Protein folding: Defining a standard set of experimental conditions and a preliminary kinetic data set of two-state proteins

Karen L. Maxwell; D. Wildes; A. Zarrine-Afsar; Miguel A. De Los Rios Rivos; Andrew G. Brown; Claire T. Friel; Linda Hedberg; Jia-Cherng Horng; Diana Bona; Erik J. Miller; Alexis Vallée-Bélisle; Ewan R. G. Main; Francesco Bemporad; Linlin Qiu; Kaare Teilum; Ngoc-Diep Vu; Aled M. Edwards; Ingo Ruczinski; Flemming M. Poulsen; Birthe Brandt Kragelund; Stephen W. Michnick; Fabrizio Chiti; Yawen Bai; Stephen J. Hagen; Luis Serrano; Mikael Oliveberg; Daniel P. Raleigh; Pernilla Wittung Stafshede; Sheena E. Radford; Sophie e. Jackson; Tobin R. Sosnick; Susan Margusee; Alan R. Davidson; Kevin W. Plaxco

doi:10.1110/ps.041205405

Protein folding: Defining a standard set of experimental conditions and a preliminary kinetic data set of two-state proteins

Karen L. Maxwell, D. Wildes, A. Zarrine-Afsar, Miguel A. De Los Rios Rivos, Andrew G. Brown, Claire T. Friel, Linda Hedberg, Jia-Cherng Horng, Diana Bona, Erik J. Miller, Alexis Vallée-Bélisle, Ewan R. G. Main, Francesco Bemporad, Linlin Qiu, Kaare Teilum, Ngoc-Diep Vu, Aled M. Edwards, Ingo Ruczinski, Flemming M. Poulsen, Birthe Brandt KragelundStephen W. Michnick, Fabrizio Chiti, Yawen Bai, Stephen J. Hagen, Luis Serrano, Mikael Oliveberg, Daniel P. Raleigh, Pernilla Wittung Stafshede, Sheena E. Radford, Sophie e. Jackson, Tobin R. Sosnick, Susan Margusee, Alan R. Davidson, Kevin W. Plaxco

164 Citations (Scopus)

Abstract

Recent years have seen the publication of both empirical and theoretical relationships predicting the rates with which proteins fold. Our ability to test and refine these relationships has been limited, however, by a variety of difficulties associated with the comparison of folding and unfolding rates, thermodynamics, and structure across diverse sets of proteins. These difficulties include the wide, potentially confounding range of experimental conditions and methods employed to date and the difficulty of obtaining correct and complete sequence and structural details for the characterized constructs. The lack of a single approach to data analysis and error estimation, or even of a common set of units and reporting standards, further hinders comparative studies of folding. In an effort to overcome these problems, we define here a

consensus

set of experimental conditions (25°C at pH 7.0, 50 mM buffer), data analysis methods, and data reporting standards that we hope will provide a benchmark for experimental studies. We take the first step in this initiative by describing the folding kinetics of 30 apparently two-state proteins or protein domains under the consensus conditions. The goal of our efforts is to set uniform standards for the experimental community and to initiate an accumulating, self-consistent data set that will aid ongoing efforts to understand the folding process.

Original language	English
Journal	Protein Science
Volume	14
Issue number	3
Pages (from-to)	602-616
ISSN	0961-8368
DOIs	https://doi.org/10.1110/ps.041205405
Publication status	Published - 2005

Access to Document

10.1110/ps.041205405

Cite this

Maxwell, K. L., Wildes, D., Zarrine-Afsar, A., Rivos, M. A. D. L. R., Brown, A. G., Friel, C. T., Hedberg, L., Horng, J-C., Bona, D., Miller, E. J., Vallée-Bélisle, A., Main, E. R. G., Bemporad, F., Qiu, L., Teilum, K., Vu, N-D., Edwards, A. M., Ruczinski, I., Poulsen, F. M., ... Plaxco, K. W. (2005). Protein folding: Defining a standard set of experimental conditions and a preliminary kinetic data set of two-state proteins. Protein Science, 14(3), 602-616. https://doi.org/10.1110/ps.041205405

Maxwell, KL, Wildes, D, Zarrine-Afsar, A, Rivos, MADLR, Brown, AG, Friel, CT, Hedberg, L, Horng, J-C, Bona, D, Miller, EJ, Vallée-Bélisle, A, Main, ERG, Bemporad, F, Qiu, L, Teilum, K, Vu, N-D, Edwards, AM, Ruczinski, I, Poulsen, FM, Kragelund, BB, Michnick, SW, Chiti, F, Bai, Y, Hagen, SJ, Serrano, L, Oliveberg, M, Raleigh, DP, Stafshede, PW, Radford, SE, Jackson, SE, Sosnick, TR, Margusee, S, Davidson, AR & Plaxco, KW 2005, 'Protein folding: Defining a standard set of experimental conditions and a preliminary kinetic data set of two-state proteins', Protein Science, vol. 14, no. 3, pp. 602-616. https://doi.org/10.1110/ps.041205405

@article{082b03706c3711dcbee902004c4f4f50,

title = "Protein folding: Defining a standard set of experimental conditions and a preliminary kinetic data set of two-state proteins",

abstract = "Recent years have seen the publication of both empirical and theoretical relationships predicting the rates with which proteins fold. Our ability to test and refine these relationships has been limited, however, by a variety of difficulties associated with the comparison of folding and unfolding rates, thermodynamics, and structure across diverse sets of proteins. These difficulties include the wide, potentially confounding range of experimental conditions and methods employed to date and the difficulty of obtaining correct and complete sequence and structural details for the characterized constructs. The lack of a single approach to data analysis and error estimation, or even of a common set of units and reporting standards, further hinders comparative studies of folding. In an effort to overcome these problems, we define here a consensus set of experimental conditions (25°C at pH 7.0, 50 mM buffer), data analysis methods, and data reporting standards that we hope will provide a benchmark for experimental studies. We take the first step in this initiative by describing the folding kinetics of 30 apparently two-state proteins or protein domains under the consensus conditions. The goal of our efforts is to set uniform standards for the experimental community and to initiate an accumulating, self-consistent data set that will aid ongoing efforts to understand the folding process.",

author = "Maxwell, {Karen L.} and D. Wildes and A. Zarrine-Afsar and Rivos, {Miguel A. De Los Rios} and Brown, {Andrew G.} and Friel, {Claire T.} and Linda Hedberg and Jia-Cherng Horng and Diana Bona and Miller, {Erik J.} and Alexis Vall{\'e}e-B{\'e}lisle and Main, {Ewan R. G.} and Francesco Bemporad and Linlin Qiu and Kaare Teilum and Ngoc-Diep Vu and Edwards, {Aled M.} and Ingo Ruczinski and Poulsen, {Flemming M.} and Kragelund, {Birthe Brandt} and Michnick, {Stephen W.} and Fabrizio Chiti and Yawen Bai and Hagen, {Stephen J.} and Luis Serrano and Mikael Oliveberg and Raleigh, {Daniel P.} and Stafshede, {Pernilla Wittung} and Radford, {Sheena E.} and Jackson, {Sophie e.} and Sosnick, {Tobin R.} and Susan Margusee and Davidson, {Alan R.} and Plaxco, {Kevin W.}",

note = "Keywords two-state • protein folding • kinetics • chevron plots • equilibrium",

year = "2005",

doi = "10.1110/ps.041205405",

language = "English",

volume = "14",

pages = "602--616",

journal = "Protein Science",

issn = "0961-8368",

publisher = "Wiley-Blackwell",

number = "3",

}

TY - JOUR

T1 - Protein folding: Defining a standard set of experimental conditions and a preliminary kinetic data set of two-state proteins

AU - Maxwell, Karen L.

AU - Wildes, D.

AU - Zarrine-Afsar, A.

AU - Rivos, Miguel A. De Los Rios

AU - Brown, Andrew G.

AU - Friel, Claire T.

AU - Hedberg, Linda

AU - Horng, Jia-Cherng

AU - Bona, Diana

AU - Miller, Erik J.

AU - Vallée-Bélisle, Alexis

AU - Main, Ewan R. G.

AU - Bemporad, Francesco

AU - Qiu, Linlin

AU - Teilum, Kaare

AU - Vu, Ngoc-Diep

AU - Edwards, Aled M.

AU - Ruczinski, Ingo

AU - Poulsen, Flemming M.

AU - Kragelund, Birthe Brandt

AU - Michnick, Stephen W.

AU - Chiti, Fabrizio

AU - Bai, Yawen

AU - Hagen, Stephen J.

AU - Serrano, Luis

AU - Oliveberg, Mikael

AU - Raleigh, Daniel P.

AU - Stafshede, Pernilla Wittung

AU - Radford, Sheena E.

AU - Jackson, Sophie e.

AU - Sosnick, Tobin R.

AU - Margusee, Susan

AU - Davidson, Alan R.

AU - Plaxco, Kevin W.

N1 - Keywords two-state • protein folding • kinetics • chevron plots • equilibrium

PY - 2005

Y1 - 2005

N2 - Recent years have seen the publication of both empirical and theoretical relationships predicting the rates with which proteins fold. Our ability to test and refine these relationships has been limited, however, by a variety of difficulties associated with the comparison of folding and unfolding rates, thermodynamics, and structure across diverse sets of proteins. These difficulties include the wide, potentially confounding range of experimental conditions and methods employed to date and the difficulty of obtaining correct and complete sequence and structural details for the characterized constructs. The lack of a single approach to data analysis and error estimation, or even of a common set of units and reporting standards, further hinders comparative studies of folding. In an effort to overcome these problems, we define here a consensus set of experimental conditions (25°C at pH 7.0, 50 mM buffer), data analysis methods, and data reporting standards that we hope will provide a benchmark for experimental studies. We take the first step in this initiative by describing the folding kinetics of 30 apparently two-state proteins or protein domains under the consensus conditions. The goal of our efforts is to set uniform standards for the experimental community and to initiate an accumulating, self-consistent data set that will aid ongoing efforts to understand the folding process.

AB - Recent years have seen the publication of both empirical and theoretical relationships predicting the rates with which proteins fold. Our ability to test and refine these relationships has been limited, however, by a variety of difficulties associated with the comparison of folding and unfolding rates, thermodynamics, and structure across diverse sets of proteins. These difficulties include the wide, potentially confounding range of experimental conditions and methods employed to date and the difficulty of obtaining correct and complete sequence and structural details for the characterized constructs. The lack of a single approach to data analysis and error estimation, or even of a common set of units and reporting standards, further hinders comparative studies of folding. In an effort to overcome these problems, we define here a consensus set of experimental conditions (25°C at pH 7.0, 50 mM buffer), data analysis methods, and data reporting standards that we hope will provide a benchmark for experimental studies. We take the first step in this initiative by describing the folding kinetics of 30 apparently two-state proteins or protein domains under the consensus conditions. The goal of our efforts is to set uniform standards for the experimental community and to initiate an accumulating, self-consistent data set that will aid ongoing efforts to understand the folding process.

U2 - 10.1110/ps.041205405

DO - 10.1110/ps.041205405

M3 - Journal article

C2 - 15689503

SN - 0961-8368

VL - 14

SP - 602

EP - 616

JO - Protein Science

JF - Protein Science

IS - 3

ER -

Protein folding: Defining a standard set of experimental conditions and a preliminary kinetic data set of two-state proteins

Abstract

Access to Document

Fingerprint

Cite this