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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 degrees 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.

SUBMITTER: Maxwell KL

PROVIDER: S-EPMC2279278 | biostudies-literature | 2005 Mar

REPOSITORIES: biostudies-literature

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

Maxwell Karen L KL Wildes David D Zarrine-Afsar Arash A De Los Rios Miguel A MA Brown Andrew G AG Friel Claire T CT Hedberg Linda L Horng Jia-Cherng JC Bona Diane D Miller Erik J EJ Vallée-Bélisle Alexis A Main Ewan R G ER Bemporad Francesco F Qiu Linlin L Teilum Kaare K Vu Ngoc-Diep ND Edwards Aled M AM Ruczinski Ingo I Poulsen Flemming M FM Kragelund Birthe B BB Michnick Stephen W SW Chiti Fabrizio F Bai Yawen Y Hagen Stephen J SJ Serrano Luis L Oliveberg Mikael M Raleigh Daniel P DP Wittung-Stafshede Pernilla P Radford Sheena E SE Jackson Sophie E SE Sosnick Tobin R TR Marqusee Susan S Davidson Alan R AR Plaxco Kevin W KW

Protein science : a publication of the Protein Society 20050202 3

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 di ...[more]

PMID: 15689503

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Project description:PurposeAdvanced ovarian cancer (AOC) and its treatment cause several symptoms and impact on patients' health-related quality of life (HRQoL). We aim to reach a consensus on the most relevant patient-reported outcome (PROs), the corresponding measures (PROMs), and measurement frequency during AOC patients' follow-up from patients' and healthcare professionals' (HCP) perspective.MethodsThe project comprised five steps: 1) a literature review, 2) a focus group with patients, 3) a nominal group with HCP, 4) two round-Delphi consultations with patients and HCP, and 5) a final meeting with HCP. Delphi questionnaire was elaborated based on literature review, focus group (n=5 patients), and nominal group (n=16 HCP). The relevance of each PRO and the appropriateness (A) and feasibility (F) of the proposed PROM were assessed (Likert scale 1=strongly agree; 9=strongly disagree). The consensus was reached when at least 75% of the panelists rated it as 'relevant', 'appropriate', or 'feasible' (score 7-9).ResultsA total of 56 HCP [51.8% Hospital Pharmacy; 41.1% Oncology; 3.6% Nursing; and 3.6% Psycho-oncology; mean time in specialty 12.5 (8.0) years] and 10 AOC patients [mean time diagnosis 5.4 (3.0) years] participated in the 1st round. All PROs achieved consensus regarding their relevance, except dry skin (58.0%). Agreement was reached for PRO-CTCAE to be used to assess fatigue (A:84.9%; F:75.8%), neuropathy (A:92.4%; F:77.3%), diarrhea (A:87.9%; F:88.7%), constipation (A:86.4%; F:75.8%), nausea (A:89.4%; F:75.8%), insomnia (A:81.8%; F:88.7%), abdominal bloating (A:82.2%; F:82.2%) and sexuality (A:78.8%; F:88.6%); EQ-5D to determine patients' HRQoL (A:87.9%; F:80.3%), pain (A:87.9%; F:75.8%) and mood (A:77.7%; F:85.5%); to assess treatment adherence the Morisky-Green (A:90.9%; F:84.9%) and the dispensing register (A:80.3%; F:80.3%) were chosen. It was agreed to note in the medical record whether the patient's treatment preferences had been considered during decision-making (A:78.8%; F:78.8%) and to use a 5-point Likert scale to assess treatment satisfaction (A:86.4%; F:86.4%). Panelists agreed (A:92.4%; F: 77.3%) to collect these PROs (1) at the time of diagnosis/relapse; (2) one month after starting treatment/change therapeutic strategy; (3) every three months during the 1st-year of treatment; and later (4) every six months until treatment completion/change.ConclusionsThe consensus reached represents the first step towards including the patient's perspective in AOC follow-up. The standardized collection of PROs in clinical practice may contribute to optimizing the follow-up of these patients and thus improving the quality of care.

Dataset Information

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

Publications

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

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