Distance measurements on spin-labelled biomacromolecules by pulsed electron paramagnetic resonance

Jeschke, Gunnar; Polyhach, Yevhen

doi:10.1039/b614920k

Cited by 583 publications

(690 citation statements)

References 70 publications

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“…The magnitude of structural difference between conformational substates can be determined by DEER spectroscopy, which measures interspin distance distributions between two nitroxides in the range of 17-70 Å (26). To explore the structural changes due to the cavity-creating mutants, pairs of R1 side chains were introduced into both 121A/133A and 138A backgrounds.…”

Section: Deer Spectroscopy Reveals Structural Differences Between Thementioning

confidence: 99%

Conformational selection and adaptation to ligand binding in T4 lysozyme cavity mutants

López

Yang

Altenbach

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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The studies presented here explore the relationship between protein packing and molecular flexibility using ligand-binding cavity mutants of T4 lysozyme. Although previously reported crystal structures of the mutants investigated show single conformations that are similar to the WT protein, site-directed spin labeling in solution reveals additional conformational substates in equilibrium exchange with a WT-like population. Remarkably, binding of ligands, including the general anesthetic halothane shifts the population to the WT-like state, consistent with a conformational selection model of ligand binding, but structural adaptation to the ligand is also apparent in one mutant. Distance mapping with double electron-electron resonance spectroscopy and the absence of ligand binding suggest that the new substates induced by the cavity-creating mutations represent alternate packing modes in which the protein fills or partially fills the cavity with side chains, including the spin label in one case; external ligands compete with the side chains for the cavity space, stabilizing the WT conformation. The results have implications for mechanisms of anesthesia, the response of proteins to hydrostatic pressure, and protein engineering.EPR | site-directed spin labeling | DEER | benzene | saturation recovery G lobular proteins have overall packing densities similar to those of crystalline solids (1) but nevertheless contain cavities and pockets that can range from a few to hundreds of cubic angstroms (2, 3). These native packing defects are generally destabilizing (4, 5), and improving the packing of the protein interior may be a general way to increase protein stability. Indeed, small-to-large mutations that fill native cavities can increase stability (6-8), but with a concomitant loss of function (7,8). Thus, cavities in the protein interior can play a critical role in function. One role of cavities may be to allow alternative packing arrangements of the core. The resulting ensemble of conformational substates could give rise to promiscuity in protein-protein interactions (9) and allosteric behavior (7,8,10). In addition, large-to-small mutations that generate cavities may have played an important role in the evolution of protein function (11).Considering the potentially important role of cavities in sculpting the energy landscape of proteins, the present study was undertaken to investigate, in solution, the structural and dynamical response of a protein to engineered cavities introduced by large-tosmall mutations. T4 lysozyme (T4L) was selected for study because of the large database of crystal structures of ligand-binding cavity mutations and the corresponding thermodynamic characterization from Matthews and coworkers (4,(12)(13)(14)(15). Remarkably, comparison of the WT and mutant structures showed very little difference or limited local relaxation near the cavity, although the mutations were strongly destabilizing (4, 15).In the present study, we examined the cavity-creating mutants L121A/L133A, L133G, and W138A in sol...

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Section: Deer Spectroscopy Reveals Structural Differences Between Thementioning

confidence: 99%

Conformational selection and adaptation to ligand binding in T4 lysozyme cavity mutants

López

Yang

Altenbach

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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“…Initially, results with reduced λ were obtained using a 5 mm dielectric ring (MD5) resonator that has large concentration sensitivity (when the sample amount is not limiting). However, the maximum microwave field‐strength is smaller than in the 3 mm split‐ring resonator (MS3) that is commonly recommended due to its absolute sensitivity (when the sample amount is a limiting factor) and higher achievable modulation depth 23. These results are described in the Supporting Information.…”

mentioning

confidence: 99%

Accurate Extraction of Nanometer Distances in Multimers by Pulse EPR

Valera

Ackermann

Pliotas

et al. 2016

Chemistry A European J

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Pulse electron paramagnetic resonance (EPR) is gaining increasing importance in structural biology. The PELDOR (pulsed electron–electron double resonance) method allows extracting distance information on the nanometer scale. Here, we demonstrate the efficient extraction of distances from multimeric systems such as membrane‐embedded ion channels where data analysis is commonly hindered by multi‐spin effects.

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“…In fact, the electronic spin gives rise to a magnetic moment that makes such molecular systems functional for various purposes. For instance, organic radicals can be used as spin probes in biomolecules [1] and are of interest as building blocks for molecular spintronics devices, [2,3] single-molecule magnets have the potential to act as molecular qubits for quantum information processing, [4] and open-shell transition metal compounds serve as catalytic centers in (bio-)inorganic chemistry, [5][6][7][8] where a change in the spin state can be an essential step in the catalytic cycle. [9] Consequently, a first-principles theory that is useful for descriptive and analytic purposes and that has the potential to be a predictive tool in theoretical studies on such chemical systems must consider the spin properties of the electronic structure.…”

Section: Introductionmentioning

confidence: 99%

Spin in density‐functional theory

Jacob¹,

Reiher²

2012

Int J of Quantum Chemistry

225

224

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The accurate description of open-shell molecules, in particular of transition metal complexes and clusters, is still an important challenge for quantum chemistry. Although density-functional theory (DFT) is widely applied in this area, the sometimes severe limitations of its currently available approximate realizations often preclude its application as a predictive theory. Here, we review the foundations of DFT applied to open-shell systems, both within the nonrelativistic and the relativistic framework. In particular, we provide an in-depth discussion of the exact theory, with a focus on the role of the spin density and possibilities for targeting specific spin states. It turns out that different options exist for setting up Kohn-Sham DFT schemes for open-shell systems, which imply different definitions of the exchangecorrelation energy functional and lead to different exact conditions on this functional. Finally, we suggest possible directions for future developments.

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Distance measurements on spin-labelled biomacromolecules by pulsed electron paramagnetic resonance

Cited by 583 publications

References 70 publications

Conformational selection and adaptation to ligand binding in T4 lysozyme cavity mutants

Conformational selection and adaptation to ligand binding in T4 lysozyme cavity mutants

Accurate Extraction of Nanometer Distances in Multimers by Pulse EPR

Spin in density‐functional theory

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