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HICL table can manipulate all proteins in human complete proteome

Zhenhua Xie
doi: https://doi.org/10.1101/093971
Zhenhua Xie
1The Shenzhen Key Laboratory of Health Sciences and Technology, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
2Green biosynthesis institute of Bontac bio-engineering(shenzhen)Co.,Ltd, Shenzhen 518102, China
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  • For correspondence: xiezh@sz.tsinghua.edu.cn
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Abstract

Background The data of human complete proteome in the databases of Universal Protein Resource (UniProt) or National Center for Biotechnology Information(NCBI) were disorderly organized and hardly handled by an ordinary biologist.

Results The HICL table enable an ordinary biologist efficiently to handle the human complete proteome with 67911 entries, to get an overview on the distribution of the physicochemical features of all proteins in the human complete proteome, to perceive the details of the distribution patterns of the physicochemical features in some protein family members and protein variants, to find some particular proteins.

Moreover, two discoveries were made via the HICL table: (1) The amino aicds(Asp,Glu) have symmetrical trend of the distributions versus pI, but the amino aicds(Arg, Lys) have local asymmetrical trend of the distributions versus pI in human complete proteome. (2) Protein sequence, besides amino acid properties, can in theory influence the modal distribution of protein isoelectric points.

Conclusion I has created the HICL table as a robust tool for orderly managing 67911 proteins in human complete proteome by their physicochemical features, the names and sequences. Any proteins with the particular physicochemical features can be screened out from the human complete proteome via the HICL table. In addition, the unbalanced distribution of the amino aicds(Arg, Lys) in high pI proteins of human complete proteome and the effect of protein sequence on modal distribution of protein isoelectric points have been discovered through the HICL table.

  • Abbreviations

    2D-PAGE
    two-dimensional polyacrylamide gel electrophoresis
    AAC
    Amino acid composition
    AAs
    amino acids
    Ala
    Alanine
    Annot1
    Annotation1
    Annot2
    Annotation2
    Arg
    Arginine
    Asp
    Aspartic acid
    Asn
    Asparagine
    Cys
    Cysteine
    DDB1
    damage-specific DNA binding protein1
    DNA
    deoxyribonucleic acid
    F-box
    a protein structural motif of about 50 amino acids that mediates protein–protein interactions
    Gln
    Glutamine
    Glu
    Glutamic acid
    Gly
    Glycine
    His
    Histidine
    HP
    Hydrophobicity
    ID
    identification
    Ile
    Isoleucine
    Leu
    Leucine
    Lys
    Lysine
    Met
    Methionine
    MS
    Mass spectrometry
    MTS
    Met-truncated sequence(derived from full protein sequence by eliminating the initial methionine)
    MW
    Molecular weight
    NCBI
    National Center for Biotechnology Information
    NO
    Number
    PDZ
    a common structural domain of 80-90 amino-acids found in the signaling proteins of bacteria, yeast, plants, viruses[1] and animals
    Phe
    Phenylalanine
    pI
    Isoelectric point
    Pfam
    a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs)
    Pro
    Proline
    Ser
    Serine
    SL
    Sequence length
    sORF
    short open reading frames
    Thr
    Threonine
    Trp
    Tryptophan
    Tyr
    Tyrosine
    UniProt
    Universal Protein Resource
    Val
    Valine
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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    Posted December 14, 2016.
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    HICL table can manipulate all proteins in human complete proteome
    Zhenhua Xie
    bioRxiv 093971; doi: https://doi.org/10.1101/093971
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    HICL table can manipulate all proteins in human complete proteome
    Zhenhua Xie
    bioRxiv 093971; doi: https://doi.org/10.1101/093971

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