1
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Kaminker R, Kaminker I, Gutekunst WR, Luo Y, Lee S, Niu J, Han S, Hawker CJ. Tuning conformation and properties of peptidomimetic backbones through dual N/C α-substitution. Chem Commun (Camb) 2018; 54:5237-5240. [PMID: 29726557 PMCID: PMC6089238 DOI: 10.1039/c8cc01356j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We demonstrate that changing the backbone between peptides, peptoids and the underexplored dual N/Cα-substituted peptoids analogues allows for control over the preferred conformation of the intrinsically disordered biomimetic oligomers. The conformation tunability is directly probed using electron paramagnetic resonance (EPR), and is shown to manifest itself in differences in the nanoparticle-oligomer hybridization propensity.
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Affiliation(s)
- R Kaminker
- Materials Research Laboratory, University of California, Santa Barbara, California 93106, USA.
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2
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Northrup JD, Mancini G, Purcell CR, Schafmeister CE. Development of Spiroligomer-Peptoid Hybrids. J Org Chem 2017; 82:13020-13033. [PMID: 29161507 DOI: 10.1021/acs.joc.7b01956] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Creating functional macromolecules that possess the diversity and functionality of proteins poses an enormous challenge, as this requires large, preorganized macromolecules to facilitate interactions. Peptoids have been shown to interact with proteins, and combinatorial libraries of peptoids have been useful in discovering new ligands for protein binding. We have created spiroligomer-peptoid hybrids that have a spirocyclic core that preorganizes functional groups in three-dimensional space. By utilizing spiroligomers, we can reduce the number of rotatable bonds between functional groups while increasing the stereochemical diversity of the molecules. We have synthesized 15 new spiroligomer monomer amines that contain two stereocenters and three functional groups (67-84% yields from a common hydantoin starting material) as well as a spiroligomer trimer 25 with six stereocenters and five functional groups. These 16 amines were used to synthesize five first-generation spiroligomer-peptoids hybrids.
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Affiliation(s)
- Justin D Northrup
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
| | - Giulia Mancini
- Department of Chemistry, University of the Sciences , Philadelphia, Pennsylvania 19104, United States
| | - Claire R Purcell
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
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3
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Marshall GR, Ballante F. Limiting Assumptions in the Design of Peptidomimetics. Drug Dev Res 2017; 78:245-267. [DOI: 10.1002/ddr.21406] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Garland R. Marshall
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
| | - Flavio Ballante
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
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4
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Pan Y, Neupane S, Farmakes J, Bridges M, Froberg J, Rao J, Qian SY, Liu G, Choi Y, Yang Z. Probing the structural basis and adsorption mechanism of an enzyme on nano-sized protein carriers. NANOSCALE 2017; 9:3512-3523. [PMID: 28244542 DOI: 10.1039/c7nr00276a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Silica nanoparticles (SiNPs) are important nano-sized, solid-state carriers/hosts to load, store, and deliver biological or pharmaceutical cargoes. They are also good potential solid supports to immobilize proteins for fundamental protein structure and dynamics studies. However, precaution is necessary when using SiNPs in these areas because adsorption might alter the activity of the cargoes, especially when enzymes are loaded. Therefore, it becomes important to understand the structural basis of the cargo enzyme activity changes, if there is any. The high complexity and dynamics of the nano-bio interface present many challenges. Reported here is a comprehensive study of the structure, dynamics, and activity of a model enzyme, T4 lysozyme, upon adsorption to a few surface-modified SiNPs using several experimental techniques. Not surprisingly, a significant activity loss on each studied SiNP was found. The structural basis of the activity loss was identified based on results from a unique technique, the Electron Paramagnetic Resonance (EPR) spectroscopy, which probes structural information regardless of the complexity. Several docking models of the enzyme on SiNPs with different surfaces, at different enzyme-to-SiNP ratios are proposed. Interestingly, we found that the adsorbed enzyme can be desorbed via pH adjustment, which highlighted the potential to use SiNPs for enzyme/protein delivery or storage due to the high capacity. In order to use SiNPs as enzyme hosts, minimizing the enzymatic activity loss upon adsorption is needed. Lastly, the work outlined here demonstrate the use of EPR in probing structural information on the complex (inorganic)nano-bio interface.
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Affiliation(s)
- Yanxiong Pan
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA.
| | - Sunanda Neupane
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA.
| | - Jasmin Farmakes
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA.
| | - Michael Bridges
- Jules Stein Eye Institute, University of California, Los Angeles, CA 90025, USA
| | - James Froberg
- Department of Physics, North Dakota State University, Fargo, ND 58108, USA
| | - Jiajia Rao
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA
| | - Steven Y Qian
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND 58108, USA
| | - Guodong Liu
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA.
| | - Yongki Choi
- Department of Physics, North Dakota State University, Fargo, ND 58108, USA
| | - Zhongyu Yang
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA.
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5
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Di Valentin M, Albertini M, Dal Farra MG, Zurlo E, Orian L, Polimeno A, Gobbo M, Carbonera D. Light-Induced Porphyrin-Based Spectroscopic Ruler for Nanometer Distance Measurements. Chemistry 2016; 22:17204-17214. [DOI: 10.1002/chem.201603666] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Indexed: 12/28/2022]
Affiliation(s)
- Marilena Di Valentin
- Dipartimento di Scienze Chimiche; Università di Padova; via Marzolo 1 35131 Padova Italy
| | - Marco Albertini
- Dipartimento di Scienze Chimiche; Università di Padova; via Marzolo 1 35131 Padova Italy
| | - Maria Giulia Dal Farra
- Dipartimento di Scienze Chimiche; Università di Padova; via Marzolo 1 35131 Padova Italy
| | - Enrico Zurlo
- Dipartimento di Scienze Chimiche; Università di Padova; via Marzolo 1 35131 Padova Italy
- Leiden Institute of Physics; Leiden University; Niels Bohrweg 2 2333 CA Leiden The Netherlands
| | - Laura Orian
- Dipartimento di Scienze Chimiche; Università di Padova; via Marzolo 1 35131 Padova Italy
| | - Antonino Polimeno
- Dipartimento di Scienze Chimiche; Università di Padova; via Marzolo 1 35131 Padova Italy
| | - Marina Gobbo
- Dipartimento di Scienze Chimiche; Università di Padova; via Marzolo 1 35131 Padova Italy
| | - Donatella Carbonera
- Dipartimento di Scienze Chimiche; Università di Padova; via Marzolo 1 35131 Padova Italy
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6
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Cheong JE, Pfeiffer CT, Northrup JD, Parker MF, Schafmeister CE. An improved, scalable synthesis of bis-amino acids. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.09.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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7
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Qi M, Hülsmann M, Godt A. Spacers for Geometrically Well-Defined Water-Soluble Molecular Rulers and Their Application. J Org Chem 2016; 81:2549-71. [DOI: 10.1021/acs.joc.6b00125] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Mian Qi
- Faculty of Chemistry and
Center for Molecular Materials (MC2), Bielefeld University, Universitätsstraße
25, 33615 Bielefeld, Germany
| | - Miriam Hülsmann
- Faculty of Chemistry and
Center for Molecular Materials (MC2), Bielefeld University, Universitätsstraße
25, 33615 Bielefeld, Germany
| | - Adelheid Godt
- Faculty of Chemistry and
Center for Molecular Materials (MC2), Bielefeld University, Universitätsstraße
25, 33615 Bielefeld, Germany
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8
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Takahashi T, Vo Ngo BC, Xiao L, Arya G, Heller MJ. Molecular mechanical properties of short-sequence peptide enzyme mimics. J Biomol Struct Dyn 2015; 34:463-74. [DOI: 10.1080/07391102.2015.1039586] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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9
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Hintze C, Schütze F, Drescher M, Mecking S. Probing of chain conformations in conjugated polymer nanoparticles by electron spin resonance spectroscopy. Phys Chem Chem Phys 2015; 17:32289-96. [DOI: 10.1039/c5cp05749c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Direct observation of individual conjugated polymer chain conformations in nanoparticles by ESR distance measurements.
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Affiliation(s)
- C. Hintze
- Department of Chemistry
- University of Konstanz
- 78464 Konstanz
- Germany
| | - F. Schütze
- Department of Chemistry
- University of Konstanz
- 78464 Konstanz
- Germany
| | - M. Drescher
- Department of Chemistry
- University of Konstanz
- 78464 Konstanz
- Germany
| | - S. Mecking
- Department of Chemistry
- University of Konstanz
- 78464 Konstanz
- Germany
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10
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Valera S, Bode BE. Strategies for the synthesis of yardsticks and abaci for nanometre distance measurements by pulsed EPR. Molecules 2014; 19:20227-56. [PMID: 25479188 PMCID: PMC6271543 DOI: 10.3390/molecules191220227] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 11/19/2014] [Accepted: 11/27/2014] [Indexed: 01/18/2023] Open
Abstract
Pulsed electron paramagnetic resonance (EPR) techniques have been found to be efficient tools for the elucidation of structure in complex biological systems as they give access to distances in the nanometre range. These measurements can provide additional structural information such as relative orientations, structural flexibility or aggregation states. A wide variety of model systems for calibration and optimisation of pulsed experiments has been synthesised. Their design is based on mimicking biological systems or materials in specific properties such as the distances themselves and the distance distributions. Here, we review selected approaches to the synthesis of chemical systems bearing two or more spin centres, such as nitroxide or trityl radicals, metal ions or combinations thereof and outline their application in pulsed EPR distance measurements.
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Affiliation(s)
- Silvia Valera
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, KY16 9ST Fife, UK
| | - Bela E Bode
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, KY16 9ST Fife, UK.
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11
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Tsvetkov YD. Nitroxyls and PELDOR: Nitroxyl radicals in pulsed electron-electron double resonance spectroscopy. J STRUCT CHEM+ 2013. [DOI: 10.1134/s0022476613070044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Sarver JL, Townsend JE, Rajapakse G, Jen-Jacobson L, Saxena S. Simulating the dynamics and orientations of spin-labeled side chains in a protein-DNA complex. J Phys Chem B 2012; 116:4024-33. [PMID: 22404310 PMCID: PMC3325110 DOI: 10.1021/jp211094n] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Site-directed spin labeling, wherein a nitroxide side chain is introduced into a protein at a selected mutant site, is increasingly employed to investigate biological systems by electron spin resonance (ESR) spectroscopy. An understanding of the packing and dynamics of the spin label is needed to extract the biologically relevant information about the macromolecule from ESR measurements. In this work, molecular dynamics (MD) simulations were performed on the spin-labeled restriction endonuclease, EcoRI in complex with DNA. Mutants of this homodimeric enzyme were previously constructed, and distance measurements were performed using the double electron electron resonance experiment. These correlated distance constraints have been leveraged with MD simulations to learn about side chain packing and preferred conformers of the spin label on sites in an α-helix and a β-strand. We found three dihedral angles of the spin label side chain to be most sensitive to the secondary structure where the spin label was located. Conformers sampled by the spin label differed between secondary structures as well. C(α)-C(α) distance distributions were constructed and used to extract details about the protein backbone mobility at the two spin labeled sites. These simulation studies enhance our understanding of the behavior of spin labels in proteins and thus expand the ability of ESR spectroscopy to contribute to knowledge of protein structure and dynamics.
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Affiliation(s)
- Jessica L. Sarver
- Department of Chemistry, University of Pittsburgh 219 Parkman Ave., Pittsburgh, PA 15260
| | - Jacqueline E. Townsend
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Ave., Pittsburgh, PA 15260
| | - Gayathri Rajapakse
- Department of Chemistry, University of Pittsburgh 219 Parkman Ave., Pittsburgh, PA 15260
| | - Linda Jen-Jacobson
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Ave., Pittsburgh, PA 15260
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh 219 Parkman Ave., Pittsburgh, PA 15260
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13
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Jeschke G, Sajid M, Schulte M, Ramezanian N, Volkov A, Zimmermann H, Godt A. Flexibility of shape-persistent molecular building blocks composed of p-phenylene and ethynylene units. J Am Chem Soc 2010; 132:10107-17. [PMID: 20590116 DOI: 10.1021/ja102983b] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ethynylene and p-phenylene are frequently employed constitutional units in constructing the backbone of nanoscopic molecules with specific shape and mechanical or electronic function. How well these properties are defined depends on the flexibility of the backbone, which can be characterized via the end-to-end distance distribution. This distribution is accessible by pulse electron paramagnetic resonance (EPR) distance measurements between spin labels that are attached at the backbone. Four sets of oligomers with different sequences of p-phenylene and ethynylene units and different spin labels were prepared using polar tagging as a tool for simple isolation of the targeted compounds. By variation of backbone length, of the sequence of p-phenylene and ethynylene units, and of the spin labels a consistent coarse-grained model for backbone flexibility of oligo(p-phenyleneethynylene)s and oligo(p-phenylenebutadiynylene)s is obtained. The relation of this harmonic segmented chain model to the worm-like chain model for shape-persistent polymers and to atomistic molecular dynamics simulations is discussed. Oligo(p-phenylenebutadiynylene)s are found to be more flexible than oligo(p-phenyleneethynylene)s, but only slightly so. The end-to-end distance distribution measured in a glassy state of the solvent at a temperature of 50 K is found to depend on the glass transition temperature of the solvent. In the range between 91 and 373 K this dependence is in quantitative agreement with expectations for flexibility due to harmonic bending. For the persistence lengths at 298 K our data predict values of (13.8 +/- 1.5) nm for poly(p-phenyleneethynylene)s and of (11.8 +/- 1.5) nm for poly(p-phenylenebutadiynylene)s.
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Affiliation(s)
- Gunnar Jeschke
- Laboratory for Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland.
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14
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Gullà SV, Sharma G, Borbat P, Freed JH, Ghimire H, Benedikt MR, Holt NL, Lorigan GA, Rege K, Mavroidis C, Budil DE. Molecular-scale force measurement in a coiled-coil peptide dimer by electron spin resonance. J Am Chem Soc 2010; 131:5374-5. [PMID: 19331323 DOI: 10.1021/ja900230w] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new method for measuring forces between small protein domains based on double electron-electron resonance (DEER) spectroscopy is demonstrated using a model peptide derived from the alpha-helical coiled-coil leucine zipper of yeast transcriptional activator GCN4. The equilibrium distribution of distances between two nitroxide spin labels rigidly attached to the helices of the dimer was determined by DEER and yielded a closing force of 100 +/- 10 pN between monomers, in excellent agreement with theoretical predictions.
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Affiliation(s)
- Stefano V Gullà
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
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15
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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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16
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17
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Maayan G. Conformational Control in Metallofoldamers: Design, Synthesis and Structural Properties. European J Org Chem 2009. [DOI: 10.1002/ejoc.200900637] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Galia Maayan
- Department of Chemistry, University of Florida, P. O. Box 117200, Gainesville, FL 32611‐7200, USA
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18
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Lovett JE, Hoffmann M, Cnossen A, Shutter ATJ, Hogben HJ, Kay CWM, Timmel CR, Anderson HL. Probing Flexibility in Porphyrin-Based Molecular Wires Using Double Electron Electron Resonance. J Am Chem Soc 2009; 131:13852-9. [DOI: 10.1021/ja905796z] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Janet E. Lovett
- Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom, Deptartment of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom, Synchrotron Radiation Source, Daresbury Laboratory, Warrington WA4 4AD, United Kingdom, Department of Chemistry,
| | - Markus Hoffmann
- Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom, Deptartment of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom, Synchrotron Radiation Source, Daresbury Laboratory, Warrington WA4 4AD, United Kingdom, Department of Chemistry,
| | - Arjen Cnossen
- Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom, Deptartment of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom, Synchrotron Radiation Source, Daresbury Laboratory, Warrington WA4 4AD, United Kingdom, Department of Chemistry,
| | - Alexander T. J. Shutter
- Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom, Deptartment of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom, Synchrotron Radiation Source, Daresbury Laboratory, Warrington WA4 4AD, United Kingdom, Department of Chemistry,
| | - Hannah J. Hogben
- Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom, Deptartment of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom, Synchrotron Radiation Source, Daresbury Laboratory, Warrington WA4 4AD, United Kingdom, Department of Chemistry,
| | - Christopher W. M. Kay
- Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom, Deptartment of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom, Synchrotron Radiation Source, Daresbury Laboratory, Warrington WA4 4AD, United Kingdom, Department of Chemistry,
| | - Christiane R. Timmel
- Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom, Deptartment of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom, Synchrotron Radiation Source, Daresbury Laboratory, Warrington WA4 4AD, United Kingdom, Department of Chemistry,
| | - Harry L. Anderson
- Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom, Deptartment of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom, Synchrotron Radiation Source, Daresbury Laboratory, Warrington WA4 4AD, United Kingdom, Department of Chemistry,
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19
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Ghimire H, McCarrick RM, Budil DE, Lorigan GA. Significantly improved sensitivity of Q-band PELDOR/DEER experiments relative to X-band is observed in measuring the intercoil distance of a leucine zipper motif peptide (GCN4-LZ). Biochemistry 2009; 48:5782-4. [PMID: 19476379 DOI: 10.1021/bi900781u] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pulsed electron double resonance (PELDOR)/double electron-electron resonance (DEER) spectroscopy is a very powerful structural biology tool in which the dipolar coupling between two unpaired electron spins (site-directed nitroxide spin-labels) is measured. These measurements are typically conducted at X-band (9.4 GHz) microwave excitation using the four-pulse DEER sequence and can often require up to 12 h of signal averaging for biological samples (depending on the spin-label concentration). In this work, we present for the first time a substantial increase in DEER sensitivity obtained by collecting DEER spectra at Q-band (34 GHz), when compared to X-band. The huge boost in sensitivity (factor of 13) demonstrated at Q-band represents a 169-fold decrease in data collection time, reveals a greatly improved frequency spectrum and higher-quality distance data, and significantly increases sample throughput. Thus, the availability of Q-band DEER spectroscopy should have a major impact on structural biology studies using site-directed spin labeling EPR techniques.
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20
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Stone K, Townsend J, Sarver J, Sapienza P, Saxena S, Jen-Jacobson L. Electron Spin Resonance Shows Common Structural Features for Different Classes ofEcoRI-DNA Complexes. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200803588] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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21
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Abstract
Proteins catalyze specific chemical reactions and carry out highly selective molecular recognition because they adopt well-defined three-dimensional structures and position chemically reactive functional groups in specific constellations. Proteins attain these well-defined structures through the complex process of protein folding. We seek to emulate these protein functions by constructing macromolecules that are easier to engineer by avoiding folding altogether. Toward that goal, we have developed an approach for the synthesis of macromolecules with programmable shapes. As described in this Account, we have constructed synthetic building blocks called bis-amino acids that we then couple through pairs of amide bonds to create water-soluble, spiroladder oligomers (bis-peptides) with well-defined three-dimensional structures. Bis-peptides use the conformational preferences of fused rings, stereochemistry, and strong covalent bonds to define their shape, unlike natural proteins and synthetic foldamers, which depend on noncovalent interactions and an unpredictable folding process to attain structure. Using these bis-amino acid monomers, we have built and characterized a number of bis-peptide nanostructures. We also constructed a molecular actuator that undergoes a large change in conformation under the control of metal exchange; the first application of bis-peptides. We are currently developing further approaches to functionalize bis-peptides as scaffolds to present well-defined constellations of functional groups. Such macromolecules could facilitate multifunctional catalysis and molecular recognition and lead to nanoscale molecular devices.
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Affiliation(s)
| | - Zachary Z. Brown
- Chemistry Department, Temple University, Philadelphia, Pennsylvania 19122
| | - Sharad Gupta
- Chemistry Department, Temple University, Philadelphia, Pennsylvania 19122
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22
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Bird GH, Pornsuwan S, Saxena S, Schafmeister CE. Distance distributions of end-labeled curved bispeptide oligomers by electron spin resonance. ACS NANO 2008; 2:1857-1864. [PMID: 19206425 DOI: 10.1021/nn800327g] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We demonstrate the synthesis of a series of spin-labeled curved oligomers to determine their end-to-end lengths and distance distributions using electron spin resonance. We synthesize shape-persistent macromolecules from conformationally restricted, asymmetric monomers that are coupled through pairs of amide bonds to create water-soluble, spiro-ladder oligomers with well-defined three-dimensional structures. We synthesized seven different macromolecules, each containing eight monomers but differing in the sequence to create macromolecules with different curved shapes. The ends of the oligomers were labeled with nitroxide spin probes, and double electron-electron resonance (DEER) electron spin resonance (ESR) experiments were carried out to obtain quantitative information about the shapes and flexibility of the oligomers. The most probable end-to-end distance of the oligomers ranges from 23 to 36 A, a range of length that we previously accessed by assembling rod-like homo-oligomers that contain 4-8 bisamino acid monomers. The relative distances measured for the oligomers confirm that, by varying the sequence of an oligomer, we are able to control its shape. The shapes of the ESR-derived population distributions allow us to compare the degree of shape persistence and flexibility of spiro-ladder oligomers to other well-studied nanoscale molecular structures such as p-phenylethynylenes.
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Affiliation(s)
- Gregory H Bird
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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23
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Schafmeister CE, Belasco LG, Brown PH. Observation of contraction and expansion in a bis(peptide)-based mechanical molecular actuator. Chemistry 2008; 14:6406-12. [PMID: 18512828 DOI: 10.1002/chem.200701942] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A novel, bis(peptide) based molecular actuator (1) has been synthesized. It is demonstrated to undergo contraction and expansion controlled by the addition and removal of Cu2+; this is demonstrated by the direct observation of a change in hydrodynamic properties by using sedimentation analysis and size exclusion chromatography. The molecule undergoes a large change in sedimentation coefficient, axial ratio, and size exclusion chromatography elution time when it binds copper. The demonstration of a controlled change in the mechanical properties of 1 make it a good starting point for the development of molecular devices that will harness changes in molecular shape and size to create molecular devices such as sensors or valves.
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24
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Qin PZ, Haworth IS, Cai Q, Kusnetzow AK, Grant GPG, Price EA, Sowa GZ, Popova A, Herreros B, He H. Measuring nanometer distances in nucleic acids using a sequence-independent nitroxide probe. Nat Protoc 2008; 2:2354-65. [PMID: 17947978 DOI: 10.1038/nprot.2007.308] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This protocol describes the procedures for measuring nanometer distances in nucleic acids using a nitroxide probe that can be attached to any nucleotide within a given sequence. Two nitroxides are attached to phosphorothioates that are chemically substituted at specific sites of DNA or RNA. Inter-nitroxide distances are measured using a four-pulse double electron-electron resonance technique, and the measured distances are correlated to the parent structures using a Web-accessible computer program. Four to five days are needed for sample labeling, purification and distance measurement. The procedures described herein provide a method for probing global structures and studying conformational changes of nucleic acids and protein/nucleic acid complexes.
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Affiliation(s)
- Peter Z Qin
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0744, USA.
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25
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Stone KM, Townsend JE, Sarver J, Sapienza PJ, Saxena S, Jen-Jacobson L. Electron spin resonance shows common structural features for different classes of EcoRI-DNA complexes. Angew Chem Int Ed Engl 2008; 47:10192-4. [PMID: 19021169 PMCID: PMC2792891 DOI: 10.1002/anie.200803588] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Katherine M. Stone
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave, Pittsburgh, PA 15260
| | - Jacqueline E. Townsend
- Department of Biological Sciences, University of Pittsburgh, 320 Clapp Hall, Pittsburgh, PA 15260
| | - Jessica Sarver
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave, Pittsburgh, PA 15260
| | - Paul J. Sapienza
- Department of Biological Sciences, University of Pittsburgh, 320 Clapp Hall, Pittsburgh, PA 15260
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave, Pittsburgh, PA 15260
| | - Linda Jen-Jacobson
- Department of Biological Sciences, University of Pittsburgh, 320 Clapp Hall, Pittsburgh, PA 15260
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26
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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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27
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Bode BE, Margraf D, Plackmeyer J, Dürner G, Prisner TF, Schiemann O. Counting the Monomers in Nanometer-Sized Oligomers by Pulsed Electron−Electron Double Resonance. J Am Chem Soc 2007; 129:6736-45. [PMID: 17487970 DOI: 10.1021/ja065787t] [Citation(s) in RCA: 164] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In a lot of cases active biomolecules are complexes of higher order, thus methods capable of counting the number of building blocks and elucidating their geometric arrangement are needed. Therefore, we experimentally validate here spin-counting via 4-pulse electron-electron double resonance (PELDOR) on well-defined test samples. Two biradicals, a symmetric and an asymmetric triradical, and a tetraradical were synthesized in a convergent reaction scheme via palladium-catalyzed cross-coupling reactions. PELDOR was then used to obtain geometric information and the number of spin centers per molecule in a single experiment. The measurement yielded the expected distances (2.2-3.8 nm) and showed that different spin-spin distances in one molecule can be resolved even if the difference amounts to only 5 A. The number of spins n has been determined to be 2.1 in both biradicals, to 3.1 and 3.0 in the symmetric and asymmetric triradicals, respectively, and to 3.9 in the tetraradical. The overall error of PELDOR spin-counting was found to be 5% for up to four spins. Thus, this method is a valuable tool to determine the number of constituting spin-bearing monomers in biologically relevant homo- and heterooligomers and how their oligomerization state and geometric arrangement changes during function.
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Affiliation(s)
- Bela E Bode
- Institute of Physical and Theoretical Chemistry, Center for Biomolecular Magnetic Resonance, J. W. Goethe-University, Frankfurt am Main, Germany
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28
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Han HJ, Sebby KB, Singel DJ, Cloninger MJ. EPR Characterization of Heterogeneously Functionalized Dendrimers. Macromolecules 2007. [DOI: 10.1021/ma070383m] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hye Jung Han
- Department of Chemistry and Biochemistry and Center for Bioinspired Nanomaterials, Montana State University, 108 Gaines Hall, Bozeman, Montana 59717
| | - Karl B. Sebby
- Department of Chemistry and Biochemistry and Center for Bioinspired Nanomaterials, Montana State University, 108 Gaines Hall, Bozeman, Montana 59717
| | - David J. Singel
- Department of Chemistry and Biochemistry and Center for Bioinspired Nanomaterials, Montana State University, 108 Gaines Hall, Bozeman, Montana 59717
| | - Mary J. Cloninger
- Department of Chemistry and Biochemistry and Center for Bioinspired Nanomaterials, Montana State University, 108 Gaines Hall, Bozeman, Montana 59717
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29
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Godt A, Schulte M, Zimmermann H, Jeschke G. How flexible are poly(para-phenyleneethynylene)s? Angew Chem Int Ed Engl 2007; 45:7560-4. [PMID: 17051574 DOI: 10.1002/anie.200602807] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Adelheid Godt
- Universität Bielefeld, Fakultät für Chemie, Universitätsstrasse 25, 33615 Bielefeld, Germany
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30
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Fafarman AT, Borbat PP, Freed JH, Kirshenbaum K. Characterizing the structure and dynamics of folded oligomers: Pulsed ESR studies of peptoid helices. Chem Commun (Camb) 2006:377-9. [PMID: 17220976 DOI: 10.1039/b612198e] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Helical peptoid oligomers were synthesized in which the positions of nitroxide radical spin probes along the backbone were systematically varied, allowing evaluation of intra-molecular distances and dynamics by electron spin resonance spectroscopy.
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Affiliation(s)
- Aaron T Fafarman
- Department of Chemistry, New York University, New York, NY 10003, USA
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31
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Godt A, Schulte M, Zimmermann H, Jeschke G. How Flexible Are Poly(para-phenyleneethynylene)s? Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200602807] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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32
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Cai Q, Kusnetzow AK, Hubbell WL, Haworth IS, Gacho GPC, Van Eps N, Hideg K, Chambers EJ, Qin PZ. Site-directed spin labeling measurements of nanometer distances in nucleic acids using a sequence-independent nitroxide probe. Nucleic Acids Res 2006; 34:4722-30. [PMID: 16966338 PMCID: PMC1635252 DOI: 10.1093/nar/gkl546] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2006] [Revised: 06/30/2006] [Accepted: 07/13/2006] [Indexed: 11/12/2022] Open
Abstract
In site-directed spin labeling (SDSL), local structural and dynamic information is obtained via electron paramagnetic resonance (EPR) spectroscopy of a stable nitroxide radical attached site-specifically to a macromolecule. Analysis of electron spin dipolar interactions between pairs of nitroxides yields the inter-nitroxide distance, which provides quantitative structural information. The development of pulse EPR methods has enabled such distance measurements up to 70 A in bio-molecules, thus opening up the possibility of SDSL global structural mapping. This study evaluates SDSL distance measurement using a nitroxide (designated as R5) that can be attached, in an efficient and cost-effective manner, to a phosphorothioate backbone position at arbitrary DNA or RNA sequences. R5 pairs were attached to selected positions of a dodecamer DNA duplex with a known NMR structure, and eight distances, ranging from 20 to 40 A, were measured using double electron-electron resonance (DEER). The measured distances correlated strongly (R2 = 0.98) with the predicted values calculated based on a search of sterically allowable R5 conformations in the NMR structure, thus demonstrating accurate distance measurements using R5. Furthermore, distance measurement in a 42 kD DNA was demonstrated. The results establish R5 as a sequence-independent probe for global structural mapping of DNA and DNA-protein complexes.
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Affiliation(s)
- Qi Cai
- Department of Chemistry , University of Southern CaliforniaLos Angeles, CA 90089-0744, USA
| | - Ana Karin Kusnetzow
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of CaliforniaLos Angeles, CA 90095, USA
| | - Wayne L. Hubbell
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of CaliforniaLos Angeles, CA 90095, USA
| | - Ian S. Haworth
- Department of Pharmaceutical Sciences, University of Southern CaliforniaLos Angeles, CA 90089, USA
| | - Gian Paola C. Gacho
- Department of Chemistry , University of Southern CaliforniaLos Angeles, CA 90089-0744, USA
| | - Ned Van Eps
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of CaliforniaLos Angeles, CA 90095, USA
| | - Kálmán Hideg
- Institute of Organic and Medical Chemistry, University of PécsH-7643, Pécs, P.O. Box 99, Hungary
| | - Eric J. Chambers
- Department of Pharmaceutical Sciences, University of Southern CaliforniaLos Angeles, CA 90089, USA
| | - Peter Z. Qin
- Department of Chemistry , University of Southern CaliforniaLos Angeles, CA 90089-0744, USA
- Department of Biological Sciences, University of Southern CaliforniaLos Angeles, CA 90089-0744, USA
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33
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Levins CG, Brown ZZ, Schafmeister CE. Maximizing the Stereochemical Diversity of Spiro-Ladder Oligomers. Org Lett 2006; 8:2807-10. [PMID: 16774262 DOI: 10.1021/ol060902q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] We introduce all stereoisomers of a bis-amino acid building block derived from trans-4-hydroxy-L-proline. This small library of monomers allows arbitrary stereochemical configuration at any chiral center within our spiro-ladder oligomers. Three tetramer oligomers containing several combinations of the monomers 1-4 were synthesized; we explored the effect of monomer sequence on scaffold conformation by NMR.
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