NMR View: A computer program for the visualization and analysis of NMR data

Johnson, B. V.; Blevins, Richard

doi:10.1007/bf00404272

Cited by 2,957 publications

(2,439 citation statements)

References 11 publications

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“…Chemical shift perturbation measurements for amide backbone resonances were calculated using Δδ = ((ΔδH) 2 + (ΔδN/5) 2 ) 0.5 and for side chain methyl groups using Δδ = ((ΔδH) 2 + (ΔδC/3.3) 2 ) 0.5 . All data were processed using 60°‐shifted cosine bell‐weighting functions using NMRPipe and NMRDraw (Delaglio et al , 1995) and were analysed using NMRViewJ (Johnson & Blevins, 1994). …”

Section: Methodsmentioning

confidence: 99%

Synergistic recruitment of UbcH7~Ub and phosphorylated Ubl domain triggers parkin activation

et al. 2018

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The E3 ligase parkin ubiquitinates outer mitochondrial membrane proteins during oxidative stress and is linked to early‐onset Parkinson's disease. Parkin is autoinhibited but is activated by the kinase PINK1 that phosphorylates ubiquitin leading to parkin recruitment, and stimulates phosphorylation of parkin's N‐terminal ubiquitin‐like (pUbl) domain. How these events alter the structure of parkin to allow recruitment of an E2~Ub conjugate and enhanced ubiquitination is an unresolved question. We present a model of an E2~Ub conjugate bound to the phospho‐ubiquitin‐loaded C‐terminus of parkin, derived from NMR chemical shift perturbation experiments. We show the UbcH7~Ub conjugate binds in the open state whereby conjugated ubiquitin binds to the RING1/IBR interface. Further, NMR and mass spectrometry experiments indicate the RING0/RING2 interface is re‐modelled, remote from the E2 binding site, and this alters the reactivity of the RING2(Rcat) catalytic cysteine, needed for ubiquitin transfer. Our experiments provide evidence that parkin phosphorylation and E2~Ub recruitment act synergistically to enhance a weak interaction of the pUbl domain with the RING0 domain and rearrange the location of the RING2(Rcat) domain to drive parkin activity.

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Section: Methodsmentioning

confidence: 99%

Synergistic recruitment of UbcH7~Ub and phosphorylated Ubl domain triggers parkin activation

et al. 2018

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“…The binding of apoMb [24][25][26][27][28][29][30][31][32][33][34][35][36] to DnaK-was tested by NMR spectroscopy via 2D 1 H-15 N HSQC-detected titrations. The binding kinetics of apoMb [24][25][26][27][28][29][30][31][32][33][34][35][36] to DnaK-is slow on the chemical shift time scale. Experiments were carried out by adding concentrated…”

Section: Methodsmentioning

confidence: 99%

“…aliquots (2 mM) of selectively 15 N-labeled apoMb [24][25][26][27][28][29][30][31][32][33][34][35][36] peptide to a solution containing a fixed amount of unlabeled DnaK-(∼0.1 mM), up to a 12.5-fold excess. Sensitivityenhanced 1 H-15 N HSQC experiments (28) were performed at 30°C on a Varian INOVA600 MHz spectrometer equipped with a 1 H{ 13 C, 15 N} triple resonance probe with a triple axis gradient.…”

Section: Methodsmentioning

confidence: 99%

“…Resonance assignments are reported elsewhere (27). ApoMb [24][25][26][27][28][29][30][31][32][33][34][35][36] NH resonance intensities for the chaperone-bound form of the peptide were followed as a function of peptide concentration. Intensities were then converted to concentrations, based on the assumption that peptide binding to DnaK-has reached saturation at 10-fold excess of peptide over DnaK-.…”

Section: Methodsmentioning

confidence: 99%

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Binding Specificity of an α-Helical Protein Sequence to a Full-Length Hsp70 Chaperone and Its Minimal Substrate-Binding Domain

et al. 2006

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Hsp70 chaperones are involved in the prevention of misfolding, and possibly the folding, of newly synthesized proteins. The members of this chaperone family are capable of interacting with polypeptide chains both co-and posttranslationally, but it is currently not clear how different structural domains of the chaperone affect binding specificity. We explored the interactions between the bacterial Hsp70, DnaK, and the sequence of a model all-R-helical globin (apoMb) by cellulose-bound peptide scanning. The binding specificity of the full-length chaperone was compared with that of its minimal substrate-binding domain, DnaK-. Six specific chaperone binding sites evenly distributed along the apoMb sequence were identified. Binding site locations are identical for the full-length chaperone and its substratebinding domain, but relative affinities differ. The binding specificity of DnaK-is only slightly decreased relative to that of full-length DnaK. DnaK's binding motif is known to comprise hydrophobic regions flanked by positively charged residues. We found that the simple fractional mean buried area correlates well with Hsp70's binding site locations along the apoMb sequence. In order to further characterize the properties of the minimal binding host, the stability of DnaK-upon chemical denaturation by urea and protons was investigated. Urea unfolding titrations yielded an apparent folding ∆G°of 3.1 ( 0.9 kcal mol -1 and an m value of 1.7 ( 0.4 kcal mol -1 M -1 .

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“…Delsuc (Delsuc, 1988), respectively. All subsequent procedures, such as spectral assignment, cross peak integration, and distance determination, were performed using the NMRVIEW program (Johnson & Blevins, 1994). Chemical shifts were measured in parts per million as observed relative to the residual CH3 resonance of acetic acid, presumed to be 2.03 ppm.…”

Section: Nmr Spectroscopymentioning

confidence: 99%

Inactive conformation of an insulin despite its wild-type sequence

et al. 1997

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The peptide group between residues B24 and B25 of insulin was replaced by an ester bond. This modification only in the backbone was meant to eliminate a structurally important H-bond between the amide proton of B25 and the carbonyl oxygen of A19. and consequently to enhance detachment of the C-terminal B-chain from the body of the molecule, exposing the underlying A-chain. According to a model derived from the effects of side-chain substitutions, main-chain shortening, and crosslinking, this conformational change is prerequisite for receptor binding.Contrary to the expectation that increased flexibility would increase receptor binding and activity, depsi-insulin ([B24-B25 CO-O]insulin) has turned out to be only 3-4% potent. In search of an explanation for this observation, the solution structure of depsi-insulin was determined by two-dimensional 'H-NMR spectroscopy. It was found that the loss of the B25-AI9 H-bond does not entail detachment of the C-terminal B-chain. On the contrary, it is overcompensated by a gain in hydrophobic interaction achieved by insertion of the Phe B25 side chain into the molecule's core. This is possible because of increased rotational freedom in the backbone owing to the ester bond. Distortion of the B20-B23 turn and an altered direction of the distal B-chain are consequences that also affect self-association. The exceptional position of the B25 side chain is thus the key feature of the depsi-insulin structure. Being buried in the interior, it is not available for guiding the interaction with the receptor, a crucial role attributed to it by the model. This seems to be the main reason why the structure of depsi-insulin represents an inactive conformation.Keywords: conformation; insulin; NMR-spectroscopy; structure Among the numerous insulin mutants and derivatives investigated in structurelfunction studies during the last 25 years, the mini proinsulins crosslinked between the amino groups of Gly AI and Lys B29 by bifunctional reagents have been particularly revealing

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NMR View: A computer program for the visualization and analysis of NMR data

Cited by 2,957 publications

References 11 publications

Synergistic recruitment of UbcH7~Ub and phosphorylated Ubl domain triggers parkin activation

Synergistic recruitment of UbcH7~Ub and phosphorylated Ubl domain triggers parkin activation

Binding Specificity of an α-Helical Protein Sequence to a Full-Length Hsp70 Chaperone and Its Minimal Substrate-Binding Domain

Inactive conformation of an insulin despite its wild-type sequence

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