1
|
Li D, Zhang Y, He Y, Zhang C, Wang J, Xiong Y, Zhang L, Liu Y, Shi P, Tian C. Protein-protein interaction analysis in crude bacterial lysates using combinational method of 19F site-specific incorporation and 19F NMR. Protein Cell 2016; 8:149-154. [PMID: 27785779 PMCID: PMC5291773 DOI: 10.1007/s13238-016-0336-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Dong Li
- Hefei National Laboratory for Physical Science at the Microscale & School of Life Science, University of Science and Technology of China, Hefei, 230026, Anhui, China
| | - Yanan Zhang
- Hefei National Laboratory for Physical Science at the Microscale & School of Life Science, University of Science and Technology of China, Hefei, 230026, Anhui, China
| | - Yao He
- Hefei National Laboratory for Physical Science at the Microscale & School of Life Science, University of Science and Technology of China, Hefei, 230026, Anhui, China
| | - Chengwei Zhang
- Hefei National Laboratory for Physical Science at the Microscale & School of Life Science, University of Science and Technology of China, Hefei, 230026, Anhui, China
| | - Jiefei Wang
- Hefei National Laboratory for Physical Science at the Microscale & School of Life Science, University of Science and Technology of China, Hefei, 230026, Anhui, China
| | - Ying Xiong
- Hefei National Laboratory for Physical Science at the Microscale & School of Life Science, University of Science and Technology of China, Hefei, 230026, Anhui, China
| | - Longhua Zhang
- Hefei National Laboratory for Physical Science at the Microscale & School of Life Science, University of Science and Technology of China, Hefei, 230026, Anhui, China
| | - Yangzhong Liu
- School of Chemistry, University of Science and Technology of China, Hefei, 230026, Anhui, China
| | - Pan Shi
- Hefei National Laboratory for Physical Science at the Microscale & School of Life Science, University of Science and Technology of China, Hefei, 230026, Anhui, China.
| | - Changlin Tian
- Hefei National Laboratory for Physical Science at the Microscale & School of Life Science, University of Science and Technology of China, Hefei, 230026, Anhui, China.
| |
Collapse
|
2
|
Sharaf NG, Gronenborn AM. (19)F-modified proteins and (19)F-containing ligands as tools in solution NMR studies of protein interactions. Methods Enzymol 2015; 565:67-95. [PMID: 26577728 DOI: 10.1016/bs.mie.2015.05.014] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
(19)F solution NMR is a powerful and versatile tool to study protein structure and protein-ligand interactions due to the favorable NMR characteristics of the (19)F atom, its absence in naturally occurring biomolecules, and small size. Protocols to introduce (19)F atoms into both proteins and their ligands are readily available and offer the ability to conduct protein-observe (using (19)F-labeled proteins) or ligand-observe (using (19)F-containing ligands) NMR experiments. This chapter provides two protocols for the (19)F-labeling of proteins, using an Escherichia coli expression system: (i) amino acid type-specific incorporation of (19)F-modified amino acids and (ii) site-specific incorporation of (19)F-modified amino acids using recombinantly expressed orthogonal amber tRNA/tRNA synthetase pairs. In addition, we discuss several applications, involving (19)F-modified proteins and (19)F-containing ligands.
Collapse
Affiliation(s)
- Naima G Sharaf
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
| |
Collapse
|
3
|
Kitevski-LeBlanc JL, Prosser RS. Current applications of 19F NMR to studies of protein structure and dynamics. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2012; 62:1-33. [PMID: 22364614 DOI: 10.1016/j.pnmrs.2011.06.003] [Citation(s) in RCA: 210] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Accepted: 07/01/2011] [Indexed: 05/20/2023]
Affiliation(s)
- Julianne L Kitevski-LeBlanc
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Rd., North Mississauga, Ontario, Canada
| | | |
Collapse
|
4
|
Yu L, Hajduk PJ, Mack J, Olejniczak ET. Structural studies of Bcl-xL/ligand complexes using 19F NMR. JOURNAL OF BIOMOLECULAR NMR 2006; 34:221-7. [PMID: 16645812 DOI: 10.1007/s10858-006-0005-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2005] [Accepted: 01/11/2006] [Indexed: 05/08/2023]
Abstract
Fluorine atoms are often incorporated into drug molecules as part of the lead optimization process in order to improve affinity or modify undesirable metabolic and pharmacokinetic profiles. From an NMR perspective, the abundance of fluorinated drug leads provides an exploitable niche for structural studies using 19F NMR in the drug discovery process. As 19F has no interfering background signal from biological sources, 19F NMR studies of fluorinated drugs bound to their protein receptors can yield easily interpretable and unambiguous structural constraints. 19F can also be selectively incorporated into proteins to obtain additional constraints for structural studies. Despite these advantages, 19F NMR has rarely been exploited for structural studies due to its broad lines in macromolecules and their ligand complexes, leading to weak signals in 1H/19F heteronuclear NOE experiments. Here we demonstrate several different experimental strategies that use 19F NMR to obtain ligand-protein structural constraints for ligands bound to the anti-apoptotic protein Bcl-xL, a drug target for anti-cancer therapy. These examples indicate the applicability of these methods to typical structural problems encountered in the drug development process.
Collapse
Affiliation(s)
- Liping Yu
- Pharmaceutical Discovery Division, GPRD, Abbott Laboratories, Abbott Park, IL 60064-6098, USA
| | | | | | | |
Collapse
|
5
|
Salopek-Sondi B, Vaughan MD, Skeels MC, Honek JF, Luck LA. (19)F NMR studies of the leucine-isoleucine-valine binding protein: evidence that a closed conformation exists in solution. J Biomol Struct Dyn 2003; 21:235-46. [PMID: 12956607 DOI: 10.1080/07391102.2003.10506919] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The leucine-isoleucine-valine binding protein (LIV) found in the periplasmic space of E. coli has been used as a structural model for a number of neuronal receptors. This "venus fly trap" type protein has been characterized by crystallography in only the open form. Herein we have labeled LIV with 5-fluorotryptophan (5F-Trp) and difluoromethionine (DFM) in order to explore the structural dynamics of this protein and the application of DFM as a potential (19)F NMR structural probe for this family of proteins. Based on mass spectrometric analysis of the protein overproduced in the presence of DFM, approximately 30% of the five LIV methionine residues were randomly substituted with the fluorinated analog. Urea denaturation experiments imply a slight decrease in protein stability when DFM is incorporated into LIV. However, the fluorinated methionine did not alter leucine-binding activity upon its incorporation into the protein. Binding of L-leucine stabilizes both the unlabeled and DFM-labeled LIV, and induces the protein to adopt a three-state unfolding model in place of the two-state process observed for the free protein. The (19)F NMR spectrum of DFM-labeled LIV gave distinct resonances for the five Met residues found in LIV. 5F-Trp labeled LIV gave a well resolved spectrum for the three Trp residues. Trp to Phe mutants defined the resonances in the spectrum. The distinct narrowing in line width of the resonances when ligand was added identified the closed form of the protein.
Collapse
|