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Keywords: NMR spectroscopy
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Articles
Biochem J (2022) 479 (5): 687–700.
Published: 16 March 2022
... License 4.0 (CC BY) . circular dichroism NMR spectroscopy peptides phosphorylation/dephosphorylation protein–protein interactions The determinants of α-helix stability are key in understanding the formation and strength of α-helix mediated protein–protein interactions (PPIs) [ 1...
Includes: Supplementary data
Articles
Biochem J (2021) 478 (14): 2871–2887.
Published: 23 July 2021
... 5 2021 18 6 2021 29 6 2021 30 6 2021 © 2021 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2021 electron transfer Geobacter multiheme cytochrome c NMR spectroscopy site-directed mutagenesis Geobacter bacteria...
Includes: Supplementary data
Articles
Biochem J (2021) 478 (5): 1009–1021.
Published: 04 March 2021
... titration calorimetry NMR spectroscopy Chemokines, a family of small molecular weight proteins (MW ∼ 10 kDa), mediate diverse roles from innate and adaptive arms of the host immune response to developmental biology, neurobiology, and tissue repair. Common to these functions is mobilizing different...
Includes: Supplementary data
Articles
Biochem J (2021) 478 (1): 197–215.
Published: 15 January 2021
... facilitating the calcium-sensitive interaction with membrane surfaces. In this work, we determined the calcium-free and calcium-bound structures of the dysferlin C2A domain using NMR spectroscopy and X-ray crystallography. We show that binding two calcium ions to this domain reduces the flexibility of the Ca 2...
Articles
Biochem J (2020) 477 (22): 4383–4395.
Published: 26 November 2020
... the Creative Commons Attribution License 4.0 (CC BY) . glycoside hydrolase NMR spectroscopy protein–ligand docking small molecule activators Tr Bgl2 The depletion of fossil fuel in combination with the increasing demand for energy worldwide has stimulated research on alternative...
Includes: Supplementary data
Articles
Biochem J (2020) 477 (17): 3147–3165.
Published: 04 September 2020
... with distinct glycoconjugates and protein counter-receptors in the cytoplasm and nucleus, as well as on the cell surface. Its structural analysis by NMR spectroscopy detected doubling of a set of particular resonances, an indicator of Gal-7 existing in two conformational states in slow exchange on the chemical...
Includes: Supplementary data
Articles
Biochem J (2020) 477 (12): 2193–2219.
Published: 22 June 2020
... structures. host–pathogen interactions NMR spectroscopy post-translational modification Ubiquitins Ubiquitin (Ub), a 76 residue protein, regulates multiple cellular pathways and is a major way of controlling protein levels in the cell [ 1–3 ]. Ub or Ub polymers are covalently attached...
Includes: Supplementary data
Articles
Biochem J (2020) 477 (9): 1613–1630.
Published: 05 May 2020
... by multinuclear NMR spectroscopy: application to a bacteriophage N-peptide/boxB RNA complex . J. Am. Chem. Soc. 119 , 6711 – 6721 10.1021/ja970224q 35 Ottiger , M. , Delaglio , F. and Bax , A. ( 1998 ) Measurement of J and dipolar couplings from simplified two-dimensional NMR spectra...
Includes: Supplementary data
Articles
Biochem J (2019) 476 (11): 1679–1694.
Published: 14 June 2019
... domains of SPAG1 in the recruitment of HSP chaperones by combining biochemical assays, ITC, NMR spectroscopy and molecular dynamics (MD) simulations. First, we propose that only two, out of the three TPR domains, are able to recruit the protein chaperones HSP70 and HSP90. We then focused on one...
Includes: Multimedia, Supplementary data
Articles
Biochem J (2019) 476 (5): 809–826.
Published: 12 March 2019
... , as a folded thioredoxin fusion protein and purified it from the cytosol. The fusion protein was cleaved and characterised by analytical ultracentrifugation, circular dichroism and nuclear magnetic resonance (NMR) spectroscopy. This showed that SPH15 is monomeric and temperature stable, with a β-sandwich...
Articles
Biochem J (2019) 476 (5): 795–808.
Published: 06 March 2019
... resistance histone acetyltransferase kanamycin NMR spectroscopy ternary complex Adaptation to the changing environment is essential for survival of living organisms and at molecular level, adaptation is an outcome of the ability of many enzymes to evolve new functions necessary for survival...
Includes: Supplementary data
Articles
Biochem J (2019) 476 (3): 613–628.
Published: 14 February 2019
... is responsible for the loss of activity of amidases at low pH values [ 49 ]. Nuclear magnetic resonance (NMR) spectroscopy is a unique technique to characterize low energy states/alternative conformations of proteins at an atomic resolution [ 18 – 21 ]. Furthermore, NMR is very much sensitive to analyze slow...
Includes: Supplementary data
Articles
Biochem J (2018) 475 (14): 2377–2393.
Published: 31 July 2018
.... Using a combined approach based on NMR spectroscopy, synthesis and in vitro testing of all Ala-scan mutants of the peptide and molecular docking/molecular dynamics, we have generated a detailed model of the AIF (370–394)/CypA complex. The model suggests us that the central region of the peptide spanning...
Includes: Supplementary data
Articles
Biochem J (2018) 475 (12): 2043–2055.
Published: 26 June 2018
... to facilitate robust and reliable identification of compounds that occupy either YAP-binding pocket or palmitate-binding pocket. Here, using NMR spectroscopy, we validated compounds that bind to these pockets and also identify the residues in mouse TEAD4 (mTEAD4) that interact with these compounds. Flufenamic...
Includes: Supplementary data
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Biochem J (2018) 475 (7): 1371–1383.
Published: 16 April 2018
...-6-P; however, its proficiency [ k uncat /( k cat / K M )] for SQ was 17 000-fold better than for Glc-6-P, revealing that Hs SQM preferentially stabilizes the SQ transition state. enzymology metabolism mutarotase NMR spectroscopy sulfoglycolysis Correspondence: Shenggen Yao ( shyao...
Includes: Supplementary data
Articles
Biochem J (2018) 475 (5): 1003–1018.
Published: 15 March 2018
... indicated formation of heterodimers as opposed to larger oligomers. 15 N- 1 H heteronuclear single quantum coherence NMR spectroscopy and molecular dynamics simulations allowed us to delineate how different galectins interact in the heterodimer. The possibility of domain exchange between galectins...
Includes: Supplementary data
Articles
Biochem J (2017) 474 (19): 3321–3338.
Published: 25 September 2017
... ) * Present address: Bayer Crop Science, Inc., Morrisville, NC, U.S.A. 14 6 2017 9 8 2017 15 8 2017 15 8 2017 © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2017 HIV-1 reverse transcriptase metamorphic NMR spectroscopy...
Includes: Supplementary data
Articles
Biochem J (2017) 474 (19): 3307–3319.
Published: 20 September 2017
..., identify by NMR spectroscopy and confirm by docking simulations, a new but cryptic phosphoinositide-binding site, comprising contiguous A1, A1′ and B helices. The addition of helix A1′, unusual among RhoGAP domains, seems to be crucial for lipid interactions. Such a site was totally unexpected inside...
Includes: Supplementary data
Articles
Biochem J (2017) 474 (17): 2977–2980.
Published: 17 August 2017
... signaling entropy NMR spectroscopy It has long been known that calcium signaling is a centerpiece for intracellular processes. The S100 proteins contain two EF-hand motifs and form signaling competent hetero- or homodimers when bound to calcium. These proteins mediate a wide range of signaling...
Articles
Biochem J (2017) 474 (11): 1853–1866.
Published: 16 May 2017
... ) 1 12 2016 11 4 2017 13 4 2017 13 4 2017 © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society 2017 Alzheimer's disease calcium signaling co-chaperone NMR spectroscopy tetratricopeptide repeat The S100 family...
Includes: Supplementary data
Articles
Biochem J (2016) 473 (20): 3451–3462.
Published: 11 October 2016
... The Author(s); published by Portland Press Limited on behalf of the Biochemical Society 2016 giant virus glycogen glycosylation NMR spectroscopy polysaccharide The giant Acanthamoeba polyphaga mimivirus is a member of the expanding family of Mimiviridae , belonging to the monophyletic...
Includes: Supplementary data
Articles
Biochem J (2016) 473 (19): 3113–3126.
Published: 27 September 2016
... the wolf spider Alopecosa marikovskyi (Lycosidae), studied by NMR spectroscopy. PT2 is composed of an N-terminal inhibitor cystine knot (ICK, or knottin) β-structural domain and a C-terminal linear cationic domain. In aqueous solution, the C-terminal fragment is hyper-flexible, whereas the knottin domain...
Includes: Supplementary data
Articles
Biochem J (2016) 473 (8): 1085–1095.
Published: 08 April 2016
... at the C-terminus. In order to obtain insights into the mechanism of chitosan recognition, the structures of DD1 and DD2 were solved by NMR spectroscopy and crystallography. DD1 and DD2 both adopted a β-sandwich fold with several loops in solution as well as in crystals. On the basis of chemical shift...
Includes: Supplementary data
Articles
Biochem J (2016) 473 (8): 1097–1110.
Published: 08 April 2016
... with enzyme domains during polyketide biosynthesis. All samples for NMR spectroscopy were prepared at concentrations of 200–800 μM in phosphate buffer supplemented with 10% D 2 O (Sigma) and 0.0025% 3,3,3-trimethylsilylpropionate (Sigma) in 5 mm Ultra-Imperial grade NMR tubes (Wilmad) to a final...
Includes: Supplementary data
Articles
Biochem J (2013) 456 (3): 397–407.
Published: 22 November 2013
... of a metallo-β-lactamase and its complex with an inhibitor, allowing the key flexible loops flanking the active site and their role in inhibitor binding to be properly defined. antibiotic resistance enzyme structure inhibitor binding metallo-β-lactamase NMR spectroscopy zinc enzyme Table 1...
Includes: Supplementary data
Articles
Biochem J (2013) 454 (3): 459–466.
Published: 29 August 2013
... protein light chain 3 beta (LC3) NMR spectroscopy optineurin protein–protein interaction selective autophagy X-ray crystallography For GST pull downs using cell lysates HEK (human embryonic kidney)-293T cells were transfected with expression constructs encoding the protein of interest using...
Includes: Supplementary data
Articles
Biochem J (2013) 449 (2): 415–425.
Published: 14 December 2012
... N)-HSQC spectrum (32 scans, 128 min recording time) was recorded after each E2lipD addition. binding-induced folding lipoate protein ligase lipoyl domain NMR spectroscopy protein–protein interaction X-ray crystallography Aerobic metabolism of 2-oxoacids and C1 metabolism...
Articles
Biochem J (2012) 445 (2): 167–174.
Published: 27 June 2012
... 5 2012 8 5 2012 © The Authors Journal compilation © 2012 Biochemical Society 2012 catalytic pocket hydrogen bonding NMR spectroscopy structure ubiquitin E2 conjugating enzymes are central components in the Ub (ubiquitin) and Ubl (Ub-like) post-translational modification...
Includes: Supplementary data
Articles
Biochem J (2011) 434 (1): 37–48.
Published: 27 January 2011
.... 1 To whom correspondence should be addressed (email gshaw1@uwo.ca ). 17 6 2010 14 11 2010 25 11 2010 25 11 2010 © The Authors Journal compilation © 2011 Biochemical Society 2011 annexin calcium-binding protein EF-hand NMR spectroscopy phospholipid-binding...
Includes: Supplementary data
Articles
Biochem J (2010) 425 (3): 513–522.
Published: 15 January 2010
.... cruzi glutathione peroxidase-like enzyme I). We also characterized the wild-type, C48G and C96G variants of TcGPXI by NMR spectroscopy and biochemical assays. Our results show that residues Cys 48 and Cys 96 are required for catalytic activity. In solution, the TcGPXI molecule readily forms a Cys 48...
Includes: Supplementary data
Articles
Biochem J (2009) 422 (2): 207–215.
Published: 13 August 2009
... 2009 7 7 2009 7 7 2009 © The Authors Journal compilation © 2009 Biochemical Society 2009 Intrinsically disordered protein NMR spectroscopy prokaryote protein degradation Pup ubiquitin Protein degradation is an important mechanism involved in broad cellular events...
Includes: Supplementary data
Articles
Biochem J (2008) 413 (2): 281–290.
Published: 26 June 2008
... 2008 Biochemical Society 2008 Bet v 1 allergen homology modelling norcoclaurine synthase NMR spectroscopy substrate binding BIAs (benzylisoquinoline alkaloids) form an important group of plant secondary metabolites including approx. 2500 different compounds. Many of these small...
Articles
Biochem J (2008) 411 (3): 571–579.
Published: 14 April 2008
... 2008 Biochemical Society 2008 Bacillus subtilis copper-mediated dimerization copper trafficking cysteine thiol luminescence NMR spectroscopy Copper is an essential metal ion involved in a wide variety of cellular processes, including oxygen transport, electron transfer, respiration...
Includes: Supplementary data
Articles
Biochem J (2008) 411 (3): 553–561.
Published: 14 April 2008
... © 2008 Biochemical Society 2008 acetylation high mobility group (HMG) box NMR spectroscopy non-histone protein site-directed mutagenesis Protein acetylation plays a critical role in the control of gene transcription. This is effected through modulation of chromatin packaging...
Articles
Biochem J (2007) 408 (3): 429–439.
Published: 28 November 2007
... Society 2007 EPR haem-binding protein haem-regulatory motif (HRM) iron regulatory protein 2 (IRP2) NMR spectroscopy proteolysis IRPs (iron regulatory proteins) are ubiquitous regulators of cellular iron homoeostasis. They are cytosolic RNA-binding proteins that post-transcriptionally...
Includes: Supplementary data
Articles
Biochem J (2007) 401 (2): 465–473.
Published: 21 December 2006
... glucose synthesis glutamine metabolism ketone body NMR spectroscopy small intestine The contribution of the liver to glucose production in normal fasted humans and animals is well established; under this situation, the liver produces glucose as a result of both gluconeogenesis mainly from...
Articles
Biochem J (2006) 399 (2): 191–198.
Published: 27 September 2006
..., London 2006 antithrombin conformation docking heparin NMR spectroscopy protein–carbohydrate interaction Heparin is a sulfated GAG (glycosaminoglycan) consisting predominantly of repeating disaccharide units of α-1,4-linked IdoA 2S [2- O -sulfated IdoA (α- L -iduronic acid)] and GlcN...
Articles
Biochem J (2005) 385 (1): 301–308.
Published: 14 December 2004
... H and 13 C one- and two-dimensional NMR spectroscopy. The structure was confirmed by mass spectrometric analysis. This compound was present at high concentrations, 44% (by weight) in hydrated leaves and 74% (by weight) in dehydrated leaves. Electron microscopy of leaf material fixed...
Articles
Biochem J (2004) 384 (1): 93–99.
Published: 09 November 2004
... ). 7 5 2004 8 7 2004 22 7 2004 22 7 2004 The Biochemical Society, London 2004 heparin-derived oligosaccharide interferon-γ (IFNγ) NMR spectroscopy protein–carbohydrate interaction IFNγ (interferon-γ) is a highly pleiotropic protein secreted mainly by activated T...
Includes: Supplementary data
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Biochem J (2002) 368 (2): 483–494.
Published: 01 December 2002
...-glycans of previously established structure accounted for 13% of total glycosylation. The remainder could be attributed to a peptidoglycan-associated secondary cell wall polymer. Structure analysis was performed using purified secondary cell wall polymer—peptidoglycan complexes. NMR spectroscopy revealed...
Articles
Biochem J (2002) 364 (3): 725–737.
Published: 15 June 2002
... been associated with fatty acid signalling, cell growth, regulation and differentiation. As a contribution to understanding the structure—function relationship, we report in the present study features of its solution structure and backbone dynamics determined by NMR spectroscopy. Applying multi...
Includes: Supplementary data
Articles
Biochem J (2002) 363 (3): 457–471.
Published: 24 April 2002
... from three to sixteen monosaccharides, were established by a combination of NMR spectroscopy, methylation analyses and matrix-assisted laser-desorption ionization—time of flight MS. Typically, some of the neutral compounds appeared to possess the core structure: Gal(β1–3)[GlcNAc(β1–6)]Gal(β1–3)[GlcNAc...
Articles
Biochem J (2002) 363 (3): 553–561.
Published: 24 April 2002
... Data Bank under accession code 1ILY. 5 11 2001 21 1 2002 15 2 2002 The Biochemical Society, London ©2002 2002 NMR spectroscopy protein structure ribosome RNA-binding protein Abbreviations used: NOE, nuclear Overhauser enhancement; NOESY, NOE spectroscopy; HSQC...
Articles
Biochem J (2001) 359 (2): 265–272.
Published: 08 October 2001
... the conformation of the 2-O-sulphated iduronic acid residue towards the skewed #S ! form. Key words: NMR spectroscopy, protein carbohydrate inter- action, solution structure. has long been a matter of controversy [8,9]. The exclusive presence of either of the two chair forms of the pyranose ring, "C % and %C...
Articles
Biochem J (2001) 354 (2): 259–266.
Published: 22 February 2001
... solution. The binding of fatty acid molecules to FABPs, which proceeds through a portal region on the protein surface, is of particular interest. In the present study we have determined the three-dimensional solution structure of human heart-type FABP by multi-dimensional heteronuclear NMR spectroscopy...
Includes: Supplementary data
Articles
Biochem J (2001) 353 (2): 181–191.
Published: 08 January 2001
.... 1 To whom correspondence should be addressed (e-mail smulev@chim.unifi.it ). 24 3 2000 26 9 2000 30 10 2000 The Biochemical Society, London © 2001 2001 haem enzyme NMR spectroscopy resonance Raman spectroscopy site-directed mutagenesis Biochem. J. (2001) 353, 181...
Articles
Biochem J (2000) 348 (3): 649–656.
Published: 07 June 2000
... neurotoxin I). Although DLPs are the major peptides in the platypus venom, little is known about their biological roles. In this study, we determined the three-dimensional structure of DLP-2 by NMR spectroscopy, with the aim of gaining insights into the natural function of the DLPs in platypus venom. The DLP...
Articles
Biochem J (2000) 346 (2): 385–391.
Published: 22 February 2000
... (‘MFBAPTA’), with dissociation constants for Ca 2+ ranging from 46 to 537 nM, have been used to measure [Ca 2+ ] i , over the range from less than 100 nM to more than 3 μ M, in Langendorff-perfused ferret hearts (30 °C, pH 7.4, paced at 1.0 Hz) by 19 F-NMR spectroscopy. Loading hearts with indicators...
Articles
Biochem J (1999) 344 (2): 495–501.
Published: 24 November 1999
... 1999 The Biochemical Society, London © 1999 1999 fluorescence NMR spectroscopy portal region site-directed mutagenesis Biochem. J. (1999) 344, 495 501 (Printed in Great Britain) 495 Functional and conformational characterization of new mutants of heart fatty acid-binding protein Aukje...
Articles
Biochem J (1999) 342 (1): 125–132.
Published: 10 August 1999
.... Key words: A-tract structure; DNA conformation; DNA dy- namics; molecular dynamics simulations; NMR spectroscopy. heat capacity (DC% p ) on binding that is consistent with the hydrophobic burial model, and agrees well with predictions of DC% p based on calculations of changes in solvent accessible...