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Tomlinson JH, Kalverda AP, Calabrese AN. Fusidic acid resistance through changes in the dynamics of the drug target. Proc Natl Acad Sci U S A 2020; 117:25523-25531. [PMID: 32999060 PMCID: PMC7568287 DOI: 10.1073/pnas.2008577117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Antibiotic resistance in clinically important bacteria can be mediated by target protection mechanisms, whereby a protein binds to the drug target and protects it from the inhibitory effects of the antibiotic. The most prevalent source of clinical resistance to the antibiotic fusidic acid (FA) is expression of the FusB family of proteins that bind to the drug target (Elongation factor G [EF-G]) and promote dissociation of EF-G from FA-stalled ribosome complexes. FusB binding causes changes in both the structure and conformational flexibility of EF-G, but which of these changes drives FA resistance was not understood. We present here detailed characterization of changes in the conformational flexibility of EF-G in response to FusB binding and show that these changes are responsible for conferring FA resistance. Binding of FusB to EF-G causes a significant change in the dynamics of domain III of EF-GC3 that leads to an increase in a minor, more disordered state of EF-G domain III. This is sufficient to overcome the steric block of transmission of conformational changes within EF-G by which FA prevents release of EF-G from the ribosome. This study has identified an antibiotic resistance mechanism mediated by allosteric effects on the dynamics of the drug target.
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Affiliation(s)
- Jennifer H Tomlinson
- School of Molecular and Cellular Biology, University of Leeds, LS2 9JT Leeds, United Kingdom;
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, United Kingdom
| | - Arnout P Kalverda
- School of Molecular and Cellular Biology, University of Leeds, LS2 9JT Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, United Kingdom
| | - Antonio N Calabrese
- School of Molecular and Cellular Biology, University of Leeds, LS2 9JT Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, United Kingdom
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2
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Beck Erlach M, Koehler J, Crusca E, Munte CE, Kainosho M, Kremer W, Kalbitzer HR. Pressure dependence of side chain 13C chemical shifts in model peptides Ac-Gly-Gly-Xxx-Ala-NH 2. JOURNAL OF BIOMOLECULAR NMR 2017; 69:53-67. [PMID: 28913741 DOI: 10.1007/s10858-017-0134-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 09/05/2017] [Indexed: 06/07/2023]
Abstract
For evaluating the pressure responses of folded as well as intrinsically unfolded proteins detectable by NMR spectroscopy the availability of data from well-defined model systems is indispensable. In this work we report the pressure dependence of 13C chemical shifts of the side chain atoms in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH2 (Xxx, one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of a number of nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200 MPa. The size of the polynomial pressure coefficients B 1 and B 2 is dependent on the type of atom and amino acid studied. For HN, N and Cα the first order pressure coefficient B 1 is also correlated to the chemical shift at atmospheric pressure. The first and second order pressure coefficients of a given type of carbon atom show significant linear correlations suggesting that the NMR observable pressure effects in the different amino acids have at least partly the same physical cause. In line with this observation the magnitude of the second order coefficients of nuclei being direct neighbors in the chemical structure also are weakly correlated. The downfield shifts of the methyl resonances suggest that gauche conformers of the side chains are not preferred with pressure. The valine and leucine methyl groups in the model peptides were assigned using stereospecifically 13C enriched amino acids with the pro-R carbons downfield shifted relative to the pro-S carbons.
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Affiliation(s)
- Markus Beck Erlach
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, 93040, Regensburg, Germany
| | - Joerg Koehler
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, 93040, Regensburg, Germany
| | - Edson Crusca
- Institute of Chemistry, São Paulo State University (UNESP), Araraquara, 14800-060, Brazil
| | - Claudia E Munte
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, 93040, Regensburg, Germany
- Physics Institute of São Carlos, University of São Paulo, São Carlos, 13566-590, Brazil
| | - Masatsune Kainosho
- Graduate School of Science and Technology, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo, 192-0397, Japan
| | - Werner Kremer
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, 93040, Regensburg, Germany
| | - Hans Robert Kalbitzer
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, 93040, Regensburg, Germany.
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3
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Buchner S, Schlundt A, Lassak J, Sattler M, Jung K. Structural and Functional Analysis of the Signal-Transducing Linker in the pH-Responsive One-Component System CadC of Escherichia coli. J Mol Biol 2015; 427:2548-2561. [DOI: 10.1016/j.jmb.2015.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 04/13/2015] [Accepted: 05/06/2015] [Indexed: 10/23/2022]
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4
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Caballero D, Smith WW, O'Hern CS, Regan L. Equilibrium transitions between side-chain conformations in leucine and isoleucine. Proteins 2015; 83:1488-99. [PMID: 26018846 DOI: 10.1002/prot.24837] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 04/30/2015] [Accepted: 05/20/2015] [Indexed: 12/12/2022]
Abstract
Despite recent improvements in computational methods for protein design, we still lack a quantitative, predictive understanding of the intrinsic probabilities for amino acids to adopt particular side-chain conformations. Surprisingly, this question has remained unsettled for many years, in part because of inconsistent results from different experimental approaches. To explicitly determine the relative populations of different side-chain dihedral angles, we performed all-atom hard-sphere Langevin Dynamics simulations of leucine (Leu) and isoleucine (Ile) dipeptide mimetics with stereo-chemical constraints and repulsive-only steric interactions between non-bonded atoms. We determine the relative populations of the different χ(1) and χ(2) dihedral angle combinations as a function of the backbone dihedral angles ϕ and ψ. We also propose, and test, a mechanism for inter-conversion between the different side-chain conformations. Specifically, we discover that some of the transitions between side-chain dihedral angle combinations are very frequent, whereas others are orders of magnitude less frequent, because they require rare coordinated motions to avoid steric clashes. For example, to transition between different values of χ(2), the Leu side-chain bond angles κ(1) and κ(2) must increase, whereas to transition in χ(1), the Ile bond angles λ(1) and λ(2) must increase. These results emphasize the importance of computational approaches in stimulating further experimental studies of the conformations of side-chains in proteins. Moreover, our studies emphasize the power of simple steric models to inform our understanding of protein structure, dynamics, and design.
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Affiliation(s)
- Diego Caballero
- Department of Physics, Yale University, New Haven, Connecticut.,Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut
| | - W Wendell Smith
- Department of Physics, Yale University, New Haven, Connecticut
| | - Corey S O'Hern
- Department of Physics, Yale University, New Haven, Connecticut.,Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut.,Department of Mechanical Engineering & Materials Science, Yale University, New Haven, Connecticut.,Department of Applied Physics, Yale University, New Haven, Connecticut
| | - Lynne Regan
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut.,Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut.,Department of Chemistry, Yale University, New Haven, Connecticut
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5
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Ab Initio Calculations of Possible γ-Gauche Effects in the 13C-NMR for Methine and Carbonyl Carbons in Precise Polyethylene Acrylic Acid Copolymers. Molecules 2013; 18:9010-20. [PMID: 23899834 PMCID: PMC6269996 DOI: 10.3390/molecules18089010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Revised: 07/19/2013] [Accepted: 07/23/2013] [Indexed: 12/03/2022] Open
Abstract
The impacts of local polymer chain conformations on the methine and carbonyl 13C-NMR chemical shifts for polyethylene acrylic acid p(E-AA) copolymers were predicted using ab initio methods. Using small molecular cluster models, the magnitude and sign of the γ-gauche torsional angle effect, along with the impact of local tetrahedral structure distortions near the carbonyl group, on the 13C-NMR chemical shifts were determined. These 13C-NMR chemical shift variations were compared to the experimental trends observed for precise p(E-AA) copolymers as a function acid group spacing and degree of zinc-neutralization in the corresponding p(E-AA) ionomers. These ab initio calculations address the future ability of 13C-NMR chemical shift variations to provide information about the local chain conformations in p(E-AA) copolymer materials.
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Iešmantavičius V, Jensen MR, Ozenne V, Blackledge M, Poulsen FM, Kjaergaard M. Modulation of the Intrinsic Helix Propensity of an Intrinsically Disordered Protein Reveals Long-Range Helix–Helix Interactions. J Am Chem Soc 2013; 135:10155-63. [DOI: 10.1021/ja4045532] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | - Malene Ringkjøbing Jensen
- Institut de Biologie Structurale Jean-Pierre Ebel, CEA-CNRS-UJF UMR 5075,
41 rue Jules Horowitz, 38027 Grenoble, France
| | - Valéry Ozenne
- Institut de Biologie Structurale Jean-Pierre Ebel, CEA-CNRS-UJF UMR 5075,
41 rue Jules Horowitz, 38027 Grenoble, France
| | - Martin Blackledge
- Institut de Biologie Structurale Jean-Pierre Ebel, CEA-CNRS-UJF UMR 5075,
41 rue Jules Horowitz, 38027 Grenoble, France
| | - Flemming M. Poulsen
- Department
of Biology, University of Copenhagen, 1017
København K, Copenhagen,
Denmark
| | - Magnus Kjaergaard
- Department
of Biology, University of Copenhagen, 1017
København K, Copenhagen,
Denmark
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7
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Kjaergaard M, Andersen L, Nielsen LD, Teilum K. A Folded Excited State of Ligand-Free Nuclear Coactivator Binding Domain (NCBD) Underlies Plasticity in Ligand Recognition. Biochemistry 2013; 52:1686-93. [DOI: 10.1021/bi4001062] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Magnus Kjaergaard
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200
Copenhagen N, Denmark
| | - Lisbeth Andersen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200
Copenhagen N, Denmark
| | - Lau Dalby Nielsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200
Copenhagen N, Denmark
| | - Kaare Teilum
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200
Copenhagen N, Denmark
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8
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Kjaergaard M, Poulsen FM, Teilum K. Is a malleable protein necessarily highly dynamic? The hydrophobic core of the nuclear coactivator binding domain is well ordered. Biophys J 2012; 102:1627-35. [PMID: 22500763 DOI: 10.1016/j.bpj.2012.02.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Revised: 01/11/2012] [Accepted: 02/06/2012] [Indexed: 02/03/2023] Open
Abstract
The nuclear coactivator binding domain of CREB binding protein folds into remarkably different structures in complex with different ligands. To understand the mechanism of the structural adaptability in the nuclear coactivator binding domain (NCBD), we have compared the dynamics of the hydrophobic core of NCBD in the ligand-free state and in a well-folded complex with the ligand activator for thyroid hormone and retinoid receptors using multiple NMR methods including methyl chemical shifts, coupling constants, and methyl order parameters. From all NMR measures, the aliphatic side chains in the hydrophobic core are slightly more dynamic in the free protein than in the complex, but have mobility comparable to the hydrophobic cores of average folded proteins. Urea titration monitored by NMR reveals that all parts of the protein, including the side-chain packing in the hydrophobic core, denatures in a single cooperative process. The molten globule characteristics of NCBD are thus restricted to a slowly fluctuating tertiary structure. Consequently, the conformational plasticity of the protein is most likely related to its low overall stability rather than an intrinsically flexible protein structure. The well-defined structure supports a model of molecular recognition dominated by conformational selection, whereas only minor structural adjustments are necessary after the association.
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Affiliation(s)
- Magnus Kjaergaard
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
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9
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Kjaergaard M, Poulsen FM, Kragelund BB. Temperature-induced transitions in disordered proteins probed by NMR spectroscopy. Methods Mol Biol 2012; 896:233-47. [PMID: 22821528 DOI: 10.1007/978-1-4614-3704-8_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Intrinsically disordered proteins are abundant in nature and perform many important physiological functions. Multidimensional NMR spectroscopy has been crucial for the understanding of the conformational properties of disordered proteins and is increasingly used to probe their conformational ensembles. Compared to folded proteins, disordered proteins are more malleable and more easily perturbed by environmental factors. Accordingly, the experimental conditions and especially the temperature modify the structural and functional properties of disordered proteins. NMR spectroscopy allows analysis of temperature-induced structural changes at residue resolution using secondary chemical shift analysis, paramagnetic relaxation enhancement, and residual dipolar couplings. This chapter discusses practical aspects of NMR studies of temperature-induced structural changes in disordered proteins.
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Affiliation(s)
- Magnus Kjaergaard
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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10
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Kjaergaard M, Poulsen FM. Disordered proteins studied by chemical shifts. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2012; 60:42-51. [PMID: 22293398 DOI: 10.1016/j.pnmrs.2011.10.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 10/06/2011] [Indexed: 05/31/2023]
Affiliation(s)
- Magnus Kjaergaard
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 København N, Denmark
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