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  1. Article ; Online: Publisher Correction: A sequence-based evolutionary distance method for Phylogenetic analysis of highly divergent proteins.

    Cao, Wei / Wu, Lu-Yun / Xia, Xia-Yu / Chen, Xiang / Wang, Zhi-Xin / Pan, Xian-Ming

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 23000

    Language English
    Publishing date 2023-12-28
    Publishing country England
    Document type Published Erratum
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-50520-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: A sequence-based evolutionary distance method for Phylogenetic analysis of highly divergent proteins.

    Cao, Wei / Wu, Lu-Yun / Xia, Xia-Yu / Chen, Xiang / Wang, Zhi-Xin / Pan, Xian-Ming

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 20304

    Abstract: Because of the limited effectiveness of prevailing phylogenetic methods when applied to highly divergent protein sequences, the phylogenetic analysis problem remains challenging. Here, we propose a sequence-based evolutionary distance algorithm termed ... ...

    Abstract Because of the limited effectiveness of prevailing phylogenetic methods when applied to highly divergent protein sequences, the phylogenetic analysis problem remains challenging. Here, we propose a sequence-based evolutionary distance algorithm termed sequence distance (SD), which innovatively incorporates site-to-site correlation within protein sequences into the distance estimation. In protein superfamilies, SD can effectively distinguish evolutionary relationships both within and between protein families, producing phylogenetic trees that closely align with those based on structural information, even with sequence identity less than 20%. SD is highly correlated with the similarity of the protein structure, and can calculate evolutionary distances for thousands of protein pairs within seconds using a single CPU, which is significantly faster than most protein structure prediction methods that demand high computational resources and long run times. The development of SD will significantly advance phylogenetics, providing researchers with a more accurate and reliable tool for exploring evolutionary relationships.
    MeSH term(s) Phylogeny ; Evolution, Molecular ; Sequence Alignment ; Biological Evolution ; Proteins/genetics ; Proteins/chemistry ; Algorithms
    Chemical Substances Proteins
    Language English
    Publishing date 2023-11-20
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-47496-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Determinants of Thermostability in Serine Hydroxymethyltransferase Identified by Principal Component Analysis.

    Leng, Fei / Wu, Lu-Yun / Lu, Chang / Pan, Xian-Ming

    Scientific reports

    2017  Volume 7, Page(s) 46463

    Abstract: Protein thermostability has received growing attention in recent years. Little is known about the determinants of thermal resistance in individual protein families. However, it is known that the mechanism is family-dependent and not identical for all ... ...

    Abstract Protein thermostability has received growing attention in recent years. Little is known about the determinants of thermal resistance in individual protein families. However, it is known that the mechanism is family-dependent and not identical for all proteins. We present a multivariate statistical analysis to find the determinants of thermostability in one protein family, the serine hydroxymethyltransferase family. Based on principal component analysis, we identified three amino acid fragments as the potential determinants of thermostability. The correlation coefficients between all the putative fragments and the protein thermostability were significant according to multivariable linear regression. Within the fragments, four critical amino acid positions were identified, and they indicated the contributions of Leu, Val, Lys, Asp, Glu, and Phe to thermostability. Moreover, we analyzed the insertions/deletions of amino acids in the sequence, which showed that thermophilic SHMTs tend to insert or delete residues in the C-terminal domain rather than the N-terminal domain. Our study provided a promising approach to perform a preliminary search for the determinants of thermophilic proteins. It could be extended to other protein families to explore their own strategies for adapting to high temperature.
    MeSH term(s) Amino Acid Sequence ; Amino Acids/chemistry ; Computer Simulation ; Enzyme Stability/genetics ; Geobacillus stearothermophilus/enzymology ; Geobacillus stearothermophilus/genetics ; Glycine Hydroxymethyltransferase/chemistry ; Glycine Hydroxymethyltransferase/genetics ; Linear Models ; Models, Molecular ; Molecular Dynamics Simulation ; Peptide Fragments/chemistry ; Peptide Fragments/genetics ; Principal Component Analysis ; Temperature
    Chemical Substances Amino Acids ; Peptide Fragments ; Glycine Hydroxymethyltransferase (EC 2.1.2.1)
    Language English
    Publishing date 2017-04-19
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/srep46463
    Database MEDical Literature Analysis and Retrieval System OnLINE

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