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Keywords: protein engineering
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Articles
Journal:
Biochemical Journal
Biochem J (2023) 480 (2): 127–140.
Published: 23 January 2023
... 2023 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2023 protein engineering signaling pathways synthetic biology More than six decades ago, Jacob and Monod proposed a groundbreaking perspective on how genetic information is organized...
Articles
Journal:
Biochemical Journal
Biochem J (2021) 478 (15): 3047–3062.
Published: 13 August 2021
... enzyme activation metalloenzymes molecular mechanisms protein engineering Metals are present as structural features in over one-third of proteins, underscoring their importance for protein structure and function [ 1 , 2 ]. The incorporation of divalent metal ions into protein structures...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2020) 477 (9): 1701–1719.
Published: 11 May 2020
... ∑ # read s mut , i where # reads mut, i is the number of reads of a mutant in library fraction i , and ∑ # reads mut, i is the sum of all the reads for all mutants in library fraction i . metalloproteases next-generation sequencing protease inhibitor protein engineering...
Includes: Supplementary data
Articles
Matthew J. Byrne, Nazia Nasir, Christine Basmadjian, Chitra Bhatia, Rory F. Cunnison, Katherine H. Carr, Corine Mas-Droux, Sharon Yeoh, Céline Cano, Richard Bayliss
Journal:
Biochemical Journal
Biochem J (2020) 477 (8): 1525–1539.
Published: 29 April 2020
... and distributed under the Creative Commons Attribution License 4.0 (CC BY) . kinases protein engineering small molecules The NIMA-related kinases (Neks) are a family of Ser/Thr protein kinases, first discovered in Aspergillus nidulans that are conserved in eukaryotes [ 1 ]. Nek7 is 1 of 11 Neks...
Articles
Journal:
Biochemical Journal
Biochem J (2020) 477 (8): 1483–1497.
Published: 29 April 2020
... to previous studies from a structural perspective. These clashes would potentially lead to reduced substrate binding affinity of McTadA, consistent with our in vitro deamination activity and binding assays. To rescue the deamination activity of McTadA, we carried out two rounds of protein engineering through...
Includes: Supplementary data
Articles
Aaron M. Collier, Yuliya Nemtsova, Narendra Kuber, Whitney Banach-Petrosky, Anurag Modak, David E. Sleat, Vikas Nanda, Peter Lobel
Journal:
Biochemical Journal
Biochem J (2020) 477 (3): 727–745.
Published: 14 February 2020
... tripeptidyl-peptidase 1 (TPP1). Progression of LINCL can be slowed or halted by enzyme replacement therapy, where recombinant human TPP1 is administered to patients. In this study, we utilized protein engineering techniques to increase the stability of recombinant TPP1 with the rationale that this may...
Includes: Supplementary data
Articles
Gloria Gamiz-Arco, Valeria A. Risso, Adela M. Candel, Alvaro Inglés-Prieto, Maria L. Romero-Romero, Eric A. Gaucher, Jose A. Gavira, Beatriz Ibarra-Molero, Jose M. Sanchez-Ruiz
Journal:
Biochemical Journal
Biochem J (2019) 476 (23): 3631–3647.
Published: 10 December 2019
... ) Transient folding intermediates characterized by protein engineering . Nature 346 , 440 – 445 10.1038/346440a0 49 Anderson , D.W. , McKeown , A.N. and Thornton , J.W. ( 2015 ) Intermolecular epistasis shaped the function and evolution of an ancient transcription factor and its...
Includes: Supplementary data
Articles
Nikolina Trstenjak, Lukas Stulik, Harald Rouha, Jakub Zmajkovic, Manuel Zerbs, Eszter Nagy, Adriana Badarau
Journal:
Biochemical Journal
Biochem J (2019) 476 (2): 275–292.
Published: 25 January 2019
... invasion protein InlA to the murine variant of its cognate receptor E-cadherin by protein engineering [ 26 ]. LukGH is the most potent leukocidin in in vitro assays and ex vivo models [ 13 , 27 – 29 ], and is present in nearly all S. aureus strains [ 27 , 30 ]. It is expressed during human...
Includes: Supplementary data
Articles
Yang Xu, Kristian Mark P. Caldo, Roman Holic, Elzbieta Mietkiewska, Jocelyn Ozga, Syed Masood Rizvi, Guanqun Chen, Randall J. Weselake
Journal:
Biochemical Journal
Biochem J (2019) 476 (1): 151–164.
Published: 15 January 2019
... of neutral lipids (Δ F TAG) as a function of OD 600 (Δ F TAG/OD 600 ). Arabidopsis thaliana error-prone PCR LACS protein engineering Saccharomyces cerevisiae Fatty acids are carboxylic acids with highly reduced acyl chains, which act as the major energy reservoir in eukaryotic...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2018) 475 (23): 3887–3901.
Published: 12 December 2018
... of the Biochemical Society 2018 homoserine malate dehydrogenase protein engineering site-directed mutagenesis synthetic biology A central challenge in the creation of a resource-efficient and sustainable bioeconomy lies in the reduction in our dependence on fossil resources and a shift in focus...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2018) 475 (7): 1335–1352.
Published: 16 April 2018
... evolution protease inhibitor protein engineering protein–protein interactions (PPIs) serine proteases Here, we constructed a combinatorial library of APPI mutants that was rich in mutations enhancing stability, affinity, specificity and rapid association. By using this YSD APPI library to conduct...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2017) 474 (1): 1–19.
Published: 22 December 2016
... sequences and limited phylogenetic trees. This review will focus, firstly, on the use of ASR to uncover links between sequence and phenotype and, secondly, on the practical application of ASR in protein engineering. Correspondence: Elizabeth M.J. Gillam ( e.gillam@uq.edu.au ) 27 5 2016 7 11...
Articles
M. Luisa Romero-Romero, Valeria A. Risso, Sergio Martinez-Rodriguez, Beatriz Ibarra-Molero, Jose M. Sanchez-Ruiz
Journal:
Biochemical Journal
Biochem J (2016) 473 (20): 3611–3620.
Published: 11 October 2016
... 2016 15 8 2016 15 8 2016 © 2016 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society 2016 protein engineering protein stability resurrected proteins thioredoxin The engineering of proteins with enhanced stability has drawn considerable...
Articles
Sabine Rauth, Dominik Hinz, Michael Börger, Markus Uhrig, Manuel Mayhaus, Matthias Riemenschneider, Arne Skerra
Journal:
Biochemical Journal
Biochem J (2016) 473 (11): 1563–1578.
Published: 27 May 2016
... candidates compared with current biopharmaceutical treatments. Aβ peptide lipocalin neurodegeneration protein engineering Alzheimer's disease (AD) is the most prevalent form of dementia, with 10% of the human population older than 65 years and 40% older than 85 years affected [ 1 ]. Apart...
Includes: Supplementary data
Articles
Itay Cohen, Olumide Kayode, Alexandra Hockla, Banumathi Sankaran, Derek C. Radisky, Evette S. Radisky, Niv Papo
Journal:
Biochemical Journal
Biochem J (2016) 473 (10): 1329–1341.
Published: 11 May 2016
... in the present study pave the way to develop new therapies targeting mesotrypsin, an enzyme that contributes to progression and metastasis of lung, prostate, breast and pancreatic cancers. cancer therapy directed evolution enzyme inhibition mesotrypsin protease inhibitor protein engineering...
Includes: Supplementary data
Articles
Christopher F. Butler, Caroline Peet, Kirsty J. McLean, Michael T. Baynham, Richard T. Blankley, Karl Fisher, Stephen E. J. Rigby, David Leys, Michael W. Voice, Andrew W. Munro
Journal:
Biochemical Journal
Biochem J (2014) 460 (2): 247–259.
Published: 13 May 2014
... in the PDB under code 4O4P. 7 1 2014 3 3 2014 4 3 2014 4 3 2014 crystal structure cytochrome P450 drug metabolism protein engineering proton pump inhibitor Replacing traditional synthetic routes to complex organic molecules using enzyme-catalysed reactions has many...
Includes: Supplementary data
Articles
Emily Golden, Rachel Paterson, Wan Jun Tie, Anandhi Anandan, Gavin Flematti, Gianluca Molla, Elena Rosini, Loredano Pollegioni, Alice Vrielink
Journal:
Biochemical Journal
Biochem J (2013) 451 (2): 217–226.
Published: 28 March 2013
.... A view of the transition state configuration of the enzyme provides important insights into the mechanism of substrate binding and catalysis. crystal structure enzyme activity protein engineering substrate specificity transition state analogue Cephalosporins are currently the most widely...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2011) 440 (1): 95–105.
Published: 27 October 2011
... protease inhibitor protein engineering Proteases that are aberrantly expressed in the tumour microenvironment represent key contributors to tumour growth and progression [ 1 ], as well as a potentially promising category of drug targets [ 2 , 3 ]. However, a major challenge in the development...
Articles
Tana Koudelakova, Eva Chovancova, Jan Brezovsky, Marta Monincova, Andrea Fortova, Jiri Jarkovsky, Jiri Damborsky
Journal:
Biochemical Journal
Biochem J (2011) 435 (2): 345–354.
Published: 29 March 2011
... ). 1 9 2010 14 1 2011 4 2 2011 4 2 2011 © The Authors Journal compilation © 2011 Biochemical Society 2011 haloalkane dehalogenase phylogenetic analysis principal component analysis protein engineering substrate specificity Enzymes are biological catalysts...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2011) 435 (1): 1–16.
Published: 15 March 2011
... © 2011 Biochemical Society 2011 procoagulant protease therapy protein degradation protein engineering trypsin fold Sequencing of the human genome revealed that more than 2% of our genes encode proteases, suggesting that these enzymes possess functions more complex than the simple...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2011) 435 (1): 55–63.
Published: 15 March 2011
...://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. avidin biotin protein engineering protein–ligand interaction streptavidin traptavidin The capture of the small molecule...
Includes: Supplementary data
Articles
Florian Nachon, Eugenie Carletti, Marielle Wandhammer, Yvain Nicolet, Lawrence M. Schopfer, Patrick Masson, Oksana Lockridge
Journal:
Biochemical Journal
Biochem J (2011) 434 (1): 73–82.
Published: 27 January 2011
... The Authors Journal compilation © 2011 Biochemical Society 2011 acetylcholinesterase bioscavenger butyrylcholinesterase organophosphorus protein engineering spontaneous reactivation Recent progress in the understanding of enzyme catalysis, through the use of structural biology and molecular...
Articles
Journal:
Biochemical Journal
Biochem J (2008) 414 (2): 205–214.
Published: 12 August 2008
... 2008 chaperonin CO 2 fixation directed evolution protein engineering RbcX ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) Rubisco [ribulose-P 2 (D-ribulose-1,5-bisphosphate) carboxylase/oxygenase; EC 4.1.1.39] is the enzyme employed by almost all photoautotrophic organisms...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2007) 404 (3): 517–524.
Published: 29 May 2007
...) or processed for SDS/PAGE (12% gels) and non-denaturing PAGE (4–12% acrylamide gradient) analysis as described previously [ 17 ]. CO 2 fixation directed evolution metabolic engineering protein engineering ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) Rubisco (ribulose-1,5...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2006) 397 (2): 305–312.
Published: 28 June 2006
.... bioluminescence assay firefly luciferase imaging Photinus pyralis protein engineering Beetle luciferases catalyse the efficient transfer of chemical energy into light via a two-step process, utilizing ATP-Mg 2+ , firefly luciferin ( D -LH 2 ) and molecular oxygen, yielding oxyluciferin (LO...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2006) 394 (1): 85–93.
Published: 27 January 2006
... The Biochemical Society, London 2006 cyclic protein cyclotide haemolytic activity kalata NMR protein engineering The cyclotides [ 1 ] are a fascinating family of plant proteins that are distinguished by a head-to-tail peptide backbone and six conserved cysteine residues that are paired to form...
Articles
Henri R. Nordlund, Vesa P. Hytönen, Jarno Hörhä, Juha A. E. Määttä, Daniel J. White, Katrin Halling, Eevaleena J. Porkka, J. Peter Slotte, Olli H. Laitinen, Markku S. Kulomaa
Journal:
Biochemical Journal
Biochem J (2005) 392 (3): 485–491.
Published: 06 December 2005
... chain. In contrast with wild-type avidin, which contains four identical avidin monomers, scAvd enables each one of the four avidin domains to be independently modified by protein engineering. Therefore the scAvd scaffold can be used to construct spatially and stoichiometrically defined pseudotetrameric...
Articles
Journal:
Biochemical Journal
Biochem J (2004) 382 (3): 885–893.
Published: 07 September 2004
... To whom correspondence should be addressed (email Lambrou@aua.gr ). The Biochemical Society, London 2004 24 2 2004 25 5 2004 11 6 2004 15 6 2004 Cibacron Blue 3GA glutathione S-transferase herbicide detoxification ligandin protein engineering triazine dye...
Articles
Journal:
Biochemical Journal
Biochem J (2003) 371 (2): 369–376.
Published: 15 April 2003
... 2003 30 1 2003 30 1 2003 The Biochemical Society, London ©2003 2003 binding affinity conformation tuning protein engineering Abbreviations used: ADAM, a disintegrin and metalloproteinase; DMEM, Dulbecco's modified Eagle's medium; ECM, extracellular matrix; EGF...
Articles
Tiila-Riikka KIEMA, Jukka P. TASKINEN, Päivi L. PIRILÄ, Kari T. KOIVURANTA, Rik K. WIERENGA, J. Kalervo HILTUNEN
Journal:
Biochemical Journal
Biochem J (2002) 367 (2): 433–441.
Published: 15 October 2002
...; mfeHAD, HAD part of MFE-1; perMFE-1, mammalian peroxisomal MFE-1; PTS-1, peroxisomal targeting signal type 1. β-oxidation lipid metabolism peroxisome protein engineering structure–function The Biochemical Society, London ©2002 2002 19 2 2002 18 6 2002 10 7 2002 10...
Articles
Journal:
Biochemical Journal
Biochem J (2002) 362 (2): 265–271.
Published: 22 February 2002
... and L-3 were found to be the major determinants of the receptor- and TTR-binding speci- ficities respectively. Thus we demonstrate that lipocalins serve as excellent scaffolds for engineering novel biological functions. Key words: vitamin A, lipocalin, protein engineering, RBP ERABP chimaera, RBP...
Articles
Journal:
Biochemical Journal
Biochem J (2001) 359 (3): 715–720.
Published: 25 October 2001
... from those of abolishing hydrogen-bond donor potential. This suggests that Trp-59 has both a local and a global stability effect by solvating a buried charge and by having a key role in the packing of the cytochrome c hydrophobic core. Key words: non-coded amino acids, protein engineering, semi...
Articles
Xiaojun REN, Shujuan GAO, Delin YOU, Hualiang HUANG, Zi LIU, Ying MU, Junqiu LIU, Yan ZHANG, Ganglin YAN, Guimin LUO, Tongshu YANG, Jiacong SHEN
Journal:
Biochemical Journal
Biochem J (2001) 359 (2): 369–374.
Published: 08 October 2001
... 6 2001 7 8 2001 The Biochemical Society, London ©2001 2001 artificial enzyme chemical mutation enzyme mimics protein engineering selenium Abbreviations used: 2F3-scFv, single-chain Fv fragment of monoclonal antibody 2F3; GPX, glutathione peroxidase; GSHPx-1, classical...
Articles
Journal:
Biochemical Journal
Biochem J (2001) 358 (1): 101–110.
Published: 08 August 2001
...2001 2001 essential dynamics herbicide detoxification molecular dynamics protein engineering Abbreviations used: CDNB, 1-chloro-2,4-dinitrobenzene; G-site, GSH binding site; GST, glutathione S-transferase; H-site, electrophile binding site; Ni-NTA, Ni 2+ -nitrilotriacetate. Biochem...
Articles
Journal:
Biochemical Journal
Biochem J (2001) 358 (1): 241–247.
Published: 08 August 2001
... be addressed (e-mail piccoli@unina.it ). 7 3 2001 10 4 2001 11 6 2001 The Biochemical Society, London ©2001 2001 antitumour agents protein engineering ribonucleases RNase inhibitor Abbreviations used: BS-RNase, bovine seminal RNase; cRI, cytosolic RNase inhibitor; DTT...
Articles
Journal:
Biochemical Journal
Biochem J (2001) 354 (2): 455–463.
Published: 22 February 2001
... properties of His- 311 are important for enzyme function. An important structural role has also been attributed to cis-Pro-288. This residue may provide the key residues Gln-287 and His-311 with the proper orientation for productive binding of formate. Key words: kinetic mechanism, protein engineering, site...
Articles
Claire LEADBEATER, Lisa MCIVER, Dominic J. CAMPOPIANO, Scott P. WEBSTER, Robert L. BAXTER, Sharon M. KELLY, Nicholas C. PRICE, Dominikus A. LYSEK, Michael A. NOBLE, Stephen K. CHAPMAN, Andrew W. MUNRO
Journal:
Biochemical Journal
Biochem J (2000) 352 (2): 257–266.
Published: 24 November 2000
... and R184 located close to the adenosine ribose 2«-phosphate group, and R144 likely to interact with the nicotinamide ribose 5«-phosphate group. Key words: coenzyme affinity, enzyme kinetics, flavodoxin NADP+ oxidoreductase, protein engineering. with other members of the ferredoxin reductase family...
Articles
Journal:
Biochemical Journal
Biochem J (2000) 350 (1): 31–39.
Published: 09 August 2000
... 25 5 2000 The Biochemical Society, London © 2000 2000 protein secretion protein engineering cell walls α-amylase Biochem. J. (2000) 350, 31 39 (Printed in Great Britain) 31 The influence of secretory-protein charge on late stages of secretion from the Gram-positive bacterium...
Articles
Journal:
Biochemical Journal
Biochem J (2000) 345 (3): 687–692.
Published: 25 January 2000
..., 504 510 34 Ricigliano, J. W. and Penning, T. M. (1990) Biochem. J. 269, 749 755 # 2000 Biochemical Society biocatalysis dehydrogenases opiates protein engineering ...
Articles
Journal:
Biochemical Journal
Biochem J (2000) 345 (2): 247–254.
Published: 10 January 2000
... of the location of the ligand on the toxin and they were found to release the restrictocin fragment efficiently on proteolysis in itro. Key words: chimaeric toxins, protease, protein engineering, targeting, toxins. an intervening specific protease recognition site made them cytotoxic [12,13]. Chimaeric toxins...
Articles
Amine ABBADI, Monika BRUMMEL, Burkhardt S. SCHüTT, Mary B. SLABAUGH, Ricardo SCHUCH, Friedrich SPENER
Journal:
Biochemical Journal
Biochem J (2000) 345 (1): 153–160.
Published: 17 December 1999
... synthesis protein engineering Biochem. J. (2000) 345, 153 160 (Printed in Great Britain) 153 Reaction mechanism of recombinant 3-oxoacyl-(acyl-carrier-protein) synthase III from Cuphea wrightii embryo, a fatty acid synthase type II condensing enzyme Amine ABBADI*, Monika BRUMMEL*, Burkhardt S. SCHU$ TT...
Articles
Journal:
Biochemical Journal
Biochem J (1999) 341 (1): 139–145.
Published: 24 June 1999
... activity, protein engineering, Vipera ammodytes ammodytes. have been used, from comparison of their primary and tertiary structures, chemical modification and the use of specific site- directed antibodies to acceptor-binding studies. Despite nu- merous attempts, toxic PLA # s still remain a complex multi...
Articles
Journal:
Biochemical Journal
Biochem J (1999) 339 (2): 309–317.
Published: 08 April 1999
... to denaturants such as guanidine HCl and urea was revealed; the wild-type protein always proved to be the most resistant. The results obtained show the importance of hydrogen bonds and ion pairs in determining protein stability and confirm that simulation methods are able to direct protein engineering in site...