Literature DB >> 23602357

Library methods for structural biology of challenging proteins and their complexes.

Darren J Hart1, Geoffrey S Waldo.   

Abstract

Genetic engineering of constructs to improve solubility or stability is a common approach, but it is often unclear how to obtain improvements. When the domain composition of a target is poorly understood, or if there are insufficient structure data to guide sited directed mutagenesis, long iterative phases of subcloning or mutation and expression often prove unsuccessful despite much effort. Random library approaches can offer a solution to this problem and involve construction of large libraries of construct variants that are analysed via screens or selections for the desired phenotype. Huge improvements in construct behaviour can be achieved rapidly with no requirement for prior knowledge of the target. Here we review the development of these experimental strategies and recent successes.
Copyright © 2013 Elsevier Ltd. All rights reserved.

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Year:  2013        PMID: 23602357      PMCID: PMC4172339          DOI: 10.1016/j.sbi.2013.03.004

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  66 in total

1.  Synthetic shuffling expands functional protein diversity by allowing amino acids to recombine independently.

Authors:  Jon E Ness; Seran Kim; Andrea Gottman; Rob Pak; Anke Krebber; Torben V Borchert; Sridhar Govindarajan; Emily C Mundorff; Jeremy Minshull
Journal:  Nat Biotechnol       Date:  2002-11-11       Impact factor: 54.908

2.  Staggered extension process (StEP) in vitro recombination.

Authors:  Anna Marie Aguinaldo; Frances Arnold
Journal:  Methods Mol Biol       Date:  2002

3.  Structure and inhibition of herpesvirus DNA packaging terminase nuclease domain.

Authors:  Marta Nadal; Philippe J Mas; Phillipe J Mas; Alexandre G Blanco; Carme Arnan; Maria Solà; Darren J Hart; Miquel Coll
Journal:  Proc Natl Acad Sci U S A       Date:  2010-08-30       Impact factor: 11.205

Review 4.  ESPRIT: an automated, library-based method for mapping and soluble expression of protein domains from challenging targets.

Authors:  Hayretin Yumerefendi; Franck Tarendeau; Philippe J Mas; Darren J Hart
Journal:  J Struct Biol       Date:  2010-03-04       Impact factor: 2.867

5.  A combinatorial method to enable detailed investigation of protein-protein interactions.

Authors:  Kate Maclagan; Rita Tommasi; Emmanuelle Laurine; Chrisostomos Prodromou; Paul C Driscoll; Laurence H Pearl; Stefanie Reich; Renos Savva
Journal:  Future Med Chem       Date:  2011-03       Impact factor: 3.808

6.  A green fluorescent protein solubility screen in E. coli reveals domain boundaries of the GTP-binding domain in the P element transposase.

Authors:  Alex Sabogal; Donald C Rio
Journal:  Protein Sci       Date:  2010-11       Impact factor: 6.725

7.  Enhancing the stability and solubility of the glucocorticoid receptor ligand-binding domain by high-throughput library screening.

Authors:  Tobias Seitz; Ralf Thoma; Guillaume A Schoch; Martine Stihle; Jörg Benz; Brigitte D'Arcy; Andrea Wiget; Armin Ruf; Michael Hennig; Reinhard Sterner
Journal:  J Mol Biol       Date:  2010-09-17       Impact factor: 5.469

8.  Expression of soluble, active fragments of the morphogenetic protein SpoIIE from Bacillus subtilis using a library-based construct screen.

Authors:  Andrea E Rawlings; Vladimir M Levdikov; Elena Blagova; Vicki L Colledge; Philippe J Mas; James Tunaley; Ludmila Vavrova; Keith S Wilson; Imrich Barak; Darren J Hart; Anthony J Wilkinson
Journal:  Protein Eng Des Sel       Date:  2010-09-03       Impact factor: 1.650

9.  CoESPRIT: a library-based construct screening method for identification and expression of soluble protein complexes.

Authors:  Yingfeng An; Patrick Meresse; Philippe J Mas; Darren J Hart
Journal:  PLoS One       Date:  2011-02-22       Impact factor: 3.240

10.  High-quality gene assembly directly from unpurified mixtures of microarray-synthesized oligonucleotides.

Authors:  Alex Y Borovkov; Andrey V Loskutov; Mark D Robida; Kristen M Day; Jose A Cano; Tien Le Olson; Hetal Patel; Kevin Brown; Preston D Hunter; Kathryn F Sykes
Journal:  Nucleic Acids Res       Date:  2010-08-06       Impact factor: 16.971

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  7 in total

1.  Structural and biophysical characterization of murine rif1 C terminus reveals high specificity for DNA cruciform structures.

Authors:  Rasa Sukackaite; Malene Ringkjøbing Jensen; Philippe J Mas; Martin Blackledge; Sara B Buonomo; Darren J Hart
Journal:  J Biol Chem       Date:  2014-03-14       Impact factor: 5.157

Review 2.  Overcoming the Solubility Problem in E. coli: Available Approaches for Recombinant Protein Production.

Authors:  Claudia Ortega; Pablo Oppezzo; Agustín Correa
Journal:  Methods Mol Biol       Date:  2022

3.  Crystallization studies of the keratin-like domain from Arabidopsis thaliana SEPALLATA 3.

Authors:  Samira Acajjaoui; Chloe Zubieta
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2013-08-19

4.  Solution structure of a soluble fragment derived from a membrane protein by shotgun proteolysis.

Authors:  Mark D Allen; Mary Christie; Peter Jones; Benjamin T Porebski; Brendan Roome; Stefan M V Freund; Ashley M Buckle; Mark Bycroft; Daniel Christ
Journal:  Protein Eng Des Sel       Date:  2015-04-15       Impact factor: 1.650

5.  Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit.

Authors:  Morgane Boone; Pathmanaban Ramasamy; Jasper Zuallaert; Robbin Bouwmeester; Berre Van Moer; Davy Maddelein; Demet Turan; Niels Hulstaert; Hannah Eeckhaut; Elien Vandermarliere; Lennart Martens; Sven Degroeve; Wim De Neve; Wim Vranken; Nico Callewaert
Journal:  Nat Commun       Date:  2021-11-05       Impact factor: 14.919

6.  Multi-position data collection and dynamic beam sizing: recent improvements to the automatic data-collection algorithms on MASSIF-1.

Authors:  Olof Svensson; Maciej Gilski; Didier Nurizzo; Matthew W Bowler
Journal:  Acta Crystallogr D Struct Biol       Date:  2018-04-24       Impact factor: 7.652

7.  Auxin sensing is a property of an unstructured domain in the Auxin Response Factor ETTIN of Arabidopsis thaliana.

Authors:  Sara Simonini; Philippe J Mas; Caroline M V S Mas; Lars Østergaard; Darren J Hart
Journal:  Sci Rep       Date:  2018-09-10       Impact factor: 4.379

  7 in total

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