cleave: Cleavage of polypeptide sequences

Description

This functions cleave polypeptide sequences. Use cleavageSites to find the cleavage sites, cleavageRanges to find the cleavage ranges and cleave to get the cleavage products.

Usage

"cleave"(x, enzym = "trypsin", missedCleavages = 0, custom = NULL, unique = TRUE)
"cleave"(x, enzym = "trypsin", missedCleavages = 0, custom = NULL, unique = TRUE)
"cleave"(x, enzym = "trypsin", missedCleavages = 0, custom = NULL, unique = TRUE)
"cleavageRanges"(x, enzym = "trypsin", missedCleavages = 0, custom = NULL)
"cleavageRanges"(x, enzym = "trypsin", missedCleavages = 0, custom = NULL)
"cleavageRanges"(x, enzym = "trypsin", missedCleavages = 0, custom = NULL)
"cleavageSites"(x, enzym = "trypsin", custom = NULL)
"cleavageSites"(x, enzym = "trypsin", custom = NULL)
"cleavageSites"(x, enzym = "trypsin", custom = NULL)

Arguments

polypeptide sequences.

enzym

character, cleavage rule.

missedCleavages

numeric, number of missed cleavages.

custom

character, of length 1 or 2. Could be used to define own cleaveage rules. The first element would be the pattern and the optional second element would be an exception (non-cleavage) pattern. Perl-like regular expressions are supported, see gregexpr for details. If custom is set the enzym is ignored.

unique

logical, if TRUE all duplicated cleavage products per peptide are removed.

Value

cleave: If x is a character it returns a list of the same length as x. Each element contains a character vector with the corresponding cleavage products of the polypeptides. If x is an AAString or an AAStringSet an AAStringSet or an AAStringSetList instance of the same length as x is returned. Each element contains an AAString or an AAStringSet instance with the corresponding cleavage products of the polypeptides.
cleavageRanges: If x is a character it returns a list of the same length as x. Each element contains a two-column matrix with the start and end positions of the peptides. If x is an AAString or an AAStringSet instance an IRanges or an IRangesList of the same length as x is returned.
cleavageSites: Returns a list of the same length as x. Each element contains an integer vector with the cleavage positions.

Overview:

Input	`cleave`	`cleavageRanges`
`cleavageSites`	`character`	`list` of `character`
`list` of `matrix`	`list` of `integer`	`AAString`
`AAStringSet`	`IRanges`	`list` of `integer`
`AAStringSet`	`AAStringSetList`	`IRangesList`
`list` of `integer`	Input	`cleave`

Details

The cleavage rules are taken from: http://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html

Cleavage rules (cleavage between P1 and P1'):

Rule name	P4	P3	P2	P1	P1'	P2'
`arg-c proteinase`	-	-	-	R	-	-
`asp-n endopeptidase`	-	-	-	-	D	-
`bnps-skatole-c`	-	-	-	W	-	-
`caspase1`	F,W,Y,L	-	H,A,T	D	not P,E,D,Q,K,R	-
`caspase2`	D	V	A	D	not P,E,D,Q,K,R	-
`caspase3`	D	M	Q	D	not P,E,D,Q,K,R	-
`caspase4`	L	E	V	D	not P,E,D,Q,K,R	-
`caspase5`	L,W	E	H	D	-	-
`caspase6`	V	E	H,I	D	not P,E,D,Q,K,R	-
`caspase7`	D	E	V	D	not P,E,D,Q,K,R	-
`caspase8`	I,L	E	T	D	not P,E,D,Q,K,R	-
`caspase9`	L	E	H	D	-	-
`caspase10`	I	E	A	D	-	-
`chymotrypsin-high`	-	-	-	F,Y	not P	-
	-	-	-	W	not M,P	-
`chymotrypsin-low`	-	-	-	F,L,Y	not P	-
	-	-	-	W	not M,P	-
	-	-	-	M	not P,Y	-
	-	-	-	H	not D,M,P,W	-
`clostripain`	-	-	-	R	-	-
`cnbr`	-	-	-	M	-	-
`enterokinase`	D,E	D,E	D,E	K	-	-
`factor xa`	A,F,G,I,L,T,V,M	D,E	G	R	-	-
`formic acid`	-	-	-	D	-	-
`glutamyl endopeptidase`	-	-	-	D	-	-
`granzyme-b`	I	E	P	D	-	-
`hydroxylamine`	-	-	-	N	G	-
`iodosobenzoic acid`	-	-	-	W	-	-
`lysc`	-	-	-	K	-	-
`lysn`	-	-	-	-	K	-
`neutrophil elastase`	-	-	-	A,V	-	-
`ntcb`	-	-	-	-	C	-
`pepsin1.3`	-	not H,K,R	not P	not R	F,L,W,Y	not P
	-	not H,K,R	not P	F,L,W,Y	-	not P
`pepsin`	-	not H,K,R	not P	not R	F,L	not P
	-	not H,K,R	not P	F,L	-	not P
`proline endopeptidase`	-	-	not H,K,R	P	not P	-
`proteinase k`	-	-	-	A,E,F,I,L,T,V,W,Y	-	-
`staphylococcal peptidase i`	-	-	not E	E	-	-
`thermolysin`	-	-	-	not D,E	A,F,I,L,M,V	-
`thrombin`	-	-	G	R	G	-
	A,F,G,I,L,T,V,M	A,F,G,I,L,T,V,W	P	R	not D,E	not D,E
`trypsin`	-	-	-	K,R	not P	-
	-	-	W	K	P	-
	-	-	M	R	P	-

Exceptions:

Rule name	Enzyme name	P4	P3	P2	P1	P1'
P2'	trypsin	-	-	C,D	K	D
-			-	-	C	K
H,Y	-			-	-	C
R	K	-			-	-
R	R	H,R	-	Rule name	Enzyme name	P4

Rule name

Enzyme name

arg-c proteinase

Arg-C proteinase

asp-n endopeptidase

Asp-N endopeptidase

bnps-skatole-c

BNPS-Skatole

caspase1

Caspase 1

caspase2

Caspase 2

caspase3

Caspase 3

caspase4

Caspase 4

caspase5

Caspase 5

caspase6

Caspase 6

caspase7

Caspase 7

caspase8

Caspase 8

caspase9

Caspase 9

caspase10

Caspase 10

chymotrypsin-high

Chymotrypsin-high specificity (C-term to [FYW], not before P)

chymotrypsin-low

Chymotrypsin-low specificity (C-term to [FYWML], not before P)

clostripain

Clostripain (Clostridiopeptidase B)

cnbr

CNBr

enterokinase

Enterokinase

factor xa

Factor Xa

formic acid

Formic acid

glutamyl endopeptidase

Glutamyl endopeptidase

granzyme-b

Granzyme B

hydroxylamine

Hydroxylamine

iodosobenzoic acid

Iodosobenzoic acid

lysc

LysC

lysn

LysN

neutrophil elastase

Neutrophil elastase

ntcb

NTCB (2-nitro-5-thiocyanobenzoic acid)

pepsin1.3

Pepsin (pH == 1.3)

pepsin

Pepsin (pH > 2)

proline endopeptidase

Proline-endopeptidase

proteinase k

Proteinase K

staphylococcal peptidase i

Staphylococcal Peptidase I

thermolysin

Thermolysin

thrombin

Thrombin

trypsin

Trypsin

References

Gasteiger E., Hoogland C., Gattiker A., Duvaud S., Wilkins M.R., Appel R.D., Bairoch A.; "Protein Identification and Analysis Tools on the ExPASy Server". (In) John M. Walker (ed): The Proteomics Protocols Handbook, Humana Press (2005). http://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html

Examples

Run this code

library("cleaver")

## Gastric juice peptide 1 (UniProtKB/Swiss-Prot: GAJU_HUMAN/P01358)
gaju <- "LAAGKVEDSD"

cleave(gaju, "trypsin")
# $LAAGKVEDSD
# [1] "LAAGK" "VEDSD"

cleavageRanges(gaju, "trypsin")
# $LAAGKVEDSD
#      start end
# [1,]     1   5
# [2,]     6  10

cleavageSites(gaju, "trypsin")
# $LAAGKVEDSD
# [1] 5

cleave(gaju, "trypsin", missedCleavages=1)
# $LAAGKVEDSD
# [1] "LAAGKVEDSD"

cleavageRanges(gaju, "trypsin", missedCleavages=1)
# $LAAGKVEDSD
#      start end
# [1,]     1  10

cleave(gaju, "trypsin", missedCleavages=0:1)
# $LAAGKVEDSD
# [1] "LAAGK" "VEDSD" "LAAGKVEDSD"

cleavageRanges(gaju, "trypsin", missedCleavages=0:1)
# $LAAGKVEDSD
#      start end
# [1,]     1   5
# [2,]     6  10
# [3,]     1  10


cleave(gaju, "pepsin")
# $LAAGKVEDSD
# [1] "LAAGKVEDSD"
# (no cleavage)


## use AAStringSet
gaju <- AAStringSet("LAAGKVEDSD")

cleave(gaju)
# AAStringSetList of length 1
# [["LAAGKVEDSD"]] LAAGK VEDSD


## Beta-enolase (UniProtKB/Swiss-Prot: ENOB_THUAL/P86978)
enob <- "SITKIKAREILD"

cleave(enob, "trypsin")
# $SITKIKAREILD
# [1] "SITK" "IK"   "AR"   "EILD"

cleave(enob, "trypsin", missedCleavages=2)
# $SITKIKAREILD
# [1] "SITKIKAR" "IKAREILD"

cleave(enob, "trypsin", missedCleavages=0:2)
# $SITKIKAREILD
# [1] "SITK"     "IK"       "AR"       "EILD"     "SITKIK"   "IKAR"
# [7] "AREILD"   "SITKIKAR" "IKAREILD"

## define own cleavage rule: cleave at K
cleave(enob, custom="K")
# $SITKIKAREILD
# [1] "SITK"   "IK"     "AREILD"

cleavageRanges(enob, custom="K")
# $SITKIKAREILD
#      start end
# [1,]     1   4
# [2,]     5   6
# [3,]     7  12

## define own cleavage rule: cleave at K but not if followed by A
cleave(enob, custom=c("K", "K(?=A)"))
# $SITKIKAREILD
# [1] "SITK"     "IKAREILD"

cleavageRanges(enob, custom=c("K", "K(?=A)"))
# $SITKIKAREILD
#      start end
# [1,]     1   4
# [2,]     5  12

cleavageSites(enob, custom=c("K", "K(?=A)"))
# $SITKIKAREILD
# [1] 4

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