Page 1 | Search Results | Biochemical Journal

1-50 of 51

Sort by

Sort Order Select

Articles

α-Helix stabilization by co-operative side chain charge-reinforced interactions to phosphoserine in a basic kinase-substrate motif

Matthew Batchelor, Robert S. Dawber, Andrew J. Wilson, Richard Bayliss

Biochem J (2022) 479 (5): 687–700.

https://doi.org/10.1042/BCJ20210812

Published: 16 March 2022

... of PPIs by phosphorylation; basic kinase-substrate motifs are common with 55 human protein kinases recognizing an Arg at a position −3 from the phosphorylated Ser, whilst the Arg ( i− 3) Ser i Lys ( i +4) is a motif found in over 2000 human proteins. circular dichroism NMR spectroscopy peptides...

View article titled, α-Helix stabilization by co-operative side chain charge-reinforced interactions to phosphoserine in a basic kinase-substrate motif

Includes: Supplementary data

Articles

Rational design of electron/proton transfer mechanisms in the exoelectrogenic bacteria Geobacter sulfurreducens

Marta A. Silva, Pilar C. Portela, Carlos A. Salgueiro

Biochem J (2021) 478 (14): 2871–2887.

https://doi.org/10.1042/BCJ20210365

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...

View article titled, Rational design of electron/proton transfer mechanisms in the exoelectrogenic bacteria Geobacter sulfurreducens

Includes: Supplementary data

Articles

Structural basis of a chemokine heterodimer binding to glycosaminoglycans

Krishna Mohan Sepuru, Krishna Rajarathnam

Biochem J (2021) 478 (5): 1009–1021.

https://doi.org/10.1042/BCJ20200927

Published: 04 March 2021

... on behalf of the Biochemical Society 2021 Correspondence: Krishna Rajarathnam ( krrajara@utmb.edu ) 30 11 2020 15 1 2021 19 1 2021 19 1 2021 chemokine glycosaminoglycans heparin heterodimer isothermal titration calorimetry NMR spectroscopy Chemokines...

View article titled, Structural basis of a chemokine heterodimer binding to glycosaminoglycans

Includes: Supplementary data

Articles

Calcium binds and rigidifies the dysferlin C2A domain in a tightly coupled manner

Yuning Wang, Roya Tadayon, Liliana Santamaria, Pascal Mercier, Chantal J. Forristal, Gary S. Shaw

Biochem J (2021) 478 (1): 197–215.

https://doi.org/10.1042/BCJ20200773

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...

View article titled, Calcium binds and rigidifies the dysferlin C2A domain in a tightly coupled manner

Articles

Fragment-derived modulators of an industrial β-glucosidase

Eleni Makraki, John F. Darby, Marta G. Carneiro, James D. Firth, Alex Heyam, Eiso AB, Peter O'Brien, Gregg Siegal, Roderick E. Hubbard

Biochem J (2020) 477 (22): 4383–4395.

https://doi.org/10.1042/BCJ20200507

Published: 26 November 2020

... by centrifugation after incubation at 13°C overnight with shaking at 200 rpm. 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...

View article titled, Fragment-derived modulators of an industrial β-glucosidase

Includes: Supplementary data

Articles

Pro4 prolyl peptide bond isomerization in human galectin-7 modulates the monomer-dimer equilibrum to affect function

Michelle C. Miller, Irina V. Nesmelova, Vladimir A. Daragan, Hans Ippel, Malwina Michalak, Aurelio Dregni, Herbert Kaltner, Jürgen Kopitz, Hans-Joachim Gabius, Kevin H. Mayo

Biochem J (2020) 477 (17): 3147–3165.

https://doi.org/10.1042/BCJ20200499

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...

View article titled, Pro4 prolyl peptide bond isomerization in human galectin-7 modulates the monomer-dimer equilibrum to affect function

Includes: Supplementary data

Articles

A novel polyubiquitin chain linkage formed by viral Ubiquitin is resistant to host deubiquitinating enzymes

Hitendra Negi, Pothula Purushotham Reddy, Vineeth Vengayil, Chhaya Patole, Sunil Laxman, Ranabir Das

Biochem J (2020) 477 (12): 2193–2219.

https://doi.org/10.1042/BCJ20200289

Published: 22 June 2020

... ) 15 4 2020 29 5 2020 29 5 2020 1 6 2020 © 2020 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2020 host–pathogen interactions NMR spectroscopy post-translational modification Ubiquitins Ubiquitin (Ub), a 76 residue...

View article titled, A novel polyubiquitin chain linkage formed by viral Ubiquitin is resistant to host deubiquitinating enzymes

Includes: Supplementary data

Articles

A local α-helix drives structural evolution of streptococcal M-protein affinity for host human plasminogen

Cunjia Qiu, Yue Yuan, Shaun W. Lee, Victoria A. Ploplis, Francis J. Castellino

Biochem J (2020) 477 (9): 1613–1630.

https://doi.org/10.1042/BCJ20200197

Published: 05 May 2020

... on behalf of the Biochemical Society 2020 bacterial receptor Gram-positive bacteria NMR spectroscopy plasminogen protein interactions protein–ligand binding Group A Streptococcus pyogenes (GAS) is a Gram-positive β-hemolytic pathogen, the natural host of which is humans...

View article titled, A local α-helix drives structural evolution of streptococcal M-protein affinity for host human plasminogen

Includes: Supplementary data

Articles

Binding properties of the quaternary assembly protein SPAG1

Marie-Eve Chagot, Raphael Dos Santos Morais, Sana Dermouche, Dorian Lefebvre, Xavier Manival, Christophe Chipot, François Dehez, Marc Quinternet

Biochem J (2019) 476 (11): 1679–1694.

https://doi.org/10.1042/BCJ20190198

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...

View article titled, Binding properties of the quaternary assembly protein SPAG1

Includes: Multimedia, Supplementary data

Articles

Structure of SPH (self-incompatibility protein homologue) proteins: a widespread family of small, highly stable, secreted proteins

Karthik V. Rajasekar, Shuangxi Ji, Rachel J. Coulthard, Jon P. Ride, Gillian L. Reynolds, Peter J. Winn, Michael J. Wheeler, Eva I. Hyde, Lorna J. Smith

Biochem J (2019) 476 (5): 809–826.

https://doi.org/10.1042/BCJ20180828

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...

View article titled, Structure of SPH (self-incompatibility protein homologue) proteins: a widespread family of small, highly stable, secreted proteins

Articles

Aminoglycoside antibiotic resistance conferred by Hpa2 of MDR Acinetobacter baumannii : an unusual adaptation of a common histone acetyltransferase

Jyoti Singh Tomar, Rama Krishna Peddinti, Ramakrishna V. Hosur

Biochem J (2019) 476 (5): 795–808.

https://doi.org/10.1042/BCJ20180791

Published: 06 March 2019

... NMR spectroscopy ternary complex Aminoglycoside antibiotic acetylation capacity of Hpa2- Ab is monitored using a DTNB reagent. Acetylation reaction involves transfer of acetyl group from acetyl-CoA to antibiotic, this leads to conversion of acetyl-CoA to CoA-SH. Reaction between DTNB...

View article titled, Aminoglycoside antibiotic resistance conferred by Hpa2 of MDR Acinetobacter baumannii : an unusual adaptation of a common histone acetyltransferase

Includes: Supplementary data

Articles

Enhanced dynamics of conformationally heterogeneous T7 bacteriophage lysozyme native state attenuates its stability and activity

Meenakshi Sharma, Nancy Jaiswal, Dinesh Kumar, Krishna Mohan Poluri

Biochem J (2019) 476 (3): 613–628.

https://doi.org/10.1042/BCJ20180703

Published: 14 February 2019

... 25 1 2019 © 2019 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2019 conformational heterogeneity endolysins NMR spectroscopy To accomplish biological functions, proteins must conserve their native state with a considerable degree...

View article titled, Enhanced dynamics of conformationally heterogeneous T7 bacteriophage lysozyme native state attenuates its stability and activity

Includes: Supplementary data

Articles

Binding mode of AIF(370–394) peptide to CypA: insights from NMR, label-free and molecular docking studies

Biancamaria Farina, Mattia Sturlese, Fabiola Mascanzoni, Andrea Caporale, Alessandra Monti, Gianluigi Di Sorbo, Roberto Fattorusso, Menotti Ruvo, Nunzianna Doti

Biochem J (2018) 475 (14): 2377–2393.

https://doi.org/10.1042/BCJ20180177

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...

View article titled, Binding mode of AIF(370–394) peptide to CypA: insights from NMR, label-free and molecular docking studies

Includes: Supplementary data

Articles

Structural and ligand-binding analysis of the YAP-binding domain of transcription factor TEAD4

Yan Li, Shuang Liu, Elizabeth Yihui Ng, Rong Li, Anders Poulsen, Jeffrey Hill, Ajaybabu V. Pobbati, Alvin W. Hung, Wanjin Hong, Thomas H. Keller, CongBao Kang

Biochem J (2018) 475 (12): 2043–2055.

https://doi.org/10.1042/BCJ20180225

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...

View article titled, Structural and ligand-binding analysis of the YAP-binding domain of transcription factor TEAD4

Includes: Supplementary data

Articles

Discovery and characterization of a sulfoquinovose mutarotase using kinetic analysis at equilibrium by exchange spectroscopy

Palika Abayakoon, James P. Lingford, Yi Jin, Christopher Bengt, Gideon J. Davies, Shenggen Yao, Ethan D. Goddard-Borger, Spencer J. Williams

Biochem J (2018) 475 (7): 1371–1383.

https://doi.org/10.1042/BCJ20170947

Published: 16 April 2018

... License 4.0 (CC BY) . enzymology metabolism mutarotase NMR spectroscopy sulfoglycolysis and is the maximum rate of reaction, reached under saturating equilibrium exchange conditions when . The rate of the mutarotation process can be expressed in terms of the Michaelis–Menten...

View article titled, Discovery and characterization of a sulfoquinovose mutarotase using kinetic analysis at equilibrium by exchange spectroscopy

Includes: Supplementary data

Articles

Adhesion/growth-regulatory galectins tested in combination: evidence for formation of hybrids as heterodimers

In Collection

Editors' pick of research highlights published in the Biochemical Journal in 2018 & 2019

Michelle C. Miller, Anna-Kristin Ludwig, Kanin Wichapong, Herbert Kaltner, Jürgen Kopitz, Hans-Joachim Gabius, Kevin H. Mayo

Biochem J (2018) 475 (5): 1003–1018.

https://doi.org/10.1042/BCJ20170658

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...

View article titled, Adhesion/growth-regulatory galectins tested in combination: evidence for formation of hybrids as heterodimers

Includes: Supplementary data

Articles

Identification of drivers for the metamorphic transition of HIV-1 reverse transcriptase

Xunhai Zheng, Geoffrey A. Mueller, Kyungmin Kim, Lalith Perera, Eugene F. DeRose, Robert E. London

Biochem J (2017) 474 (19): 3321–3338.

https://doi.org/10.1042/BCJ20170480

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...

View article titled, Identification of drivers for the metamorphic transition of HIV-1 reverse transcriptase

Includes: Supplementary data

Articles

Structural evidence of a phosphoinositide-binding site in the Rgd1-RhoGAP domain

Denis Martinez, Béatrice Langlois d'Estaintot, Thierry Granier, James Tolchard, Cécile Courrèges, Valérie Prouzet-Mauléon, Michel Hugues, Bernard Gallois, François Doignon, Benoît Odaert

Biochem J (2017) 474 (19): 3307–3319.

https://doi.org/10.1042/BCJ20170331

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...

View article titled, Structural evidence of a phosphoinositide-binding site in the Rgd1-RhoGAP domain

Includes: Supplementary data

Articles

New insight on the S100A1–STIP1 complex highlights the important relationship between allostery and entropy in protein function

Nathaniel V. Nucci

Biochem J (2017) 474 (17): 2977–2980.

https://doi.org/10.1042/BCJ20170275

Published: 17 August 2017

... binding to the TPR domains of STIP1 also suggest possible changes in backbone dynamics for the entropically driven S100A1–STIP1-binding process. allosteric regulation calcium signaling entropy NMR spectroscopy It has long been known that calcium signaling is a centerpiece for intracellular...

View article titled, New insight on the S100A1–STIP1 complex highlights the important relationship between allostery and entropy in protein function

Articles

Molecular basis for the interaction between stress-inducible phosphoprotein 1 (STIP1) and S100A1

Andrzej Maciejewski, Vania F. Prado, Marco A.M. Prado, Wing-Yiu Choy

Biochem J (2017) 474 (11): 1853–1866.

https://doi.org/10.1042/BCJ20161055

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 present study employed...

View article titled, Molecular basis for the interaction between stress-inducible phosphoprotein 1 (STIP1) and S100A1

Includes: Supplementary data

Articles

Giant mimivirus R707 encodes a glycogenin paralogue polymerizing glucose through α- and β-glycosidic linkages

Anna J. Rommel, Andreas J. Hülsmeier, Simon Jurt, Thierry Hennet

Biochem J (2016) 473 (20): 3451–3462.

https://doi.org/10.1042/BCJ20160280

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 ANOVA with multiple comparisons was used and P < 0.05 was considered statistically significant. GraphPad Prism 6 software...

View article titled, Giant mimivirus R707 encodes a glycogenin paralogue polymerizing glucose through α- and β-glycosidic linkages

Includes: Supplementary data

Articles

Structure of purotoxin-2 from wolf spider: modular design and membrane-assisted mode of action in arachnid toxins

Peter B. Oparin, Kirill D. Nadezhdin, Antonina A. Berkut, Alexander S. Arseniev, Eugene V. Grishin, Alexander A. Vassilevski

Biochem J (2016) 473 (19): 3113–3126.

https://doi.org/10.1042/BCJ20160573

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...

View article titled, Structure of purotoxin-2 from wolf spider: modular design and membrane-assisted mode of action in arachnid toxins

Includes: Supplementary data

Articles

Mechanism of chitosan recognition by CBM32 carbohydrate-binding modules from a Paenibacillus sp. IK-5 chitosanase/glucanase

Shoko Shinya, Shigenori Nishimura, Yoshihito Kitaoku, Tomoyuki Numata, Hisashi Kimoto, Hideo Kusaoke, Takayuki Ohnuma, Tamo Fukamizo

Biochem J (2016) 473 (8): 1085–1095.

https://doi.org/10.1042/BCJ20160045

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...

View article titled, Mechanism of chitosan recognition by CBM32 carbohydrate-binding modules from a Paenibacillus sp. IK-5 chitosanase/glucanase

Includes: Supplementary data

Articles

Sticky swinging arm dynamics: studies of an acyl carrier protein domain from the mycolactone polyketide synthase

Steven Vance, Olga Tkachenko, Ben Thomas, Mona Bassuni, Hui Hong, Daniel Nietlispach, William Broadhurst

Biochem J (2016) 473 (8): 1097–1110.

https://doi.org/10.1042/BCJ20160041

Published: 08 April 2016

... biosynthesis. acyl carrier protein mycolactone NMR spectroscopy 4′-phosphopantetheine type I polyketide synthase Type I modular polyketide synthases (PKSs) are large, multi-domain complexes responsible for generating natural products with a spectrum of medically important activities...

View article titled, Sticky swinging arm dynamics: studies of an acyl carrier protein domain from the mycolactone polyketide synthase

Includes: Supplementary data

Articles

Solution structures of the Bacillus cereus metallo-β-lactamase BcII and its complex with the broad spectrum inhibitor R -thiomandelic acid

Andreas Ioannis Karsisiotis, Christian F. Damblon, Gordon C. K. Roberts

Biochem J (2013) 456 (3): 397–407.

https://doi.org/10.1042/BJ20131003

Published: 22 November 2013

... and structure determination of larger molecules J. Magn. Reson. 1990 86 210 216 35 Zwahlen C. Legault P. Vincent S. B. F. Greenblatt J. Konrat R. Kay L. E. Methods for measurement of intermolecular NOEs by multinuclear NMR spectroscopy: application to a bacteriophage λ N...

View article titled, Solution structures of the Bacillus cereus metallo-β-lactamase BcII and its complex with the broad spectrum inhibitor R -thiomandelic acid

Includes: Supplementary data

Articles

Structural basis for phosphorylation-triggered autophagic clearance of Salmonella

Vladimir V. Rogov, Hironori Suzuki, Evgenij Fiskin, Philipp Wild, Andreas Kniss, Alexis Rozenknop, Ryuichi Kato, Masato Kawasaki, David G. McEwan, Frank Löhr, Peter Güntert, Ivan Dikic, Soichi Wakatsuki, Volker Dötsch

Biochem J (2013) 454 (3): 459–466.

https://doi.org/10.1042/BJ20121907

Published: 29 August 2013

... at 257.5 nm and verified by 1D-NMR spectroscopy. The titration schemes were adopted to have optimum precision and signal intensity at the given temperature. Usually 16–26 steps were used, proportional to the molar enthalpy values. All structural NMR experiments were performed at 288 K on Bruker...

View article titled, Structural basis for phosphorylation-triggered autophagic clearance of Salmonella

Includes: Supplementary data

Articles

Post-translational modification in the archaea: structural characterization of multi-enzyme complex lipoylation

Mareike G. Posner, Abhishek Upadhyay, Susan J. Crennell, Andrew J. A. Watson, Steve Dorus, Michael J. Danson, Stefan Bagby

Biochem J (2013) 449 (2): 415–425.

https://doi.org/10.1042/BJ20121150

Published: 14 December 2012

... that, unlike E. coli LplA, bovine apo-LPT adopts the same relative N- and C-terminal domain orientations as lipoyl-AMP-bound LPT [ 13 ]. binding-induced folding lipoate protein ligase lipoyl domain NMR spectroscopy protein–protein interaction X-ray crystallography Aerobic metabolism of 2...

View article titled, Post-translational modification in the archaea: structural characterization of multi-enzyme complex lipoylation

Articles

Architecture of the catalytic HPN motif is conserved in all E2 conjugating enzymes

Benjamin W. Cook, Gary S. Shaw

Biochem J (2012) 445 (2): 167–174.

https://doi.org/10.1042/BJ20120504

Published: 27 June 2012

... catalytic pocket hydrogen bonding NMR spectroscopy structure ubiquitin High-resolution structures of 25 different human E2 conjugating enzymes have been determined using X-ray crystallography and NMR spectroscopy. Despite this wealth of high-resolution information, there is no consensus...

View article titled, Architecture of the catalytic HPN motif is conserved in all E2 conjugating enzymes

Includes: Supplementary data

Articles

Identification of regions responsible for the open conformation of S100A10 using chimaeric S100A11–S100A10 proteins

Liliana Santamaria-Kisiel, Gary S. Shaw

Biochem J (2011) 434 (1): 37–48.

https://doi.org/10.1042/BJ20100887

Published: 27 January 2011

... and adopt a more open conformation as in Ca 2+ −S100A11. Figure 3 Calcium-induced conformational changes in the S100A11 chimaeric proteins monitored by NMR spectroscopy Comparison of 1 H- 15 N-HSQC spectra for ( A ) S100A11, ( B ) S100A11 N66C,E75S , ( C ) S100A11 LI and ( D ) S100A11 H3,H4...

View article titled, Identification of regions responsible for the open conformation of S100A10 using chimaeric S100A11–S100A10 proteins

Includes: Supplementary data

Articles

Structural insights into the catalytic mechanism of Trypanosoma cruzi GPXI (glutathione peroxidase-like enzyme I)

Shreenal Patel, Syeed Hussain, Richard Harris, Sunita Sardiwal, John M. Kelly, Shane R. Wilkinson, Paul C. Driscoll, Snezana Djordjevic

Biochem J (2010) 425 (3): 513–522.

https://doi.org/10.1042/BJ20091167

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...

View article titled, Structural insights into the catalytic mechanism of Trypanosoma cruzi GPXI (glutathione peroxidase-like enzyme I)

Includes: Supplementary data

Articles

Pup, a prokaryotic ubiquitin-like protein, is an intrinsically disordered protein

Shanhui Liao, Qiang Shang, Xuecheng Zhang, Jiahai Zhang, Chao Xu, Xiaoming Tu

Biochem J (2009) 422 (2): 207–215.

https://doi.org/10.1042/BJ20090738

Published: 13 August 2009

..., PafA is assumed to be a Pup ligase, which catalyses the ATP-dependent ligation of the terminal γ-carboxylate of glutamate to lysines [ 19 ]. © The Authors Journal compilation © 2009 Biochemical Society 2009 Intrinsically disordered protein NMR spectroscopy prokaryote protein degradation...

View article titled, Pup, a prokaryotic ubiquitin-like protein, is an intrinsically disordered protein

Includes: Supplementary data

Articles

Conformation, catalytic site, and enzymatic mechanism of the PR10 allergen-related enzyme norcoclaurine synthase

Hanna Berkner, Kristian Schweimer, Irena Matecko, Paul Rösch

Biochem J (2008) 413 (2): 281–290.

https://doi.org/10.1042/BJ20080306

Published: 26 June 2008

... according to amide–amide NOEs (nuclear Overhauser effects) observed between the respective backbone amide protons. Bet v 1 allergen homology modelling norcoclaurine synthase NMR spectroscopy substrate binding BIAs (benzylisoquinoline alkaloids) form an important group of plant...

View article titled, Conformation, catalytic site, and enzymatic mechanism of the PR10 allergen-related enzyme norcoclaurine synthase

Articles

Structure and Cu(I)-binding properties of the N-terminal soluble domains of Bacillus subtilis CopA

Chloe Singleton, Lucia Banci, Simone Ciofi-Baffoni, Leonardo Tenori, Margaret A. Kihlken, Ruth Boetzel, Nick E. Le Brun

Biochem J (2008) 411 (3): 571–579.

https://doi.org/10.1042/BJ20071620

Published: 14 April 2008

...). Chromosomal DNA from B. subtilis strain 1A1 (Bacillus Genetic Stock Center, Columbus, OH, U.S.A.) was isolated as described previously [ 17 ]. Bacillus subtilis copper-mediated dimerization copper trafficking cysteine thiol luminescence NMR spectroscopy Copper is an essential metal...

View article titled, Structure and Cu(I)-binding properties of the N-terminal soluble domains of Bacillus subtilis CopA

Includes: Supplementary data

Articles

A critical role in structure-specific DNA binding for the acetylatable lysine residues in HMGB1

René Assenberg, Michelle Webb, Edward Connolly, Katherine Stott, Matthew Watson, Josie Hobbs, Jean O. Thomas

Biochem J (2008) 411 (3): 553–561.

https://doi.org/10.1042/BJ20071613

Published: 14 April 2008

... and purified ( Figure 1 d) as described previously for the A domain [ 12 ], AB di-domain [ 21 ] and full-length HMGB1 [ 25 ]. The effect of the double mutation on the isolated A domain structure was checked by CD spectroscopy and two-dimensional NMR spectroscopy. Gel-retardation assays were used to assess...

View article titled, A critical role in structure-specific DNA binding for the acetylatable lysine residues in HMGB1

Articles

Human iron regulatory protein 2 is easily cleaved in its specific domain: consequences for the haem binding properties of the protein

Camille Dycke, Catherine Bougault, Jacques Gaillard, Jean-Pierre Andrieu, Kostas Pantopoulos, Jean-Marc Moulis

Biochem J (2007) 408 (3): 429–439.

https://doi.org/10.1042/BJ20070983

Published: 28 November 2007

... 7 2007 28 8 2007 31 8 2007 31 8 2007 © The Authors Journal compilation © 2007 Biochemical Society 2007 EPR haem-binding protein haem-regulatory motif (HRM) iron regulatory protein 2 (IRP2) NMR spectroscopy proteolysis IRPs (iron regulatory proteins...

View article titled, Human iron regulatory protein 2 is easily cleaved in its specific domain: consequences for the haem binding properties of the protein

Includes: Supplementary data

Articles

Glutamine gluconeogenesis in the small intestine of 72 h-fasted adult rats is undetectable

Guy Martin, Bernard Ferrier, Agnès Conjard, Mireille Martin, Rémi Nazaret, Michelle Boghossian, Fadi Saadé, Claire Mancuso, Daniel Durozard, Gabriel Baverel

Biochem J (2007) 401 (2): 465–473.

https://doi.org/10.1042/BJ20061148

Published: 21 December 2006

... glucose synthesis glutamine metabolism ketone body NMR spectroscopy small intestine Since the viability of isolated rat enterocytes is limited with time [ 8 ], our segments were incubated for 20 and 30 min, but, for accuracy purposes, these short incubation times were compensated...

View article titled, Glutamine gluconeogenesis in the small intestine of 72 h-fasted adult rats is undetectable

Articles

Conformational transitions induced in heparin octasaccharides by binding with antithrombin III

Marco Guerrini, Sara Guglieri, Daniela Beccati, Giangiacomo Torri, Christian Viskov, Pierre Mourier

Biochem J (2006) 399 (2): 191–198.

https://doi.org/10.1042/BJ20060656

Published: 27 September 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 NS,6S ( N ,6-O...

View article titled, Conformational transitions induced in heparin octasaccharides by binding with antithrombin III

Articles

The predominant polyphenol in the leaves of the resurrection plant Myrothamnus flabellifolius , 3,4,5 tri- O -galloylquinic acid, protects membranes against desiccation and free radical-induced oxidation

John P. MOORE, Kim L. WESTALL, Neil RAVENSCROFT, Jill M. FARRANT, George G. LINDSEY, Wolf F. BRANDT

Biochem J (2005) 385 (1): 301–308.

https://doi.org/10.1042/BJ20040499

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...

View article titled, The predominant polyphenol in the leaves of the resurrection plant Myrothamnus flabellifolius , 3,4,5 tri- O -galloylquinic acid, protects membranes against desiccation and free radical-induced oxidation

Articles

NMR characterization of the interaction between the C-terminal domain of interferon-γ and heparin-derived oligosaccharides

Cécile VANHAVERBEKE, Jean-Pierre SIMORRE, Rabia SADIR, Pierre GANS, Hugues LORTAT-JACOB

Biochem J (2004) 384 (1): 93–99.

https://doi.org/10.1042/BJ20040757

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...

View article titled, NMR characterization of the interaction between the C-terminal domain of interferon-γ and heparin-derived oligosaccharides

Includes: Supplementary data

Articles

The first biantennary bacterial secondary cell wall polymer and its influence on S-layer glycoprotein assembly

Christian STEINDL, Christina SCHÄFFER, Thomas WUGEDITSCH, Michael GRANINGER, Irena MATECKO, Norbert MÜLLER, Paul MESSNER

Biochem J (2002) 368 (2): 483–494.

https://doi.org/10.1042/bj20020988

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...

View article titled, The first biantennary bacterial secondary cell wall polymer and its influence on S-layer glycoprotein assembly

Articles

Solution structure and backbone dynamics of human epidermal-type fatty acid-binding protein (E-FABP)

Luis H. GUTIÉRREZ-GONZÁLEZ, Christian LUDWIG, Carsten HOHOFF, Martin RADEMACHER, Thorsten HANHOFF, Heinz RÜTERJANS, Friedrich SPENER, Christian LÜCKE

Biochem J (2002) 364 (3): 725–737.

https://doi.org/10.1042/bj20020039

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...

View article titled, Solution structure and backbone dynamics of human epidermal-type fatty acid-binding protein (E-FABP)

Includes: Supplementary data

Articles

The solution structure of ribosomal protein L18 from Thermus thermophilus reveals a conserved RNA-binding fold

Esmeralda A. WOESTENENK, George M. GONGADZE, Dmitry V. SHCHERBAKOV, Alexey V. RAK, Maria B. GARBER, Torleif HÄRD, Helena BERGLUND

Biochem J (2002) 363 (3): 553–561.

https://doi.org/10.1042/bj3630553

Published: 24 April 2002

... in both proteins. We suggest that the L18 fold recognizes a specific RNA motif and that the resulting RNA protein-recognition module is tolerant to varia- tions in sequence. Key words: NMR spectroscopy, protein structure, ribosome, RNA-binding protein. information of the structure and dynamics...

View article titled, The solution structure of ribosomal protein L18 from Thermus thermophilus reveals a conserved RNA-binding fold

Articles

Species specificity of O-linked carbohydrate chains of the oviducal mucins in amphibians: structural analysis of neutral oligosaccharide alditols released by reductive β-elimination from the egg-jelly coats of Rana clamitans

Florence DELPLACE, Emmanuel MAES, Jérôme LEMOINE, Gérard STRECKER

Biochem J (2002) 363 (3): 457–471.

https://doi.org/10.1042/bj3630457

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...

View article titled, Species specificity of O-linked carbohydrate chains of the oviducal mucins in amphibians: structural analysis of neutral oligosaccharide alditols released by reductive β-elimination from the egg-jelly coats of Rana clamitans

Articles

Conformation of heparin pentasaccharide bound to antithrombin III

Miloš HRICOVÍNI, Marco GUERRINI, Antonella BISIO, Giangiacomo TORRI, Maurice PETITOU, Benito CASU

Biochem J (2001) 359 (2): 265–272.

https://doi.org/10.1042/bj3590265

Published: 08 October 2001

...-glycoside of A respectively) glycosidic linkages. Evidence is also provided that the protein drives the conformation of the 2-O-sulphated iduronic acid residue towards the skewed 2 S 0 form. 21 5 2001 25 6 2001 8 8 2001 The Biochemical Society, London ©2001 2001 NMR spectroscopy...

View article titled, Conformation of heparin pentasaccharide bound to antithrombin III

Articles

Spin-system heterogeneities indicate a selected-fit mechanism in fatty acid binding to heart-type fatty acid-binding protein (H-FABP)

Christian LÜCKE, Martin RADEMACHER, Aukje W. ZIMMERMAN, Herman T. B. VAN MOERKERK, Jacques H. VEERKAMP, Heinz RÜTERJANS

Biochem J (2001) 354 (2): 259–266.

https://doi.org/10.1042/bj3540259

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...

View article titled, Spin-system heterogeneities indicate a selected-fit mechanism in fatty acid binding to heart-type fatty acid-binding protein (H-FABP)

Includes: Supplementary data

Articles

Haem-linked interactions in horseradish peroxidase revealed by spectroscopic analysis of the Phe-221→Met mutant

Barry D. HOWES, Nigel C. VEITCH, Andrew T. SMITH, Christopher G. WHITE, Giulietta SMULEVICH

Biochem J (2001) 353 (2): 181–191.

https://doi.org/10.1042/bj3530181

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...

View article titled, Haem-linked interactions in horseradish peroxidase revealed by spectroscopic analysis of the Phe-221→Met mutant

Articles

Defensin-like peptide-2 from platypus venom: member of a class of peptides with a distinct structural fold

Allan M. TORRES, Greg M. DE PLATER, Magnus DOVERSKOG, Liesl C. BIRINYI-STRACHAN, Graham M. NICHOLSON, Clifford H. GALLAGHER, Philip W. KUCHEL

Biochem J (2000) 348 (3): 649–656.

https://doi.org/10.1042/bj3480649

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...

View article titled, Defensin-like peptide-2 from platypus venom: member of a class of peptides with a distinct structural fold

Articles

Estimation of systolic and diastolic free intracellular Ca2+ by titration of Ca2+ buffering in the ferret heart

Heide L. KIRSCHENLOHR, Andrew A. GRACE, Jamie I. VANDENBERG, James C. METCALFE, Gerry A. SMITH

Biochem J (2000) 346 (2): 385–391.

https://doi.org/10.1042/bj3460385

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...

View article titled, Estimation of systolic and diastolic free intracellular Ca2+ by titration of Ca2+ buffering in the ferret heart

Articles

Functional and conformational characterization of new mutants of heart fatty acid-binding protein

Aukje W. ZIMMERMAN, Martin RADEMACHER, Heinz RüTERJANS, Christian LüCKE, Jacques H. VEERKAMP

Biochem J (1999) 344 (2): 495–501.

https://doi.org/10.1042/bj3440495

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...

View article titled, Functional and conformational characterization of new mutants of heart fatty acid-binding protein

Articles

Solution structure and dynamics of the A-T tract DNA decamer duplex d(GGTAATTACC) 2 : implications for recognition by minor groove binding drugs

Clare E. BOSTOCK-SMITH, Charles A. LAUGHTON, Mark S. SEARLE

Biochem J (1999) 342 (1): 125–132.

https://doi.org/10.1042/bj3420125

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...

View article titled, Solution structure and dynamics of the A-T tract DNA decamer duplex d(GGTAATTACC) 2 : implications for recognition by minor groove binding drugs

Email alerts

CONNECT

EXPLORE

This Feature Is Available To Subscribers Only