1
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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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2
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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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3
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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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4
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Krumkacheva O, Bagryanskaya E. EPR-based distance measurements at ambient temperature. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 280:117-126. [PMID: 28579097 DOI: 10.1016/j.jmr.2017.02.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 02/23/2017] [Accepted: 02/24/2017] [Indexed: 05/24/2023]
Abstract
Pulsed dipolar (PD) EPR spectroscopy is a powerful technique allowing for distance measurements between spin labels in the range of 2.5-10.0nm. It was proposed more than 30years ago, and nowadays is widely used in biophysics and materials science. Until recently, PD EPR experiments were limited to cryogenic temperatures (T<80K). Recently, application of spin labels with long electron spin dephasing time at room temperature such as triarylmethyl radicals and nitroxides with bulky substituents at a position close to radical centers enabled measurements at room temperature and even at physiologically relevant temperatures by PD EPR as well as other approaches based on EPR (e.g., relaxation enhancement; RE). In this paper, we review the features of PD EPR and RE at ambient temperatures, in particular, requirements on electron spin phase memory time, ways of immobilization of biomolecules, the influence of a linker between the spin probe and biomolecule, and future opportunities.
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Affiliation(s)
- Olesya Krumkacheva
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Pr. Lavrentjeva 9, Novosibirsk 630090, Russian Federation; Novosibirsk State University, Pirogova Street 2, Novosibirsk 630090, Russian Federation; International Tomography Center SB RAS, Institutskaya 3A, Novosibirsk 630090, Russian Federation.
| | - Elena Bagryanskaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Pr. Lavrentjeva 9, Novosibirsk 630090, Russian Federation; Novosibirsk State University, Pirogova Street 2, Novosibirsk 630090, Russian Federation.
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5
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Yang Z, Bridges MD, López CJ, Rogozhnikova OY, Trukhin DV, Brooks EK, Tormyshev V, Halpern HJ, Hubbell WL. A triarylmethyl spin label for long-range distance measurement at physiological temperatures using T1 relaxation enhancement. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 269:50-54. [PMID: 27214582 PMCID: PMC4958593 DOI: 10.1016/j.jmr.2016.05.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 05/09/2016] [Accepted: 05/10/2016] [Indexed: 05/19/2023]
Abstract
Site-directed spin labeling (SDSL) in combination with electron paramagnetic resonance (EPR) spectroscopy has become an important tool for measuring distances in proteins on the order of a few nm. For this purpose pairs of spin labels, most commonly nitroxides, are site-selectively introduced into the protein. Recent efforts to develop new spin labels are focused on tailoring the intrinsic properties of the label to either extend the upper limit of measurable distances at physiological temperature, or to provide a unique spectral lineshape so that selective pairwise distances can be measured in a protein or complex containing multiple spin label species. Triarylmethyl (TAM) radicals are the foundation for a new class of spin labels that promise to provide both capabilities. Here we report a new methanethiosulfonate derivative of a TAM radical that reacts rapidly and selectively with an engineered cysteine residue to generate a TAM containing side chain (TAM1) in high yield. With a TAM1 residue and Cu(2+) bound to an engineered Cu(2+) binding site, enhanced T1 relaxation of TAM should enable measurement of interspin distances up to 50Å at physiological temperature. To achieve favorable TAM1-labeled protein concentrations without aggregation, proteins are tethered to a solid support either site-selectively using an unnatural amino acid or via native lysine residues. The methodology is general and readily extendable to complex systems, including membrane proteins.
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Affiliation(s)
- Zhongyu Yang
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael D Bridges
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Carlos J López
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Olga Yu Rogozhnikova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia
| | - Dmitry V Trukhin
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia
| | - Evan K Brooks
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Victor Tormyshev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Howard J Halpern
- The Center for EPR Imaging in vivo Physiology, Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL 60637, USA.
| | - Wayne L Hubbell
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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6
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Jones CE, Berliner LJ. Nitroxide Spin-Labelling and Its Role in Elucidating Cuproprotein Structure and Function. Cell Biochem Biophys 2016; 75:195-202. [PMID: 27342129 DOI: 10.1007/s12013-016-0751-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 06/11/2016] [Indexed: 10/21/2022]
Abstract
Copper is one of the most abundant biological metals, and its chemical properties mean that organisms need sophisticated and multilayer mechanisms in place to maintain homoeostasis and avoid deleterious effects. Studying copper proteins requires multiple techniques, but electron paramagnetic resonance (EPR) plays a key role in understanding Cu(II) sites in proteins. When spin-labels such as aminoxyl radicals (commonly referred to as nitroxides) are introduced, then EPR becomes a powerful technique to monitor not only the coordination environment, but also to obtain structural information that is often not readily available from other techniques. This information can contribute to explaining how cuproproteins fold and misfold. The theory and practice of EPR can be daunting to the non-expert; therefore, in this mini review, we explore how nitroxide spin-labelling can be used to help the inorganic biochemist gain greater understanding of cuproprotein structure and function in vitro and how EPR imaging may help improve understanding of copper homoeostasis in vivo.
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Affiliation(s)
- Christopher E Jones
- The School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2759, Australia.
| | - Lawrence J Berliner
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, 80208-0183, USA
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7
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Evans EGB, Pushie MJ, Markham KA, Lee HW, Millhauser GL. Interaction between Prion Protein's Copper-Bound Octarepeat Domain and a Charged C-Terminal Pocket Suggests a Mechanism for N-Terminal Regulation. Structure 2016; 24:1057-67. [PMID: 27265848 DOI: 10.1016/j.str.2016.04.017] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/19/2016] [Accepted: 04/20/2016] [Indexed: 11/29/2022]
Abstract
Copper plays a critical role in prion protein (PrP) physiology. Cu(2+) binds with high affinity to the PrP N-terminal octarepeat (OR) domain, and intracellular copper promotes PrP expression. The molecular details of copper coordination within the OR are now well characterized. Here we examine how Cu(2+) influences the interaction between the PrP N-terminal domain and the C-terminal globular domain. Using nuclear magnetic resonance and copper-nitroxide pulsed double electron-electron resonance, with molecular dynamics refinement, we localize the position of Cu(2+) in its high-affinity OR-bound state. Our results reveal an interdomain cis interaction that is stabilized by a conserved, negatively charged pocket of the globular domain. Interestingly, this interaction surface overlaps an epitope recognized by the POM1 antibody, the binding of which drives rapid cerebellar degeneration mediated by the PrP N terminus. The resulting structure suggests that the globular domain regulates the N-terminal domain by binding the Cu(2+)-occupied OR within a complementary pocket.
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Affiliation(s)
- Eric G B Evans
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - M Jake Pushie
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada
| | - Kate A Markham
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Hsiau-Wei Lee
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Glenn L Millhauser
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
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8
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Copper-based pulsed dipolar ESR spectroscopy as a probe of protein conformation linked to disease states. Biophys J 2015; 107:1669-74. [PMID: 25296320 DOI: 10.1016/j.bpj.2014.07.068] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 07/18/2014] [Accepted: 07/30/2014] [Indexed: 11/21/2022] Open
Abstract
We demonstrate the ability of pulsed dipolar electron spin resonance (ESR) spectroscopy (PDS) to report on the conformation of Cu-Zn superoxide dismutase (SOD1) through the sensitive measurement of dipolar interactions between inherent Cu(2+) ions. Although the extent and the anisotropy of the Cu ESR spectrum provides challenges for PDS, Ku-band (17.3 GHz) double electron-electron resonance and double-quantum coherence variants of PDS coupled with distance reconstruction methods recover Cu-Cu distances in good agreement with crystal structures. Moreover, Cu-PDS measurements expose distinct differences between the conformational properties of wild-type SOD1 and a single-residue variant (I149T) that leads to the disease amyotrophic lateral sclerosis (ALS). The I149T protein displays a broader Cu-Cu distance distribution within the SOD1 dimer compared to wild-type. In a nitroxide (NO)-labeled sample, distance distributions obtained from Cu-Cu, Cu-NO, and NO-NO separations reveal increased structural heterogeneity within the protein and a tendency for mutant dimers to associate. In contrast, perturbations caused by the ALS mutation are completely masked in the crystal structure of I149T. Thus, PDS readily detects alterations in metalloenzyme solution properties not easily deciphered by other methods and in doing so supports the notion that increased range of motion and associations of SOD1 ALS variants contribute to disease progression.
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9
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Kuzhelev AA, Trukhin DV, Krumkacheva OA, Strizhakov RK, Rogozhnikova OY, Troitskaya TI, Fedin MV, Tormyshev VM, Bagryanskaya EG. Room-Temperature Electron Spin Relaxation of Triarylmethyl Radicals at the X- and Q-Bands. J Phys Chem B 2015; 119:13630-13640. [PMID: 26001103 DOI: 10.1021/acs.jpcb.5b03027] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Triarylmethyl radicals (trityls, TAMs) represent a relatively new class of spin labels. The long relaxation of trityls at room temperature in liquid solutions makes them a promising alternative for traditional nitroxides. In this work we have synthesized a series of TAMs including perdeuterated Finland trityl (D36 form), mono-, di-, and triester derivatives of Finland-D36 trityl, the deuterated form of OX63, the dodeca-n-butyl homologue of Finland trityl, and triamide derivatives of Finland trityl with primary and secondary amines attached. We have studied room-temperature relaxation properties of these TAMs in liquids using pulsed electron paramagnetic resonance (EPR) at two microwave frequency bands. We have found the clear dependence of phase memory time (Tm ∼ T2) on the magnetic field: room-temperature Tm values are ∼1.5-2.5 times smaller at the Q-band (34 GHz, 1.2 T) than at the X-band (9 GHz, 0.3 T). This trend is ascribed to the contribution from g-anisotropy that is negligible at lower magnetic fields but comes into play at the Q-band. In agreement with this, the difference between T1 and Tm becomes more pronounced at the Q-band than at the X-band due to increased contributions from incomplete motional averaging of g-anisotropy. Linear dependence of (1/Tm - 1/T1) on viscosity implies that g-anisotropy is modulated by rotational motion of the trityl radical. On the basis of the analysis of previous data and results of the present work, we conclude that, in the general situation where the spin label is at least partly mobile, the X-band is most suitable for application of trityls for room-temperature pulsed EPR distance measurements.
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Affiliation(s)
- Andrey A Kuzhelev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Dmitry V Trukhin
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Olesya A Krumkacheva
- International Tomography Center SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Rodion K Strizhakov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
| | - Olga Yu Rogozhnikova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Tatiana I Troitskaya
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Matvey V Fedin
- International Tomography Center SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Victor M Tormyshev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Elena G Bagryanskaya
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
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10
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Yang Z, Bridges M, Lerch MT, Altenbach C, Hubbell WL. Saturation Recovery EPR and Nitroxide Spin Labeling for Exploring Structure and Dynamics in Proteins. Methods Enzymol 2015; 564:3-27. [DOI: 10.1016/bs.mie.2015.07.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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11
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Bagryanskaya EG, Krumkacheva OA, Fedin MV, Marque SR. Development and Application of Spin Traps, Spin Probes, and Spin Labels. Methods Enzymol 2015; 563:365-96. [DOI: 10.1016/bs.mie.2015.06.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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12
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13
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Yang Z, Jiménez-Osés G, López CJ, Bridges MD, Houk KN, Hubbell WL. Long-range distance measurements in proteins at physiological temperatures using saturation recovery EPR spectroscopy. J Am Chem Soc 2014; 136:15356-65. [PMID: 25290172 PMCID: PMC4227719 DOI: 10.1021/ja5083206] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Indexed: 11/28/2022]
Abstract
Site-directed spin labeling in combination with EPR is a powerful method for providing distances on the nm scale in biological systems. The most popular strategy, double electron-electron resonance (DEER), is carried out at cryogenic temperatures (50-80 K) to increase the short spin-spin relaxation time (T2) upon which the technique relies. A challenge is to measure long-range distances (20-60 Å) in proteins near physiological temperatures. Toward this goal we are investigating an alternative approach based on the distance-dependent enhancement of spin-lattice relaxation rate (T1(-1)) of a nitroxide spin label by a paramagnetic metal. With a commonly used nitroxide side chain (R1) and Cu(2+), it has been found that interspin distances ≤25 Å can be determined in this way (Jun et al. Biochemistry 2006, 45, 11666). Here, the upper limit of the accessible distance is extended to ≈40 Å using spin labels with long T1, a high-affinity 5-residue Cu(2+) binding loop inserted into the protein sequence, and pulsed saturation recovery to measure relaxation enhancement. Time-domain Cu(2+) electron paramagnetic resonance, quantum mechanical calculations, and molecular dynamics simulations provide information on the structure and geometry of the Cu(2+) loop and indicate that the metal ion is well-localized in the protein. An important aspect of these studies is that both Cu(2+)/nitroxide DEER at cryogenic temperatures and T1 relaxation measurements at room temperature can be carried out on the same sample, allowing both validation of the relaxation method and assessment of the effect of freezing on protein structure.
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Affiliation(s)
- Zhongyu Yang
- Jules Stein Eye Institute and Department of
Chemistry and Biochemistry, University of
California, Los Angeles, California 90095, United States
| | - Gonzalo Jiménez-Osés
- Jules Stein Eye Institute and Department of
Chemistry and Biochemistry, University of
California, Los Angeles, California 90095, United States
| | - Carlos J. López
- Jules Stein Eye Institute and Department of
Chemistry and Biochemistry, University of
California, Los Angeles, California 90095, United States
| | | | - K. N. Houk
- Jules Stein Eye Institute and Department of
Chemistry and Biochemistry, University of
California, Los Angeles, California 90095, United States
| | - Wayne L. Hubbell
- Jules Stein Eye Institute and Department of
Chemistry and Biochemistry, University of
California, Los Angeles, California 90095, United States
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14
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Hubbell WL, López CJ, Altenbach C, Yang Z. Technological advances in site-directed spin labeling of proteins. Curr Opin Struct Biol 2013; 23:725-33. [PMID: 23850140 DOI: 10.1016/j.sbi.2013.06.008] [Citation(s) in RCA: 229] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 06/12/2013] [Indexed: 12/23/2022]
Abstract
Molecular flexibility over a wide time range is of central importance to the function of many proteins, both soluble and membrane. Revealing the modes of flexibility, their amplitudes, and time scales under physiological conditions is the challenge for spectroscopic methods, one of which is site-directed spin labeling EPR (SDSL-EPR). Here we provide an overview of some recent technological advances in SDSL-EPR related to investigation of structure, structural heterogeneity, and dynamics of proteins. These include new classes of spin labels, advances in measurement of long range distances and distance distributions, methods for identifying backbone and conformational fluctuations, and new strategies for determining the kinetics of protein motion.
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Affiliation(s)
- Wayne L Hubbell
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, United States.
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15
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Lueders P, Jäger H, Hemminga MA, Jeschke G, Yulikov M. Distance Measurements on Orthogonally Spin-Labeled Membrane Spanning WALP23 Polypeptides. J Phys Chem B 2013; 117:2061-8. [DOI: 10.1021/jp311287t] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Petra Lueders
- Laboratory of Physical Chemistry, ETH Zurich, Switzerland
| | - Heidrun Jäger
- Laboratory
of Biophysics, Wageningen University, Wageningen,
The Netherlands
| | - Marcus A. Hemminga
- Laboratory
of Biophysics, Wageningen University, Wageningen,
The Netherlands
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zurich, Switzerland
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, ETH Zurich, Switzerland
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16
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Mansiaux Y, Joseph AP, Gelly JC, de Brevern AG. Assignment of PolyProline II conformation and analysis of sequence--structure relationship. PLoS One 2011; 6:e18401. [PMID: 21483785 PMCID: PMC3069088 DOI: 10.1371/journal.pone.0018401] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 03/07/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Secondary structures are elements of great importance in structural biology, biochemistry and bioinformatics. They are broadly composed of two repetitive structures namely α-helices and β-sheets, apart from turns, and the rest is associated to coil. These repetitive secondary structures have specific and conserved biophysical and geometric properties. PolyProline II (PPII) helix is yet another interesting repetitive structure which is less frequent and not usually associated with stabilizing interactions. Recent studies have shown that PPII frequency is higher than expected, and they could have an important role in protein-protein interactions. METHODOLOGY/PRINCIPAL FINDINGS A major factor that limits the study of PPII is that its assignment cannot be carried out with the most commonly used secondary structure assignment methods (SSAMs). The purpose of this work is to propose a PPII assignment methodology that can be defined in the frame of DSSP secondary structure assignment. Considering the ambiguity in PPII assignments by different methods, a consensus assignment strategy was utilized. To define the most consensual rule of PPII assignment, three SSAMs that can assign PPII, were compared and analyzed. The assignment rule was defined to have a maximum coverage of all assignments made by these SSAMs. Not many constraints were added to the assignment and only PPII helices of at least 2 residues length are defined. CONCLUSIONS/SIGNIFICANCE The simple rules designed in this study for characterizing PPII conformation, lead to the assignment of 5% of all amino as PPII. Sequence-structure relationships associated with PPII, defined by the different SSAMs, underline few striking differences. A specific study of amino acid preferences in their N and C-cap regions was carried out as their solvent accessibility and contact patterns. Thus the assignment of PPII can be coupled with DSSP and thus opens a simple way for further analysis in this field.
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Affiliation(s)
- Yohann Mansiaux
- INSERM, UMR-S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Paris, France
- Université Paris Diderot - Paris 7, Paris, France
- Institut National de la Transfusion Sanguine (INTS), Paris, France
| | - Agnel Praveen Joseph
- INSERM, UMR-S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Paris, France
- Université Paris Diderot - Paris 7, Paris, France
- Institut National de la Transfusion Sanguine (INTS), Paris, France
| | - Jean-Christophe Gelly
- INSERM, UMR-S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Paris, France
- Université Paris Diderot - Paris 7, Paris, France
- Institut National de la Transfusion Sanguine (INTS), Paris, France
| | - Alexandre G. de Brevern
- INSERM, UMR-S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Paris, France
- Université Paris Diderot - Paris 7, Paris, France
- Institut National de la Transfusion Sanguine (INTS), Paris, France
- * E-mail:
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17
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Yang Z, Kise D, Saxena S. An Approach towards the Measurement of Nanometer Range Distances Based on Cu2+ Ions and ESR. J Phys Chem B 2010; 114:6165-74. [DOI: 10.1021/jp911637s] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhongyu Yang
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Drew Kise
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
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18
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Xue Y, Podkorytov IS, Rao DK, Benjamin N, Sun H, Skrynnikov NR. Paramagnetic relaxation enhancements in unfolded proteins: theory and application to drkN SH3 domain. Protein Sci 2009; 18:1401-24. [PMID: 19544584 DOI: 10.1002/pro.153] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Site-directed spin labeling in combination with paramagnetic relaxation enhancement (PRE) measurements is one of the most promising techniques for studying unfolded proteins. Since the pioneering work of Gillespie and Shortle (J Mol Biol 1997;268:158), PRE data from unfolded proteins have been interpreted using the theory that was originally developed for rotational spin relaxation. At the same time, it can be readily recognized that the relative motion of the paramagnetic tag attached to the peptide chain and the reporter spin such as (1)H(N) is best described as a translation. With this notion in mind, we developed a number of models for the PRE effect in unfolded proteins: (i) mutual diffusion of the two tethered spheres, (ii) mutual diffusion of the two tethered spheres subject to a harmonic potential, (iii) mutual diffusion of the two tethered spheres subject to a simulated mean-force potential (Smoluchowski equation); (iv) explicit-atom molecular dynamics simulation. The new models were used to predict the dependences of the PRE rates on the (1)H(N) residue number and static magnetic field strength; the results are appreciably different from the Gillespie-Shortle model. At the same time, the Gillespie-Shortle approach is expected to be generally adequate if the goal is to reconstruct the distance distributions between (1)H(N) spins and the paramagnetic center (provided that the characteristic correlation time is known with a reasonable accuracy). The theory has been tested by measuring the PRE rates in three spin-labeled mutants of the drkN SH3 domain in 2M guanidinium chloride. Two modifications introduced into the measurement scheme-using a reference compound to calibrate the signals from the two samples (oxidized and reduced) and using peak volumes instead of intensities to determine the PRE rates-lead to a substantial improvement in the quality of data. The PRE data from the denatured drkN SH3 are mostly consistent with the model of moderately expanded random-coil protein, although part of the data point toward a more compact structure (local hydrophobic cluster). At the same time, the radius of gyration reported by Choy et al. (J Mol Biol 2002;316:101) suggests that the protein is highly expanded. This seemingly contradictory evidence can be reconciled if one assumes that denatured drkN SH3 forms a conformational ensemble that is dominated by extended conformations, yet also contains compact (collapsed) species. Such behavior is apparently more complex than predicted by the model of a random-coil protein in good solvent/poor solvent.
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Affiliation(s)
- Yi Xue
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
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19
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Schweitzer-Stenner R. Distribution of conformations sampled by the central amino acid residue in tripeptides inferred from amide I band profiles and NMR scalar coupling constants. J Phys Chem B 2009; 113:2922-32. [PMID: 19243204 DOI: 10.1021/jp8087644] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The conformational preference of individual amino acid residues in the unfolded state of peptides and proteins is the subject of a continuous debate. Research has mostly been focused on alanine, owing to its abundance in proteins and its relevance for the understanding of helix <----> coil transitions. In the current study, we have analyzed the amide I band profiles of the IR, isotropic and anisotropic Raman, and VCD profiles of trialanine in terms of a conformational model which, for the first time, explicitly considers the entire ensemble of possible conformations rather than representative structures. The distribution function utilized for a satisfactory simulation of the amide I band profiles was found to also reproduce a set of five J coupling constants reported by Graf et al. (Graf, J.; et al. J. Am. Chem. Soc. 2007, 129, 1179). The results of our analysis reveal a PPII fraction of approximately 0.84 for the central alanine residue, which strongly corroborates the notion that alanine has a very high PPII propensity, exceeding the values obtained from restricted coil libraries. We performed a similar analysis for trivaline and found that the dominant fraction of its central residue is a beta-strand. The fraction of the respective distribution is 0.68. The remaining fraction contains contributions from helical and PPII conformations. The results of our analysis enable us to decide on the suitability of force fields used for MD simulations of short alanine-containing peptides. The paper establishes vibrational spectroscopy as a suitable method to explore the energy landscape of amino acid residues.
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Affiliation(s)
- Reinhard Schweitzer-Stenner
- Department of Chemistry, Drexel University, 32nd and Chestnut Streets, Philadelphia, Pennsylvania 19104, USA.
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20
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Rajapandian V, Raman SS, Hakkim V, Parthasarathi R, Subramanian V. Molecular mechanics and molecular dynamics study on azurin using extensible and systematic force field (ESFF). ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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Essiz SG, Coalson RD. Dynamic Linear Response Theory for Conformational Relaxation of Proteins. J Phys Chem B 2009; 113:10859-69. [DOI: 10.1021/jp900745u] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Sebnem G. Essiz
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Rob D. Coalson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
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22
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Jäger H, Koch A, Maus V, Spiess HW, Jeschke G. Relaxation-based distance measurements between a nitroxide and a lanthanide spin label. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2008; 194:254-263. [PMID: 18674941 DOI: 10.1016/j.jmr.2008.07.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Revised: 07/15/2008] [Accepted: 07/15/2008] [Indexed: 05/26/2023]
Abstract
Distance measurements by electron paramagnetic resonance techniques between labels attached to biomacromolecules provide structural information on systems that cannot be crystallized or are too large to be characterized by NMR methods. However, existing techniques are limited in their distance range and sensitivity. It is anticipated by theoretical considerations that these limits could be extended by measuring the enhancement of longitudinal relaxation of a nitroxide label due to a lanthanide complex label at cryogenic temperatures. The relaxivity of the dysprosium complex with the macrocyclic ligand DOTA can be determined without direct measurements of longitudinal relaxation rates of the lanthanide and without recourse to model compounds with well defined distance by analyzing the dependence of relaxation enhancement on either temperature or concentration in homogeneous glassy frozen solutions. Relaxivities determined by the two calibration techniques are in satisfying agreement with each other. Error sources for both techniques are examined. A distance of about 2.7 nm is measured in a model compound of the type nitroxide-spacer-lanthanide complex and is found in good agreement with the distance in a modeled structure. Theoretical considerations suggest that an increase of the upper distance limit requires measurements at lower fields and temperatures.
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Affiliation(s)
- H Jäger
- Max Planck Institute for Polymer Research, Mainz, Germany
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23
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Cheng MH, Coalson RD, Cascio M, Kurnikova M. Computational prediction of ion permeation characteristics in the glycine receptor modified by photo-sensitive compounds. J Comput Aided Mol Des 2008; 22:563-70. [PMID: 18368498 PMCID: PMC2822900 DOI: 10.1007/s10822-008-9200-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2007] [Accepted: 02/18/2008] [Indexed: 11/27/2022]
Abstract
We conduct computational analyses of ion permeation characteristics in a model glycine receptor (GlyR) modified by photo-sensitive compounds. In particular, we consider hypothetical attachment to the channel of charge-neutral chemical groups which can be photo-activated by shining light of an appropriate wavelength on the system. After illumination, the attached molecules become charged via a photodissociation process or excited into a charge-separated state (thus generating a significant electric dipole). We carry out Brownian Dynamics simulations of ion flow through the channel in the presence of the additional charges generated in this fashion. Based on these calculations, we predict that photo-activation of appropriately positioned photo-sensitive compounds near the channel mouth can significantly modify the rate of ion permeation and the current rectification ratio. Possible implications for GlyR-based device designs are briefly discussed.
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Affiliation(s)
- Mary Hongying Cheng
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Rob D. Coalson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Michael Cascio
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Maria Kurnikova
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15260, USA
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24
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Raman SS, Vijayaraj R, Parthasarathi R, Subramanian V. Helix forming tendency of valine substituted poly-alanine: a molecular dynamics investigation. J Phys Chem B 2008; 112:9100-4. [PMID: 18597521 DOI: 10.1021/jp7119813] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In this study, classical molecular dynamics simulations have been carried out on the valine (guest) substituted poly alanine (host) using the host-guest peptide approach to understand the role of valine in the formation and stabilization of helix. Valine has been substituted in the host peptide starting from N terminal to C terminal. Various structural parameters have been obtained from the molecular dynamics simulation to understand the tolerance of helical motif to valine. Depending on the position of valine in the host peptide, it stabilizes (or destabilizes) the formation of the helical structure. The substitution of valine in the poly alanine at some positions has no effect on the helix formation (deformation). It is interesting to observe the coexistence of 3 10 and alpha-helix in the peptides due to the dynamical nature of the hydrogen bonding interaction and sterical interactions.
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Affiliation(s)
- S Sundar Raman
- Chemical Laboratory, Central Leather Research Institute, Adyar, Chennai 600 020 India
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25
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Schiemann O, Prisner TF. Long-range distance determinations in biomacromolecules by EPR spectroscopy. Q Rev Biophys 2007; 40:1-53. [PMID: 17565764 DOI: 10.1017/s003358350700460x] [Citation(s) in RCA: 423] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy provides a variety of tools to study structures and structural changes of large biomolecules or complexes thereof. In order to unravel secondary structure elements, domain arrangements or complex formation, continuous wave and pulsed EPR methods capable of measuring the magnetic dipole coupling between two unpaired electrons can be used to obtain long-range distance constraints on the nanometer scale. Such methods yield reliably and precisely distances of up to 80 A, can be applied to biomolecules in aqueous buffer solutions or membranes, and are not size limited. They can be applied either at cryogenic or physiological temperatures and down to amounts of a few nanomoles. Spin centers may be metal ions, metal clusters, cofactor radicals, amino acid radicals, or spin labels. In this review, we discuss the advantages and limitations of the different EPR spectroscopic methods, briefly describe their theoretical background, and summarize important biological applications. The main focus of this article will be on pulsed EPR methods like pulsed electron-electron double resonance (PELDOR) and their applications to spin-labeled biosystems.
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Affiliation(s)
- Olav Schiemann
- Institute of Physical and Theoretical Chemistry, Center for Biomolecular Magnetic Resonance, J. W. Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany.
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26
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Schweitzer-Stenner R, Measey TJ. The alanine-rich XAO peptide adopts a heterogeneous population, including turn-like and polyproline II conformations. Proc Natl Acad Sci U S A 2007; 104:6649-54. [PMID: 17416675 PMCID: PMC1871840 DOI: 10.1073/pnas.0700006104] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2007] [Indexed: 11/18/2022] Open
Abstract
The solution structure of the hepta-alanine polypeptide Ac-X(2)A(7)O(2)-NH(2) (XAO) has been a matter of controversy in the current literature. On one side of the argument is a claim that the peptide adopts a mostly polyproline II (PPII) structure, with a <20% population of beta conformations at room temperature [Shi Z, Olson CA, Rose GA, Baldwin RL, Kallenbach NR (2002) Proc Natl Acad Sci USA 99:9190-9195], whereas the other side of the argument insists that the peptide exists as an ensemble of conformations, including multiple beta-turn structures [Makowska J, Rodziewicz-Motowidlo S, Baginska K, Vila JA, Liwo A, Chmurzynski L, Scheraga HA (2006) Proc Natl Acad Sci USA 103:1744-1749]. We have used an excitonic coupling model to simulate the amide I band of the FTIR, vibrational circular dichroism, and isotropic and anisotropic Raman spectra of XAO, where, for each residue, the backbone dihedral angle varphi was constrained by using the reported (3)J(CalphaHNH) values and a modified Karplus relation. The best reproduction of the experimental data could only be achieved by assuming an ensemble of conformations, which contains various beta-turn conformations ( approximately 26%), in addition to beta-strand ( approximately 23%) and PPII ( approximately 50%) conformations. PPII is the dominant conformation in segments not involved in turn formations. Most of the residues were found to sample the bridge region connecting the PPII and right-handed helix troughs in the Ramachandran plot, which is part of the very heterogeneous ensemble of conformations generally termed type IV beta-turn.
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