aminoAcidProperties - Calculates amino acid chemical properties for sequence data

Description

aminoAcidProperties calculates amino acid sequence physicochemical properties, including length, hydrophobicity, bulkiness, polarity, aliphatic index, net charge, acidic residue content, basic residue content, and aromatic residue content.

Usage

aminoAcidProperties(
data,
property = c("length", "gravy", "bulk", "aliphatic", "polarity", "charge", "basic",
"acidic", "aromatic"),
seq = "junction",
nt = TRUE,
trim = FALSE,
label = NULL,
...
)

Arguments

data
data.frame containing sequence data.
property
vector strings specifying the properties to be calculated. Defaults to calculating all defined properties.
seq
character name of the column containing input sequences.
nt
boolean, TRUE if the sequences (or sequence) are DNA and will be translated.
trim
if TRUE remove the first and last codon/amino acids from each sequence before calculating properties. If FALSE do not modify input sequences.
label
name of sequence region to add as prefix to output column names.
…
additional named arguments to pass to the functions gravy, bulk, aliphatic, polar or charge.

Value

A modified data data.frame with the following columns:

  • *_aa_length: number of amino acids.
  • *_aa_gravy: grand average of hydrophobicity (gravy) index.
  • *_aa_bulk: average bulkiness of amino acids.
  • *_aa_aliphatic: aliphatic index.
  • *_aa_polarity: average polarity of amino acids.
  • *_aa_charge: net charge.
  • *_aa_basic: fraction of informative positions that are Arg, His or Lys.
  • *_aa_acidic: fraction of informative positions that are Asp or Glu.
  • *_aa_aromatic: fraction of informative positions that are His, Phe, Trp or Tyr.

Where * is the value from label or the name specified for seq if label=NULL.

Details

For all properties except for length, non-informative positions are excluded, where non-informative is defined as any character in c("X", "-", ".", "*").

The scores for gravy, bulkiness and polarity are calculated as simple averages of the scores for each informative positions. The basic, acid and aromatic indices are calculated as the fraction of informative positions falling into the given category.

The aliphatic index is calculated using the Ikai, 1980 method.

The net charge is calculated using the method of Moore, 1985, excluding the N-terminus and C-terminus charges, and normalizing by the number of informative positions. The default pH for the calculation is 7.4.

The following data sources were used for the default property scores:

  • hydropathy: Kyte & Doolittle, 1982.
  • bulkiness: Zimmerman et al, 1968.
  • polarity: Grantham, 1974.
  • pK: EMBOSS.

References

  1. Zimmerman JM, Eliezer N, Simha R. The characterization of amino acid sequences in proteins by statistical methods. J Theor Biol 21, 170-201 (1968).
  2. Grantham R. Amino acid difference formula to help explain protein evolution. Science 185, 862-864 (1974).
  3. Ikai AJ. Thermostability and aliphatic index of globular proteins. J Biochem 88, 1895-1898 (1980).
  4. Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. J Mol Biol 157, 105-32 (1982).
  5. Moore DS. Amino acid and peptide net charges: A simple calculational procedure. Biochem Educ 13, 10-11 (1985).
  6. Wu YC, et al. High-throughput immunoglobulin repertoire analysis distinguishes between human IgM memory and switched memory B-cell populations. Blood 116, 1070-8 (2010).
  7. Wu YC, et al. The relationship between CD27 negative and positive B cell populations in human peripheral blood. Front Immunol 2, 1-12 (2011).
  8. https://emboss.sourceforge.net/apps/cvs/emboss/apps/iep.html

Examples

# Subset example data
db <- ExampleDb[c(1,10,100), c("sequence_id", "junction")]

# Calculate default amino acid properties from DNA sequences
aminoAcidProperties(db, seq="junction")


     sequence_id
1 GN5SHBT02D2WUN
2 GN5SHBT08JP7HP
3 GN5SHBT05HH5SE
                                                                                       junction
1 TGTGCGAGAGTCAAGCGAAGAGGTTGGCGAAGGAACTCACTATGGTTCGGGGAGTCCACACCTAGCGATGCCCACCGATGGTTCGACCCCTGG
2             TGTGCGAGAGATCGGTATTATTGTGGTGGTGACTGCTATTCCCCCCTACCCCAGTACTACTACTACGGTATGGACGTCTGG
3                                     TGTGCGAGTGCCTGTAGCAGTGGTGGCTGCTACGAGGAGAACTGGCTCGACCCCTGG
  junction_aa_length junction_aa_gravy junction_aa_bulk junction_aa_aliphatic
1                 31        -1.2612903         14.72194             0.2838710
2                 27        -0.7037037         14.50222             0.2888889
3                 19        -0.3684211         13.18053             0.3105263
  junction_aa_polarity junction_aa_charge junction_aa_basic junction_aa_acidic
1             8.687097           4.038916        0.25806452         0.09677419
2             7.874074          -1.233769        0.07407407         0.11111111
3             8.284211          -3.221436        0.00000000         0.15789474
  junction_aa_aromatic
1            0.2258065
2            0.2962963
3            0.1578947


# Calculate default amino acid properties from amino acid sequences
# Use a custom output column prefix
db$junction_aa <- translateDNA(db$junction)
aminoAcidProperties(db, seq="junction_aa", label="junction", nt=FALSE)


     sequence_id
1 GN5SHBT02D2WUN
2 GN5SHBT08JP7HP
3 GN5SHBT05HH5SE
                                                                                       junction
1 TGTGCGAGAGTCAAGCGAAGAGGTTGGCGAAGGAACTCACTATGGTTCGGGGAGTCCACACCTAGCGATGCCCACCGATGGTTCGACCCCTGG
2             TGTGCGAGAGATCGGTATTATTGTGGTGGTGACTGCTATTCCCCCCTACCCCAGTACTACTACTACGGTATGGACGTCTGG
3                                     TGTGCGAGTGCCTGTAGCAGTGGTGGCTGCTACGAGGAGAACTGGCTCGACCCCTGG
                      junction_aa junction_aa_length junction_aa_gravy
1 CARVKRRGWRRNSLWFGESTPSDAHRWFDPW                 31        -1.2612903
2     CARDRYYCGGDCYSPLPQYYYYGMDVW                 27        -0.7037037
3             CASACSSGGCYEENWLDPW                 19        -0.3684211
  junction_aa_bulk junction_aa_aliphatic junction_aa_polarity
1         14.72194             0.2838710             8.687097
2         14.50222             0.2888889             7.874074
3         13.18053             0.3105263             8.284211
  junction_aa_charge junction_aa_basic junction_aa_acidic junction_aa_aromatic
1           4.038916        0.25806452         0.09677419            0.2258065
2          -1.233769        0.07407407         0.11111111            0.2962963
3          -3.221436        0.00000000         0.15789474            0.1578947



# Use the Grantham, 1974 side chain volume scores from the seqinr package
# Set pH=7.0 for the charge calculation
# Calculate only average volume and charge
# Remove the head and tail amino acids from the junction, thus making it the CDR3
library(seqinr)
data(aaindex)
x <- aaindex[["GRAR740103"]]$I
# Rename the score vector to use single-letter codes
names(x) <- translateStrings(names(x), ABBREV_AA)
# Calculate properties
aminoAcidProperties(db, property=c("bulk", "charge"), seq="junction", 
trim=TRUE, label="cdr3", bulkiness=x, pH=7.0)

     sequence_id
1 GN5SHBT02D2WUN
2 GN5SHBT08JP7HP
3 GN5SHBT05HH5SE
                                                                                       junction
1 TGTGCGAGAGTCAAGCGAAGAGGTTGGCGAAGGAACTCACTATGGTTCGGGGAGTCCACACCTAGCGATGCCCACCGATGGTTCGACCCCTGG
2             TGTGCGAGAGATCGGTATTATTGTGGTGGTGACTGCTATTCCCCCCTACCCCAGTACTACTACTACGGTATGGACGTCTGG
3                                     TGTGCGAGTGCCTGTAGCAGTGGTGGCTGCTACGAGGAGAACTGGCTCGACCCCTGG
                      junction_aa cdr3_aa_bulk cdr3_aa_charge
1 CARVKRRGWRRNSLWFGESTPSDAHRWFDPW     85.00000       4.242920
2     CARDRYYCGGDCYSPLPQYYYYGMDVW     79.76000      -1.064488
3             CASACSSGGCYEENWLDPW     58.79412      -3.058792

See also

See countPatterns for counting the occurance of specific amino acid subsequences. See gravy, bulk, aliphatic, polar and charge for functions that calculate the included properties individually.