seqinr (version 3.4-5)

pmw: Protein Molecular Weight

Description

With default parameter values, returns the apparent molecular weight of one mole (6.0221415 e+23) of the input protein expressed in gram at see level on Earth with terrestrial isotopic composition.

Usage

pmw(seqaa, Ar = c(C = 12.0107, H = 1.00794, O = 15.9994,
N = 14.0067, P = 30.973762, S = 32.065), gravity = 9.81,
unit = "gram", checkseqaa = TRUE)

Arguments

seqaa

a protein sequence as a vector of single chars. Allowed values are "*ACDEFGHIKLMNPQRSTVWY", non allowed values are ignored.

Ar

a named vector for the mean relative atomic masses of CHONPS atoms. Defaults values are from to the natural terrestrial sources according to the 43rd IUPAC General Assembly in Beijing, China in August 2005 (See http://iupac.org/category/recent-releases/ for updates).

gravity

gravitational field constant in standard units. Defaults to 9.81 m/s2, that is to the average value at see level on Earth. Negative values are not allowed.

unit

a string that could be "gram" to get the result in grams (1 g = 0.001 kg) or "N" to get the result in Newton units (1 N = 1 kg.m/s2).

checkseqaa

if TRUE pmw() warns if a non-allowed character in seqaa is found.

Value

The protein molecular weight as a single numeric value.

Details

Algorithm

Computing the molecular mass of a protein is close to a linear form on amino-acid frequencies, but not exactly since we have to remove n - 1 water molecules for peptidic bound formation.

Cysteine

All cysteines are supposed to be in reduced (-SH) form.

Methionine

All methionines are supposed to be not oxidized.

Modifications

No post-traductional modifications (such as phosphorylations) are taken into account.

Rare

Rare amino-acids (pyrolysine and selenocysteine) are not handled.

Warning

Do not use defaults values for Ar to compute the molecular mass of alien's proteins: the isotopic composition for CHONPS atoms could be different from terrestrial data in a xenobiotic context. Some aliens are easily offended, make sure not to initiate one more galactic war by repporting wrong results.

References

citation("seqinr")

See Also

s2c, c2s, aaa, a

Examples

# NOT RUN {
allowed <- s2c("*ACDEFGHIKLMNPQRSTVWY") # All allowed chars in a protein
pmw(allowed)
all.equal(pmw(allowed), 2395.71366) # Should be true on most platforms
#
# Compute the apparent molecular weight on Moon surface:
#
pmw(allowed, g = 1.6)
#
# Compute the apparent molecular weight in absence of gravity:
#
pmw(allowed, g = 0) # should be zero
#
# Reports results in Newton units:
#
pmw(allowed, unit = "N")
#
# Compute the mass in kg of one mol of this protein:
#
pmw(allowed)/10^3
#
# Compute the mass for all amino-acids:
#
sapply(allowed[-1], pmw) -> aamw
names(aamw) <- aaa(names(aamw))
aamw
# }