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Articles

Maximizing the performance of protein-based fluorescent biosensors

Fu Chai, Dazhou Cheng, Yusuke Nasu, Takuya Terai, Robert E. Campbell

Biochem Soc Trans (2023) 51 (4): 1585–1595.

https://doi.org/10.1042/BST20221413

Published: 11 July 2023

... and the Biochemical Society under a transformative agreement with Individual. biosensors chemical biology fluorescence microscopy fluorescent proteins protein engineering signaling The 1994 demonstration that the green fluorescent protein (GFP) could be recombinantly and functionally expressed...

View articletitled, Maximizing the performance of protein-based fluorescent biosensors

Articles

Frankenstein Cas9: engineering improved gene editing systems

Pascal D. Vos, Aleksandra Filipovska, Oliver Rackham

Biochem Soc Trans (2022) 50 (5): 1505–1516.

https://doi.org/10.1042/BST20220873

Published: 28 October 2022

... it an adaptable gene editing system, it has many characteristics that could be improved for use in biotechnology. Cas9 exhibits significant off-target activity and low on-target nuclease activity in certain contexts. Scientists have undertaken ambitious protein engineering campaigns to bypass these limitations...

View articletitled, Frankenstein Cas9: engineering improved gene editing systems

Articles

Artificial protein assemblies with well-defined supramolecular protein nanostructures

Suyeong Han, Yongwon Jung

Biochem Soc Trans (2021) 49 (6): 2821–2830.

https://doi.org/10.1042/BST20210808

Published: 23 November 2021

... of the Biochemical Society 2021 protein assembly protein engineering protein nanostructures Proteins are versatile, major building blocks for diverse high-order biomolecule structures in nature, and there are also many supramolecular protein only assemblies with a wide range of structures...

View articletitled, Artificial protein assemblies with well-defined supramolecular protein nanostructures

Articles

Writing and erasing O- GlcNAc from target proteins in cells

Yun Ge, Christina M. Woo

Biochem Soc Trans (2021) 49 (6): 2891–2901.

https://doi.org/10.1042/BST20210865

Published: 16 November 2021

... deglycosylation glycosylation O -GlcNAc post translational modification protein engineering O- GlcNAc is a monosaccharide post-translational modification (PTM) installed on thousands of nucleocytoplasmic and mitochondrial proteins at multiple serine or threonine residues in eukaryotic cells [ 1...

View articletitled, Writing and erasing O- GlcNAc from target proteins in cells

Articles

Challenges and approaches to studying pore-forming proteins

Joshua T. Benton, Charles Bayly-Jones

Biochem Soc Trans (2021) 49 (6): 2749–2765.

https://doi.org/10.1042/BST20210706

Published: 08 November 2021

.... agricultural bioscience imaging techniques membrane proteins nanotechnology pore-forming toxins protein engineering Pore-forming proteins (PFPs) represent a highly diverse and growing class of molecules identified in all kingdoms of life ( Figure 1 ). Examples include the MACPF/CDC, aerolysin...

View articletitled, Challenges and approaches to studying pore-forming proteins

Articles

Engineering with NanoLuc: a playground for the development of bioluminescent protein switches and sensors

Lieuwe Biewenga, Bas J.H.M. Rosier, Maarten Merkx

Biochem Soc Trans (2020) 48 (6): 2643–2655.

https://doi.org/10.1042/BST20200440

Published: 26 November 2020

... NanoLuc-based sensors and switches with a focus on the underlying protein engineering approaches. We discuss the advantages and disadvantages of various strategies with respect to sensor sensitivity, modularity, and dynamic range of the sensor and provide a perspective on future strategies...

View articletitled, Engineering with NanoLuc: a playground for the development of bioluminescent protein switches and sensors

Articles

Engineered protein switches for exogenous control of gene expression

Shaun Spisak, Marc Ostermeier

Biochem Soc Trans (2020) 48 (5): 2205–2212.

https://doi.org/10.1042/BST20200441

Published: 20 October 2020

... © 2020 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2020 protein engineering protein switches transcription factors Chimeric transcription factors have also recently been used as a tool to aid in natural product discovery [ 31 ]. Genome...

View articletitled, Engineered protein switches for exogenous control of gene expression

Articles

Engineered peptide ligases for cell signaling and bioconjugation

Clara L. Frazier, Amy M. Weeks

Biochem Soc Trans (2020) 48 (3): 1153–1165.

https://doi.org/10.1042/BST20200001

Published: 15 June 2020

... enzymes with naturally evolved peptide ligation activity. Here, we provide a review of key natural peptide ligases and proteases engineered to favor peptide ligation activity. We cover the protein engineering approaches used to generate and improve these tools, along with recent biological applications...

View articletitled, Engineered peptide ligases for cell signaling and bioconjugation

Articles

Better together: building protein oligomers naturally and by design

Rebecca E.A. Gwyther, D. Dafydd Jones, Harley L. Worthy

Biochem Soc Trans (2019) 47 (6): 1773–1780.

https://doi.org/10.1042/BST20190283

Published: 05 December 2019

... of the Biochemical Society 2019 expanded genetic code oligomerization protein complexes protein engineering structural biology synthetic biology Oligomeric proteins complexes are the most common structural form of proteins found in nature. Taking inspiration from nature new artificial protein...

View articletitled, Better together: building protein oligomers naturally and by design

Articles

Engineering quorum quenching enzymes: progress and perspectives

Shereen A. Murugayah, Monica L. Gerth

Biochem Soc Trans (2019) 47 (3): 793–800.

https://doi.org/10.1042/BST20180165

Published: 07 May 2019

...-review, we have focused on efforts to engineer enzymes that disrupt quorum sensing by inactivating acyl-homoserine lactone signalling molecules. We review different approaches for protein engineering and provide examples of how these engineering approaches have been used to tailor the stability...

View articletitled, Engineering quorum quenching enzymes: progress and perspectives

Articles

Protein engineering: the potential of remote mutations

Matthew Wilding, Nansook Hong, Matthew Spence, Ashley M. Buckle, Colin J. Jackson

Biochem Soc Trans (2019) 47 (2): 701–711.

https://doi.org/10.1042/BST20180614

Published: 22 March 2019

... of the protein, i.e. regions remote from the active- or ligand-binding site, is often ignored. However, there is a growing body of literature that reports on, and rationalises, the successful engineering of proteins at remote sites. This minireview will discuss the current state of the art in protein engineering...

View articletitled, Protein engineering: the potential of remote mutations

Articles

Engineering of receptor-binding proteins in bacteriophages and phage tail-like bacteriocins

Dorien Dams, Lone Brøndsted, Zuzanna Drulis-Kawa, Yves Briers

Biochem Soc Trans (2019) 47 (1): 449–460.

https://doi.org/10.1042/BST20180172

Published: 19 February 2019

... 21 1 2019 28 1 2019 © 2019 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2019 phage phage tail-like bacteriocin protein engineering receptor-binding protein synthetic biology tailocin Bacteriophages (phages) are bacteria...

View articletitled, Engineering of receptor-binding proteins in bacteriophages and phage tail-like bacteriocins

Articles

Membrane protein engineering to the rescue

Andrea E. Rawlings

Biochem Soc Trans (2018) 46 (6): 1541–1549.

https://doi.org/10.1042/BST20180140

Published: 31 October 2018

... way of working with membrane proteins was to optimise the environment to suit the protein, through the use of different detergents, solubilising additives, and other adaptations. However, with innovative protein engineering methodologies, the membrane proteins themselves are now being adapted to suit...

View articletitled, Membrane protein engineering to the rescue

Articles

Approaches to single-molecule studies of metalloprotein electron transfer using scanning probe-based techniques

Martin Elliott, D. Dafydd Jones

Biochem Soc Trans (2018) 46 (1): 1–9.

https://doi.org/10.1042/BST20170229

Published: 22 December 2017

.... photosystem I) that generally have to be produced through recombinant cellular methods. Instead, protein engineering can be employed together with recombinant protein production. © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2018 electron transfer...

View articletitled, Approaches to single-molecule studies of metalloprotein electron transfer using scanning probe-based techniques

Articles

Let there be light: how to use photoswitchable cross-linker to reprogram proteins

Daniel Hoersch

Biochem Soc Trans (2017) 45 (3): 831–837.

https://doi.org/10.1042/BST20160386

Published: 15 June 2017

... of the Biochemical Society 2017 allosteric regulation azobenzene molecular machine photoswitch protein engineering The fundamental basis of the ‘molecular tweezer’ engineering strategy lies in the photo-physical properties of the azobenzene group. It exists in two isomerization states...

View articletitled, Let there be light: how to use photoswitchable cross-linker to reprogram proteins

Articles

Selection platforms for directed evolution in synthetic biology

Pedro A.G. Tizei, Eszter Csibra, Leticia Torres, Vitor B. Pinheiro

Biochem Soc Trans (2016) 44 (4): 1165–1175.

https://doi.org/10.1042/BST20160076

Published: 15 August 2016

... biology [ 4 ] or xenobiology [ 9 , 10 ]. Beyond improving our understanding of life and its origins, these modifications can be applied to novel biocontainment strategies [ 9 – 11 ], therapeutic agents [ 12 , 13 ] and protein engineering [ 14 ]. Partitioning of a diversified population...

View articletitled, Selection platforms for directed evolution in synthetic biology

Articles

Membrane proteins: always an insoluble problem?

Andrea E. Rawlings

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

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) . This review has so far focused on IMPs which normally reside within lipid membranes and which can, by elaborate protein engineering methods, be made to exist in a water soluble form without the addition...

View articletitled, Membrane proteins: always an insoluble problem?

Articles

BrisSynBio: a BBSRC/EPSRC-funded Synthetic Biology Research Centre

Kathleen R. Sedgley, Paul R. Race, Derek N. Woolfson

Biochem Soc Trans (2016) 44 (3): 689–691.

https://doi.org/10.1042/BST20160004

Published: 09 June 2016

... Society and distributed under the Creative Commons Attribution Licence 4.0 (CC BY) . biotechnology molecular modelling protein design protein engineering synthetic biology BrisSynBio is supported by £13.6 million from Biotechnology and Biological Sciences Research Council (BBSRC...

View articletitled, BrisSynBio: a BBSRC/EPSRC-funded Synthetic Biology Research Centre

Articles

Glycosyltransferase engineering for carbohydrate synthesis

John B. McArthur, Xi Chen

Biochem Soc Trans (2016) 44 (1): 129–142.

https://doi.org/10.1042/BST20150200

Published: 09 February 2016

... future opportunities to better understand GT domain–domain interactions. carbohydrate directed evolution enzymatic synthesis glycosyltransferase mutagenesis protein engineering A growing appreciation for the important biological roles and the therapeutic potential of carbohydrates...

View articletitled, Glycosyltransferase engineering for carbohydrate synthesis

Articles

Dissecting and reprogramming the folding and assembly of tandem-repeat proteins

Pamela J.E. Rowling, Elin M. Sivertsson, Albert Perez-Riba, Ewan R.G. Main, Laura S. Itzhaki

Biochem Soc Trans (2015) 43 (5): 881–888.

https://doi.org/10.1042/BST20150099

Published: 09 October 2015

... the native state from the N-terminus. 1 Correspondence may be addressed to either author (email [email protected] and [email protected] ) . 13 5 2015 © 2015 Authors; published by Portland Press Limited 2015 ankyrin protein design protein engineering protein folding tandem...

View articletitled, Dissecting and reprogramming the folding and assembly of tandem-repeat proteins

Articles

ProxiMAX randomization: a new technology for non-degenerate saturation mutagenesis of contiguous codons

Mohammed Ashraf, Laura Frigotto, Matthew E. Smith, Seema Patel, Marcus D. Hughes, Andrew J. Poole, Husam R.M. Hebaishi, Christopher G. Ullman, Anna V. Hine

Biochem Soc Trans (2013) 41 (5): 1189–1194.

https://doi.org/10.1042/BST20130123

Published: 23 September 2013

..., distribution and reproduction in any medium, provided the original work is properly cited. antibody engineering gene library MAX randomization overlap PCR protein engineering saturation mutagenesis For this longer loop, both right-hand and left-hand acceptors were employed to build two...

View articletitled, ProxiMAX randomization: a new technology for non-degenerate saturation mutagenesis of contiguous codons

Includes: Supplementary data

Articles

Rewiring cell signalling through chimaeric regulatory protein engineering

Baojun Wang, Mauricio Barahona, Martin Buck, Jörg Schumacher

Biochem Soc Trans (2013) 41 (5): 1195–1200.

https://doi.org/10.1042/BST20130138

Published: 23 September 2013

... is properly cited. bacterial enhancer binding protein cell signalling chimaeric protein protein engineering synthetic biology two-component signalling system In another study, Bashor et al. [ 27 ] constructed a synthetic scaffold protein device to systematically reshape response dynamics...

View articletitled, Rewiring cell signalling through chimaeric regulatory protein engineering

Articles

Genetically encoding phenyl azide chemistry: new uses and ideas for classical biochemistry

Samuel Reddington, Peter Watson, Pierre Rizkallah, Eric Tippmann, D. Dafydd Jones

Biochem Soc Trans (2013) 41 (5): 1177–1182.

https://doi.org/10.1042/BST20130094

Published: 23 September 2013

... or [email protected] ). 31 5 2013 © 2013 The Authors 2013 Click chemistry expanded genetic code p -azido- L -phenylalanine phenyl azide photocontrol protein engineering Uaas (unnatural amino acids) provide a powerful approach to expand the functionality of the proteome...

View articletitled, Genetically encoding phenyl azide chemistry: new uses and ideas for classical biochemistry

Articles

The alternative oxidases: simple oxidoreductase proteins with complex functions

Luke Young, Tomoo Shiba, Shigeharu Harada, Kiyoshi Kita, Mary S. Albury, Anthony L. Moore

Biochem Soc Trans (2013) 41 (5): 1305–1311.

https://doi.org/10.1042/BST20130073

Published: 23 September 2013

... 2013 The Authors 2013 di-iron carboxylate protein electron transfer protein engineering respiration ubiquinol oxidase It is generally recognized that the distribution of the AOX (alternative oxidase) is substantially wider than previously thought [ 1 ]. In addition to being ubiquitous...

View articletitled, The alternative oxidases: simple oxidoreductase proteins with complex functions

Articles

Rational design of FRET sensor proteins based on mutually exclusive domain interactions

Maarten Merkx, Misha V. Golynskiy, Laurens H. Lindenburg, Jan L. Vinkenborg

Biochem Soc Trans (2013) 41 (5): 1201–1205.

https://doi.org/10.1042/BST20130128

Published: 23 September 2013

... 2013 The Authors 2013 fluorescent sensor Förster resonance energy transfer (FRET) intracellular imaging protein engineering synthetic biology Figure 3 A modular design approach for engineering protein switches Using mutually exclusive interactions between input and output domains...

View articletitled, Rational design of FRET sensor proteins based on mutually exclusive domain interactions

Articles

Engineering oxidoreductases: maquette proteins designed from scratch

Bruce R. Lichtenstein, Tammer A. Farid, Goutham Kodali, Lee A. Solomon, J.L. Ross Anderson, Molly M. Sheehan, Nathan M. Ennist, Bryan A. Fry, Sarah E. Chobot, Chris Bialas, Joshua A. Mancini, Craig T. Armstrong, Zhenyu Zhao, Tatiana V. Esipova, David Snell, Sergei A. Vinogradov, Bohdana M. Discher, Christopher C. Moser, P. Leslie Dutton

Biochem Soc Trans (2012) 40 (3): 561–566.

https://doi.org/10.1042/BST20120067

Published: 22 May 2012

... oxidative chemistry that is the basis of multi-electron oxidative and reductive catalysis. 1 To whom correspondence should be addressed (email [email protected] ). 6 3 2012 electron transfer maquette oxidoreductase protein design protein engineering synthetic protein...

View articletitled, Engineering oxidoreductases: maquette proteins designed from scratch

Articles

Rational design and protein engineering of growth factors for regenerative medicine and tissue engineering

Andrew J. Moss, Shikha Sharma, Nicholas P.J. Brindle

Biochem Soc Trans (2009) 37 (4): 717–721.

https://doi.org/10.1042/BST0370717

Published: 22 July 2009

... specificity and action. Rational and combinatorial protein engineering techniques allow introduction of additional features into these synthetic growth molecules, as well as natural growth factors, which significantly enhance their therapeutic utility. Figure 1 RTK activation ( A ) Schematic...

View articletitled, Rational design and protein engineering of growth factors for regenerative medicine and tissue engineering

Articles

Controlling complexity and water penetration in functional de novo protein design

J.L. Ross Anderson, Ronald L. Koder, Christopher C. Moser, P. Leslie Dutton

Biochem Soc Trans (2008) 36 (6): 1106–1111.

https://doi.org/10.1042/BST0361106

Published: 19 November 2008

... novo protein design have illustrated how such control can be incorporated into the design process and have paved the way for the synthesis of nascent enzymatic activity in these systems. abzyme de novo protein design haem maquette protein engineering water penetration Figure 3 Haem...

View articletitled, Controlling complexity and water penetration in functional de novo protein design

Articles

Protein engineering applications of industrially exploitable enzymes: Geobacillus stearothermophilus LDH and Candida methylica FDH

N.G. Karagüler, R.B. Sessions, B. Binay, E.B. Ordu, A.R. Clarke

Biochem Soc Trans (2007) 35 (6): 1610–1615.

https://doi.org/10.1042/BST0351610

Published: 23 November 2007

... disadvantages in the large-scale production of chirally pure compounds. We have applied two routes of protein engineering studies to improve the properties of these two enzymes, namely DNA shuffling and site-directed mutagenesis. Altering the substrate specificity of bs LDH by DNA shuffling and changing...

View articletitled, Protein engineering applications of industrially exploitable enzymes: Geobacillus stearothermophilus LDH and Candida methylica FDH

Articles

Developing chemokine mutants with improved proteoglycan affinity and knocked-out GPCR activity as anti-inflammatory recombinant drugs

H. Potzinger, E. Geretti, B. Brandner, V. Wabitsch, A.-M. Piccinini, A. Rek, A.J. Kungl

Biochem Soc Trans (2006) 34 (3): 435–437.

https://doi.org/10.1042/BST0340435

Published: 22 May 2006

... Society 2006 anti-inflammatory drug chemokine mutant glycomics glycosaminoglycan G-protein-coupled receptor (GPCR) protein engineering Chemokines induce cell migration and activation by binding to specific cell surface, seven-transmembrane-spanning GPCRs (G-protein-coupled receptors...

View articletitled, Developing chemokine mutants with improved proteoglycan affinity and knocked-out GPCR activity as anti-inflammatory recombinant drugs

Articles

Choice of biocatalyst form for scalable processes

J.M. Woodley

Biochem Soc Trans (2006) 34 (2): 301–303.

https://doi.org/10.1042/BST0340301

Published: 20 March 2006

... in relation to the choice to be made. Recent developments in cell and protein engineering as well as reactor and process engineering are discussed in addition. 1 email [email protected] 25 11 2005 © 2006 The Biochemical Society 2006 biocatalytic process catalyst cost cell...

View articletitled, Choice of biocatalyst form for scalable processes

Articles

Lipids in and around photosynthetic reaction centres

P.K. Fyfe, M.R. Jones

Biochem Soc Trans (2005) 33 (5): 924–930.

https://doi.org/10.1042/BST0330924

Published: 26 October 2005

..., and a similar lipid–chlorophyll bonding interaction has recently been seen in LHC II (light harvesting complex II), the major antenna complex associated with PS-II [ 20 , 33 ]. 8 6 2005 © 2005 The Biochemical Society 2005 detergent lipid membrane protein protein engineering reaction...

View articletitled, Lipids in and around photosynthetic reaction centres

Articles

Rewiring photosynthesis: engineering wrong-way electron transfer in the purple bacterial reaction centre

M.C. Wakeham, M.R. Jones

Biochem Soc Trans (2005) 33 (4): 851–857.

https://doi.org/10.1042/BST0330851

Published: 01 August 2005

... of ubiquinone-6 in order to selectively reconstitute the Q B ubiquinone [ 56 – 58 ], or purified using the detergent Deriphat 160-C that allows retention of the Q B ubiquinone [ 57 , 58 ]. bacteriochlorophyll electron transfer membrane protein photosynthetic bacteria protein engineering reaction...

View articletitled, Rewiring photosynthesis: engineering wrong-way electron transfer in the purple bacterial reaction centre

Articles

Engineering substrate recognition in catalysis by cytochrome P450cam

S.G. Bell, X. Chen, F. Xu, Z. Rao, L.-L. Wong

Biochem Soc Trans (2003) 31 (3): 558–562.

https://doi.org/10.1042/bst0310558

Published: 01 June 2003

... Focused Meeting held at St. Andrews University, 12–14 January 2003 7 March 2003 © 2003 Biochemical Society 2003 chloroaromatic compound crystal structure cytochrome P450 enzyme P450 monooxygenase protein engineering terpene Abbreviations used: PeCB, pentachlorobenzene...

View articletitled, Engineering substrate recognition in catalysis by cytochrome P450cam

Articles

Control of electron transfer in neuronal NO synthase

S. Daff, M. A. Noble, D. H. Craig, S. L. Rivers, S. K. Chapman, A. W. Munro, S. Fujiwara, E. Rozhkova, I. Sagami, T. Shimizu

Biochem Soc Trans (2001) 29 (2): 147–152.

https://doi.org/10.1042/bst0290147

Published: 01 May 2001

... be addressed (e-mail [email protected] ) 15 11 2000 © 2001 Biochemical Society 2001 autoinhibitory domain cytochrome P450 nitric oxide protein engineering NOS, nitric oxide synthase nNOS, iNOS and eNOS, neuronal, induced and endothelial NOS P450, cytochrome P450 BM3, Bacillus...

View articletitled, Control of electron transfer in neuronal NO synthase

Articles

Mutagenesis of a plastidial lysophosphatidic acid acyltransferase

S. Maisonneuve, J.-J. Bessoule, R. Lessire, M. Delseny, T. J. Roscoe

Biochem Soc Trans (2000) 28 (6): 961–964.

https://doi.org/10.1042/bst0280961

Published: 01 December 2000

... To whom correspondence should be addressed (e-mail [email protected] ) 21 6 2000 © 2000 Biochemical Society 2000 protein engineering LPAAT, lysophosphatidic acid acyltransferase Biotechnological Aspects: Complex Lipids 5 Eccleston, V. S. and Harwood, J. L. ( 1995) Biochim...

View articletitled, Mutagenesis of a plastidial lysophosphatidic acid acyltransferase

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