ArticleProceedings of the National Academy of Sciences of the United States of America2008
A stringent test for hydrophobicity scales: two proteins with 88% sequence identity but different structure and function.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 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
7 citing papers in PubMed, 20 citations in OpenAlex.
- The Contribution of Hydrophobic Interactions to Conformational Changes of Inward/Outward Transmembrane Transport Proteins.Membranes · 2022Article
- Learning the relationship between nanoscale chemical patterning and hydrophobicity.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- A minireview on the perturbation effects of polar groups to direct nanoscale hydrophobic interaction and amphiphilic peptide assembly.RSC advances · 2021Review
- Rapid fabrication of precise high-throughput filters from membrane protein nanosheets.Nature materials · 2020Article
- Hydrophobicity of proteins and nanostructured solutes is governed by topographical and chemical context.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Examination of the quality of various force fields and solvation models for the equilibrium simulations of GA88 and GB88.Journal of molecular modeling · 2016Article
- Scaling and self-organized criticality in proteins II.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
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 at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. In their classic article, Kyte and Doolittle (KD) concluded that the "simplicity and graphic nature of hydrophobicity scales make them very useful tools for the evaluation of protein structures." In practice, however, attempts to develop hydrophobicity scales (for example, compatible with classical force fields (CFF) in calculating the energetics of protein folding) have encountered many difficulties. Here, we suggest an entirely different approach based on the idea that proteins are self-organized networks, subject to evolving finite-scale criticality (like some network glasses). We test this proposal against two small proteins that are delicately balanced between alpha and alpha/beta structures, with different functions encoded with only 12% of their amino acids. This example explains why protein structure prediction is so challenging, and it provides a severe test for the accuracy and content of hydrophobicity scales. This method confirms KD's evaluation and at the same time suggests that protein structure, dynamics, and function can be best discussed without using CFF.
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.