Corrigendum to “The cytochrome <i>c</i> peroxidase and cytochrome <i>c</i> encounter complex: The other side of the story” [FEBS Lett. 588 (2014) 1873–1878]

Schilder, Jesika T.; Löhr, Frank; Schwalbe, Harald; Ubbink, Marcellus

doi:10.1016/j.febslet.2015.06.018

Cited by 6 publications

(14 citation statements)

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“…15,24,34−36 Volkov, Ubbink, and colleagues have made resonance assignments for essentially all of the backbone amide groups ( 1 H and 15 N) in CcP and cyanoCcP by using isotopically enriched CcP. 36,37 The chemical shifts of the amide resonances are sensitive to the chemical environment, and, upon binding of yCc at high ionic strength, where only 1:1 complex formation is expected, significant changes in the chemical shift positions of a number of the CcP amide groups have been observed. 36−38 The size of the chemical shifts is related to the lifetime of the complex, and the largest chemical shifts indicate that yCc occupies a single orientation within the complex for a significant fraction of the time.…”

Section: ■ Discussionmentioning

confidence: 99%

Binding of Yeast Cytochrome c to Forty-Four Charge-Reversal Mutants of Yeast Cytochrome c Peroxidase: Isothermal Titration Calorimetry

et al. 2015

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Previously, we constructed, expressed, and purified 46 charge-reversal mutants of yeast cytochrome c peroxidase (CcP) and determined their electronic absorption spectra, their reaction with H2O2, and their steady-state catalytic properties [ Pearl , N. M. et al. (2008) Biochemistry 47 , 2766 - 2775 ]. Forty-four of the mutants involve the conversion of either an aspartate or glutamate residue to a lysine residue, while two are positive-to-negative mutations, R31E and K149D. In this paper, we report on a calorimetric study of the interaction of each charge-reversal mutant (excluding the internal mutants D76K and D235K) with recombinant yeast iso-1 ferricytochrome c(C102T) (yCc) under conditions where only one-to-one yCc/CcP complex formation is observed. Thirteen of the 44 surface-site charge-reversal mutants decrease the binding affinity for yCc by a factor of 2 or more. Eight of the 13 mutations (E32K, D33K, D34K, E35K, E118K, E201K, E290K, E291K) occur within, or on the immediate periphery, of the crystallographically defined yCc binding site [ Pelletier , H. and Kraut , J. (1992) Science 258 , 1748 - 1755 ], three of the mutations (D37K, E98K, E209K) are slightly removed from the crystallographic site, and two of the mutations (D165K, D241K) occur on the "back-side" of CcP. The current study is consistent with a model for yCc binding to CcP in which yCc binds predominantly near the region defined by crystallographic structure of the 1:1 yCc-CcP complex, whether as a stable electron-transfer active complex or as part of a dynamic encounter complex.

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Section: ■ Discussionmentioning

confidence: 99%

Binding of Yeast Cytochrome c to Forty-Four Charge-Reversal Mutants of Yeast Cytochrome c Peroxidase: Isothermal Titration Calorimetry

et al. 2015

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“…For the proteins used in the NMR experiments, 15 N- and 15 N, 13 C-enriched minimal media were prepared as described previously 59 . Uniformly isotopically enriched MPS1 samples were produced as following.…”

Section: Methodsmentioning

confidence: 99%

Interactions between N-Terminal Modules in MPS1 Enable Spindle Checkpoint Silencing

Pachis

Hiruma

Perrakis

et al. 2018

Preprint

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14Faithful chromosome segregation relies on the ability of the spindle assembly checkpoint 15 (SAC) to delay anaphase onset until all chromosomes are attached to the mitotic spindle via 16 their kinetochores. MPS1 kinase is recruited to unattached kinetochores to initiate SAC 17 signaling, and is removed from kinetochores once stable microtubule attachments have been 18 formed to allow normal mitotic progression. Here we show that a helical fragment within the 19 kinetochore-targeting NTE module of MPS1 is required for interactions with kinetochores, 20 and also forms intramolecular interactions with its adjacent TPR domain. Bypassing this NTE-21 TPR interaction results in high MPS1 levels at kinetochores due to loss of regulatory input into 22Monopolar spindle 1 (MPS1) kinase is the major orchestrator of SAC signaling 12 . It is 53 recruited to unattached kinetochores where it autoactivates and subsequently 54 phosphorylates its kinetochore substrates in order to recruit downstream SAC components 55 and enable MCC production 2,13-17 . MPS1 phosphorylates multiple residues on at least three 56 proteins involved in the recruitment cascade (Knl1, Bub1, Mad1) 18-23 and may subsequently 57 also directly impact MCC complex stability and its binding to the APC/C 24 . Besides its role in 58 the SAC, MPS1 is also involved in the regulation of chromosome biorientation [25][26][27][28] . 59 MPS1 contains in its N-terminus an N-terminal extension (NTE) sequence module 60 followed by a tetratricopeptide repeat (TRP) domain. Although the NTE provides the 61 predominant localization signal, both modules are involved in MPS1's ability to localize to 62 kinetochores via direct binding to members of the NDC80 complex [29][30][31][32][33][34] . The mitotic kinase 63 Aurora B plays an important role in promoting MPS1 kinetochore localization 27,35 , at least in 64 part by alleviating an inhibitory effect that the TPR imposes on kinetochore binding via the 65 NTE 31 . MPS1 signaling at kinetochores diminishes upon microtubule binding due to 66 competition between MPS1 and microtubules for binding to the NDC80 complex. Aided by 67 high turnover of kinetochore MPS1 36,37 , this results in reduced ability of MPS1 molecules to 68 re-bind kinetochores once they are occupied by microtubules 32,33 . In this way SAC signaling 69 is disrupted at its most upstream point -a mechanism that, alongside other ways of SAC 70 silencing, eventually causes full SAC inactivation and anaphase onset [38][39][40][41][42][43][44][45][46][47][48] . 71The localization of MPS1 to kinetochores and regulation thereof are crucial for the SAC, 72 yet much is still unknown about the mechanisms that dictate it. Here, we set out to examine 73 the potential interplay between the different N-terminal regions in MPS1 and determine how 74 they regulate its kinetochore levels. We report the presence of a helical fragment in the NTE 75 of MPS1 that is important for its kinetochore localization, and we detect a direct 76 intramolecular interaction between the NTE and TPR...

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“…The genes for the yeast CcP C128A containing mutations NC38, NC200 and TC288 14 were sub-cloned in the pET28aCcP plasmid and were expressed to produce CcP, which was purified as described previously. 16 The yields were 40 mg L À1 for NC38 [ 2 H 15 N], 20 mg L À1 for NC200 [ 15 N] and 120 mg L À1 for TC288 [ 2 H 15 N] in minimal media. A pUC19 based plasmid containing the S. cerevisiae iso-1cytochrome c gene was used to produce Cc, which was purified according to published procedures.…”

Section: Protein Sample Preparationmentioning

confidence: 99%

“…The CcP mutants were tagged with MTS, MTSL or pyMTSL, as described previously. 14,16 The tagging efficiency was determined by mass spectroscopy to be essentially 100% and SLs at these positions have previously been shown not to interfere with Cc-CcP complex formation. 14…”

Section: Protein Sample Preparationmentioning

confidence: 99%

“…The aim of this work is to establish whether PRE data alone are sufficient for accurate rigid body docking of two proteins that form a dynamic complex. The Cc-CcP complex spends approximately 30% of the time in an encounter state; 14,[16][17][18][19] therefore, the PRE represent not only the well-defined stereospecific state but also the encounter state. We investigate the role of SL mobility by comparing MTSL to pyMTSL, as well as by comparing the use of a single SL conformer to the use of an ensemble of conformers when the orientations are either fixed or mobile during the calculations.…”

Section: Introductionmentioning

confidence: 99%

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Protein docking using an ensemble of spin labels optimized by intra-molecular paramagnetic relaxation enhancement

Schilder

Liu

Kumar

et al. 2016

Phys. Chem. Chem. Phys.

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Paramagnetic NMR is a useful technique to study proteins and protein complexes and the use of paramagnetic relaxation enhancement (PRE) for this purpose has become wide-spread. PREs are commonly generated using paramagnetic spin labels (SLs) that contain an unpaired electron in the form of a nitroxide radical, with 1-oxyl-2,2,5,5-tetramethyl-2,5-dihydropyrrol-3-ylmethyl methane thiosulfonate (MTSL) being the most popular tag. The inherent flexibility of the SL causes sampling of several conformations in solution, which can be problematic as over- or underestimation of the spatial distribution of the unpaired electron in structural calculations will lead to errors in the distance restraints. We investigated the effect of this mobility on the accuracy of protein-protein docking calculations using intermolecular PRE data by comparing MTSL and the less mobile 3-methanesulfonilthiomethyl-4-(pyridin-3-yl)-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-1-yloxyl (pyMTSL) on the dynamic complex of cytochrome c and cytochrome c peroxidase. No significant differences were found between the two SLs. Docking was performed using either single or multiple conformers and either fixed or flexible SLs. It was found that mobility of the SLs is the limiting factor for obtaining accurate solutions. Optimization of SL conformer orientations using intra-molecular PRE improves the accuracy of docking.

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Corrigendum to “The cytochrome c peroxidase and cytochrome c encounter complex: The other side of the story” [FEBS Lett. 588 (2014) 1873–1878]

Cited by 6 publications

References 0 publications

Binding of Yeast Cytochrome c to Forty-Four Charge-Reversal Mutants of Yeast Cytochrome c Peroxidase: Isothermal Titration Calorimetry

Binding of Yeast Cytochrome c to Forty-Four Charge-Reversal Mutants of Yeast Cytochrome c Peroxidase: Isothermal Titration Calorimetry

Interactions between N-Terminal Modules in MPS1 Enable Spindle Checkpoint Silencing

Protein docking using an ensemble of spin labels optimized by intra-molecular paramagnetic relaxation enhancement

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