| membpos {Peptides} | R Documentation |
Compute theoretically the class of a protein sequence
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
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
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