ArticleProtein science : a publication of the Protein Society2006
An amino acid "transmembrane tendency" scale that approaches the theoretical limit to accuracy for prediction of transmembrane helices: relationship to biological hydrophobicity.
Article in Protein science : a publication of the Protein Society, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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Who cites it
73 citing papers in PubMed.
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- Controllable Generation of Pathogen-Specific Antimicrobial Peptides Through Knowledge-Aware Prompt Diffusion Model.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
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- Exploring Uniform, Dual, and Dynamic Topologies of Membrane Proteins by Substituted Cysteine Accessibility Method (SCAM™).Methods in molecular biology (Clifton, N.J.) · 2024Article
- Visualization of Self-Assembly and Hydration of a β-Hairpin through Integrated Small and Wide-Angle Neutron Scattering.Biomacromolecules · 2023Article
- Exome sequencing in retinal dystrophy patients reveals a novel candidate gene ER membrane protein complex subunit 3.Heliyon · 2023Article
- Interpreting the molecular mechanisms of disease variants in human transmembrane proteins.Biophysical journal · 2023Article
- A TAle of Two Pathways: Tail-Anchored Protein Insertion at the Endoplasmic Reticulum.Cold Spring Harbor perspectives in biology · 2023Review
- Lipocalin 2 - mutation screen and serum levels in patients with anorexia nervosa or obesity and in lean individuals.Frontiers in endocrinology · 2023Article
- Prediction and bioactivity of small-molecule antimicrobial peptides fromFrontiers in microbiology · 2023Article
- Comparative Study of the Solid-Liquid Interfacial Adsorption of Proteins in Their Native and Amyloid Forms.International journal of molecular sciences · 2022Article
- Structurally derived universal mechanism for the catalytic cycle of the tail-anchored targeting factor Get3.Nature structural & molecular biology · 2022Article
- Traditional and Computational Screening of Non-Toxic Peptides and Approaches to Improving Selectivity.Pharmaceuticals (Basel, Switzerland) · 2022Review
13 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
Hydrophobicity analyses applied to databases of soluble and transmembrane (TM) proteins of known structure were used to resolve total genomic hydrophobicity profiles into (helical) TM sequences and mainly "subhydrophobic" soluble components. This information was used to define a refined "hydrophobicity"-type TM sequence prediction scale that should approach the theoretical limit of accuracy. The refinement procedure involved adjusting scale values to eliminate differences between the average amino acid composition of populations TM and soluble sequences of equal hydrophobicity, a required property of a scale having maximum accuracy. Application of this procedure to different hydrophobicity scales caused them to collapse to essentially a single TM tendency scale. As expected, when different scales were compared, the TM tendency scale was the most accurate at predicting TM sequences. It was especially highly correlated (r = 0.95) to the biological hydrophobicity scale, derived experimentally from the percent TM conformation formed by artificial sequences passing though the translocon. It was also found that resolution of total genomic sequence data into TM and soluble components could be used to define the percent probability that a sequence with a specific hydrophobicity value forms a TM segment. Application of the TM tendency scale to whole genomic data revealed an overlap of TM and soluble sequences in the "semihydrophobic" range. This raises the possibility that a significant number of proteins have sequences that can switch between TM and non-TM states. Such proteins may exist in moonlighting forms having properties very different from those of the predominant conformation.
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