ArticleThe journal of physical chemistry. B2012
Simulating the dynamics and orientations of spin-labeled side chains in a protein-DNA complex.
Article in The journal of physical chemistry. B, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Rational Design of a Cu(II) Spin Label Improves the Sensitivity of Distance Measurements.The journal of physical chemistry letters · 2025Article
- Protein Modeling with DEER Spectroscopy.Annual review of biophysics · 2025Review
- Modeling of Cu(II)-based protein spin labels using rotamer libraries.Physical chemistry chemical physics : PCCP · 2024Article
- Copper coordination states affect the flexibility of copper Metallochaperone Atox1: Insights from molecular dynamics simulations.Protein science : a publication of the Protein Society · 2022Article
- Comparative evaluation of spin-label modeling methods for protein structural studies.Biophysical journal · 2022Article
- Benchmark Test and Guidelines for DEER/PELDOR Experiments on Nitroxide-Labeled Biomolecules.Journal of the American Chemical Society · 2021Article
- Rotameric preferences of a protein spin label at edge-strand β-sheet sites.Protein science : a publication of the Protein Society · 2016Article
- The double-histidine Cu²⁺-binding motif: a highly rigid, site-specific spin probe for electron spin resonance distance measurements.Angewandte Chemie (International ed. in English) · 2015Article
- New developments in spin labels for pulsed dipolar EPR.Molecules (Basel, Switzerland) · 2014Review
- Pulsed electron double resonance in structural studies of spin-labeled nucleic acids.Acta naturae · 2013Article
- Tunable, mixed-resolution modeling using library-based Monte Carlo and graphics processing units.Journal of chemical theory and computation · 2012Article
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Authors and funding
5 authors.
Funding
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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