Liu_Lab

Selection of proteins with desired functions from the natural proteome libraries and synthetic protein libraries

Professor Liu’s research interests include functional proteomics approaches to the definition of protein-protein interaction networks, the identification of enzyme-substrate and drug-protein target interactions at a proteome-wide scale, and screening for antibody-like affinity molecules for biomarkers using in vitro protein selection technology. The projects in Liu’s group are funded by the National Institute of Neurological Disorders and Stroke, the American Cancer Society, the National Cancer Institute,  the National Institure on Drug Abuse and NIH Roadmap.

 

The Liu lab uses in vitro protein selection strategies to address biological problems on a proteome-wide scale. The major tool used in the lab is a novel technique called mRNA display, in which a protein is covalently linked to the 3′ end of its own mRNA. Because of this physical link, mRNA display provides a rapid and powerful means of identifying protein-protein interactions by amplifying or enriching for interacting proteins based on functional characteristics. Our research interests focus on the following fields:

  1. Deciphering the signaling pathways mediated by proteases and by Ca2+ using systems biology approaches. We address the problems using mRNA-displayed proteomes from human, mouse, Drosophila, and C. elegans. Current projects in the lab include: (a) to identify the family member-specific natural substrate repertoire of different caspases and granzymes; (b) to decipher the signaling pathways of several regulatory proteins identified from the selection; and (C) to identify potential drug targets that are involved in the pathogenesis of cancer and neurodegenerative diseases.
  2. Developing novel protein therapeutics that can be used in tumor diagnosis and treatment. We use molecular evolution approaches to develop novel antibody mimics, on the basis of the scaffolds of several stable protein domains and non-mammalian antibodies, that bind to biomarkers on the surface of cancer cells. We conjugate these target-binding antibody mimics to small molecule drugs or nanoparticles for the targeted delivery of therapeutic agents.
  3. Identifying the protein targets of drugs or drug candidates whose action mechanisms are unknown. We combine molecular proteomic and chemical biology approaches to identify the protein targets of drugs whose target-binding affinities are modest. Current project in this field is a collaborative effort with the Kohn lab to identify the targets of anti-epilepsy drug lacosamide from the proteome of mouse.

The Liu lab is at Division of Medicinal Chemistry and Natural Products at the School of Pharmacy. The lab is also affiliated to the Carolina Center for Genome Sciences and the Carolina Center of Cancer Nanotechnology Excellence. The projects in the Liu lab are funded by the National Institute of Neurological Disorders and Stroke, the American Cancer Society, the National Cancer Institute, and the National Institute of Diabetes and Digestive and Kidney Diseases.

Current Projects

This project aims at identifying from the human proteome the proteins that interact with calmodulin in a Ca2+-dependent or Ca2+-independent manner. We have finished the proteome-wide selection and are now focusing on a few novel CaM-binding proteins that mediate different signaling pathways, including the AKT, apoptosis,  and ubiquitin-proteasome pathways. The project is supported by the American Cancer Society.
This project aims at identifying from the C. elegans proteome the proteins that interact with calmodulin in a Ca2+-dependent or Ca2+-independent manner.  The project is supported by the American Cancer Society.

This project aims at identifying from the human proteome the family member-specific natural substrate repertoire of each caspase in the mammalian caspase family. The project is funded by the National Institute of Neurological Disorders and Stroke. We have finished the proteome-wide selections of the downstream substrates of the following caspase members:
1. Caspase-2
2. Caspase-3
3. Caspase-6
4. Caspase-8
5. Caspase-9
6. Caspase-10

This project aims at identifying the downstream substrates of CED-3 and putative CSP-1B from the proteome of C. elegans.
This project aims at identifying from the human proteome the downstream substrates that are specifically cleaved by granzyme A or granzyme B, but not by caspases.
This project aims at the in vitro selection and optimization of tumor biomarker-binding single-domain antibody mimics from various mRNA-displayed protein  libraries. The project is funded by the National Cancer Institute.
This project aims at the identification of the protein target(s) of a novel anti-epilepsy drug lacosamide. This is a collaborative project with the Kohn lab at UNC Eshelman School of Pharmacy. The project is funded by the National Institute of Neurological Disorders and Stroke.

Grants

5R01 NS047650 (PI: Liu) from NIH/NINDS
Identification of caspase substrates from human proteome

RSG-TBE-06-073 (PI: Liu) from American Cancer Society
Novel calmodulin-binding proteins in regulating ubiquitin-proteasome system

5U54 CA119343 (PI: Juliano) from NIH/NCI
The Combinatorial Library Research Core of the Carolina Center of Cancer Nanotechnology Excellence (C-CCNE)
Role: PI of the Combinatorial Library Screening Core

5R01NS054112 (PI: Kohn) from NIH/NINDS
Methods to Identify Targets of the Neurological Agent (R)-Lacosamide
Role: Co-PI

5R21 DA025702 (PI: Liu) from NIDA/NIH

Identification of the interactome of methylated histones from human proteome

Shen, X., Valencia, C. A., Szostak, J. W., Dong, B., and Liu, R. (2005) “Scanning the Human Proteome for Calmodulin-binding Proteins”; Proceedings of the National Academy of Sciences of US, 102, 5969-5974.

Dong, B., Valencia, C. A., and Liu, R. (2007) “Ca2+/CaM Directly Interacts with the PH Domain of AKT1”; Journal of Biological Chemistry, 282 (34), 25131-40.

Huang, B. and Liu, R. (2007) “Comparison of mRNA-Display Based Selections Using Synthetic Peptide and Natural Protein Libraries”, Biochemistry, 46 (35), 10102-10112.

Ju, W., Valencia, C. A., Pang, H., Ke, Y., Gao, W., Dong, B., and Liu, R. (2007) “Proteome-wide Identification of Member-specific Natural Substrate Repertoire of Caspases”; Proceedings of the National Academy of Sciences of US, 104, 14294-14299.

Kim, J. S., Valencia, C. A., Liu, R., and Lin, W. (2007) “Highly-Efficient Purification of Native Polyhistidine-Tagged Proteins by Multivalent NTA-Modified Magnetic Nanoparticles”, Bioconjugate Chemistry, 18 (2), 333-341.

Valencia, C. A., Ju, W., and Liu, R. (2007) “Matrin 3 is a Ca2+/Calmodulin-binding Protein Cleaved by Caspases”, Biochemical and Biophysical Research Communications, 361 (2), 281-286.

Valencia, C. A., Bailey, C., and Liu, R. (2007) “Novel Zebrafish Caspase-3 Substrates”, Biochemical and Biophysical Research Communications, 361 (2), 311-316.

Duan, J., Wu, J., Valencia, C. A., and Liu, R. (2007) “Fibronectin Type III Domain Based Monobody with High Avidity”, Biochemistry, 46 (44), 12656-12664.

Valencia, C. A., Cotten, S. W., and Liu, R. (2007) “Cleavage of BNIP-2 and BNIP-XL by Caspases”, Biochemical and Biophysical Research Communications, 364 (3), 495-501.

Valencia, C. A., Cotten, S. W., Duan, J., and Liu, R. (2008) “Modulation of Nucleobindin-1 and Nucleobindin-2 by Caspases”, FEBS Letters, 582 (2), 286-290.

Dong, B. and Liu, R. (2008) “Characterization of Endogenous and Recombinant Human Calpain-10”, Biochimie, 90, 1362-1371.

Shen, X., Valencia, C. A., Gao, W., Cotten, S.W., Dong, B., Huang, B., and Liu, R. (2008) “Ca2+/calmodulin-binding Proteins from the C. elegans Proteome”; Cell Calcium, 43 (5), 444-456.

Valencia, C. A., Cotten, S. W., Dong, B., and Liu, R. (2008) “mRNA-display-based Selections for Proteins with Desired Functions: A Protease-Substrate Case Study” (Review), Biotechnology Progress 24 (3), 561-569.

Liu, R., Kay, B.K., Jiang, S., and Chen, S. (2009) “Smart Molecules for Nanoparticle Delivery: Targeting and Nonspecific Binding” (Review), MRS Bulletin, 34 (6), 432-440.

Park, K., Liu, R., and Kohn, H. (2009) “Useful Tools for Biomolecule Isolation, Detection, and Identification: Acylhydrazone-Based Cleavable Linkers”, Chemistry & Biology, 16 (7), 763-772.

Rihe Liu, Ph.D.

(919) 843-3635 rliu@email.unc.edu

Rihe Liu received his bachelor’s degree in polymer physics from the University of Science and Technology of China in 1988. He did his graduate work from 1992 to 1996 with Professor Leslie E. Orgel at the Salk Institute for Biological Studies and received his PhD in biochemistry from the University of California at San Diego.