About: Chemical property based sequence characterization of PpcA and its homolog proteins PpcB-E: A mathematical approach

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About: Chemical property based sequence characterization of PpcA and its homolog proteins PpcB-E: A mathematical approach Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Chemical property based sequence characterization of PpcA and its homolog proteins PpcB-E: A mathematical approach
Creator	Choudhury, Pabitra Das, Jayanta
Source	PMC
abstract	Periplasmic c7 type cytochrome A (PpcA) protein is determined in Geobacter sulfurreducens along with its other four homologs (PpcB-E). From the crystal structure viewpoint the observation emerges that PpcA protein can bind with Deoxycholate (DXCA), while its other homologs do not. But it is yet to be established with certainty the reason behind this from primary protein sequence information. This study is primarily based on primary protein sequence analysis through the chemical basis of embedded amino acids. Firstly, we look for the chemical group specific score of amino acids. Along with this, we have developed a new methodology for the phylogenetic analysis based on chemical group dissimilarities of amino acids. This new methodology is applied to the cytochrome c7 family members and pinpoint how a particular sequence is differing with others. Secondly, we build a graph theoretic model on using amino acid sequences which is also applied to the cytochrome c7 family members and some unique characteristics and their domains are highlighted. Thirdly, we search for unique patterns as subsequences which are common among the group or specific individual member. In all the cases, we are able to show some distinct features of PpcA that emerges PpcA as an outstanding protein compared to its other homologs, resulting towards its binding with deoxycholate. Similarly, some notable features for the structurally dissimilar protein PpcD compared to the other homologs are also brought out. Further, the five members of cytochrome family being homolog proteins, they must have some common significant features which are also enumerated in this study.
has issue date	2017-03-31(xsd:dateTime)
bibo:doi	10.1371/journal.pone.0175031
bibo:pmid	28362850
has license	cc-by
sha1sum (hex)	7f3106f6c5402784319dd722bbbaaa5f5b59df1f
schema:url	https://doi.org/10.1371/journal.pone.0175031
resource representing a document's title	Chemical property based sequence characterization of PpcA and its homolog proteins PpcB-E: A mathematical approach
has PubMed Central identifier	PMC5376323
has PubMed identifier	28362850
schema:publication	PLoS One
resource representing a document's body	covid:7f3106f6c5402784319dd722bbbaaa5f5b59df1f#body_text
is schema:about of	named entity 'emerges' named entity 'chemical' named entity 'basis' named entity 'PpcA' named entity 'Chemical property' named entity 'homolog' named entity 'ITS' named entity 'PPCA' named entity 'PROTEINS' named entity 'PROTEIN SEQUENCE' named entity 'EMBEDDED' named entity 'LOOK' named entity 'GEOBACTER SULFURREDUCENS' named entity 'FAMILY MEMBERS' named entity 'CYTOCHROME A' named entity 'HAVE' named entity 'INFORMATION' named entity 'NEW' named entity 'APPLIED' named entity 'METHODOLOGY' named entity 'DETERMINED' named entity 'PROTEIN ' named entity 'SCORE' named entity 'CERTAINTY' named entity 'PARTICULAR' named entity 'PINPOINT' named entity 'CHEMICAL' named entity 'CRYSTAL STRUCTURE' named entity 'BASIS' named entity 'BIND' named entity 'SEQUENCE' named entity 'VIEWPOINT' named entity 'FIRSTLY' named entity 'TYPE' named entity 'DEOXYCHOLATE' named entity 'PRIMARY' named entity 'PROTEIN SEQUENCE ANALYSIS' named entity 'SEQUENCE' named entity 'HOW' named entity 'BUT' named entity 'HOMOLOG' named entity 'MATHEMATICAL' named entity 'CHEMICAL PROPERTY' named entity 'PPCB' named entity 'PROTEIN CAN' named entity 'BASED' named entity 'ESTABLISHED' named entity 'DO NOT' named entity 'OBSERVATION' named entity 'CHARACTERIZATION' named entity 'APPROACH' named entity 'STUDY' named entity 'ITS' named entity 'REASON' named entity 'SPECIFIC' named entity 'AMINO ACIDS' named entity 'CYTOCHROME C7' named entity 'BASED' named entity 'PPCA' named entity 'PERIPLASMIC' named entity 'CHEMICAL GROUP' named entity 'PHYLOGENETIC ANALYSIS' named entity 'sequence' named entity 'This' named entity 'chemical group' named entity 'methodology' named entity 'chemical group' named entity 'certainty' named entity 'amino acids' named entity 'observation' named entity 'PpcA' named entity 'amino acids' named entity 'cytochrome' named entity 'crystal structure' named entity 'protein sequence analysis' named entity 'Threonine' named entity 'PpcA' named entity 'amino acid' named entity 'amino acids' named entity 'amino acid'

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