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Structural and functional studies of LaIT2, an antimicrobial and insecticidal peptide from Liocheles australasiae. Toxicon 2022; 214:8-17. [DOI: 10.1016/j.toxicon.2022.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 04/11/2022] [Accepted: 04/20/2022] [Indexed: 11/23/2022]
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Brath U, Lau K, Van Petegem F, Erdélyi M. Mapping the sevoflurane-binding sites of calmodulin. Pharmacol Res Perspect 2014; 2:5. [PMID: 25505574 PMCID: PMC4186402 DOI: 10.1002/prp2.25] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 01/06/2014] [Indexed: 11/21/2022] Open
Abstract
General anesthetics, with sevoflurane (SF) being the first choice inhalational anesthetic agent, provide reversible, broad depressor effects on the nervous system yet have a narrow margin of safety. As characterization of low-affinity binding interactions of volatile substances is exceptionally challenging with the existing methods, none of the numerous cellular targets proposed as chief protagonists in anesthesia could yet be confirmed. The recognition that most critical functions modulated by volatile anesthetics are under the control of intracellular Ca2+ concentration, which in turn is primarily regulated by calmodulin (CaM), motivated us for characterization of the SF–CaM interaction. Solution NMR (Nuclear Magnetic Resonance) spectroscopy was used to identify SF-binding sites using chemical shift displacement, NOESY and heteronuclear Overhauser enhancement spectroscopy (HOESY) experiments. Binding affinities were measured using ITC (isothermal titration calorimetry). SF binds to both lobes of (Ca2+)4-CaM with low mmol/L affinity whereas no interaction was observed in the absence of Ca2+. SF does not affect the calcium binding of CaM. The structurally closely related SF and isoflurane are shown to bind to the same clefts. The SF-binding clefts overlap with the binding sites of physiologically relevant ion channels and bioactive small molecules, but the binding affinity suggests it could only interfere with very weak CaM targets.
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Affiliation(s)
- Ulrika Brath
- Department of Chemistry and Molecular Biology and the Swedish NMR Centre, University of Gothenburg SE-412 96, Gothenburg, Sweden
| | - Kelvin Lau
- Department of Biochemistry and Molecular Biology, University of British Columbia Vancouver, British Columbia, V6T 1Z3, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, University of British Columbia Vancouver, British Columbia, V6T 1Z3, Canada
| | - Máté Erdélyi
- Department of Chemistry and Molecular Biology and the Swedish NMR Centre, University of Gothenburg SE-412 96, Gothenburg, Sweden
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Brath U, Akke M. Differential responses of the backbone and side-chain conformational dynamics in FKBP12 upon binding the transition-state analog FK506: implications for transition-state stabilization and target protein recognition. J Mol Biol 2009; 387:233-44. [PMID: 19361439 DOI: 10.1016/j.jmb.2009.01.047] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2008] [Revised: 01/12/2009] [Accepted: 01/23/2009] [Indexed: 10/21/2022]
Abstract
FKBP12 serves a dual role as a peptidyl-prolyl cis-trans isomerase and as a modulator of several cell signaling pathways. The macrolide FK506 is a transition-state analog of the catalyzed reaction and displaces FKBP12 from its natural target proteins. We compared the conformational exchange dynamics of the backbone and methyl-bearing side chains of FKBP12 in the free and FK506-bound states using NMR relaxation-dispersion experiments. Our results show that the free enzyme exchanges between the ground state and an excited state that resembles the ligand-bound state or Michaelis complex. In FK506-bound FKBP12, the backbone is confined to a single conformation, while conformational exchange prevails for many methyl groups. The residual side-chain dynamics in the transition-state analog-bound state suggests that the transition-state ensemble involves multiple conformations, a finding that challenges the long-standing concept of conformational restriction in the transition-state complex. Furthermore, exchange between alternative conformations is observed in the bound state for an extended network of methyl groups that includes locations remote from the active site. Several of these locations are known to be important for interactions with cellular target proteins, including calcineurin and the ryanodine receptor, suggesting that the conformational heterogeneity might play a role in the promiscuous binding of FKBP12 to different targets.
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Affiliation(s)
- Ulrika Brath
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, Lund, Sweden
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Brath U, Akke M, Yang D, Kay LE, Mulder FAA. Functional Dynamics of Human FKBP12 Revealed by Methyl 13C Rotating Frame Relaxation Dispersion NMR Spectroscopy. J Am Chem Soc 2006; 128:5718-27. [PMID: 16637639 DOI: 10.1021/ja0570279] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Transverse relaxation dispersion NMR spectroscopy can provide atom-specific information about time scales, populations, and the extent of structural reorganization in proteins under equilibrium conditions. A method is described that uses side-chain methyl groups as local reporters for conformational transitions taking place in the microsecond regime. The experiment measures carbon nuclear spin relaxation rates in the presence of continuous wave off-resonance irradiation, in proteins uniformly enriched with 13C, and partially randomly labeled with 2H. The method was applied to human FK-506 binding protein (FKBP12), which uses a common surface for binding substrates in its dual role as both an immunophilin and folding assistant. Conformational dynamics on a time scale of approximately 130 micros were detected for methyl groups located in the substrate binding pocket, demonstrating its plasticity in the absence of substrate. The spatial arrangement of affected side-chain atoms suggests that substrate recognition involves the rapid relative movement of the subdomain comprising residues Ala81-Thr96 and that the observed dynamics play an important role in facilitating the interaction of this protein with its many partners, including calcineurin.
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Affiliation(s)
- Ulrika Brath
- Department of Biophysical Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden
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Mueller GA, Kirby TW, DeRose EF, London RE. NMR assignment of protein side chains using residue-correlated labeling and NOE spectra. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2003; 165:237-247. [PMID: 14643705 DOI: 10.1016/j.jmr.2003.08.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A new approach for the isotopic labeling of proteins is proposed that aims to facilitate side chain resonance assignments. Residue-correlated (RC) labeling is achieved by the expression of a protein on a medium containing a mixture of labeled, e.g., [U-13C,15N]amino acids, and NMR silent, [U-2H]amino acids. De novo synthesis of amino acids was suppressed by feedback inhibition by the amino acids in the growth medium and by the addition of beta-chloro-L-alanine, a transaminase inhibitor. Incorporation of these amino acids into synthesized proteins results in a relative diminution of inter-residue NOE interactions and a relative enhancement of intra-residue NOEs. Comparison of the resulting NOE spectra with those obtained from a uniformly labeled sample allows identification of intra-residue NOE peaks. Thus, this approach provides direct information for sidechain assignments in the NOE spectra, which are subsequently used for structural analysis. We have demonstrated the feasibility of this strategy for the 143 amino acid nuclease inhibitor NuiA, both at 35 degrees C, corresponding to a rotational correlation time of 9.5 ns, and at 5 degrees C, corresponding to a rotational correlation time of 22 ns.
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Affiliation(s)
- Geoffrey A Mueller
- National Institute of Environmental Health Sciences, Laboratory of Structural Biology, 111 Alexander Drive, PO Box 12233 MD MR-01, Research Triangle Park, NC 27709, USA
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Zwahlen C, Vincent SJF, Gardner KH, Kay LE. Significantly Improved Resolution for NOE Correlations from Valine and Isoleucine (Cγ2) Methyl Groups in 15N,13C- and 15N,13C,2H-Labeled Proteins. J Am Chem Soc 1998. [DOI: 10.1021/ja9742601] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Catherine Zwahlen
- Contribution from the Protein Engineering Network Centers of Excellence and Departments of Molecular and Medical Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, Biochemistry Research, Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8, and Program in Molecular Biology and Cancer, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
| | - Sébastien J. F. Vincent
- Contribution from the Protein Engineering Network Centers of Excellence and Departments of Molecular and Medical Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, Biochemistry Research, Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8, and Program in Molecular Biology and Cancer, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
| | - Kevin H. Gardner
- Contribution from the Protein Engineering Network Centers of Excellence and Departments of Molecular and Medical Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, Biochemistry Research, Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8, and Program in Molecular Biology and Cancer, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
| | - Lewis E. Kay
- Contribution from the Protein Engineering Network Centers of Excellence and Departments of Molecular and Medical Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, Biochemistry Research, Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8, and Program in Molecular Biology and Cancer, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
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Nicholson LK, Kay LE, Baldisseri DM, Arango J, Young PE, Bax A, Torchia DA. Dynamics of methyl groups in proteins as studied by proton-detected 13C NMR spectroscopy. Application to the leucine residues of staphylococcal nuclease. Biochemistry 1992; 31:5253-63. [PMID: 1606149 DOI: 10.1021/bi00138a003] [Citation(s) in RCA: 205] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This paper describes the application of recently developed nuclear magnetic resonance (NMR) pulse sequences to obtain information about the internal dynamics of isotopically enriched hydrophobic side chains in proteins. The two-dimensional spectra provided by the pulse sequences enable one to make accurate measurements of nuclear Overhauser effects (NOE) and longitudinal (T1) and transverse (T2) relaxation times of enriched methyl carbons in proteins. Herein, these techniques are used to investigate the internal dynamics of the 11 leucine side chains of staphylococcal nuclease (SNase), a small enzyme having Mr = 16.8K, in the absence and presence of ligands thymidine 3',5'-bisphosphate (pdTp) and Ca2+. We report the synthesis of [5,5'-13C2]leucine, the preparation of SNase containing the labeled leucine, the sequential assignment of the leucine methyl carbons and protons in the liganded and unliganded proteins, and the measurement of the 13C T1, T2, and NOE values for the SNase leucine methyl carbons. Analysis of the relaxation parameters using the formalism of Lipari and Szabo shows that the internal motions of the leucine methyl carbons are characterized by effective correlation times tau f (5-80 ps) and tau s (less than 2 ns). The fast motion is identified with the rapid rotation of the methyl group about the C gamma-C delta bond axis, while the slow motion is associated with reorientation of the C gamma-C delta bond axis itself. The mean squared order parameters associated with the latter motion, Ss2, lie in the range 0.34-0.92. The values of Ss2 correlate reasonably well with the temperature factors of the leucine methyl carbons obtained from the crystal structures, but some are smaller than anticipated on the basis of the fact that nearly all leucine methyl carbons are buried and have temperature factors no larger than that of the leucine backbone atoms. Five leucine residues in liganded SNase and eight in unliganded SNase have values of Ss2 less than 0.71. These order parameters correspond to large amplitude motions (angular excursions of 27-67 degrees) of the C gamma-C delta bond axis. These results indicate that, in solution, the internal motions of the leucine side chains of SNase are significantly larger than suggested by the X-ray structures or by qualitative analysis of NOESY spectra. Comparison of Ss2 values obtained from liganded and unliganded SNase reveals a strong correlation between delta Ss2 and distance between the leucine methyl carbon and the ligands.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- L K Nicholson
- Bone Research Branch, National Institute of Dental Research, National Institutes of Health, Bethesda, Maryland 20892
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