mtsslSuite:<i>In silico</i>spin labelling, trilateration and distance-constrained rigid body docking in PyMOL

Hagelueken, Gregor; Abdullin, Dinar; Ward, Roger; Schiemann, Olav

doi:10.1080/00268976.2013.809804

Cited by 60 publications

(73 citation statements)

References 36 publications

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“…MtsslWizard searches for ensembles of possible MTSSL rotamers that do not clash with a static model of the protein. The program contains a sub-program called MtsslDock (Hagelueken et al, , 2013, which allows the user to dock two macromolecules based on a set of intermolecular distances obtained from DEER measurements. MtsslDock uses a mixed genetic and evolutionary algorithm to find docking models between two macromolecules (e.g., two BAX monomers or two BAX dimers) that agree with the experimental distance data.…”

Section: Activation Of Bax By Bimbh3mentioning

confidence: 99%

Solution Structure of Apoptotic BAX Oligomer: Oligomerization Likely Precedes Membrane Insertion

Sung

Lai

et al. 2015

Structure

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Proapoptotic BAX protein is largely cytosolic in healthy cells, but it oligomerizes and translocates to mitochondria upon receiving apoptotic stimuli. A long-standing challenge has been the inability to capture any structural information beyond the onset of activation. Here, we present solution structures of an activated BAX oligomer by means of spectroscopic and scattering methods, providing details about the monomer-monomer interfaces in the oligomer and how the oligomer is assembled from homodimers. We show that this soluble oligomer undergoes a direct conversion into membrane-inserted oligomer, which has the ability of inducing apoptosis and structurally resembles a membrane-embedded oligomer formed from BAX monomers in lipid environment. Structural differences between the soluble and the membrane-inserted oligomers are manifested in the C-terminal helices. Our data suggest an alternative pathway of apoptosis in which BAX oligomer formation occurs prior to membrane insertion.

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Section: Activation Of Bax By Bimbh3mentioning

confidence: 99%

Solution Structure of Apoptotic BAX Oligomer: Oligomerization Likely Precedes Membrane Insertion

Sung

Lai

et al. 2015

Structure

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“…This simplifies the treatment of large-scale conformational transitions, where rigid domains move with respect to each other [4], and of rigid-body docking [23,26,32]. In integrative modelling, the approximation of the local environment can be iteratively improved [33].…”

Section: From Distance Distributions To Modelsmentioning

confidence: 99%

“…Such problems can be overdetermined by distance distribution restraints. The two-body problem can be solved by a genetic algorithm implemented in mtsslSuite [32], by a complete grid search [23,26], or by an Xplor-NIH [47]-based protocol [48]. For more than two bodies, the RigiFlex approach has been proposed [26].…”

Section: Model Building With Epr Restraintsmentioning

confidence: 99%

The contribution of modern EPR to structural biology

Jeschke

2018

Emerging Topics in Life Sciences

133

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Electron paramagnetic resonance (EPR) spectroscopy combined with site-directed spin labelling is applicable to biomolecules and their complexes irrespective of system size and in a broad range of environments. Neither short-range nor long-range order is required to obtain structural restraints on accessibility of sites to water or oxygen, on secondary structure, and on distances between sites. Many of the experiments characterize a static ensemble obtained by shock-freezing. Compared with characterizing the dynamic ensemble at ambient temperature, analysis is simplified and information loss due to overlapping timescales of measurement and system dynamics is avoided. The necessity for labelling leads to sparse restraint sets that require integration with data from other methodologies for building models. The double electron-electron resonance experiment provides distance distributions in the nanometre range that carry information not only on the mean conformation but also on the width of the native ensemble. The distribution widths are often inconsistent with Anfinsen's concept that a sequence encodes a single native conformation defined at atomic resolution under physiological conditions.

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“…The corresponding PRONOX algorithm is available for MTSL attached to cysteine residues in proteins . A similar accessible-volume algorithm is used by MtsslWizard (Hagelueken, Ward, Naismith, & Schiemann, 2012). These algorithms provide similar prediction accuracy as first-generation rotamer libraries ( Jeschke, 2013), but none of the existing approaches is easy to interface with existing programs for generation of atomic resolution structures from NMR data.…”

Section: Modeling Spin-label Conformationsmentioning

confidence: 99%

Combining NMR and EPR to Determine Structures of Large RNAs and Protein–RNA Complexes in Solution

Duss

Yulikov

Allain

et al. 2015

Methods in Enzymology

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mtsslSuite:In silicospin labelling, trilateration and distance-constrained rigid body docking in PyMOL

Cited by 60 publications

References 36 publications

Solution Structure of Apoptotic BAX Oligomer: Oligomerization Likely Precedes Membrane Insertion

Solution Structure of Apoptotic BAX Oligomer: Oligomerization Likely Precedes Membrane Insertion

The contribution of modern EPR to structural biology

Combining NMR and EPR to Determine Structures of Large RNAs and Protein–RNA Complexes in Solution

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