membpos: Compute theoretically the class of a protein sequence

Description Usage Arguments Details Value References Examples

Description

This function calculates the theoretical class of a protein sequence based on the relationship between the hydrophobic moment and hydrophobicity scale proposed by Eisenberg (1984).

Usage

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membpos(seq, angle = 100)

Arguments

seq

An amino-acids sequence

angle

A protein rotational angle

Details

Eisenberg et al. (1982) found a correlation between hydrophobicity and hydrophobic moment that defines the protein section as globular, transmembrane or superficial. The function calculates the hydrophobicity (H) and hydrophobic moment (uH) based on the standardized scale of Eisenberg (1984) using windows of 11 amino acids for calculate the theoretical fragment type.

Value

A data frame for each sequence given with the calculated class for each window of eleven amino-acids

References

Eisenberg, David. "Three-dimensional structure of membrane and surface proteins." Annual review of biochemistry 53.1 (1984): 595-623.

D. Eisenberg, R. M. Weiss, and T. C. Terwilliger. The helical hydrophobic moment: A measure of the amphiphilicity of a helix. Nature, 299(5881):371-374, 1982. [p7, 8]

Examples

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membpos(seq = "ARQQNLFINFCLILIFLLLI",angle = 100)
#       Pep        H     uH       MembPos
# 1 ARQQNLFINFCL 0.083 0.353      Globular
# 2 RQQNLFINFCLI 0.147 0.317      Globular
# 3 QQNLFINFCLIL 0.446 0.274      Globular
# 4 QNLFINFCLILI 0.632 0.274 Transmembrane
# 5 NLFINFCLILIF 0.802 0.253       Surface
# 6 LFINFCLILIFL 0.955 0.113 Transmembrane
# 7 FINFCLILIFLL 0.955 0.113 Transmembrane
# 8 INFCLILIFLLL 0.944 0.108 Transmembrane
# 9 NFCLILIFLLLI 0.944 0.132 Transmembrane

membpos(seq = "ARQQNLFINFCLILIFLLLI",angle = 160)
#       Pep        H     uH    MembPos
# 1 ARQQNLFINFCL 0.083 0.467  Globular
# 2 RQQNLFINFCLI 0.147 0.467  Globular
# 3 QQNLFINFCLIL 0.446 0.285  Globular
# 4 QNLFINFCLILI 0.632 0.358  Surface
# 5 NLFINFCLILIF 0.802 0.358  Surface
# 6 LFINFCLILIFL 0.955 0.269  Surface
# 7 FINFCLILIFLL 0.955 0.269  Surface
# 8 INFCLILIFLLL 0.944 0.257  Surface
# 9 NFCLILIFLLLI 0.944 0.229  Surface


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