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Articles

Aurora A binds to the transactivation domain of c-Myc and recognizes the phosphorylated N-terminal degron motif

Nidhi Joshi, Katie M. Dunleavy, Kaitlin M. Beel, Tiffany A. Engel, Andrew R. Thompson, Felix L. John, David D. Thomas, Nicholas M. Levinson

Biochem J (2025) 482 (08): 369–381.

https://doi.org/10.1042/BCJ20240726

Published: 16 April 2025

.... Here we show, using NMR and Förster resonance energy transfer experiments, that AurA binds to c-Myc through several discrete interactions spanning 145 residues within its TAD. AurA binding to c-Myc is enhanced by phosphorylation of the T58/S62 degron, demonstrating that the kinase recognizes the pool...

View articletitled, Aurora A binds to the transactivation domain of c-Myc and recognizes the phosphorylated N-terminal degron motif

Includes: Supplementary data

Articles

CORM-3 induces DNA damage through Ru(II) binding to DNA

Rhiannon F. Lyon, Hannah M. Southam, Clare R. Trevitt, Chunyan Liao, Sherif F. El-Khamisy, Robert K. Poole, Mike P. Williamson

Biochem J (2022) 479 (13): 1429–1439.

https://doi.org/10.1042/BCJ20220254

Published: 04 July 2022

... amino acids and thus prevents accumulation of CORM-3 into the cells. We conclude that CORM-3 leads to DNA damage over the relatively short timeframe of this experiment, which is less than 30 min. cancer cisplatin CORM DNA damage NMR ruthenium Organometallic complexes have long been...

View articletitled, CORM-3 induces DNA damage through Ru(II) binding to DNA

Articles

Mobility shift-based electrophoresis coupled with fluorescent detection enables real-time enzyme analysis of carbohydrate sulfatase activity

Dominic P. Byrne, James A. London, Patrick A. Eyers, Edwin A. Yates, Alan Cartmell

Biochem J (2021) 478 (4): 735–748.

https://doi.org/10.1042/BCJ20200952

Published: 18 February 2021

... and inhibition parameters and is based on existing microfluidic technology coupled to a new synthetic fluorescent 6S-GlcNAc carbohydrate substrate. Furthermore, we compare this technique, in terms of both time and resources, to high-performance anion exchange chromatography and NMR-based methods, which...

View articletitled, Mobility shift-based electrophoresis coupled with fluorescent detection enables real-time enzyme analysis of carbohydrate sulfatase activity

Articles

Biochemical and NMR characterization of the interactions of Vav2–SH2 domain with lipids and the EphA2 juxtamembrane region on membrane

Liang Ge, Bo Wu, Youjia Zhang, Jiarong Wang, Hongxin Zhao, Junfeng Wang

Biochem J (2020) 477 (19): 3791–3801.

https://doi.org/10.1042/BCJ20200300

Published: 12 October 2020

... site in Vav2–SH2 domain was identified by NMR chemical shift perturbation experiments using the head groups of PI(4,5)P2 and PI(3,4,5)P3, both of which bind to Vav2–SH2 with millimolar binding affinities. In addition, the interaction between Vav2–SH2 and the phosphorylated juxtamembrane region (JM...

View articletitled, Biochemical and NMR characterization of the interactions of Vav2–SH2 domain with lipids and the EphA2 juxtamembrane region on membrane

Includes: Supplementary data

Articles

Comparative structure, dynamics and evolution of acyl-carrier proteins from Borrelia burgdorferi , Brucella melitensis and Rickettsia prowazekii

Ravi P. Barnwal, Mandeep Kaur, Alec Heckert, Janeka Gartia, Gabriele Varani

Biochem J (2020) 477 (2): 491–508.

https://doi.org/10.1042/BCJ20190797

Published: 31 January 2020

... the structure, dynamics and evolution of ACPs from three human pathogens: Borrelia burgdorferi , Brucella melitensis and Rickettsia prowazekii , which could facilitate the discovery of new inhibitors of ACP function in pathogenic bacteria. All NMR experiments were conducted at 25°C on Bruker Avance 500...

View articletitled, Comparative structure, dynamics and evolution of acyl-carrier proteins from Borrelia burgdorferi , Brucella melitensis and Rickettsia prowazekii

Includes: Supplementary data

Articles

Solution structure of TbTFIIS2-2 PWWP domain from Trypanosoma brucei and its binding to H4K17me3 and H3K32me3

Rui Wang, Jie Gao, Jiahai Zhang, Xuecheng Zhang, Chao Xu, Shanhui Liao, Xiaoming Tu

Biochem J (2019) 476 (2): 421–431.

https://doi.org/10.1042/BCJ20180870

Published: 31 January 2019

... factors . In the present study, the solution structure of TbTFIIS2-2 PWWP domain was determined by NMR spectroscopy. TbTFIIS2-2 PWWP domain adopts a global fold containing a ﬁve-strand β-barrel and two C-terminal α-helices similar to other PWWP domains. Moreover, through systematic screening, we revealed...

View articletitled, Solution structure of TbTFIIS2-2 PWWP domain from Trypanosoma brucei and its binding to H4K17me3 and H3K32me3

Includes: Supplementary data

Articles

Solution structure of TbCentrin4 from Trypanosoma brucei and its interactions with Ca 2+ and other centrins

Fangzhen Shan, Kaiqin Ye, Jiahai Zhang, Shanhui Liao, Xuecheng Zhang, Chao Xu, Xiaoming Tu

Biochem J (2018) 475 (23): 3763–3778.

https://doi.org/10.1042/BCJ20180752

Published: 06 December 2018

... brucei , TbCentrin4 is mainly localized in basal bodies and bi-lobe structure, and is involved in the processes coordinating karyokinesis and cytokinesis. In the present study, we solved the solution structure of TbCentrin4 using NMR (nuclear magnetic resonance) spectroscopy. TbCentrin4 contains four EF...

View articletitled, Solution structure of TbCentrin4 from Trypanosoma brucei and its interactions with Ca 2+ and other centrins

Includes: Supplementary data

Articles

Thermodynamic and functional characterization of the periplasmic triheme cytochrome PpcA from Geobacter metallireducens

Tomás M. Fernandes, Leonor Morgado, Carlos A. Salgueiro

Biochem J (2018) 475 (17): 2861–2875.

https://doi.org/10.1042/BCJ20180457

Published: 14 September 2018

... of five periplasmic triheme cytochromes, which are important to bridge the electron transfer from the cytoplasmic donors to the extracellular acceptors. Using NMR and visible spectroscopic techniques, a detailed thermodynamic characterization of PpcA was obtained, including the determination of the heme...

View articletitled, Thermodynamic and functional characterization of the periplasmic triheme cytochrome PpcA from Geobacter metallireducens

Includes: Supplementary data

Articles

Redox- and pH-linked conformational changes in triheme cytochrome PpcA from Geobacter sulfurreducens

Leonor Morgado, Marta Bruix, P. Raj Pokkuluri, Carlos A. Salgueiro, David L. Turner

Biochem J (2017) 474 (2): 231–246.

https://doi.org/10.1042/BCJ20160932

Published: 06 January 2017

.... This functional mechanism requires control of both the redox state and the protonation state. In the present study, isotope-labeled PpcA was produced and the three-dimensional structure of PpcA in the oxidized form was determined by NMR. This is the first solution structure of a G. sulfurreducens cytochrome...

View articletitled, Redox- and pH-linked conformational changes in triheme cytochrome PpcA from Geobacter sulfurreducens

Includes: Supplementary data

Articles

The combination of sequence-specific and nonspecific DNA-binding modes of transcription factor SATB1

Kazuhiko Yamasaki, Tomoko Yamasaki

Biochem J (2016) 473 (19): 3321–3339.

https://doi.org/10.1042/BCJ20160236

Published: 27 September 2016

... in a sequence-specific binding mode) did not affect the binding affinity significantly. The NMR analyses and computational modeling of the homeodomain, however, revealed the tertiary structure and DNA-binding mode that are typical of homeodomains capable of sequence-specific binding. We believe that the lack...

View articletitled, The combination of sequence-specific and nonspecific DNA-binding modes of transcription factor SATB1

Includes: Supplementary data

Articles

The N-terminal ubiquitin-binding region of ubiquitin-specific protease 28 modulates its deubiquitination function: NMR structural and mechanistic insights

Yi Wen, Li Shi, Yiluan Ding, Rong Cui, Wen-tian He, Hong-yu Hu, Naixia Zhang

Biochem J (2015) 471 (2): 155–165.

https://doi.org/10.1042/BJ20150088

Published: 02 October 2015

.... It is of interest that an additional small ubiquitin-like modifier (SUMO)-interacting motif (SIM) is located next to its UIM. To date, the functional role of the Usp28 UBR is still not understood. To elucidate the regulatory mechanism of the UBR on the full functional display of Usp28, in the present study, NMR...

View articletitled, The N-terminal ubiquitin-binding region of ubiquitin-specific protease 28 modulates its deubiquitination function: NMR structural and mechanistic insights

Includes: Supplementary data

Articles

The solution structure of the MANEC-type domain from hepatocyte growth factor activator inhibitor-1 reveals an unexpected PAN/apple domain-type fold

Zebin Hong, Michal Nowakowski, Chris Spronk, Steen V. Petersen, Peter A. Andreasen, Wiktor Koźmiński, Frans A.A. Mulder, Jan K. Jensen

Biochem J (2015) 466 (2): 299–309.

https://doi.org/10.1042/BJ20141236

Published: 20 February 2015

... present the NMR solution structure of the MANEC domain from HAI-1, the first three-dimensional (3D) structure from the MANEC domain family. Unexpectedly, MANEC is a new subclass of the PAN/apple domain family, with its own unifying features, such as two additional disulfide bonds, two extended loop...

View articletitled, The solution structure of the MANEC-type domain from hepatocyte growth factor activator inhibitor-1 reveals an unexpected PAN/apple domain-type fold

Includes: Supplementary data

Articles

The structural basis of DNA binding by the single-stranded DNA-binding protein from Sulfolobus solfataricus

Roland Gamsjaeger, Ruvini Kariawasam, Adrian X. Gimenez, Christine Touma, Elysse McIlwain, Ray E. Bernardo, Nicholas E. Shepherd, Sandro F. Ataide, Qihan Dong, Derek J. Richard, Malcolm F. White, Liza Cubeddu

Biochem J (2015) 465 (2): 337–346.

https://doi.org/10.1042/BJ20141140

Published: 06 January 2015

... differences in the molecular mechanism of ssDNA binding. We have determined the structure of the SsoSSB OB domain bound to ssDNA by NMR spectroscopy. We reveal that ssDNA recognition is modulated by base-stacking of three key aromatic residues, in contrast with the OB domains of human RPA and the recently...

View articletitled, The structural basis of DNA binding by the single-stranded DNA-binding protein from Sulfolobus solfataricus

Includes: Supplementary data

Articles

Solution structures and dynamics of ADF/cofilins UNC-60A and UNC-60B from Caenorhabditis elegans

Vaibhav Kumar Shukla, Ashish Kabra, Diva Maheshwari, Rahul Yadav, Anupam Jain, Sarita Tripathi, Shoichiro Ono, Dinesh Kumar, Ashish Arora

Biochem J (2015) 465 (1): 63–78.

https://doi.org/10.1042/BJ20140923

Published: 12 December 2014

... medium containing [ 15 N]ammonium sulphate and [ 13 C]glucose (CIL) as the sole nitrogen and carbon sources respectively. NMR samples of 13 C/ 15 N-labelled UNC-60A and UNC-60B were prepared at a concentration of approximately 0.65 mM and 1.0 mM respectively in NMR buffer (20 mM sodium phosphate, pH...

View articletitled, Solution structures and dynamics of ADF/cofilins UNC-60A and UNC-60B from Caenorhabditis elegans

Includes: Supplementary data

Articles

Structural basis of conformational transitions in the active site and 80′s loop in the FK506-binding protein FKBP12

Sourajit M. Mustafi, Matthew Brecher, Jing Zhang, Hongmin Li, David M. Lemaster, Griselda Hernández

Biochem J (2014) 458 (3): 525–536.

https://doi.org/10.1042/BJ20131429

Published: 28 February 2014

...Sourajit M. Mustafi; Matthew Brecher; Jing Zhang; Hongmin Li; David M. Lemaster; Griselda Hernández The extensive set of NMR doublings exhibited by the immunophilin FKBP12 (FK506-binding protein 12) arose from a slow transition to the cis -peptide configuration at Gly 89 near the tip of the 80′s...

View articletitled, Structural basis of conformational transitions in the active site and 80′s loop in the FK506-binding protein FKBP12

Includes: Supplementary data

Articles

Secret of the major birch pollen allergen Bet v 1: identification of the physiological ligand

Christian Seutter von Loetzen, Thomas Hoffmann, Maximilian J. Hartl, Kristian Schweimer, Wilfried Schwab, Paul Rösch, Olivia Hartl-Spiegelhauer

Biochem J (2014) 457 (3): 379–390.

https://doi.org/10.1042/BJ20130413

Published: 10 January 2014

... the specificity of Q3OS binding. Elucidation of the binding site by NMR combined with a computational model resulted in a more detailed understanding and shed light on the physiological function of Bet v 1. We postulate that the binding of Q3OS to Bet v 1 plays an important, but as yet unclear, role during...

View articletitled, Secret of the major birch pollen allergen Bet v 1: identification of the physiological ligand

Includes: Supplementary data

Articles

Analysing the visible conformational substates of the FK506-binding protein FKBP12

Sourajit M. Mustafi, Hui Chen, Hongmin Li, David M. LeMaster, Griselda Hernández

Biochem J (2013) 453 (3): 371–380.

https://doi.org/10.1042/BJ20130276

Published: 12 July 2013

...Sourajit M. Mustafi; Hui Chen; Hongmin Li; David M. LeMaster; Griselda Hernández The 1 H- 15 N 2D NMR correlation spectrum of the widely studied FK506-binding protein FKBP12 (FK506-binding protein of 12 kDa) contains previously unreported peak doublings for at least 31 residues that arise from...

View articletitled, Analysing the visible conformational substates of the FK506-binding protein FKBP12

Articles

High-resolution NMR studies of structure and dynamics of human ERp27 indicate extensive interdomain flexibility

Nader T. Amin, A. Katrine Wallis, Stephen A. Wells, Michelle L. Rowe, Richard A. Williamson, Mark J. Howard, Robert B. Freedman

Biochem J (2013) 450 (2): 321–332.

https://doi.org/10.1042/BJ20121635

Published: 15 February 2013

... of two thioredoxin-fold domains homologous with the non-catalytic b and b ′ domains of PDI. The structure in solution of the N-terminal b -like domain of ERp27 was solved using high-resolution NMR data. The structure confirms that it has the thioredoxin fold and that ERp27 is a member of the PDI family...

View articletitled, High-resolution NMR studies of structure and dynamics of human ERp27 indicate extensive interdomain flexibility

Includes: Supplementary data

Articles

Ca 2+ enhances Aβ polymerization rate and fibrillar stability in a dynamic manner

Kristoffer Brännström, Anders Öhman, Malin Lindhagen-Persson, Anders Olofsson

Biochem J (2013) 450 (1): 189–197.

https://doi.org/10.1042/BJ20121583

Published: 24 January 2013

... and reversible manner enhances both the elongation rate and fibrillar stability, where specifically the ‘dock and lock’ phase mechanism is enhanced. Through NMR analysis we found that Ca 2+ affects the fibrillar architecture. In addition, and unexpectedly, we found that Ca 2+ does not bind the free Aβ monomer...

View articletitled, Ca 2+ enhances Aβ polymerization rate and fibrillar stability in a dynamic manner

Articles

An unusual antithrombin-binding heparin octasaccharide with an additional 3-O-sulfated glucosamine in the active pentasaccharide sequence

Marco Guerrini, Stefano Elli, Pierre Mourier, Timothy R. Rudd, Davide Gaudesi, Benito Casu, Christian Boudier, Giangiacomo Torri, Christian Viskov

Biochem J (2013) 449 (2): 343–351.

https://doi.org/10.1042/BJ20121309

Published: 14 December 2012

... semuloparin, in which both glucosamine residues of the pentasaccharide moiety located at the non-reducing end bear 3- O -sulfate groups. Two-dimensional and STD (saturation transfer difference) NMR experiments clearly confirmed its structure and identified its ligand epitope binding to antithrombin...

View articletitled, An unusual antithrombin-binding heparin octasaccharide with an additional 3-O-sulfated glucosamine in the active pentasaccharide sequence

Includes: Supplementary data

Articles

Buckwheat trypsin inhibitor with helical hairpin structure belongs to a new family of plant defence peptides

Peter B. Oparin, Konstantin S. Mineev, Yakov E. Dunaevsky, Alexander S. Arseniev, Mikhail A. Belozersky, Eugene V. Grishin, Tsezi A. Egorov, Alexander A. Vassilevski

Biochem J (2012) 446 (1): 69–77.

https://doi.org/10.1042/BJ20120548

Published: 27 July 2012

... with thioredoxin. The 3D (three-dimensional) structure of the peptide in solution was determined by NMR spectroscopy, revealing two antiparallel α-helices stapled by disulfide bonds. Together with VhTI, a trypsin inhibitor from veronica ( Veronica hederifolia ), BWI-2c represents a new family of protease...

View articletitled, Buckwheat trypsin inhibitor with helical hairpin structure belongs to a new family of plant defence peptides

Articles

The disordered N-terminal region of dengue virus capsid protein contains a lipid-droplet-binding motif

Ivo C. Martins, Francisco Gomes-Neto, André F. Faustino, Filomena A. Carvalho, Fabiana A. Carneiro, Patricia T. Bozza, Ronaldo Mohana-Borges, Miguel A. R. B. Castanho, Fábio C. L. Almeida, Nuno C. Santos, Andrea T. Da Poian

Biochem J (2012) 444 (3): 405–415.

https://doi.org/10.1042/BJ20112219

Published: 29 May 2012

... no vaccine or specific treatment is available. We used NMR, zeta potential measurements and atomic force microscopy to study the structural features of the interaction between dengue virus C (capsid) protein and LDs (lipid droplets), organelles crucial for infectious particle formation. C protein-binding...

View articletitled, The disordered N-terminal region of dengue virus capsid protein contains a lipid-droplet-binding motif

Includes: Supplementary data

Articles

Revealing the structural origin of the redox-Bohr effect: the first solution structure of a cytochrome from Geobacter sulfurreducens

Leonor Morgado, Vítor B. Paixão, Marianne Schiffer, P. Raj Pokkuluri, Marta Bruix, Carlos A. Salgueiro

Biochem J (2012) 441 (1): 179–187.

https://doi.org/10.1042/BJ20111103

Published: 14 December 2011

... for ATP synthesis in the presence of extracellular electron acceptors. In the present study, 15 N-labelled PpcA was produced and NMR spectroscopy was used to determine its solution structure in the fully reduced state, its backbone dynamics and the pH-dependent conformational changes. The structure...

View articletitled, Revealing the structural origin of the redox-Bohr effect: the first solution structure of a cytochrome from Geobacter sulfurreducens

Includes: Supplementary data

Articles

Structural changes in the BH3 domain of SOUL protein upon interaction with the anti-apoptotic protein Bcl-xL

Emmanuele Ambrosi, Stefano Capaldi, Michele Bovi, Gianmaria Saccomani, Massimiliano Perduca, Hugo L. Monaco

Biochem J (2011) 438 (2): 291–301.

https://doi.org/10.1042/BJ20110257

Published: 12 August 2011

... identified in the protein, thus making it a potential new member of the BH3-only protein family. In the present study, we provide NMR, SPR (surface plasmon resonance) and crystallographic evidence that a peptide spanning residues 147–172 in SOUL interacts with the anti-apoptotic protein Bcl-xL. We have...

View articletitled, Structural changes in the BH3 domain of SOUL protein upon interaction with the anti-apoptotic protein Bcl-xL

Includes: Supplementary data

Articles

The structure of a Burkholderia pseudomallei immunophilin–inhibitor complex reveals new approaches to antimicrobial development

Isobel H. Norville, Katherine O'Shea, Mitali Sarkar-Tyson, Suxin Zheng, Richard W. Titball, Gabriele Varani, Nicholas J. Harmer

Biochem J (2011) 437 (3): 413–422.

https://doi.org/10.1042/BJ20110345

Published: 13 July 2011

... isomerase activity and are inhibited by drugs including rapamycin and tacrolimus. We determined the structure of the Mip homologue [BpML1 ( Burkholderia pseudomallei Mip-like protein 1)] from the human pathogen and biowarfare threat B. pseudomallei by NMR and X-ray crystallography. The crystal structure...

View articletitled, The structure of a Burkholderia pseudomallei immunophilin–inhibitor complex reveals new approaches to antimicrobial development

Includes: Supplementary data

Articles

Solution structure of the Taf14 YEATS domain and its roles in cell growth of Saccharomyces cerevisiae

Wen Zhang, Jiahai Zhang, Xuecheng Zhang, Chao Xu, Xiaoming Tu

Biochem J (2011) 436 (1): 83–90.

https://doi.org/10.1042/BJ20110004

Published: 27 April 2011

... NMR spectroscopy. The Taf14 YEATS domain adopts a global fold of an elongated β-sandwich, similar to the Yaf9 YEATS domain. However, the Taf14 YEATS domain differs significantly from the Yaf9 YEATS domain in some aspects, which might indicate different structural classes of the YEATS domain family...

View articletitled, Solution structure of the Taf14 YEATS domain and its roles in cell growth of Saccharomyces cerevisiae

Includes: Supplementary data

Articles

Domain interactions of the transcription–translation coupling factor Escherichia coli NusG are intermolecular and transient

Björn M. Burmann, Ulrich Scheckenhofer, Kristian Schweimer, Paul Rösch

Biochem J (2011) 435 (3): 783–789.

https://doi.org/10.1042/BJ20101679

Published: 13 April 2011

... Aquifex aeolicus NusG, with a secondary structure that is highly similar to E. coli NusG shows direct interaction between its N- and C-terminal domains in a domain-swapped dimer. In the present study, we performed NMR paramagnetic relaxation enhancement measurements and identified interdomain interactions...

View articletitled, Domain interactions of the transcription–translation coupling factor Escherichia coli NusG are intermolecular and transient

Includes: Supplementary data

Articles

Determinants of activity in glutaredoxins: an in vitro evolved Grx1-like variant of Escherichia coli Grx3

Tobias H. Elgán, Anne-Gaëlle Planson, Jon Beckwith, Peter Güntert, Kurt D. Berndt

Biochem J (2010) 430 (3): 487–495.

https://doi.org/10.1042/BJ20100289

Published: 27 August 2010

... in a Grx1-like protein [Ortenberg, Gon, Porat and Beckwith (2004) Proc. Natl. Acad. Sci. U.S.A. 101 , 7439–7944]. To uncover the structural basis of this change in activity, we have compared wild-type and mutant Grx3 using CD and NMR spectroscopy. Ligand-induced stability measurements demonstrate...

View articletitled, Determinants of activity in glutaredoxins: an in vitro evolved Grx1-like variant of Escherichia coli Grx3

Articles

Formation of transient dimers by a retroviral protease

Maximilian J. Hartl, Kristian Schweimer, Martin H. Reger, Stephan Schwarzinger, Jochen Bodem, Paul Rösch, Birgitta M. Wöhrl

Biochem J (2010) 427 (2): 197–203.

https://doi.org/10.1042/BJ20091451

Published: 29 March 2010

... darunavir and tipranavir, known to prevent HIV-1 PR dimerization in cells, had no effect on foamy virus protease in vitro . 1 H- 15 N HSQC (heteronuclear single quantum coherence) NMR analysis of PRshort indicates that cholic acid binds in the proposed PRshort dimerization interface and appears to impair...

View articletitled, Formation of transient dimers by a retroviral protease

Articles

Dimer–dimer stacking interactions are important for nucleic acid binding by the archaeal chromatin protein Alba

Clare Jelinska, Biljana Petrovic-Stojanovska, W. John Ingledew, Malcolm F. White

Biochem J (2010) 427 (1): 49–55.

https://doi.org/10.1042/BJ20091841

Published: 15 March 2010

... 60 . In the present study we map perturbation of the polypeptide backbone of Alba upon binding to DNA and RNA by NMR, and demonstrate the central role of Phe 60 in forming the dimer–dimer interface. Site-directed spin labelling and pulsed ESR are used to confirm that an end-to-end, dimer–dimer...

View articletitled, Dimer–dimer stacking interactions are important for nucleic acid binding by the archaeal chromatin protein Alba

Articles

Chicken ileal bile-acid-binding protein: a promising target of investigation to understand binding co-operativity across the protein family

Mara Guariento, Michael Assfalg, Serena Zanzoni, Dimitrios Fessas, Renato Longhi, Henriette Molinari

Biochem J (2010) 425 (2): 413–424.

https://doi.org/10.1042/BJ20091209

Published: 23 December 2009

... isothermal titration calorimetry experiments and validated on the basis of both protein-observed and ligand-observed NMR titration data. It emerges that a singly bound protein is relatively abundant at low ligand/protein molar ratios assessing the absence of strong co-operativity. Both the measured...

View articletitled, Chicken ileal bile-acid-binding protein: a promising target of investigation to understand binding co-operativity across the protein family

Includes: Supplementary data

Articles

Structure of human insulin-like peptide 5 and characterization of conserved hydrogen bonds and electrostatic interactions within the relaxin framework

Linda M. Haugaard-Jönsson, Mohammed Akhter Hossain, Norelle L. Daly, David J. Craik, John D. Wade, K. Johan Rosengren

Biochem J (2009) 419 (3): 619–627.

https://doi.org/10.1042/BJ20082353

Published: 14 April 2009

... potency and appears to be the endogenous ligand for this receptor, on the basis of overlapping expression profiles and their apparent co-evolution. In the present study, we have used solution-state NMR to characterize the three-dimensional structure of synthetic human INSL5. The structure reveals...

View articletitled, Structure of human insulin-like peptide 5 and characterization of conserved hydrogen bonds and electrostatic interactions within the relaxin framework

Includes: Supplementary data

Articles

Amide solvent protection analysis demonstrates that amyloid-β(1–40) and amyloid-β(1–42) form different fibrillar structures under identical conditions

Anders Olofsson, Malin Lindhagen-Persson, A. Elisabeth Sauer-Eriksson, Anders Öhman

Biochem J (2007) 404 (1): 63–70.

https://doi.org/10.1042/BJ20061561

Published: 26 April 2007

.... In the present study we have used quenched hydrogen/deuterium-exchange NMR experiments to probe the structure of Aβ(1–40) fibrils. The fibrils were prepared and analysed identically as in our previous study on Aβ(1–42) fibrils, allowing a direct comparison of the two fibrillar structures. The solvent protection...

View articletitled, Amide solvent protection analysis demonstrates that amyloid-β(1–40) and amyloid-β(1–42) form different fibrillar structures under identical conditions

Articles

Myotonia-related mutations in the distal C-terminus of ClC-1 and ClC-0 chloride channels affect the structure of a poly-proline helix

María J. Macías, Oscar Teijido, Giovanni Zifarelli, Pau Martin, Ximena Ramirez-Espain, Antonio Zorzano, Manuel Palacín, Michael Pusch, Raúl Estévez

Biochem J (2007) 403 (1): 79–87.

https://doi.org/10.1042/BJ20061230

Published: 13 March 2007

... of these mutants is reduced in Xenopus oocytes compared with wild-type ClC-1. Functional, biochemical and NMR spectroscopy studies revealed that the CTD region encompasses a segment conserved in most voltage-dependent CLC channels that folds with a secondary structure containing a short type II poly-proline helix...

View articletitled, Myotonia-related mutations in the distal C-terminus of ClC-1 and ClC-0 chloride channels affect the structure of a poly-proline helix

Includes: Supplementary data

Articles

A reassessment of copper(II) binding in the full-length prion protein

Mark A. Wells, Graham S. Jackson, Samantha Jones, Laszlo L. P. Hosszu, C. Jeremy Craven, Anthony R. Clarke, John Collinge, Jonathan P. Waltho

Biochem J (2006) 399 (3): 435–444.

https://doi.org/10.1042/BJ20060458

Published: 13 October 2006

... mild acidification to pH 5.5 selects in favour of the low occupancy, multiple imidazole binding mode. We have used NMR to resolve how Cu 2+ binds to the full-length prion protein under mildly acidic conditions where multiple histidine co-ordination is dominant. We show that at pH 5.5 the protein binds...

View articletitled, A reassessment of copper(II) binding in the full-length prion protein

Includes: Supplementary data

Articles

Structural plasticity of the cyclic-cystine-knot framework: implications for biological activity and drug design

Richard J. Clark, Norelle L. Daly, David J. Craik

Biochem J (2006) 394 (1): 85–93.

https://doi.org/10.1042/BJ20051691

Published: 27 January 2006

... 2005 21 11 2005 21 11 2005 The Biochemical Society, London 2006 cyclic protein cyclotide haemolytic activity kalata NMR protein engineering Human type A erythrocytes were washed with PBS and centrifuged at 150 g for 30 s in a microcentrifuge several times until...

View articletitled, Structural plasticity of the cyclic-cystine-knot framework: implications for biological activity and drug design

Articles

Interactions between the plasma membrane and the antimicrobial peptide HP (2-20) and its analogues derived from Helicobacter pylori

Kwang H. Lee, Dong G. Lee, Yoonkyung Park, Dong-Il Kang, Song Y. Shin, Kyung-Soo Hahm, Yangmee Kim

Biochem J (2006) 394 (1): 105–114.

https://doi.org/10.1042/BJ20051574

Published: 27 January 2006

... by replacement of Phe 5 or Leu 11 with serine was accompanied by a reduction in antimicrobial activity. Analysis of the tertiary structures of the peptides in SDS micelles by NMR spectroscopy revealed that they have a well-defined α-helical structure. Among the analogues, anal-3 has the longest α-helix, from Val...

View articletitled, Interactions between the plasma membrane and the antimicrobial peptide HP (2-20) and its analogues derived from Helicobacter pylori

Includes: Supplementary data

Articles

Structure of the zinc finger domain encompassing residues 13–51 of the nucleocapsid protein from simian immunodeficiency virus

Nelly Morellet, Hervé Meudal, Serge Bouaziz, Bernard Pierre Roques

Biochem J (2006) 393 (3): 725–732.

https://doi.org/10.1042/BJ20051203

Published: 13 January 2006

... of antiviral drugs, the structure of (13-51)NCp8 (zinc finger domain of NCp8, encompassing residues 13–51) from SIVlhoest was determined by NMR to appraise the influence of major differences in the sequence, since Glu 21 , Gly 43 and Met 46 in NCp7 are replaced by Pro, Glu and Phe respectively...

View articletitled, Structure of the zinc finger domain encompassing residues 13–51 of the nucleocapsid protein from simian immunodeficiency virus

Articles

Kalata B8, a novel antiviral circular protein, exhibits conformational flexibility in the cystine knot motif

Norelle L. Daly, Richard J. Clark, Manuel R. Plan, David J. Craik

Biochem J (2006) 393 (3): 619–626.

https://doi.org/10.1042/BJ20051371

Published: 13 January 2006

... was achieved using Edman degradation. Samples for 1 H NMR measurements contained approx. 1 mM peptide in 90% water/10% 2 H 2 O (v/v) at approx. pH 3. 2 H 2 O (99.9 and 99.99%) was obtained from Cambridge Isotope Laboratories (Woburn, MA, U.S.A.). Spectra were recorded between 280 and 320 K...

View articletitled, Kalata B8, a novel antiviral circular protein, exhibits conformational flexibility in the cystine knot motif

Includes: Supplementary data

Articles

The N-terminal 26-residue fragment of human programmed cell death 5 protein can form a stable α-helix having unique electrostatic potential character

Dongsheng Liu, Hongwei Yao, Yaoyao Chen, Yingang Feng, Yingyu Chen, Jinfeng Wang

Biochem J (2005) 392 (1): 47–54.

https://doi.org/10.1042/BJ20050688

Published: 08 November 2005

... in this study to better understand its tertiary structure. The spectroscopic studies using CD and hetero- and homo-nuclear NMR methods determine a stable α-helix formed by Asp 3 –Ala 19 of PDCD5-(1–26). The N-terminal residues Asp 3 –Ala 19 of PDCD5 were then affirmed to have the capacity to form a stable α...

View articletitled, The N-terminal 26-residue fragment of human programmed cell death 5 protein can form a stable α-helix having unique electrostatic potential character

Articles

Structural and functional studies of vertebrate metallothioneins: cross-talk between domains in the absence of physical contact

Clemente Capasso, Vincenzo Carginale, Orlando Crescenzi, Daniela Di Maro, Roberta Spadaccini, Piero Andrea Temussi, Elio Parisi

Biochem J (2005) 391 (1): 95–103.

https://doi.org/10.1042/BJ20050335

Published: 26 September 2005

... of the isolated recombinant domains constituting Notothenia coriiceps and mouse MTs, and compared them with those of the corresponding whole MTs. NMR spectra of the separated domains of N. coriiceps are almost superimposable on those of the parent MT, suggesting an apparent lack of interaction between the two...

View articletitled, Structural and functional studies of vertebrate metallothioneins: cross-talk between domains in the absence of physical contact

Articles

Interaction between the bacterial nucleoid associated proteins Hha and H-NS involves a conformational change of Hha

Jesús GARCÍA, Tiago N. CORDEIRO, José M. NIETO, Ignacio PONS, Antonio JUÁREZ, Miquel PONS

Biochem J (2005) 388 (3): 755–762.

https://doi.org/10.1042/BJ20050002

Published: 07 June 2005

... that proteins of the Hha family are essential elements for H-NS-regulated gene expression. Hha has been shown to bind H-NS, although the details for this interaction are still unknown. In the present paper, we report fluorescence anisotropy and NMR studies of the interaction between Hha and H-NS 64...

View articletitled, Interaction between the bacterial nucleoid associated proteins Hha and H-NS involves a conformational change of Hha

Articles

An unusual fold for potassium channel blockers: NMR structure of three toxins from the scorpion Opisthacanthus madagascariensis

Benjamin CHAGOT, Cyril PIMENTEL, Li DAI, Joost PIL, Jan TYTGAT, Terumi NAKAJIMA, Gerardo CORZO, Hervé DARBON, Gilles FERRAT

Biochem J (2005) 388 (1): 263–271.

https://doi.org/10.1042/BJ20041705

Published: 10 May 2005

... the amplitude of the K + current of the rat channels Kv1.1 and Kv1.2, as well as human Kv1.3. We also determine the solution structure of three of the toxins by use of two-dimensional proton NMR techniques followed by distance geometry and molecular dynamics. The structures of these three peptides display...

View articletitled, An unusual fold for potassium channel blockers: NMR structure of three toxins from the scorpion Opisthacanthus madagascariensis

Articles

The C-terminal domain of the HIV-1 regulatory protein Vpr adopts an antiparallel dimeric structure in solution via its leucine-zipper-like domain

Sarah BOURBIGOT, Hervé BELTZ, Jérôme DENIS, Nelly MORELLET, Bernard P. ROQUES, Yves MÉLY, Serge BOUAZIZ

Biochem J (2005) 387 (2): 333–341.

https://doi.org/10.1042/BJ20041759

Published: 05 April 2005

... is implicated in properties of the protein such as DNA interaction and apoptosis via interaction with the adenine nucleotide translocator. To understand the specific interactions of Vpr-(52–96), the ability of this peptide to dimerize via a leucine-zipper mechanism has been investigated, by NMR and fluorescence...

View articletitled, The C-terminal domain of the HIV-1 regulatory protein Vpr adopts an antiparallel dimeric structure in solution via its leucine-zipper-like domain

Includes: Supplementary data

Articles

Hepatitis A virus proteinase 3C binding to viral RNA: correlation with substrate binding and enzyme dimerization

Hannelore PETERS, Yuri Y. KUSOV, Sonja MEYER, Andrew J. BENIE, Englbert BÄUML, Maike WOLFF, Christoph RADEMACHER, Thomas PETERS, Verena GAUSS-MÜLLER

Biochem J (2005) 385 (2): 363–370.

https://doi.org/10.1042/BJ20041153

Published: 07 January 2005

... resonance (SPR) NMR The comprehensive characterization of the multiple functions of 3C is of prime importance for the understanding of the finely tuned steps of protein and RNA synthesis in the viral life cycle. Our initial experiments were therefore aimed at characterizing HAV 3C binding to viral RNA...

View articletitled, Hepatitis A virus proteinase 3C binding to viral RNA: correlation with substrate binding and enzyme dimerization

Articles

Structural characterization of Escherichia coli sensor histidine kinase EnvZ: the periplasmic C-terminal core domain is critical for homodimerization

Ahmad KHORCHID, Masayori INOUYE, Mitsuhiko IKURA

Biochem J (2005) 385 (1): 255–264.

https://doi.org/10.1042/BJ20041125

Published: 14 December 2004

... 9 2004 9 9 2004 The Biochemical Society, London 2005 bacterial signal transduction membrane receptor NMR osmolarity stress response Bacterial response to environmental changes is essential for their survival. The two-component regulatory systems (also referred...

View articletitled, Structural characterization of Escherichia coli sensor histidine kinase EnvZ: the periplasmic C-terminal core domain is critical for homodimerization

Includes: Supplementary data

Articles

The stereospecificity and catalytic efficiency of the tryptophan synthase-catalysed exchange of the α-protons of amino acids

Máire E. NíBEILLIÚ, J. Paul G. MALTHOUSE

Biochem J (2004) 381 (3): 847–852.

https://doi.org/10.1042/BJ20040388

Published: 27 July 2004

...Máire E. NíBEILLIÚ; J. Paul G. MALTHOUSE 13 C-NMR has been used to follow the tryptophan synthase (EC 4.2.1.20) catalysed hydrogen–deuterium exchange of the pro-2R and pro-2S protons of [2- 13 C]glycine at pH 7.8. 1 H-NMR has also been used to follow the tryptophan-synthase-catalysed hydrogen...

View articletitled, The stereospecificity and catalytic efficiency of the tryptophan synthase-catalysed exchange of the α-protons of amino acids

Articles

Biochemical analysis of the processive mechanism for epimerization of alginate by mannuronan C-5 epimerase AlgE4

Cristiana CAMPA, Synnøve HOLTAN, Nadra NILSEN, Tonje M. BJERKAN, Bjørn T. STOKKE, Gudmund SKJÅK-BRÆK

Biochem J (2004) 381 (1): 155–164.

https://doi.org/10.1042/BJ20031265

Published: 22 June 2004

... attack or a processive mode of action. Based on methodologies involving specific degrading enzymes, NMR, electrospray ionisation mass spectrometry and capillary electrophoresis we show here that on average 10 residues are epimerised for each enzyme–substrate encounter. A subsite model for the enzyme...

View articletitled, Biochemical analysis of the processive mechanism for epimerization of alginate by mannuronan C-5 epimerase AlgE4

Articles

Kinetic and structural characterization of a product complex of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase from Escherichia coli

Arnaud GARÇON, Alun BERMINGHAM, Lu-Yun LIAN, Jeremy P. DERRICK

Biochem J (2004) 380 (3): 867–873.

https://doi.org/10.1042/bj20031850

Published: 15 June 2004

... to the enzyme, and the second phase with a slow event that occurs after the reaction has taken place. The HPPK–DHPPP and HPPK–DHPPP–AMP complexes were examined by NMR, and the binding site for DHPPP partially mapped from changes in chemical shifts identified from two dimensional 1 H/ 15 N heteronuclear single...

View articletitled, Kinetic and structural characterization of a product complex of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase from Escherichia coli

Articles

Solution conformation of alpha-conotoxin GIC, a novel potent antagonist of alpha3beta2 nicotinic acetylcholine receptors

Seung-Wook CHI, Do-Hyoung KIM, Baldomero M. OLIVERA, J. Michael McINTOSH, Kyou-Hoon HAN

Biochem J (2004) 380 (2): 347–352.

https://doi.org/10.1042/bj20031792

Published: 01 June 2004

... selectivity for neuronal versus muscle subtype [McIntosh, Dowell, Watkins, Garrett, Yoshikami, and Olivera (2002) J. Biol. Chem. 277 , 33610–33615]. We have now determined the three-dimensional solution structure of α-conotoxin GIC by NMR spectroscopy. The structure of α-conotoxin GIC is well defined...

View articletitled, Solution conformation of alpha-conotoxin GIC, a novel potent antagonist of alpha3beta2 nicotinic acetylcholine receptors

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