1
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Richardson JS, Williams CJ, Chen VB, Prisant MG, Richardson DC. The bad and the good of trends in model building and refinement for sparse-data regions: pernicious forms of overfitting versus good new tools and predictions. Acta Crystallogr D Struct Biol 2023; 79:1071-1078. [PMID: 37921807 PMCID: PMC10833350 DOI: 10.1107/s2059798323008847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 10/09/2023] [Indexed: 11/04/2023] Open
Abstract
Model building and refinement, and the validation of their correctness, are very effective and reliable at local resolutions better than about 2.5 Å for both crystallography and cryo-EM. However, at local resolutions worse than 2.5 Å both the procedures and their validation break down and do not ensure reliably correct models. This is because in the broad density at lower resolution, critical features such as protein backbone carbonyl O atoms are not just less accurate but are not seen at all, and so peptide orientations are frequently wrongly fitted by 90-180°. This puts both backbone and side chains into the wrong local energy minimum, and they are then worsened rather than improved by further refinement into a valid but incorrect rotamer or Ramachandran region. On the positive side, new tools are being developed to locate this type of pernicious error in PDB depositions, such as CaBLAM, EMRinger, Pperp diagnosis of ribose puckers, and peptide flips in PDB-REDO, while interactive modeling in Coot or ISOLDE can help to fix many of them. Another positive trend is that artificial intelligence predictions such as those made by AlphaFold2 contribute additional evidence from large multiple sequence alignments, and in high-confidence parts they provide quite good starting models for loops, termini or whole domains with otherwise ambiguous density.
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Affiliation(s)
- Jane S. Richardson
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA
| | | | - Vincent B. Chen
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA
| | - Michael G. Prisant
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA
| | - David C. Richardson
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA
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2
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Yang Z, Stein RA, Pink M, Madzelan P, Ngendahimana T, Rajca S, Wilson MA, Eaton SS, Eaton GR, Mchaourab HS, Rajca A. Cucurbit[7]uril Enhances Distance Measurements of Spin-Labeled Proteins. J Am Chem Soc 2023; 145:25726-25736. [PMID: 37963181 PMCID: PMC10961179 DOI: 10.1021/jacs.3c09184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
We report complex formation between the chloroacetamide 2,6-diazaadamantane nitroxide radical (ClA-DZD) and cucurbit[7]uril (CB-7), for which the association constant in water, Ka = 1.9 × 106 M-1, is at least 1 order of magnitude higher than the previously studied organic radicals. The radical is highly immobilized by CB-7, as indicated by the increase in the rotational correlation time, τrot, by a factor of 36, relative to that in the buffer solution. The X-ray structure of ClA-DZD@CB-7 shows the encapsulated DZD guest inside the undistorted CB-7 host, with the pendant group protruding outside. Upon addition of CB-7 to T4 Lysozyme (T4L) doubly spin-labeled with the iodoacetamide derivative of DZD, we observe the increase in τrot and electron spin coherence time, Tm, along with the narrowing of interspin distance distributions. Sensitivity of the DEER measurements at 83 K increases by a factor 4-9, compared to the common spin label such as MTSL, which is not affected by CB-7. Interspin distances of 3 nm could be reliably measured in water/glycerol up to temperatures near the glass transition/melting temperature of the matrix at 200 K, thus bringing us closer to the goal of supramolecular recognition-enabled long-distance DEER measurements at near physiological temperatures. The X-ray structure of DZD-T4L 65 at 1.12 Å resolution allows for unambiguous modeling of the DZD label (0.88 occupancy), indicating an undisturbed structure and conformation of the protein.
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Affiliation(s)
- Zhimin Yang
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Richard A. Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Maren Pink
- IUMSC, Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
| | - Peter Madzelan
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Thacien Ngendahimana
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Suchada Rajca
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Mark A. Wilson
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Sandra S. Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Gareth R. Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Hassane S. Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Andrzej Rajca
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
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3
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Chen M, Kálai T, Cascio D, Bridges MD, Whitelegge JP, Elgeti M, Hubbell WL. A Highly Ordered Nitroxide Side Chain for Distance Mapping and Monitoring Slow Structural Fluctuations in Proteins. APPLIED MAGNETIC RESONANCE 2023; 55:251-277. [PMID: 38357006 PMCID: PMC10861403 DOI: 10.1007/s00723-023-01618-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/06/2023] [Accepted: 09/09/2023] [Indexed: 02/16/2024]
Abstract
Site-directed spin labeling electron paramagnetic resonance (SDSL-EPR) is an established tool for exploring protein structure and dynamics. Although nitroxide side chains attached to a single cysteine via a disulfide linkage are commonly employed in SDSL-EPR, their internal flexibility complicates applications to monitor slow internal motions in proteins and to structure determination by distance mapping. Moreover, the labile disulfide linkage prohibits the use of reducing agents often needed for protein stability. To enable the application of SDSL-EPR to the measurement of slow internal dynamics, new spin labels with hindered internal motion are desired. Here, we introduce a highly ordered nitroxide side chain, designated R9, attached at a single cysteine residue via a non-reducible thioether linkage. The reaction to introduce R9 is highly selective for solvent-exposed cysteine residues. Structures of R9 at two helical sites in T4 Lysozyme were determined by X-ray crystallography and the mobility in helical sequences was characterized by EPR spectral lineshape analysis, Saturation Transfer EPR, and Saturation Recovery EPR. In addition, interspin distance measurements between pairs of R9 residues are reported. Collectively, all data indicate that R9 will be useful for monitoring slow internal structural fluctuations, and applications to distance mapping via dipolar spectroscopy and relaxation enhancement methods are anticipated. Supplementary Information The online version contains supplementary material available at 10.1007/s00723-023-01618-8.
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Affiliation(s)
- Mengzhen Chen
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 USA
| | - Tamás Kálai
- Institute of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Pécs, Szigeti St. 12, Pecs, 7624 Hungary
| | - Duilio Cascio
- Department of Biological Chemistry, UCLA-DOE Institute, Howard Hughes Medical Institute, and Molecular Biology Institute, University of California, Los Angeles, CA 90095 USA
| | - Michael D. Bridges
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 USA
| | - Julian P. Whitelegge
- The Pasarow Mass Spectrometry Laboratory, David Geffen School of Medicine, The Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095 USA
| | - Matthias Elgeti
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 USA
- Present Address: Institute for Drug Discovery, Leipzig University Medical Center, Härtelstr. 16-18, 04107 Leipzig, Germany
| | - Wayne L. Hubbell
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 USA
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4
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Yang Z, Stein RA, Pink M, Madzelan P, Ngendahimana T, Rajca S, Wilson MA, Eaton SS, Eaton GR, Mchaourab HS, Rajca A. Cucurbit[7]uril Enhances Distance Measurements of Spin-Labeled Proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.22.554361. [PMID: 37662277 PMCID: PMC10473685 DOI: 10.1101/2023.08.22.554361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
We report complex formation between the chloroacetamide 2,6-diazaadamantane nitroxide radical (ClA-DZD) and cucurbit[7]uril (CB-7), for which the association constant in water, Ka = 1.9 × 106 M-1, is at least one order of magnitude higher than the previously studied organic radicals. The radical is highly immobilized by CB-7, as indicated by the increase of the rotational correlation time, τrot, by a factor of 36, relative to that in the buffer solution. The X-ray structure of ClA-DZD@CB-7 shows the encapsulated DZD guest inside the undistorted CB-7 host, with the pendant group protruding outside. Upon addition of CB-7 to T4 Lysozyme (T4L) doubly spin-labeled with the iodoacetamide derivative of DZD, we observe the increase in τrot and electron spin coherence time, Tm, along with the narrowing of inter-spin distance distributions. Sensitivity of the DEER measurements at 83 K increases by a factor 4 - 9, compared to the common spin label such as MTSL, which is not affected by CB-7. Inter-spin distances of 3-nm could be reliably measured in water/glycerol up to temperatures near the glass transition/melting temperature of the matrix at 200 K, thus bringing us closer to the goal of supramolecular recognition-enabled long-distance DEER measurements at near physiological temperatures. The X-ray structure of DZD-T4L 65 at 1.12 Å resolution allows for unambiguous modeling of the DZD label (0.88 occupancy), indicating undisturbed structure and conformation of the protein.
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Affiliation(s)
- Zhimin Yang
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Richard A. Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Maren Pink
- IUMSC, Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
| | - Peter Madzelan
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Thacien Ngendahimana
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Suchada Rajca
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Mark A. Wilson
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Sandra S. Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Gareth R. Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Hassane S. Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Andrzej Rajca
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
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5
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Xi K, Zhu L. Automated Path Searching Reveals the Mechanism of Hydrolysis Enhancement by T4 Lysozyme Mutants. Int J Mol Sci 2022; 23:ijms232314628. [PMID: 36498954 PMCID: PMC9736071 DOI: 10.3390/ijms232314628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/16/2022] [Accepted: 11/19/2022] [Indexed: 11/25/2022] Open
Abstract
Bacteriophage T4 lysozyme (T4L) is a glycosidase that is widely applied as a natural antimicrobial agent in the food industry. Due to its wide applications and small size, T4L has been regarded as a model system for understanding protein dynamics and for large-scale protein engineering. Through structural insights from the single conformation of T4L, a series of mutations (L99A,G113A,R119P) have been introduced, which have successfully raised the fractional population of its only hydrolysis-competent excited state to 96%. However, the actual impact of these substitutions on its dynamics remains unclear, largely due to the lack of highly efficient sampling algorithms. Here, using our recently developed travelling-salesman-based automated path searching (TAPS), we located the minimum-free-energy path (MFEP) for the transition of three T4L mutants from their ground states to their excited states. All three mutants share a three-step transition: the flipping of F114, the rearrangement of α0/α1 helices, and final refinement. Remarkably, the MFEP revealed that the effects of the mutations are drastically beyond the expectations of their original design: (a) the G113A substitution not only enhances helicity but also fills the hydrophobic Cavity I and reduces the free energy barrier for flipping F114; (b) R119P barely changes the stability of the ground state but stabilizes the excited state through rarely reported polar contacts S117OG:N132ND2, E11OE1:R145NH1, and E11OE2:Q105NE2; (c) the residue W138 flips into Cavity I and further stabilizes the excited state for the triple mutant L99A,G113A,R119P. These novel insights that were unexpected in the original mutant design indicated the necessity of incorporating path searching into the workflow of rational protein engineering.
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6
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Liu Y, Biczysko M, Moriarty NW. A radical approach to radicals. Acta Crystallogr D Struct Biol 2022; 78:43-51. [PMID: 34981760 DOI: 10.1107/s2059798321010809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 10/18/2021] [Indexed: 11/10/2022] Open
Abstract
Nitroxide radicals are characterized by a long-lived spin-unpaired electronic ground state and are strongly sensitive to their chemical surroundings. Combined with electron paramagnetic resonance spectroscopy, these electronic features have led to the widespread application of nitroxide derivatives as spin labels for use in studying protein structure and dynamics. Site-directed spin labelling requires the incorporation of nitroxides into the protein structure, leading to a new protein-ligand molecular model. However, in protein crystallographic refinement nitroxides are highly unusual molecules with an atypical chemical composition. Because macromolecular crystallography is almost entirely agnostic to chemical radicals, their structural information is generally less accurate or even erroneous. In this work, proteins that contain an example of a radical compound (Chemical Component Dictionary ID MTN) from the nitroxide family were re-refined by defining its ideal structural parameters based on quantum-chemical calculations. The refinement results show that this procedure improves the MTN ligand geometries, while at the same time retaining higher agreement with experimental data.
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Affiliation(s)
- Youjia Liu
- International Center for Quantum and Molecular Structures, Shanghai University, Shanghai 200444, People's Republic of China
| | - Malgorzata Biczysko
- International Center for Quantum and Molecular Structures, Shanghai University, Shanghai 200444, People's Republic of China
| | - Nigel W Moriarty
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
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7
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Maleckis A, Herath ID, Otting G. Synthesis of 13C/ 19F/ 2H labeled indoles for use as tryptophan precursors for protein NMR spectroscopy. Org Biomol Chem 2021; 19:5133-5147. [PMID: 34032255 DOI: 10.1039/d1ob00611h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Synthesis of indoles labeled with 13C-1H and 13C-19F spin pairs is described. All syntheses utilize inexpensive carbon-13C dioxide as the 13C isotope source. Ruthenium-mediated ring-closing metathesis is the key step in construction of the 13C containing indole carbocycle. Fluorine is introduced via electrophilic fluorination at the 7-position and via palladium-mediated cross-coupling at the 4-position. Indole and fluoroindoles are viable tryptophan precursors for in vivo protein expression. We show that they are viable also in in vitro protein synthesis using standard E. coli S30 extracts. Incorporation of the synthesized 13C-1H and 13C-19F spin pair labeled tryptophans into proteins enables high-resolution and high-sensitivity nuclear magnetic resonance (NMR) spectroscopy.
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Affiliation(s)
- Ansis Maleckis
- Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006, Riga, Latvia.
| | - Iresha D Herath
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
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8
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Torricella F, Pierro A, Mileo E, Belle V, Bonucci A. Nitroxide spin labels and EPR spectroscopy: A powerful association for protein dynamics studies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140653. [PMID: 33757896 DOI: 10.1016/j.bbapap.2021.140653] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 01/01/2023]
Abstract
Site-Directed Spin Labelling (SDSL) technique is based on the attachment of a paramagnetic label onto a specific position of a protein (or other bio-molecules) and the subsequent study by Electron Paramagnetic Resonance (EPR) spectroscopy. In particular, continuous-wave EPR (cw-EPR) spectra can detect the local conformational dynamics for proteins under various conditions. Moreover, pulse-EPR experiments on doubly spin-labelled proteins allow measuring distances between spin centres in the 1.5-8 nm range, providing information about structures and functions. This review focuses on SDSL-EPR spectroscopy as a structural biology tool to investigate proteins using nitroxide labels. The versatility of this spectroscopic approach for protein structural characterization has been demonstrated through the choice of recent studies. The main aim is to provide a general overview of the technique, particularly for non-experts, to spread the applicability of this technique in various fields of structural biology.
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Affiliation(s)
- F Torricella
- CERM-Magnetic Resonance Center, Department of Chemistry, University of Florence, via L.Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - A Pierro
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France
| | - E Mileo
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France
| | - V Belle
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France
| | - A Bonucci
- CERM-Magnetic Resonance Center, Department of Chemistry, University of Florence, via L.Sacconi 6, 50019 Sesto Fiorentino, Italy; Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France.
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9
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Martin PD, Svensson B, Thomas DD, Stoll S. Trajectory-Based Simulation of EPR Spectra: Models of Rotational Motion for Spin Labels on Proteins. J Phys Chem B 2019; 123:10131-10141. [PMID: 31693365 DOI: 10.1021/acs.jpcb.9b02693] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Direct time-domain simulation of continuous-wave (CW) electron paramagnetic resonance (EPR) spectra from molecular dynamics (MD) trajectories has become increasingly popular, especially for proteins labeled with nitroxide spin labels. Due to the time-consuming nature of simulating adequately long MD trajectories, two approximate methods have been developed to reduce the MD-trajectory length required for modeling EPR spectra: hindered Brownian diffusion (HBD) and hidden Markov models (HMMs). Here, we assess the accuracy of these two approximate methods relative to direct simulations from MD trajectories for three spin-labeled protein systems (a simple helical peptide, a soluble protein, and a membrane protein) and two nitroxide spin labels with differing mobilities (R1 and 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid (TOAC)). We find that the HMMs generally outperform HBD. Although R1 dynamics partially resembles hindered Brownian diffusion, HMMs accommodate the multiple dynamic time scales for the transitions between rotameric states of R1 that cannot be captured accurately by a HBD model. The MD trajectories of the TOAC-labeled proteins show that its dynamics closely resembles slow multisite exchange between twist-boat and chair ring puckering states. This motion is modeled well by HMM but not by HBD. All MD-trajectory data processing, stochastic trajectory simulations, and CW EPR spectral simulations are implemented in EasySpin, a free software package for MATLAB.
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Affiliation(s)
| | | | | | - Stefan Stoll
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
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10
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Consentius P, Loll B, Gohlke U, Alings C, Müller C, Müller R, Teutloff C, Heinemann U, Kaupp M, Wahl MC, Risse T. Internal Dynamics of the 3-Pyrroline-N-Oxide Ring in Spin-Labeled Proteins. J Phys Chem Lett 2017; 8:1113-1117. [PMID: 28221042 DOI: 10.1021/acs.jpclett.6b02971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Site-directed spin labeling is a versatile tool to study structure as well as dynamics of proteins using EPR spectroscopy. Methanethiosulfonate (MTS) spin labels tethered through a disulfide linkage to an engineered cysteine residue were used in a large number of studies to extract structural as well as dynamic information on the protein from the rotational dynamics of the nitroxide moiety. The ring itself was always considered to be a rigid body. In this contribution, we present a combination of high-resolution X-ray crystallography and EPR spectroscopy of spin-labeled protein single crystals demonstrating that the nitroxide ring inverts fast at ambient temperature while exhibiting nonplanar conformations at low temperature. We have used quantum chemical calculations to explore the potential energy that determines the ring dynamics as well as the impact of the geometry on the magnetic parameters probed by EPR spectroscopy.
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Affiliation(s)
- Philipp Consentius
- Institute of Chemistry and Biochemistry, Freie Universität Berlin , Takustraße 3, 14195 Berlin, Germany
| | - Bernhard Loll
- Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Freie Universität Berlin , Takustraße 6, 14195 Berlin, Germany
| | - Ulrich Gohlke
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association , Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Claudia Alings
- Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Freie Universität Berlin , Takustraße 6, 14195 Berlin, Germany
| | - Carsten Müller
- Institute of Chemistry and Biochemistry, Freie Universität Berlin , Takustraße 3, 14195 Berlin, Germany
| | - Robert Müller
- Institute of Chemistry, Technische Universität Berlin , Sekr. C7, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Christian Teutloff
- Department of Physics, Freie Universität Berlin , Arnimallee 14, D-14195 Berlin, Germany
- Berlin Joint EPR Laboratory, Freie Universität Berlin , 14195 Berlin, Germany
| | - Udo Heinemann
- Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Freie Universität Berlin , Takustraße 6, 14195 Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association , Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Martin Kaupp
- Institute of Chemistry, Technische Universität Berlin , Sekr. C7, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Markus C Wahl
- Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Freie Universität Berlin , Takustraße 6, 14195 Berlin, Germany
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography , Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Thomas Risse
- Institute of Chemistry and Biochemistry, Freie Universität Berlin , Takustraße 3, 14195 Berlin, Germany
- Berlin Joint EPR Laboratory, Freie Universität Berlin , 14195 Berlin, Germany
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11
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Consentius P, Gohlke U, Loll B, Alings C, Heinemann U, Wahl MC, Risse T. Combining EPR spectroscopy and X-ray crystallography to elucidate the structure and dynamics of conformationally constrained spin labels in T4 lysozyme single crystals. Phys Chem Chem Phys 2017; 19:20723-20734. [DOI: 10.1039/c7cp03144k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Unraveling structural and dynamic details of spin labeled proteins using a combination of single crystal EPR spectroscopy and X-ray crystallography.
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Affiliation(s)
- Philipp Consentius
- Freie Universität Berlin
- Institute of Chemistry and Biochemistry
- 14195 Berlin
- Germany
| | - Ulrich Gohlke
- Medicine in the Helmholtz Association
- 13125 Berlin
- Germany
| | - Bernhard Loll
- Freie Universität Berlin
- Institute of Chemistry and Biochemistry
- Laboratory of Structural Biochemistry
- 14195 Berlin
- Germany
| | - Claudia Alings
- Freie Universität Berlin
- Institute of Chemistry and Biochemistry
- Laboratory of Structural Biochemistry
- 14195 Berlin
- Germany
| | - Udo Heinemann
- Freie Universität Berlin
- Institute of Chemistry and Biochemistry
- 14195 Berlin
- Germany
- Medicine in the Helmholtz Association
| | - Markus C. Wahl
- Freie Universität Berlin
- Institute of Chemistry and Biochemistry
- Laboratory of Structural Biochemistry
- 14195 Berlin
- Germany
| | - Thomas Risse
- Freie Universität Berlin
- Institute of Chemistry and Biochemistry
- 14195 Berlin
- Germany
- Berlin Joint EPR Laboratory, Freie Universität Berlin
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