ArticlePLoS computational biology2006
Prediction of amyloidogenic and disordered regions in protein chains.
Article in PLoS computational biology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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Who cites it
61 citing papers in PubMed, 173 citations in OpenAlex.
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- Sequence-Based Prediction of Protein Phase Separation: The Role of Beta-Pairing Propensity.Biomolecules · 2022Article
- The Increased Amyloidogenicity of Spike RBD and pH-Dependent Binding to ACE2 May Contribute to the Transmissibility and Pathogenic Properties of SARS-CoV-2 Omicron as Suggested by In Silico Study.International journal of molecular sciences · 2022Article
- A comprehensive mini-review on amyloidogenesis of different SARS-CoV-2 proteins and its effect on amyloid formation in various host proteins.3 Biotech · 2022Review
- Bioinformatics Methods in Predicting Amyloid Propensity of Peptides and Proteins.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Investigating the Disordered and Membrane-Active Peptide A-Cage-C Using Conformational Ensembles.Molecules (Basel, Switzerland) · 2021Article
- A theoretical study of polymorphism in VQIVYK fibrils.Biophysical journal · 2021Article
- Repeats in S1 Proteins: Flexibility and Tendency for Intrinsic Disorder.International journal of molecular sciences · 2019Article
- Acid-denatured small heat shock protein HdeA fromThe Journal of biological chemistry · 2019Article
- Modulation of the aggregation of an amyloidogenic sequence by flanking-disordered region in the intrinsically disordered antigen merozoite surface protein 2.European biophysics journal : EBJ · 2019Article
- Desmin and Cardiac Disease: An Unfolding Story.Circulation research · 2018Article
- Proteome-scale understanding of relationship between homo-repeat enrichments and protein aggregation properties.PloS one · 2018Article
- Factors affecting the physical stability (aggregation) of peptide therapeutics.Interface focus · 2017Review
- Oligomerization of FVFLM peptides and their ability to inhibit beta amyloid peptides aggregation: consideration as a possible model.Physical chemistry chemical physics : PCCP · 2017Article
- Comparative genome analyses of mycobacteria give better insights into their evolution.PloS one · 2017Article
- The C-terminus hot spot region helps in the fibril formation of bacteriophage-associated hyaluronate lyase (HylP2).Scientific reports · 2015Article
- Amyloid-Forming Properties of Human Apolipoproteins: Sequence Analyses and Structural Insights.Advances in experimental medicine and biology · 2015Review
- PASTA 2.0: an improved server for protein aggregation prediction.Nucleic acids research · 2014Article
- Advantages of proteins being disordered.Protein science : a publication of the Protein Society · 2014Review
- Hot spots in apolipoprotein A-II misfolding and amyloidosis in mice and men.FEBS letters · 2014Article
1 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The determination of factors that influence protein conformational changes is very important for the identification of potentially amyloidogenic and disordered regions in polypeptide chains. In our work we introduce a new parameter, mean packing density, to detect both amyloidogenic and disordered regions in a protein sequence. It has been shown that regions with strong expected packing density are responsible for amyloid formation. Our predictions are consistent with known disease-related amyloidogenic regions for eight of 12 amyloid-forming proteins and peptides in which the positions of amyloidogenic regions have been revealed experimentally. Our findings support the concept that the mechanism of amyloid fibril formation is similar for different peptides and proteins. Moreover, we have demonstrated that regions with weak expected packing density are responsible for the appearance of disordered regions. Our method has been tested on datasets of globular proteins and long disordered protein segments, and it shows improved performance over other widely used methods. Thus, we demonstrate that the expected packing density is a useful value with which one can predict both intrinsically disordered and amyloidogenic regions of a protein based on sequence alone. Our results are important for understanding the structural characteristics of protein folding and misfolding.
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Registered trials
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