ArticleProceedings of the National Academy of Sciences of the United States of America2004
Integrating folding kinetics and protein function: biphasic kinetics and dual binding specificity in a WW domain.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
33 citing papers in PubMed.
- Gas-Binding Studies of Class 1 Sugar Beet Phytoglobin and C86A Mutant Using Isothermal Spectral Shifts in High-Precision Microliter Assay.International journal of molecular sciences · 2025Article
- Atomistic Simulations of Functionalized Nano-Materials for Biosensors Applications.International journal of molecular sciences · 2022Review
- Funneled energy landscape unifies principles of protein binding and evolution.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- New Insights into Folding, Misfolding, and Nonfolding Dynamics of a WW Domain.The journal of physical chemistry. B · 2020Article
- A quantitative connection of experimental and simulated folding landscapes by vibrational spectroscopy.Chemical science · 2018Article
- The effects of tether placement on antibody stability on surfaces.The Journal of chemical physics · 2017Article
- Exploring Protein-Nanoparticle Interactions with Coarse-Grained Protein Folding Models.Small (Weinheim an der Bergstrasse, Germany) · 2017Article
- The Dependence of Carbohydrate-Aromatic Interaction Strengths on the Structure of the Carbohydrate.Journal of the American Chemical Society · 2016Article
- The Role of Electrostatic Interactions in Folding of β-Proteins.Journal of the American Chemical Society · 2016Article
- Preventing fibril formation of a protein by selective mutation.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Evaluation of conformational changes in diabetes-associated mutation in insulin a chain: a molecular dynamics study.Proteins · 2015Article
- WW domain folding complexity revealed by infrared spectroscopy.Biochemistry · 2014Article
- Dynamics of an ultrafast folding subdomain in the context of a larger protein fold.Journal of the American Chemical Society · 2013Article
- Local vs global motions in protein folding.Journal of chemical theory and computation · 2013Article
- Allosteric control in a metalloprotein dramatically alters function.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Folding pathways of a knotted protein with a realistic atomistic force field.PLoS computational biology · 2013Article
- Understanding the folding-function tradeoff in proteins.PloS one · 2013Article
- Effects of mutation, truncation, and temperature on the folding kinetics of a WW domain.Journal of molecular biology · 2012Article
- Strand swapping regulates the iron-sulfur cluster in the diabetes drug target mitoNEET.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation.Current opinion in structural biology · 2011Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Because of the association of beta-sheet formation with the initiation and propagation of amyloid diseases, model systems have been sought to further our understanding of this process. WW domains have been proposed as one such model system. Whereas the folding of the WW domains from human Yes-associated protein (YAP) and Pin have been shown to obey single-exponential kinetics, the folding of the WW domain from formin-binding protein (FBP) 28 has been shown to proceed via biphasic kinetics. From an analysis of free-energy landscapes from atomic-level molecular dynamics simulations, the biphasic folding kinetics observed in the FBP WW domain may be traced to the ability of this WW domain to adopt two slightly different forms of packing in its hydrophobic core. This conformational change is propagated along the peptide backbone and affects the position of a tryptophan residue shown in other WW domains to play a key role in binding. The WW domains of Pin and YAP do not support more than one type of packing each, leading to monophasic folding kinetics. The ability of the FBP WW domain to assume two different types of packing may, in turn, explain the capacity of this WW domain to bind two classes of ligand, a property that is not shared by other WW domains. These findings lead to the hypothesis that lability with respect to conformations separated by an observable barrier as a requirement for function is incompatible with the ability of a protein to fold via single-exponential kinetics.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.