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Hattori Y, Heidenreich D, Ono Y, Sugiki T, Yokoyama KI, Suzuki EI, Fujiwara T, Kojima C. Protein 19F-labeling using transglutaminase for the NMR study of intermolecular interactions. JOURNAL OF BIOMOLECULAR NMR 2017; 68:271-279. [PMID: 28756478 DOI: 10.1007/s10858-017-0125-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 07/14/2017] [Indexed: 06/07/2023]
Abstract
The preparation of stable isotope-labeled proteins is important for NMR studies, however, it is often hampered in the case of eukaryotic proteins which are not readily expressed in Escherichia coli. Such proteins are often conveniently investigated following post-expression chemical isotope tagging. Enzymatic 15N-labeling of glutamine side chains using transglutaminase (TGase) has been applied to several proteins for NMR studies. 19F-labeling is useful for interaction studies due to its high NMR sensitivity and susceptibility. Here, 19F-labeling of glutamine side chains using TGase and 2,2,2-trifluoroethylamine hydrochloride was established for use in an NMR study. This enzymatic 19F-labeling readily provided NMR detection of protein-drug and protein-protein interactions with complexes of about 100 kDa since the surface residues provided a good substrate for TGase. The 19F-labeling method was 3.5-fold more sensitive than 15N-labeling, and could be combined with other chemical modification techniques such as lysine 13C-methylation. 13C-dimethylated-19F-labeled FKBP12 provided more accurate information concerning the FK506 binding site.
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Affiliation(s)
- Yoshikazu Hattori
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka, 565-0871, Japan
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihamaboji, 180, Yamashiro-cho, Tokushima, 770-8514, Japan
| | - David Heidenreich
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka, 565-0871, Japan
- Institute for Pharmaceutical Chemistry and Buchmann Institute for Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 9, 60438, Frankfurt am Main, Germany
| | - Yuki Ono
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka, 565-0871, Japan
| | - Toshihiko Sugiki
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka, 565-0871, Japan
| | - Kei-Ichi Yokoyama
- Institute for Innovation Ajinomoto Co., Inc, Suzuki-cho 1-1, Kawasaki-ku, Kawasaki, 210-8681, Japan
| | - Ei-Ichiro Suzuki
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya-ku, Yokohama, 240-8501, Japan
| | - Toshimichi Fujiwara
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka, 565-0871, Japan
| | - Chojiro Kojima
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka, 565-0871, Japan.
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya-ku, Yokohama, 240-8501, Japan.
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Reckel S, Lopez JJ, Löhr F, Glaubitz C, Dötsch V. In-Cell Solid-State NMR as a Tool to Study Proteins in Large Complexes. Chembiochem 2012; 13:534-7. [DOI: 10.1002/cbic.201100721] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Indexed: 11/06/2022]
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Allison JR, van Gunsteren WF. A method to explore protein side chain conformational variability using experimental data. Chemphyschem 2010; 10:3213-28. [PMID: 19882615 DOI: 10.1002/cphc.200900400] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Experimentally measured values of molecular properties or observables of biomolecules such as proteins are generally averages over time and space, which do not contain sufficient information to determine the underlying conformational distribution of the molecules in solution. The relationship between experimentally measured NMR (3)J-coupling values and the corresponding dihedral angle values is a particularly complicated case due to its nonlinear, multiple-valued nature. Molecular dynamics (MD) simulations at constant temperature can generate Boltzmann ensembles of molecular structures that are free from a priori assumptions about the nature of the underlying conformational distribution. They suffer, however, from limited sampling with respect to time and conformational space. Moreover, the quality of the obtained structures is dependent on the choice of force field and solvation model. A recently proposed method that uses time-averaging with local-elevation (LE) biasing of the conformational search provides an elegant means of overcoming these three problems. Using a set of side chain (3)J-coupling values for the FK506 binding protein (FKBP), we first investigate the uncertainty in the angle values predicted theoretically. We then propose a simple MD-based technique to detect inconsistencies within an experimental data set and identify degrees of freedom for which conformational averaging takes place or for which force field parameters may be deficient. Finally, we show that LE MD is the best method for producing ensembles of structures that, on average, fit the experimental data.
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Affiliation(s)
- Jane R Allison
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zurich, Switzerland
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Etezady-Esfarjani T, Hiller S, Villalba C, Wüthrich K. Cell-free protein synthesis of perdeuterated proteins for NMR studies. JOURNAL OF BIOMOLECULAR NMR 2007; 39:229-38. [PMID: 17846899 DOI: 10.1007/s10858-007-9188-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2007] [Accepted: 08/17/2007] [Indexed: 05/17/2023]
Abstract
Cell-free protein synthesis protocols for uniformly deuterated proteins typically yield low, non-uniform deuteration levels. This paper introduces an E. coli cell-extract, D-S30, which enables efficient production of proteins with high deuteration levels for all non-labile hydrogen atom positions. Potential applications of the new protocol may include production of proteins with selective isotope-labeling of selected amino acid residues on a perdeuterated background for studies of enzyme active sites or for ligand screening in drug discovery projects, as well as the synthesis of perdeuterated polypeptides for NMR spectroscopy with large supra-molecular structures. As an illustration, it is demonstrated that the 800-kDa chaperonine GroEL synthesized with the D-S30 cell-free system had a uniform deuteration level of about 95% and assembled into its biologically active oligomeric form.
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Abstract
The effect of non-random conformational averaging in the urea-unfolded state on the folding pathway has been investigated in a variant of the FK506 binding protein with three additional residues at the amino terminus (FKBP(*)). Three mutations (asparagine, aspartate, and threonine) were introduced into position Q53 to enhance formation of non-native helix observed in this part of the protein in the urea-unfolded state. NMR analysis showed minor structural changes in the native state of each mutant, but additional medium-range alphaN(i,i+2) of each mutant nuclear Overhauser enhancements were observed in the urea-unfolded state that were not in FKBP(*), indicating that the mutations had a more substantial effect on the unfolded state ensemble than on the native state ensemble. Isothermal equilibrium denaturation measurements showed that the Q53T and Q53D mutants were destabilized, whereas the Q53N mutant was stabilized relative to FKBP(*) with little change in the equilibrium m values. The unfolding rates of Q53N and Q53T were similar to that of FKBP(*), but Q53D unfolded twice as fast as FKBP(*). In contrast, the mutations had a more pronounced effect on the refolding kinetics. Q53N refolded slightly faster and exhibited a kinetic folding intermediate similar to that of FKBP(*). The Q53D and Q53T mutants also refolded faster than FKBP(*) but lacked the folding intermediate, indicating that these mutants experienced a different folding trajectory and transition state than FKBP(*) and Q53N. The refolding kinetic Phi values were 0.74, 1.4 and 7.9 for Q53N, Q53T, and Q53D, respectively. The data point to Q53 functioning as a gatekeeper residue in the folding of FKBP(*). This study shows that perturbing the unfolded state ensemble via mutagenesis can provide insights into residues that play important roles in the folding pathway, and represents an attractive strategy for mapping the high-energy portions of the folding energy landscape.
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Affiliation(s)
- Alla Korepanova
- Graduate Program in Molecular Biophysics, Florida State University, 501 MBB 4380, Tallahassee, FL 32306-4380, USA
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6
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Burkhard P, Hommel U, Sanner M, Walkinshaw MD. The discovery of steroids and other novel FKBP inhibitors using a molecular docking program. J Mol Biol 1999; 287:853-8. [PMID: 10222195 DOI: 10.1006/jmbi.1999.2621] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The molecular docking computer program SANDOCK was used to screen small molecule three-dimensional databases in the hunt for novel FKBP inhibitors. Spectroscopic measurements confirmed binding of over 20 compounds to the target protein, some with dissociation constants in the low micromolar range. The discovery that FK506 binding protein is a steroid binding protein may be of wider biological significance. Two-dimensional NMR was used to determine the steroid binding mode and confirmed the interactions predicted by the docking program.
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Affiliation(s)
- P Burkhard
- Structural Biochemistry Unit, Edinburgh University, Michael Swann Building, Edinburgh, Kings Buildings, EH9 3JR, UK
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7
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Asakura T, Demura M, Date T, Miyashita N, Ogawa K, Williamson MP. NMR study of silk I structure ofBombyx mori silk fibroin with15N- and13C-NMR chemical shift contour plots. Biopolymers 1997. [DOI: 10.1002/(sici)1097-0282(199702)41:2<193::aid-bip6>3.0.co;2-o] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Yu L, Fesik SW. pH titration of the histidine residues of cyclophilin and FK506 binding protein in the absence and presence of immunosuppressant ligands. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1209:24-32. [PMID: 7524680 DOI: 10.1016/0167-4838(94)90132-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Histidine residues in immunophilins, particularly His-126 of cyclophilin (CyP) and His-87 of the FK506 binding protein (FKBP), have been suggested to play important roles in ligand binding and peptidyl prolyl cis-trans isomerase (PPiase) catalysis. The charged states of the histidine residues in FKBP and CyP, which were characterized by their pKa values, have been determined in the absence and presence of the immunosuppressant ligands, ascomycin and cyclosporin A (CsA), respectively, by using a heteronuclear two-dimensional NMR method. Overall, the histidine residues in FKBP and CyP are very acidic with pKa values ranging from < or = 2.8 to 6.5, indicating that they are predominantly uncharged at physiological pH. To our knowledge, the pKa value of < or = 2.8 determined from this study is the lowest pKa reported for the free imidazole ring of the histidine residues in proteins. The abnormally acidic pKa's of His-25 in FKBP and His-54 in CyP could be explained by their highly positively charged environments. His-87 of FKBP, which is located in the FK506 binding pocket, was found to exist in two forms in free FKBP with pKa values of 5.9 and 6.5 for the major and minor forms, respectively. His-126, which is part of the CsA and substrate binding site, has a pKa of 6.3 in free CyP. The pKa values of these two histidine residues in the free proteins are higher than the pKa's obtained for the peptidyl prolyl cis-trans isomerase (PPiase) activity of these enzymes, indicating that the acid/base characters of His-87 of FKBP and His-126 of CyP are not essential in the PPiase catalysis. The hydrogen bonding of the histidine imidazole rings and the effect of hydrophobicity upon changes in pKa values are discussed.
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Affiliation(s)
- L Yu
- Pharmaceutical Discovery Division, Abbott Laboratories, Abbott Park, IL 60064
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9
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Curley RW, Panigot MJ, Hansen AP, Fesik SW. Stereospecific assignments of glycine in proteins by stereospecific deuteration and 15N labeling. JOURNAL OF BIOMOLECULAR NMR 1994; 4:335-340. [PMID: 7517241 DOI: 10.1007/bf00179344] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A method is described for stereospecifically assigning the alpha-protons of glycine residues in proteins. The approach involves the stereospecific deuteration and 15N labeling of glycine and subsequent selective incorporation of this residue into the protein. The stereospecific assignments of the glycine alpha-protons are obtained from a comparison of a 3D 15N-resolved TOCSY spectrum of the uniformly 15N-labeled protein with a 2D/3D 15N-edited TOCSY spectrum of the protein, containing the stereospecifically deuterated and 15N-labeled glycine. The approach is demonstrated by stereospecifically assigning the glycine alpha-protons of the FK506 binding protein when bound to the immunosuppressant ascomycin.
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Cheng JW, Lepre CA, Moore JM. 15N NMR relaxation studies of the FK506 binding protein: dynamic effects of ligand binding and implications for calcineurin recognition. Biochemistry 1994; 33:4093-100. [PMID: 7512379 DOI: 10.1021/bi00180a001] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Backbone dynamics of the ligand- (FK506-) bound protein FKBP-12 (107 amino acids) have been examined using 15N relaxation data derived from inverse-detected two-dimensional 1H-15N NMR spectra. A model free formalism [Lipari & Szabo (1982) J. Am. Chem. Soc. 104, 4546-4559] was used to derive the generalized order parameter (S2), the effective correlation time for internal motions (tau e), and the chemical-exchange line width (R(ex)) based on the measured 15N relaxation rate constants (R1, R2) and 1H-15N heteronuclear NOEs. The final optimized overall correlation time (tau m) was 9.0 ns. The average order parameter (S2) describing the amplitude of motions on the picosecond time scale was found to be 0.88 +/- 0.04, indicating that internal flexibility is restricted along the entire polypeptide chain. In contrast to results obtained for uncomplexed FKBP, the 80's loop (residues 82-87) surrounding the ligand binding site was found to be rigidly fixed, indicating that internal motions at this site are damped significantly due to stabilizing noncovalent interactions with the FK506 molecule. Structural implications of these differences in picosecond mobility as well as possible implications for calcineurin recognition are discussed.
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Affiliation(s)
- J W Cheng
- Vertex Pharmaceuticals Incorporated, Cambridge, Massachusetts 02139-4211
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Pilot-Matias TJ, Pratt SD, Lane BC. High-level synthesis of the 12-kDa human FK506-binding protein in Escherichia coli using translational coupling. Gene X 1993; 128:219-25. [PMID: 7685727 DOI: 10.1016/0378-1119(93)90566-l] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The gene encoding the 12-kDa cytosolic form of human FK506-binding protein (hFKBP-12) was isolated from a Jurkat T-cell cDNA library and expressed in three different non-fusion systems in Escherichia coli. Expression of recombinant hFKBP-12 (re-hFKBP-12) from the trc promoter vector, pKK233-2, yielded low levels of protein. A second system, which utilized a modified lac promoter and a stronger ribosome-binding site, showed greatly improved expression. A third system, utilizing translational coupling to an upstream segment of kdsB under the control of this modified lac promoter, produced re-hFKPB-12 at a very high level. The re-hFKBP-12 produced via translational coupling was soluble and was shown to have the authentic N terminus. The level of active re-hFKBP-12 produced from this vector was estimated to be 50% of total soluble protein, based on competition with the fusion protein, CKS::re-hFKBP-12, for binding to ascomycin-C22-carboxymethyloxime-alkaline phosphatase.
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