Studying the Structure and Dynamics of Biomolecules by Using Soluble Paramagnetic Probes

Hocking, Henry G.; Zangger, Klaus; Madl, Tobias

doi:10.1002/cphc.201300219

Cited by 54 publications

(52 citation statements)

References 89 publications

(145 reference statements)

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“…However, a discordant result was obtained when the lipophilic 16-DSA was used as the paramagnetic probe (note that an apolar probe was not employed in the previous study (Kim et al, 2012) of the isolated β3 TM): for 16-DSA, little difference was observed between the membrane topology and tilt of β3-WT and the β3-K716E mutant (Figure 4C and Figure 4—figure supplement 1). This led us to recall literature showing that chelate probes such as Mn(II)-EDDA and Gd(III)-DTPA sometimes have an exposed ligand site that can transiently associate with anions such as Glu and Asp side chain carboxylates (Hocking et al, 2013). To test this possibility, we repeated the Gd(III)-DTPA probe experiment under conditions in which excess (10 mM) free EDTA was added to the solution to cap any free ligand sites in Gd(III)-DTPA, thereby suppressing any direct binding of protein carboxyl sides to the open ligand site in the lanthanide ion chelate.…”

Section: Resultsmentioning

confidence: 99%

Implications of the differing roles of the β1 and β3 transmembrane and cytoplasmic domains for integrin function

Mathew

Jiang

et al. 2016

eLife

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Integrins are transmembrane receptors composed of α and β subunits. Although most integrins contain β1, canonical activation mechanisms are based on studies of the platelet integrin, αIIbβ3. Its inactive conformation is characterized by the association of the αIIb transmembrane and cytosolic domain (TM/CT) with a tilted β3 TM/CT that leads to activation when disrupted. We show significant structural differences between β1 and β3 TM/CT in bicelles. Moreover, the ‘snorkeling’ lysine at the TM/CT interface of β subunits, previously proposed to regulate αIIbβ3 activation by ion pairing with nearby lipids, plays opposite roles in β1 and β3 integrin function and in neither case is responsible for TM tilt. A range of affinities from almost no interaction to the relatively high avidity that characterizes αIIbβ3 is seen between various α subunits and β1 TM/CTs. The αIIbβ3-based canonical model for the roles of the TM/CT in integrin activation and function clearly does not extend to all mammalian integrins.DOI: http://dx.doi.org/10.7554/eLife.18633.001

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Section: Resultsmentioning

confidence: 99%

Implications of the differing roles of the β1 and β3 transmembrane and cytoplasmic domains for integrin function

Mathew

Jiang

et al. 2016

eLife

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“…[5] ThesPRE technique has been used to assess the structures of proteins and protein complexes. [5] ThesPRE technique has been used to assess the structures of proteins and protein complexes.…”

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confidence: 99%

Protein Structural Ensembles Visualized by Solvent Paramagnetic Relaxation Enhancement

Gong

Guo

et al. 2016

Angew Chem Int Ed

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A protein can be in different conformations when fulfilling its function. Yet depiction of protein structural ensembles remains difficult. Here we show that the accurate measurement of solvent paramagnetic relaxation enhancement (sPRE) in the presence of an inert paramagnetic cosolute allows the assessment of protein dynamics. Demonstrated with two multi-domain proteins, we present a method to characterize protein microsecond-millisecond dynamics based on the analysis of the sPRE. Provided with the known structures of a protein, our method uncovers an ensemble of structures that fully accounts for the observed sPRE. In conjunction with molecular dynamics simulations, our method can identify protein alternative conformation that has only been theorized before. Together, our method expands the application of sPRE beyond structural characterization of rigid proteins and complements the established PRE NMR technique.

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“…Gd(DTPA-BMA) is an inert, water-soluble, paramagnetic compound that displays no specific binding to micelles or peptides (20,58). In solution, this compound enhances the relaxation rates of nuclei exposed to solvent through PRE.…”

Section: Analysis Of Trp3 Dynamics By Means Of Relaxation Parametersmentioning

confidence: 99%

“…PRE measurements can provide information about the orientation of peptides inserted in micelles (20,58). As proposed by Respondek et al (20), PRE experimental values can be modeled by Eq.…”

Section: Analysis Of Peptide Location and Orientation In The Micellesmentioning

confidence: 99%

Structural and Dynamic Insights of the Interaction between Tritrpticin and Micelles: An NMR Study

Santos

Moraes

Nakaie

et al. 2016

Biophysical Journal

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A large number of antimicrobial peptides (AMPs) acts with high selectivity and specificity through interactions with membrane lipid components. These peptides undergo complex conformational changes in solution; upon binding to an interface, one major conformation is stabilized. Here we describe a study of the interaction between tritrpticin (TRP3), a cathelicidin AMP, and micelles of different chemical composition. The peptide's structure and dynamics were examined using one-dimensional and two-dimensional NMR. Our data showed that the interaction occurred by conformational selection and the peptide acquired similar structures in all systems studied, despite differences in detergent headgroup charge or dipole orientation. Fluorescence and paramagnetic relaxation enhancement experiments showed that the peptide is located in the interface region and is slightly more deeply inserted in 1-myristoyl-2-hydroxy-sn-glycero-3-phospho-1 0 -rac-glycerol (LMPG, anionic) than in 1-lauroyl-2-hydroxy-sn-glycero-3-phosphocholine (LLPC, zwitterionic) micelles. Moreover, the tilt angle of an assumed helical portion of the peptide is similar in both systems. In previous work we proposed that TRP3 acts by a toroidal pore mechanism. In view of the high hydrophobic core exposure, hydration, and curvature presented by micelles, the conformation of TRP3 in these systems could be related to the peptide's conformation in the toroidal pore.

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Studying the Structure and Dynamics of Biomolecules by Using Soluble Paramagnetic Probes

Cited by 54 publications

References 89 publications

Implications of the differing roles of the β1 and β3 transmembrane and cytoplasmic domains for integrin function

Implications of the differing roles of the β1 and β3 transmembrane and cytoplasmic domains for integrin function

Protein Structural Ensembles Visualized by Solvent Paramagnetic Relaxation Enhancement

Structural and Dynamic Insights of the Interaction between Tritrpticin and Micelles: An NMR Study

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