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Articles

The Nrd1–Nab3–Sen1 transcription termination complex from a structural perspective

Belén Chaves-Arquero, José Manuel Pérez-Cañadillas

Biochem Soc Trans (2023) BST20221418.

DOI: https://doi.org/10.1042/BST20221418

Published: 24 May 2023

... domain SD split domain TRAMP Trf4/5 Air1/2 Mtr4 polyadenylation complex CUTs Nab3 Nrd1 pervasive transcription protein structure Sen1 References 1 Kuehner , J.N. , Pearson , E.L. and Moore , C. ( 2011 ) Unravelling the means to an end: RNA...

View article titled, The Nrd1–Nab3–Sen1 transcription termination complex from a structural perspective

Articles

The building blocks of caveolae revealed: caveolins finally take center stage

Anne K. Kenworthy

Biochem Soc Trans (2023) 51 (2): 855–869.

DOI: https://doi.org/10.1042/BST20221298

Published: 21 April 2023

... article published by Portland Press Limited on behalf of the Biochemical Society and distributed under the Creative Commons Attribution License 4.0 (CC BY) . caveolae caveolins cell membranes cryo-electron microscopy membrane proteins protein structure A critical step forward...

View article titled, The building blocks of caveolae revealed: caveolins finally take center stage

Articles

Structural analysis of mycobacterial electron transport chain complexes by cryoEM

Yingke Liang, John L. Rubinstein

Biochem Soc Trans (2023) 51 (1): 183–193.

DOI: https://doi.org/10.1042/BST20220611

Published: 20 January 2023

... chain membrane proteins Mycobacterium tuberculosis protein structure Bacteria of the genus Mycobacterium include pathogenic species such as M. tuberculosis , M. leprae , M. avium , M. abscessus (sometimes called Mycobacteroides abscessus ), and M. ulcerans, as well as non-pathogenic...

View article titled, Structural analysis of mycobacterial electron transport chain complexes by cryoEM

Articles

Unveiling the mechanisms and biosynthesis of a novel nickel-pincer enzyme

Shramana Chatterjee, Santhosh Gatreddi, Swati Gupta, Jorge L. Nevarez, Joel A. Rankin, Aiko Turmo, Jian Hu, Robert P. Hausinger

Biochem Soc Trans (2022) 50 (4): 1187–1196.

DOI: https://doi.org/10.1042/BST20220490

Published: 12 August 2022

.... Thus, lactate racemase is the founding member of a large family of NPN-containing enzymes. biosynthesis coenzymes cofactors nickel protein structure racemase Lactate racemase (Lar) interconverts the l - and d -isomers of lactic acid ( Figure 1A ) [ 1 ]. These 2-hydroxyacids...

View article titled, Unveiling the mechanisms and biosynthesis of a novel nickel-pincer enzyme

Articles

Drug repurposing in silico screening platforms

Jonathan G.L. Mullins

Biochem Soc Trans (2022) 50 (2): 747–758.

DOI: https://doi.org/10.1042/BST20200967

Published: 14 March 2022

... computational biology drug discovery and design molecular docking platforms protein structure Drug repurposing possesses great advantages in terms of establishing new therapeutic options for specific disorders by exploiting drugs used for other conditions that are already known to be largely safe...

View article titled, Drug repurposing in silico screening platforms

Articles

Conformational ensembles of intrinsically disordered proteins and flexible multidomain proteins

F. Emil Thomasen, Kresten Lindorff-Larsen

Biochem Soc Trans (2022) 50 (1): 541–554.

DOI: https://doi.org/10.1042/BST20210499

Published: 07 February 2022

... protein conformations, models to calculate experimental observables from protein structure, and methods to refine ensembles against experimental data. We also provide examples of recent applications of integrative conformational ensemble determination to study IDPs and multidomain proteins and suggest...

View article titled, Conformational ensembles of intrinsically disordered proteins and flexible multidomain proteins

Articles

Tall tails: cryo-electron microscopy of phage tail DNA ejection conduits

Joshua M. Hardy, Rhys A. Dunstan, Trevor Lithgow, Fasséli Coulibaly

Biochem Soc Trans (2022) 50 (1): 459–22W.

DOI: https://doi.org/10.1042/BST20210799

Published: 07 February 2022

... of the Biochemical Society and distributed under the Creative Commons Attribution License 4.0 (CC BY) . bacteriophages cryo-electron microscopy protein structure structural biology virology Bacteriophages, or phages, infect prokaryotes and are the most abundant biological entity on the planet [ 1...

View article titled, Tall tails: cryo-electron microscopy of phage tail DNA ejection conduits

Articles

Solid state NMR of membrane proteins: methods and applications

Vivien Yeh, Boyan B. Bonev

Biochem Soc Trans (2021) 49 (4): 1505–1513.

DOI: https://doi.org/10.1042/BST20200070

Published: 16 August 2021

... and membrane protein studies, which uniquely provides information on structure, interactions and dynamics of membrane proteins. High resolution approaches are discussed in conjunction with applications of NMR methods to studies of membrane lipid and protein structure and interactions. Signal enhancement...

View article titled, Solid state NMR of membrane proteins: methods and applications

Articles

Plant asparaginyl endopeptidases and their structural determinants of function

Samuel G. Nonis, Joel Haywood, Joshua S. Mylne

Biochem Soc Trans (2021) 49 (2): 965–976.

DOI: https://doi.org/10.1042/BST20200908

Published: 05 March 2021

... protein structure proteolysis Asparaginyl endopeptidases (AEPs) are cysteine proteases of the C13 family (clan CD) that cleave at the carboxyl-terminal side of Asx (Asp or Asn). First discovered in legume plants [ 1 ], these enzymes were thus categorised as legumains (EC 3.4.22.34) [ 2...

View article titled, Plant asparaginyl endopeptidases and their structural determinants of function

Articles

Developments in tandem ion mobility mass spectrometry

Charles Eldrid, Konstantinos Thalassinos

Biochem Soc Trans (2020) 48 (6): 2457–2466.

DOI: https://doi.org/10.1042/BST20190788

Published: 18 December 2020

... (CC BY) . Open access for this article was enabled by the participation of University College London in an all-inclusive Read & Publish pilot with Portland Press and the Biochemical Society under a transformative agreement with JISC. ion mobility mass spectrometry protein structure...

View article titled, Developments in tandem ion mobility mass spectrometry

Articles

Does it take two to tango? RING domain self-association and activity in TRIM E3 ubiquitin ligases

Filippo Fiorentini, Diego Esposito, Katrin Rittinger

Biochem Soc Trans (2020) 48 (6): 2615–2624.

DOI: https://doi.org/10.1042/BST20200383

Published: 10 November 2020

... pilot with Portland Press and the Biochemical Society under a transformative agreement with JISC. protein structure ring ligases TRIM proteins ubiquitin ligases An abundance of cellular functions is controlled by the attachment of a 76-residue ubiquitin (Ub) molecule to a protein...

View article titled, Does it take two to tango? RING domain self-association and activity in TRIM E3 ubiquitin ligases

Includes: Supplementary data

Articles

Elevator-type mechanisms of membrane transport

Alisa A. Garaeva, Dirk J. Slotboom

Biochem Soc Trans (2020) 48 (3): 1227–1241.

DOI: https://doi.org/10.1042/BST20200290

Published: 05 May 2020

... by the participation of University of Groningen in an all-inclusive Read & Publish pilot with Portland Press and the Biochemical Society. membrane proteins protein structure transport Structural studies of membrane transporters from diverse protein families have revealed that alternating access...

View article titled, Elevator-type mechanisms of membrane transport

Articles

Structure and mechanism of the ESCRT pathway AAA+ ATPase Vps4

Han Han, Christopher P. Hill

Biochem Soc Trans (2019) 47 (1): 37–45.

DOI: https://doi.org/10.1042/BST20180260

Published: 15 January 2019

... BY-NC-ND) . AAA proteins cryo-electron microscopy endosomal sorting protein disassembly protein structure E ndosomal S orting C omplex R equired for T ransport (ESCRT) pathways drive membrane fission in numerous cellular processes, including cytokinesis, multivesicular...

View article titled, Structure and mechanism of the ESCRT pathway AAA+ ATPase Vps4

Articles

Transporter oligomerisation: roles in structure and function

Cristina Cecchetti, Euan Pyle, Bernadette Byrne

Biochem Soc Trans (2019) 47 (1): 433–440.

DOI: https://doi.org/10.1042/BST20180316

Published: 21 December 2018

... published by Portland Press Limited on behalf of the Biochemical Society and distributed under the Creative Commons Attribution License 4.0 (CC BY) . function membrane lipid oligomerisation protein structure transporter Integral membrane transporters play key roles in the effective...

View article titled, Transporter oligomerisation: roles in structure and function

Articles

The molecular mechanism of DHHC protein acyltransferases

Mitra S. Rana, Chul-Jin Lee, Anirban Banerjee

Biochem Soc Trans (2019) 47 (1): 157–167.

DOI: https://doi.org/10.1042/BST20180429

Published: 17 December 2018

... ( anirban.banerjee@nih.gov ) 28 9 2018 1 11 2018 6 11 2018 © 2019 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2019 acyl coenzyme A palmitoylation protein lipidation protein structure S-acylation transmembrane proteins DHHC-PATs...

View article titled, The molecular mechanism of DHHC protein acyltransferases

Articles

Structural biology and structure–function relationships of membrane proteins

Rosana Reis, Isabel Moraes

Biochem Soc Trans (2019) 47 (1): 47–61.

DOI: https://doi.org/10.1042/BST20180269

Published: 17 December 2018

... ( isabel.moraes@npl.co.uk ) 7 8 2018 22 10 2018 29 10 2018 © 2019 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2019 drug discovery membrane proteins protein structure structure–function relationship Membrane proteins (MP) are a large...

View article titled, Structural biology and structure–function relationships of membrane proteins

Articles

The structural basis of cystic fibrosis

Xin Meng, Jack Clews, Eleanor R. Martin, Anca D. Ciuta, Robert C. Ford

Biochem Soc Trans (2018) 46 (5): 1093–1098.

DOI: https://doi.org/10.1042/BST20180296

Published: 28 August 2018

...]. The structural basis of CF will be discussed in this article. cystic fibrosis transmembrane conductance regulator ion channel protein structure transmembrane proteins Initial structural studies were carried out over a decade ago on the soluble CFTR domains studied in isolation from...

View article titled, The structural basis of cystic fibrosis

Articles

Membrane proteins: always an insoluble problem?

Andrea E. Rawlings

Biochem Soc Trans (2016) 44 (3): 790–795.

DOI: https://doi.org/10.1042/BST20160025

Published: 09 June 2016

... of the Biochemical Society and distributed under the Creative Commons Attribution Licence 4.0 (CC BY) . membrane proteins protein engineering protein stability protein structure Integral membrane proteins (IMPs) exist within lipid membranes. Current estimates suggest that between 15 and 30% of open...

View article titled, Membrane proteins: always an insoluble problem?

Articles

O-GlcNAc transferase inhibitors: current tools and future challenges

Riccardo Trapannone, Karim Rafie, Daan M.F. van Aalten

Biochem Soc Trans (2016) 44 (1): 88–93.

DOI: https://doi.org/10.1042/BST20150189

Published: 09 February 2016

... ], rendering the enzyme inactive. inhibitor O-linked N -acetylglucosamine (O-GlcNAc) O-linked N -acetylglucosamine (O-GlcNAc) transferase post-translational modification protein structure signal transduction Figure 1 Chemical structures discussed in this review UDP–5S–GlcNAc...

View article titled, O-GlcNAc transferase inhibitors: current tools and future challenges

Articles

In search of the boundary between repetitive and non-repetitive protein sequences

François D. Richard, Andrey V. Kajava

Biochem Soc Trans (2015) 43 (5): 807–811.

DOI: https://doi.org/10.1042/BST20150073

Published: 09 October 2015

...; published by Portland Press Limited 2015 bioinformatics protein structure proteome scoring function tandem repeats Table 1 Scores used to assess TR MSAs Gaps are considered as twenty-first amino acids. Given an MSA of n repeat units, of length l , a fractional frequency can...

View article titled, In search of the boundary between repetitive and non-repetitive protein sequences

Articles

ABC transporter research: going strong 40 years on

Frederica L. Theodoulou, Ian D. Kerr

Biochem Soc Trans (2015) 43 (5): 1033–1040.

DOI: https://doi.org/10.1042/BST20150139

Published: 09 October 2015

... or ian.kerr@nottingham.ac.uk ). 3 6 2015 ATP-binding cassette (ABC) transporter disease multi-drug resistance protein structure transport mechanism The ATP-binding cassette (ABC) transporter field emerged from studies on nutrient uptake in bacteria in the 1970’s with the biochemical...

View article titled, ABC transporter research: going strong 40 years on

Articles

Structural biology of moonlighting: lessons from antibodies

Andrew C.R. Martin

Biochem Soc Trans (2014) 42 (6): 1704–1708.

DOI: https://doi.org/10.1042/BST20140211

Published: 17 November 2014

... compilation © 2014 Biochemical Society 2014 antibodies complementarity determining regions evolution moonlighting protein structure The traditional dogma of biology has been that DNA is copied into RNA which encodes a protein with a single function. Over the last 10–15 years, this dogma has...

View article titled, Structural biology of moonlighting: lessons from antibodies

Articles

Bacterial glyoxalase I enzymes: structural and biochemical investigations

John F. Honek

Biochem Soc Trans (2014) 42 (2): 479–484.

DOI: https://doi.org/10.1042/BST20130285

Published: 20 March 2014

... exist. The further investigation of the metal control of Glo1 by its protein structure continue to intrigue investigators not only for the enzyme's fundamental enzymology and the role that molecular structure plays in metal binding and activation, but also its importance in MG control and its role...

View article titled, Bacterial glyoxalase I enzymes: structural and biochemical investigations

Includes: Multimedia, Supplementary data

Articles

On the road to improve the bioremediation and electricity-harvesting skills of Geobacter sulfurreducens : functional and structural characterization of multihaem cytochromes

Leonor Morgado, Ana P. Fernandes, Joana M. Dantas, Marta A. Silva, Carlos A. Salgueiro

Biochem Soc Trans (2012) 40 (6): 1295–1301.

DOI: https://doi.org/10.1042/BST20120099

Published: 21 November 2012

... the thermodynamic parameters are determined, it is possible to evaluate the contribution of each microstate and their relevance to the electron-transfer mechanism. extracellular electron transfer Geobacter sulfurreducens multihaem cytochrome nuclear magnetic resonance (NMR) protein structure...

View article titled, On the road to improve the bioremediation and electricity-harvesting skills of Geobacter sulfurreducens : functional and structural characterization of multihaem cytochromes

Includes: Supplementary data

Articles

The fine details of evolution

Roman A. Laskowski, Janet M. Thornton, Michael J.E. Sternberg

Biochem Soc Trans (2009) 37 (4): 723–726.

DOI: https://doi.org/10.1042/BST0370723

Published: 22 July 2009

... To whom correspondence should be addressed (email roman@ebi.ac.uk ). gene duplication horizontal gene transfer phosphorylation protein evolution protein network protein structure In the 150 years since On the Origin of Species [ 1 ] was published, we have learnt much about...

View article titled, The fine details of evolution

Articles

Structural and functional restraints in the evolution of protein families and superfamilies

Sungsam Gong, Catherine L. Worth, G. Richard J. Bickerton, Semin Lee, Duangrudee Tanramluk, Tom L. Blundell

Biochem Soc Trans (2009) 37 (4): 727–733.

DOI: https://doi.org/10.1042/BST0370727

Published: 22 July 2009

...://creativecommons.org/licenses/by-nc/2.5/ ) which permits unrestricted non-commercial use, distribution and reproduction in any medium, provided the original work is properly cited. buried residue hydrogen bond local structural environment protein evolution protein structure An understanding...

View article titled, Structural and functional restraints in the evolution of protein families and superfamilies

Articles

The effects of conformational heterogeneity on the binding of the Notch intracellular domain to effector proteins: a case of biologically tuned disorder

Angela Bertagna, Dima Toptygin, Ludwig Brand, Doug Barrick

Biochem Soc Trans (2008) 36 (2): 157–166.

DOI: https://doi.org/10.1042/BST0360157

Published: 20 March 2008

... disorder Notch signalling protein–protein interaction protein structure The Notch pathway is a transmembrane signal transduction pathway used in cell-fate determination in metazoan development, homoeostasis and stem-cell maintenance and differentiation. Through Notch signalling, neighbouring...

View article titled, The effects of conformational heterogeneity on the binding of the Notch intracellular domain to effector proteins: a case of biologically tuned disorder

Articles

Computational approaches to the identification of heparin-binding sites on the surfaces of proteins

M. Forster, B. Mulloy

Biochem Soc Trans (2006) 34 (3): 431–434.

DOI: https://doi.org/10.1042/BST0340431

Published: 22 May 2006

..., at Laboratory for Molecular Structure, NIBSC (email bmulloy@nibsc.ac.uk ). 19 12 2005 © 2006 The Biochemical Society 2006 docking heparan sulphate heparin protein structure protein surface simulated annealing The complex glycosaminoglycan HS (heparan sulphate) [ 1 ] is found...

View article titled, Computational approaches to the identification of heparin-binding sites on the surfaces of proteins

Articles

Active and inactive conformations of the epidermal growth factor receptor

K.M. Ferguson

Biochem Soc Trans (2004) 32 (5): 742–745.

DOI: https://doi.org/10.1042/BST0320742

Published: 26 October 2004

...-mean-square deviation RTK receptor tyrosine kinase TGFα transforming growth factor-α ErbB receptor extracellular domain growth factor mechanism-based inhibitor protein structure target-specific drug Recent structural data have led to the proposal of a novel model...

View article titled, Active and inactive conformations of the epidermal growth factor receptor

Articles

Circular dichroism and synchrotron radiation circular dichroism spectroscopy: tools for drug discovery

B.A. Wallace, Robert W. Janes

Biochem Soc Trans (2003) 31 (3): 631–633.

DOI: https://doi.org/10.1042/bst0310631

Published: 01 June 2003

...B.A. Wallace; Robert W. Janes CD spectroscopy is an established and valuable technique for examining protein structure, dynamics and folding. Because of its ability to sensitively detect conformational changes, it has important potential for drug discovery, enabling screening for ligand and drug...

View article titled, Circular dichroism and synchrotron radiation circular dichroism spectroscopy: tools for drug discovery

Articles

Membrane properties and amyloid fibril formation of lung surfactant protein C

J. Johansson

Biochem Soc Trans (2001) 29 (4): 601–606.

DOI: https://doi.org/10.1042/bst0290601

Published: 01 August 2001

... © 2001 Biochemical Society 2001 amyloid-β peptide α-helix → β-strand transition prion protein protein structure secondary structure prediction Aβ, amyloid-β ES, electrospray PAP, pulmonary alveolar proteinosis PrP, prion protein SP-C, surfactant protein C DPPC...

View article titled, Membrane properties and amyloid fibril formation of lung surfactant protein C

Articles

Searching for the ideal forms of proteins

W. R. Taylor

Biochem Soc Trans (2000) 28 (2): 264–269.

DOI: https://doi.org/10.1042/bst0280264

Published: 01 February 2000

... of the algorithm, it will be possible to compare all of these against the Protein Structure Database and determine the extent to which the current ideal forms can account for the variety of protein structure. Analysis of the remainder should provide a base for the development of further forms. 1 9 1999...

View article titled, Searching for the ideal forms of proteins

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The Nrd1–Nab3–Sen1 transcription termination complex from a structural perspective

The building blocks of caveolae revealed: caveolins finally take center stage

Structural analysis of mycobacterial electron transport chain complexes by cryoEM

Unveiling the mechanisms and biosynthesis of a novel nickel-pincer enzyme

Drug repurposing in silico screening platforms

Conformational ensembles of intrinsically disordered proteins and flexible multidomain proteins

Tall tails: cryo-electron microscopy of phage tail DNA ejection conduits

Solid state NMR of membrane proteins: methods and applications

Plant asparaginyl endopeptidases and their structural determinants of function

Developments in tandem ion mobility mass spectrometry

Does it take two to tango? RING domain self-association and activity in TRIM E3 ubiquitin ligases

Elevator-type mechanisms of membrane transport

Structure and mechanism of the ESCRT pathway AAA+ ATPase Vps4

Transporter oligomerisation: roles in structure and function

The molecular mechanism of DHHC protein acyltransferases

Structural biology and structure–function relationships of membrane proteins

The structural basis of cystic fibrosis

Membrane proteins: always an insoluble problem?

O-GlcNAc transferase inhibitors: current tools and future challenges

In search of the boundary between repetitive and non-repetitive protein sequences

ABC transporter research: going strong 40 years on

Structural biology of moonlighting: lessons from antibodies

Bacterial glyoxalase I enzymes: structural and biochemical investigations

On the road to improve the bioremediation and electricity-harvesting skills of Geobacter sulfurreducens : functional and structural characterization of multihaem cytochromes

The fine details of evolution

Structural and functional restraints in the evolution of protein families and superfamilies

The effects of conformational heterogeneity on the binding of the Notch intracellular domain to effector proteins: a case of biologically tuned disorder

Computational approaches to the identification of heparin-binding sites on the surfaces of proteins

Active and inactive conformations of the epidermal growth factor receptor

Circular dichroism and synchrotron radiation circular dichroism spectroscopy: tools for drug discovery

Membrane properties and amyloid fibril formation of lung surfactant protein C

Searching for the ideal forms of proteins

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