ArticleBMC structural biology2014
Sequence analysis on the information of folding initiation segments in ferredoxin-like fold proteins.
Article in BMC structural biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 14 citations in OpenAlex.
- Conserved structural topologies in RNase A-like and trypsin-like serine proteases: a sequence-based folding analysis.BMC molecular and cell biology · 2025Article
- Decoding an Amino Acid Sequence to Extract Information on Protein Folding.Molecules (Basel, Switzerland) · 2022Review
- Slowest-first protein translation scheme: Structural asymmetry and co-translational folding.Biophysical journal · 2021Article
- Structure, Assembly, and Function of Tripartite Efflux and Type 1 Secretion Systems in Gram-Negative Bacteria.Chemical reviews · 2021Review
- Analyses of the folding sites of irregular β-trefoil fold proteins through sequence-based techniques and Gō-model simulations.BMC molecular and cell biology · 2020Article
- A new technique for predicting intrinsically disordered regions based on average distance map constructed with inter-residue average distance statistics.BMC structural biology · 2019Article
- Evolution of a protein folding nucleus.Protein science : a publication of the Protein Society · 2016Article
- Structure-based design of combinatorial mutagenesis libraries.Protein science : a publication of the Protein Society · 2015Article
- Implication of the cause of differences in 3D structures of proteins with high sequence identity based on analyses of amino acid sequences and 3D structures.BMC research notes · 2014Article
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWhile some studies have shown that the 3D protein structures are more conservative than their amino acid sequences, other experimental studies have shown that even if two proteins share the same topology, they may have different folding pathways. There are many studies investigating this issue with molecular dynamics or Go-like model simulations, however, one should be able to obtain the same information by analyzing the proteins' amino acid sequences, if the sequences contain all the information about the 3D structures. In this study, we use information about protein sequences to predict the location of their folding segments. We focus on proteins with a ferredoxin-like fold, which has a characteristic topology. Some of these proteins have different folding segments.
resultsDespite the simplicity of our methods, we are able to correctly determine the experimentally identified folding segments by predicting the location of the compact regions considered to play an important role in structural formation. We also apply our sequence analyses to some homologues of each protein and confirm that there are highly conserved folding segments despite the homologues' sequence diversity. These homologues have similar folding segments even though the homology of two proteins' sequences is not so high.
conclusionOur analyses have proven useful for investigating the common or different folding features of the proteins studied.
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