link]]
- Dai, Z.; Tao, Y.; Brenowitz, M. D.; Girvin, M.E.; Lai, J. R.* Conditional Trimerization and Lytic Activity of HIV-1 gp41 Variants Containing the Membrane-Associated Segments. Biochemistry, 2015, 54, 1589-1599. [[Journal link]]
- Nyakatura, E. K.; Frei, J. C.; Lai, J. R.* Chemical and Structural Aspects of Ebola Virus Entry Inhbitors. ACS Infect. Dis., 2015, 1, 42-52. [[Journal link]]
- Chen, G.+; Koellhoffer, J. F.+; Zak, S. E.+; Frei, J. C.; Liu, N.; Long, H.; Yi, W.; Nagar, K.; Pan, G.; Chandran, K.; Dye, J. M.; Sidhu, S. S.; Lai, J. R.* Synthetic Antibodies with a Human Framework that Protect Mice from Lethal Sudan Ebolavirus Challenge. ACS Chem. Biol., 2014, 9, 2263-2273. [[Journal link]] Press coverage of this work: NY1, NY Daily News, FrontPageAfrica, Chemical & Engineering News, Quartz, Infection Control Today, Einstein1, Einstein2.
- Higgins, C. D.; Malashkevich, V. N.; Almo, S. C.; Lai. J. R.* Influcence of a Heptad Repeat Stutter on the pH-Dependent Conformational Behavior of the Central Coiled-Coil from Influenza Hemagglutinin HA2. Proteins, 2014, 82, 2220-2229. [[Journal link]]
- Koellhoffer, J. F.+; Dai, Z+; Malashkevich, V. N.; Stenglein, M. D.; Liu, Y.; Toro, R.; Harrison, J. S.; Chandran, K.; DeRisi, J. L.; Almo, S. C.; Lai, J. R.* Structural Characterization of the Glycoprotein GP2 Core Domain from the CAS Virus, a Novel Arenavirus-like Species. J. Mol. Biol., 2014, 426, 1452-1468. [[Journal link]]
- Koellhoffer, J. F.; Higgins, C. D.; Lai, J. R.* Protein Engineering Strategies for the Development of Viral Vaccines and Immunotherapeutics. FEBS Lett. 2014, 588, 298-307. [[Journal link]]
- Liu, Y.; Higgins, C. D.; Overstreet, C. M.; Rai, K. R.; Chiorazzi, N.*; Lai, J. R.* Peptides that Bind Specifically to an Antibody from a Chronic Lymphocytic Leukemia Clone Expressing Unmutated Immunoglobulin Variable Region Genes. Mol. Medicine, 2013, 19, 245-252. [[Journal link]]
- Higgins, C. D.; Koellhoffer, J. F.; Chandran, K.; Lai, J. R.* C-Peptide Inhibitors of Ebola virus Glycoprotein-Mediated Cell Entry: Effects of Conjugation to Cholesterol and Side Chain-Side Chain Crosslinking. Bioorg. Med. Chem. Lett, 2013, 23, 5356-5360. [[Journal link]]
- Harrison, J. S.*; Higgins, C. D.; O'Meara, M. J.; Koellhoffer, J. F.; Kuhlman, B. A.; Lai, J. R.* Role of Electrostatic Repulsion in Controlling pH-Dependent Conformational Changes of Viral Fusion Proteins. Structure, 2013, 21, 1085-1096. [[Journal link]]
- Regula, L. K.; Harris, R.; Wang, F.; Higgins, C. D.; Koellhoffer, J. K.; Zhao, Y.; Chandran, K.; Gao, J.; Girvin, M. E.; Lai, J. R.* Conformational Properties of Peptides Corresponding to the Ebolavirus GP2 Membrane-Proximal External Region in the Presence of Micelle-Forming Surfactants and Lipids. Biochemistry, 2013, 52, 3393-3404. [[Journal link]]
- Stewart, A.; Harrison, J. S.; Regula, L. K.; Lai, J. R.* Side Chain Requirements for Affinity and Specificity in D5, an HIV-1 Antibody Derived from the VH1-69 Germline Segment. BMC Biochemistry, 2013, 4, 9. [[Journal link]]
- Koellhoffer, J. L.+; Chen, G.+; Sandesara, R. G.+; Bale, S.; Saphire, E. O.; Chandran, K.*; Sidhu, S. S.*; Lai, J. R.* Two Synthetic Antibodies that Recognize and Neutralize Distinct Proteolytic Forms of the Ebola Virus Glycoprotein. ChemBioChem, 2012, 13, 2549-2557. [[Journal link]]
- Koellhoffer, J. K.; Malashkevich, V. N.; Harrison, J. S.; Toro, R.; Bhosle, R. C.; Chandran, K.; Almo, S. C.; Lai, J. R.* Crystal Structure of the Marburg Virus GP2 Core Domain in its Post-Fusion Conformation. Biochemistry, 2012, 51, 7665-7775. [[Journal link]]
- Harrison, J. S.; Koellhoffer, J. K.; Chandran, K.; Lai, J. R.* Marburg Virus Glycoprotein GP2: pH-Dependent Stability of the Ectodomain alpha-Helical Bundle. Biochemistry, 2012, 51, 2515-2525. [[Journal link]]
- Stewart, A.; Liu, Y.; Lai, J. R.* A Strategy for Phage Display Selection of Functional Domain-Exchanged Immunoglobulin Scaffolds with High Affinity for Glycan Targets. J. Immunol. Methods., 2012, 376, 150-155. [[Journal link]]
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