Literature DB >> 23764454

Folding the proteome.

Esther Braselmann1, Julie L Chaney, Patricia L Clark.   

Abstract

Protein folding is an essential prerequisite for protein function and hence cell function. Kinetic and thermodynamic studies of small proteins that refold reversibly were essential for developing our current understanding of the fundamentals of protein folding mechanisms. However, we still lack sufficient understanding to accurately predict protein structures from sequences, or the effects of disease-causing mutations. To date, model proteins selected for folding studies represent only a small fraction of the complexity of the proteome and are unlikely to exhibit the breadth of folding mechanisms used in vivo. We are in urgent need of new methods - both theoretical and experimental - that can quantify the folding behavior of a truly broad set of proteins under in vivo conditions. Such a shift in focus will provide a more comprehensive framework from which to understand the connections between protein folding, the molecular basis of disease, and cell function and evolution.
Copyright © 2013 Elsevier Ltd. All rights reserved.

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Year:  2013        PMID: 23764454      PMCID: PMC3691291          DOI: 10.1016/j.tibs.2013.05.001

Source DB:  PubMed          Journal:  Trends Biochem Sci        ISSN: 0968-0004            Impact factor:   13.807


  76 in total

1.  Cotranslational folding increases GFP folding yield.

Authors:  Krastyu G Ugrinov; Patricia L Clark
Journal:  Biophys J       Date:  2010-04-07       Impact factor: 4.033

2.  Beta-barrel proteins that reside in the Escherichia coli outer membrane in vivo demonstrate varied folding behavior in vitro.

Authors:  Nancy K Burgess; Thuy P Dao; Ann Marie Stanley; Karen G Fleming
Journal:  J Biol Chem       Date:  2008-07-19       Impact factor: 5.157

3.  Problem solved* (*sort of).

Authors:  Robert F Service
Journal:  Science       Date:  2008-08-08       Impact factor: 47.728

4.  Predicting protein folding rates from geometric contact and amino acid sequence.

Authors:  Zheng Ouyang; Jie Liang
Journal:  Protein Sci       Date:  2008-04-23       Impact factor: 6.725

5.  Protein folding stability and dynamics imaged in a living cell.

Authors:  Simon Ebbinghaus; Apratim Dhar; J Douglas McDonald; Martin Gruebele
Journal:  Nat Methods       Date:  2010-02-28       Impact factor: 28.547

Review 6.  Models of macromolecular crowding effects and the need for quantitative comparisons with experiment.

Authors:  Adrian H Elcock
Journal:  Curr Opin Struct Biol       Date:  2010-02-16       Impact factor: 6.809

7.  Cotranslational folding promotes beta-helix formation and avoids aggregation in vivo.

Authors:  Michael S Evans; Ian M Sander; Patricia L Clark
Journal:  J Mol Biol       Date:  2008-07-22       Impact factor: 5.469

8.  Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm.

Authors:  Sean R McGuffee; Adrian H Elcock
Journal:  PLoS Comput Biol       Date:  2010-03-05       Impact factor: 4.475

Review 9.  Linking folding and binding.

Authors:  Peter E Wright; H Jane Dyson
Journal:  Curr Opin Struct Biol       Date:  2009-01-20       Impact factor: 6.809

Review 10.  Folding scene investigation: membrane proteins.

Authors:  Paula J Booth; Paul Curnow
Journal:  Curr Opin Struct Biol       Date:  2009-01-20       Impact factor: 6.809

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  49 in total

1.  Fold and flexibility: what can proteins' mechanical properties tell us about their folding nucleus?

Authors:  Sophie Sacquin-Mora
Journal:  J R Soc Interface       Date:  2015-11-06       Impact factor: 4.118

Review 2.  Hydrogen-deuterium exchange mass spectrometry reveals folding and allostery in protein-protein interactions.

Authors:  Cesar A Ramirez-Sarmiento; Elizabeth A Komives
Journal:  Methods       Date:  2018-04-06       Impact factor: 3.608

Review 3.  The Mechanism and Function of Group II Chaperonins.

Authors:  Tom Lopez; Kevin Dalton; Judith Frydman
Journal:  J Mol Biol       Date:  2015-04-30       Impact factor: 5.469

4.  Conformational transitions in the glycine-bound GluN1 NMDA receptor LBD via single-molecule FRET.

Authors:  David R Cooper; Drew M Dolino; Henriette Jaurich; Bo Shuang; Swarna Ramaswamy; Caitlin E Nurik; Jixin Chen; Vasanthi Jayaraman; Christy F Landes
Journal:  Biophys J       Date:  2015-07-07       Impact factor: 4.033

5.  Protein folding in the cell, from atom to organism.

Authors:  Jeffrey L Brodsky; Patricia L Clark
Journal:  FASEB J       Date:  2014-12       Impact factor: 5.191

6.  Proteins in the cell.

Authors:  Patricia L Clark
Journal:  Protein Sci       Date:  2019-07       Impact factor: 6.725

7.  Quantitative determination of ribosome nascent chain stability.

Authors:  Avi J Samelson; Madeleine K Jensen; Randy A Soto; Jamie H D Cate; Susan Marqusee
Journal:  Proc Natl Acad Sci U S A       Date:  2016-11-07       Impact factor: 11.205

8.  Network analysis of synonymous codon usage.

Authors:  Khalique Newaz; Gabriel Wright; Jacob Piland; Jun Li; Patricia L Clark; Scott J Emrich; Tijana Milenković
Journal:  Bioinformatics       Date:  2020-12-08       Impact factor: 6.937

9.  The ribosome destabilizes native and non-native structures in a nascent multidomain protein.

Authors:  Kaixian Liu; Joseph E Rehfus; Elliot Mattson; Christian M Kaiser
Journal:  Protein Sci       Date:  2017-05-19       Impact factor: 6.725

Review 10.  Comparing protein folding in vitro and in vivo: foldability meets the fitness challenge.

Authors:  Karan S Hingorani; Lila M Gierasch
Journal:  Curr Opin Struct Biol       Date:  2014-01-14       Impact factor: 6.809

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