53 research outputs found
The role of a disulfide bridge in the stability and folding kinetics of Arabidopsis thaliana cytochrome c6A
Cytochrome c 6A is a eukaryotic member of the Class I cytochrome c family possessing a high structural homology with photosynthetic cytochrome c 6 from cyanobacteria, but structurally and functionally distinct through the presence of a disulfide bond and a heme mid-point redox potential of + 71 mV (vs normal hydrogen electrode). The disulfide bond is part of a loop insertion peptide that forms a cap-like structure on top of the core α-helical fold. We have investigated the contribution of the disulfide bond to thermodynamic stability and (un)folding kinetics in cytochrome c 6A from Arabidopsis thaliana by making comparison with a photosynthetic cytochrome c 6 from Phormidium laminosum and through a mutant in which the Cys residues have been replaced with Ser residues (C67/73S). We find that the disulfide bond makes a significant contribution to overall stability in both the ferric and ferrous heme states. Both cytochromes c 6A and c 6 fold rapidly at neutral pH through an on-pathway intermediate. The unfolding rate for the C67/73S variant is significantly increased indicating that the formation of this region occurs late in the folding pathway. We conclude that the disulfide bridge in cytochrome c 6A acts as a conformational restraint in both the folding intermediate and native state of the protein and that it likely serves a structural rather than a previously proposed catalytic role. © 2011 Elsevier B.V. All rights reserved
Quantitative first principles calculations of protein circular dichroism in the near-ultraviolet
Vibrational structure in the near-UV circular dichroism (CD) spectra of proteins is an important source of information on protein conformation and can be exploited to study structure and folding. A fully quantitative theory of the relationship between protein conformation and optical spectroscopy would facilitate deeper interpretation and insights into biophysical and simulation studies of protein dynamics and folding. We have developed new models of the aromatic side chain chromophores toluene, p-cresol and 3-methylindole, which incorporate ab initio calculations of the Franck-Condon effect into first principles calculations of CD using an exciton approach. The near-UV CD spectra of 40 proteins are calculated with the new parameter set and the correlation between the computed and the experimental intensity from 270 to 290 nm is much improved. The contribution of individual chromophores to the CD spectra has been calculated for several mutants and in many cases helps rationalize changes in their experimental spectra. Considering conformational flexibility by using families of NMR structures leads to further improvements for some proteins and illustrates an informative level of sensitivity to side chain conformation. In several cases, the near-UV CD calculations can distinguish the native protein structure from a set of computer-generated misfolded decoy structures
Release the BEESTS: Bayesian Estimation of Ex-Gaussian STop-Signal Reaction Time Distributions
The stop-signal paradigm is frequently used to study response inhibition. Inthis paradigm, participants perform a two-choice response time task wherethe primary task is occasionally interrupted by a stop-signal that promptsparticipants to withhold their response. The primary goal is to estimatethe latency of the unobservable stop response (stop signal reaction timeor SSRT). Recently, Matzke, Dolan, Logan, Brown, and Wagenmakers (inpress) have developed a Bayesian parametric approach that allows for theestimation of the entire distribution of SSRTs. The Bayesian parametricapproach assumes that SSRTs are ex-Gaussian distributed and uses Markovchain Monte Carlo sampling to estimate the parameters of the SSRT distri-bution. Here we present an efficient and user-friendly software implementa-tion of the Bayesian parametric approach —BEESTS— that can be appliedto individual as well as hierarchical stop-signal data. BEESTS comes withan easy-to-use graphical user interface and provides users with summarystatistics of the posterior distribution of the parameters as well various diag-nostic tools to assess the quality of the parameter estimates. The softwareis open source and runs on Windows and OS X operating systems. In sum,BEESTS allows experimental and clinical psychologists to estimate entiredistributions of SSRTs and hence facilitates the more rigorous analysis ofstop-signal data
Turning the Hands of Time Again: A Purely Confirmatory Replication Study and a Bayesian Analysis
In a series of four experiments, Topolinski and Sparenberg (2012; TS) found support for the conjecture that clockwise movements induce psychological states of temporal progression and an orientation toward the future and novelty. Here we report the results of a preregistered replication attempt of Experiment 2 from TS. Participants turned kitchen rolls either clockwise or counterclockwise while answering items from a questionnaire assessing openness to experience. Data from 102 participants showed that the effect went slightly in the direction opposite to that predicted by TS, and a preregistered Bayes factor hypothesis test revealed that the data were 10.76 times more likely under the null hypothesis than under the alternative hypothesis. Our findings illustrate the theoretical importance and practical advantages of preregistered Bayes factor replication studies, both for psychological science and for empirical work in general
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