Literature DB >> 21498105

Protein stability by number: high-throughput and statistical approaches to one of protein science's most difficult problems.

Thomas J Magliery1, Jason J Lavinder, Brandon J Sullivan.   

Abstract

Most proteins are only barely stable, which impedes research, complicates therapeutic applications, and makes proteins susceptible to pathologically destabilizing mutations. Our ability to predict the thermodynamic consequences of even single point mutations is still surprisingly limited, and established methods of measuring stability are slow. Recent advances are bringing protein stability studies into the high-throughput realm. Some methods are based on inferential read-outs such as activity, proteolytic resistance or split-protein fragment reassembly. Other methods use miniaturization of direct measurements, such as intrinsic fluorescence, H/D exchange, cysteine reactivity, aggregation and hydrophobic dye binding (DSF). Protein engineering based on statistical analysis (consensus and correlated occurrences of amino acids) is promising, but much work remains to understand and implement these methods.
Copyright © 2011 Elsevier Ltd. All rights reserved.

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Year:  2011        PMID: 21498105      PMCID: PMC3110604          DOI: 10.1016/j.cbpa.2011.03.015

Source DB:  PubMed          Journal:  Curr Opin Chem Biol        ISSN: 1367-5931            Impact factor:   8.822


  70 in total

1.  Visualization of interactions among bZIP and Rel family proteins in living cells using bimolecular fluorescence complementation.

Authors:  Chang-Deng Hu; Yurii Chinenov; Tom K Kerppola
Journal:  Mol Cell       Date:  2002-04       Impact factor: 17.970

2.  Allosteric determinants in guanine nucleotide-binding proteins.

Authors:  Mark E Hatley; Steve W Lockless; Scott K Gibson; Alfred G Gilman; Rama Ranganathan
Journal:  Proc Natl Acad Sci U S A       Date:  2003-11-17       Impact factor: 11.205

3.  Rapid expression and purification of 100 nmol quantities of active protein using cell-free protein synthesis.

Authors:  Michael C Jewett; James R Swartz
Journal:  Biotechnol Prog       Date:  2004 Jan-Feb

Review 4.  Combinatorial approaches to protein stability and structure.

Authors:  Thomas J Magliery; Lynne Regan
Journal:  Eur J Biochem       Date:  2004-05

5.  Beyond consensus: statistical free energies reveal hidden interactions in the design of a TPR motif.

Authors:  Thomas J Magliery; Lynne Regan
Journal:  J Mol Biol       Date:  2004-10-22       Impact factor: 5.469

Review 6.  Dominant forces in protein folding.

Authors:  K A Dill
Journal:  Biochemistry       Date:  1990-08-07       Impact factor: 3.162

Review 7.  Hydrogen bonding, hydrophobicity, packing, and protein folding.

Authors:  G D Rose; R Wolfenden
Journal:  Annu Rev Biophys Biomol Struct       Date:  1993

8.  Instrumentation for automated determination of protein stability.

Authors:  W E Stites; M P Byrne; J Aviv; M Kaplan; P M Curtis
Journal:  Anal Biochem       Date:  1995-05-01       Impact factor: 3.365

9.  Sequence statistics reliably predict stabilizing mutations in a protein domain.

Authors:  B Steipe; B Schiller; A Plückthun; S Steinbacher
Journal:  J Mol Biol       Date:  1994-07-15       Impact factor: 5.469

10.  Monitoring protein stability and aggregation in vivo by real-time fluorescent labeling.

Authors:  Zoya Ignatova; Lila M Gierasch
Journal:  Proc Natl Acad Sci U S A       Date:  2003-12-30       Impact factor: 11.205

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  23 in total

1.  High-throughput identification of protein mutant stability computed from a double mutant fitness landscape.

Authors:  Nicholas C Wu; C Anders Olson; Ren Sun
Journal:  Protein Sci       Date:  2015-12-08       Impact factor: 6.725

2.  Biophysical Inference of Epistasis and the Effects of Mutations on Protein Stability and Function.

Authors:  Jakub Otwinowski
Journal:  Mol Biol Evol       Date:  2018-10-01       Impact factor: 16.240

3.  A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function.

Authors:  Carlos L Araya; Douglas M Fowler; Wentao Chen; Ike Muniez; Jeffery W Kelly; Stanley Fields
Journal:  Proc Natl Acad Sci U S A       Date:  2012-10-03       Impact factor: 11.205

4.  Consensus design of a NOD receptor leucine rich repeat domain with binding affinity for a muramyl dipeptide, a bacterial cell wall fragment.

Authors:  Rachael Parker; Ana Mercedes-Camacho; Tijana Z Grove
Journal:  Protein Sci       Date:  2014-04-17       Impact factor: 6.725

5.  Protein Evolution is Potentially Governed by Protein Stability: Directed Evolution of an Esterase from the Hyperthermophilic Archaeon Sulfolobus tokodaii.

Authors:  Ryo Kurahashi; Satoshi Sano; Kazufumi Takano
Journal:  J Mol Evol       Date:  2018-04-20       Impact factor: 2.395

6.  Stabilizing proteins from sequence statistics: the interplay of conservation and correlation in triosephosphate isomerase stability.

Authors:  Brandon J Sullivan; Tran Nguyen; Venuka Durani; Deepti Mathur; Samantha Rojas; Miriam Thomas; Trixy Syu; Thomas J Magliery
Journal:  J Mol Biol       Date:  2012-05-01       Impact factor: 5.469

7.  Deep mutational scanning: a new style of protein science.

Authors:  Douglas M Fowler; Stanley Fields
Journal:  Nat Methods       Date:  2014-08       Impact factor: 28.547

8.  Ligands for glaucoma-associated myocilin discovered by a generic binding assay.

Authors:  Susan D Orwig; Pamela V Chi; Yuhong Du; Shannon E Hill; Marchello A Cavitt; Amrithaa Suntharalingam; Katherine C Turnage; Chad A Dickey; Stefan France; Haian Fu; Raquel L Lieberman
Journal:  ACS Chem Biol       Date:  2013-12-09       Impact factor: 5.100

Review 9.  Protein stability: computation, sequence statistics, and new experimental methods.

Authors:  Thomas J Magliery
Journal:  Curr Opin Struct Biol       Date:  2015-08       Impact factor: 6.809

10.  SDM: a server for predicting effects of mutations on protein stability.

Authors:  Arun Prasad Pandurangan; Bernardo Ochoa-Montaño; David B Ascher; Tom L Blundell
Journal:  Nucleic Acids Res       Date:  2017-07-03       Impact factor: 16.971

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