Pulse Dipolar Electron Spin Resonance: Distance Measurements

Borbat, Peter P.; Freed, Jack H.

doi:10.1007/430_2012_82

Cited by 79 publications

(99 citation statements)

References 150 publications

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“…Pulsed dipolar experiments, such as double electron-electron resonance (DEER) spectroscopy and double quantum coherence (DQC) have gained in popularity and can generate accurate distance information [44]. These techniques can measure distances in the range 15-80 Å and are undertaken at cryogenic temperatures which minimize complications due to motion of the protein/peptide and increase the spin-spin relaxation time.…”

Section: Using Epr To Determine a Copper(ii)-nitroxide Distancementioning

confidence: 99%

Nitroxide Spin-Labelling and Its Role in Elucidating Cuproprotein Structure and Function

Jones

Berliner

2016

Cell Biochem Biophys

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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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Section: Using Epr To Determine a Copper(ii)-nitroxide Distancementioning

confidence: 99%

Nitroxide Spin-Labelling and Its Role in Elucidating Cuproprotein Structure and Function

Jones

Berliner

2016

Cell Biochem Biophys

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“…This structural study uses pulse dipolar spectroscopy (PDS) implemented at the current state of the art (1)(2)(3) to understand the change in physical structure of a stem-loop oligonucleotide from HIV-1. The stem-loop structure is found in the TAR (transactivation response) region of TAR DNA and TAR RNA.…”

Section: Introductionmentioning

confidence: 99%

Pulse Dipolar ESR of Doubly Labeled Mini TAR DNA and Its Annealing to Mini TAR RNA

Sun

Borbat

Grigoryants

et al. 2015

Biophysical Journal

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Pulse dipolar electron-spin resonance in the form of double electron electron resonance was applied to strategically placed, site-specifically attached pairs of nitroxide spin labels to monitor changes in the mini TAR DNA stem-loop structure brought on by the HIV-1 nucleocapsid protein NCp7. The biophysical structural evidence was at Ångstrom-level resolution under solution conditions not amenable to crystallography or NMR. In the absence of complementary TAR RNA, double labels located in both the upper and the lower stem of mini TAR DNA showed in the presence of NCp7 a broadened distance distribution between the points of attachment, and there was evidence for several conformers. Next, when equimolar amounts of mini TAR DNA and complementary mini TAR RNA were present, NCp7 enhanced the annealing of their stem-loop structures to form duplex DNA-RNA. When duplex TAR DNA-TAR RNA formed, double labels initially located 27.5 Å apart at the 3'- and 5'-termini of the 27-base mini TAR DNA relocated to opposite ends of a 27 bp RNA-DNA duplex with 76.5 Å between labels, a distance which was consistent with the distance between the two labels in a thermally annealed 27-bp TAR DNA-TAR RNA duplex. Different sets of double labels initially located 26-27 Å apart in the mini TAR DNA upper stem, appropriately altered their interlabel distance to ~35 Å when a 27 bp TAR DNA-TAR RNA duplex formed, where the formation was caused either through NCp7-induced annealing or by thermal annealing. In summary, clear structural evidence was obtained for the fraying and destabilization brought on by NCp7 in its biochemical function as an annealing agent and for the detailed structural change from stem-loop to duplex RNA-DNA when complementary RNA was present.

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“…The echo is then modulated by the dipolar frequency providing sensitivity to distances. In DQC all pulses are applied at the same frequency, and it is important that all pulses should be intense in order to excite as many spins as possible [14,18,19].…”

Section: Introductionmentioning

confidence: 99%

A simple double quantum coherence ESR sequence that minimizes nuclear modulations in Cu2+-ion based distance measurements

Ruthstein

Shin

et al. 2015

Journal of Magnetic Resonance

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Double quantum coherence (DQC) ESR is a sensitive method to measure magnetic dipolar interactions between spin labels. However, the DQC experiment on Cu(2+) centers presents a challenge at X-band. The Cu(2+) centers are usually coordinated to histidine residues in proteins. The electron-nuclear interaction between the Cu(2+) ion and the remote nitrogen in the imidazole ring can interfere with the electron-electron dipolar interaction. Herein, we report on a modified DQC experiment that has the advantage of reduced contributions from electron-nuclear interactions, which enhances the resolution of the DQC signal to the electron-electron dipolar modulations. The modified pulse-sequence is verified on Cu(2+)-NO system in a polyalanine-based peptide and on a coupled Cu(2+) system in a polyproline-based peptide. The modified DQC data were compared with the DEER data and good agreement was found.

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Pulse Dipolar Electron Spin Resonance: Distance Measurements

Cited by 79 publications

References 150 publications

Nitroxide Spin-Labelling and Its Role in Elucidating Cuproprotein Structure and Function

Nitroxide Spin-Labelling and Its Role in Elucidating Cuproprotein Structure and Function

Pulse Dipolar ESR of Doubly Labeled Mini TAR DNA and Its Annealing to Mini TAR RNA

A simple double quantum coherence ESR sequence that minimizes nuclear modulations in Cu2+-ion based distance measurements

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