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Using VIPT-jump to distinguish between different folding mechanisms: application to BBL and a Trpzip.

ABSTRACT: Protein folding involves a large number of sequential molecular steps or conformational substates. Thus, experimental characterization of the underlying folding energy landscape for any given protein is difficult. Herein, we present a new method that can be used to determine the major characteristics of the folding energy landscape in question, e.g., to distinguish between activated and barrierless downhill folding scenarios. This method is based on the idea that the conformational relaxation kinetics of different folding mechanisms at a given final condition will show different dependences on the initial condition. We show, using both simulation and experiment, that it is possible to differentiate between disparate kinetic folding models by comparing temperature jump (T-jump) relaxation traces obtained with a fixed final temperature and varied initial temperatures, which effectively varies the initial potential (VIP) of the system of interest. We apply this method (hereafter refer to as VIPT-jump) to two model systems, tryptophan zipper (Trpzip)-2c and BBL, and our results show that BBL exhibits characteristics of barrierless downhill folding, whereas Trpzip-2c folding encounters a free energy barrier. In addition, using the T-jump data of BBL we are able to provide, via Langevin dynamics simulations, a realistic estimate of its conformational diffusion coefficient.

SUBMITTER: Lin CW

PROVIDER: S-EPMC3706100 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature

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Using VIPT-jump to distinguish between different folding mechanisms: application to BBL and a Trpzip.

Lin Chun-Wei CW Culik Robert M RM Gai Feng F

Journal of the American Chemical Society 20130514 20

Protein folding involves a large number of sequential molecular steps or conformational substates. Thus, experimental characterization of the underlying folding energy landscape for any given protein is difficult. Herein, we present a new method that can be used to determine the major characteristics of the folding energy landscape in question, e.g., to distinguish between activated and barrierless downhill folding scenarios. This method is based on the idea that the conformational relaxation ki ...[more]

PMID: 23642153

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Project description:Background:The vertical jump is used to estimate sports performance capabilities and physical fitness in children, elderly, non-athletic and injured individuals. Different jump techniques and measurement tools are available to assess vertical jump height and peak power; however, their use is limited by access to laboratory settings, excessive cost and/or time constraints thus making these tools oftentimes unsuitable for field assessment. A popular field test uses the Vertec and the Sargent vertical jump with countermovement; however, new low cost, easy to use tools are becoming available, including the My Jump iOS mobile application (app). The purpose of this study was to assess the reliability of the My Jump relative to values obtained by the Vertec for the Sargent stand and reach vertical jump (VJ) test. Methods:One hundred and thirty-five healthy participants aged 18-39 years (94 males, 41 females) completed three maximal Sargent VJ with countermovement that were simultaneously measured using the Vertec and the My Jump. Jump heights were quantified for each jump and peak power was calculated using the Sayers equation. Four separate ICC estimates and their 95% confidence intervals were used to assess reliability. Two analyses (with jump height and calculated peak power as the dependent variables, respectively) were based on a single rater, consistency, two-way mixed-effects model, while two others (with jump height and calculated peak power as the dependent variables, respectively) were based on a single rater, absolute agreement, two-way mixed-effects model. Results:Moderate to excellent reliability relative to the degree of consistency between the Vertec and My Jump values was found for jump height (ICC = 0.813; 95% CI [0.747-0.863]) and calculated peak power (ICC = 0.926; 95% CI [0.897-0.947]). However, poor to good reliability relative to absolute agreement for VJ height (ICC = 0.665; 95% CI [0.050-0.859]) and poor to excellent reliability relative to absolute agreement for peak power (ICC = 0.851; 95% CI [0.272-0.946]) between the Vertec and My Jump values were found; Vertec VJ height, and thus, Vertec calculated peak power values, were significantly higher than those calculated from My Jump values (p < 0.0001). Discussion:The My Jump app may provide a reliable measure of vertical jump height and calculated peak power in multiple field and laboratory settings without the need of costly equipment such as force plates or Vertec. The reliability relative to degree of consistency between the Vertec and My Jump app was moderate to excellent. However, the reliability relative to absolute agreement between Vertec and My Jump values contained significant variation (based on CI values), thus, it is recommended that either the My Jump or the Vertec be used to assess VJ height in repeated measures within subjects' designs; these measurement tools should not be considered interchangeable within subjects or in group measurement designs.

Dataset Information

Using VIPT-jump to distinguish between different folding mechanisms: application to BBL and a Trpzip.

Publications

Using VIPT-jump to distinguish between different folding mechanisms: application to BBL and a Trpzip.

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