Project1-27.02.
2018
##Proteins(Cytosolic and Membrane) and PCA analysis
library(bio3d)
library(peptider)
library(Peptides)
#Membrane Protein-
p.memb<-read.pdb("2jqy")
s.p.memb<-pdbseq(p.memb)
s.p.memb
##Aadescriptors-Compute 66 descriptors for each amino acid of a protein
sequence
desc1<-aaDescriptors(s.p.memb)
summary(desc1)
#Thermostability value of membrane protein-depends on the relative volume of
side chains of aliphatic amino acids Isoleucine, Alanine, Valine and Leucine.
The aliphatic index needs to be calculated.
ai_p.memb<-aIndex(s.p.memb)
ai_p.memb
ai_p.memb<-which(ai_p.memb!=0)
ai_p.memb
l.seq1<-length(s.p.memb)
l.seq1
therm.stability.mem<-sum(ai_p.memb)/l.seq1
therm.stability.mem
#Protein Interaction-Potential Protein Interaction Index is calculated by
using function Boman.
mem.p.interaction<-boman(s.p.memb)
mem.p.interaction
memp.bin.point<- sum(mem.p.interaction)/l.seq1
memp.bin.point
#Since bin point is 2.275(<2.68), it can be concluded that protein-protein
interaction is slightly less, for two proteins to interact.
##Cytosolic protein
cyt.p<-read.pdb("3ibv")
seq.cyt.p<-pdbseq(cyt.p)
seq.cyt.p
##Aadescriptors-Compute 66 descriptors for each amino acid of a protein
sequence
desc2<-aaDescriptors(seq.cyt.p)
summary(desc2)
#Thermostability value of membrane protein-depends on the relative volume of
side chains of aliphatic amino acids Isoleucine, Alanine, Valine and Leucine.
The aliphatic index needs to be calculated.
ai.cyt.p<-aIndex(seq.cyt.p)
ai.cyt.p
ai.cyt.p<-which(ai.cyt.p!=0)
ai.cyt.p
l.seq2<-length(seq.cyt.p)
l.seq2
therm.stability.cyt<-sum(ai.cyt.p)/l.seq2
therm.stability.cyt
#Protein Interaction-Potential Protein Interaction Index is calculated by
using function Boman.
cyt.p.interaction<-boman(seq.cyt.p)
cyt.p.interaction
cytp.bin.point<- sum(cyt.p.interaction)/l.seq2
cytp.bin.point
#Since bin point is 1.084(<2.68), it can be concluded that protein-protein
interaction is hugely less due to a lower affininty.
#A function for protein pca
protein.pca<-function(seq){
library("bio3d")
library("Peptides")
ch<-charge(seq, pH = 7, pKscale = "Lehninger")
p.interaction<-boman(seq)
ampI<-hmoment(seq, angle = 100, window = 11)
hy<-hydrophobicity(seq, scale = "KyteDoolittle")
pI<-pI(seq,pKscale = "Lehninger")
mw<-mw(seq, monoisotopic = FALSE)
pro<-cbind(ch, p.interaction,ampI,hy,pI,mw)
colnames(pro)<-c("CHARGE","P-
P","AMPIPHILLICITY","HYDRPHOBICITY","ISOELECTRIC","MOL WEIGHT")
p<-cbind(seq,pro)
colnames(p)<-c("AA","CHARGE","P-
P","AMPIPHILLICITY","HYDRPHOBICITY","ISOELECTRIC","MOL WEIGHT")
pr.pca<-prcomp(pro)
return(pr.pca)}
#A function for protein analysis of different properties
p.property<-function(seq){
library("bio3d")
library("Peptides")
ch<-charge(seq, pH = 7, pKscale = "Lehninger")
p.interaction<-boman(seq)
ampI<-hmoment(seq, angle = 100, window = 11)
hy<-hydrophobicity(seq, scale = "KyteDoolittle")
pI<-pI(seq,pKscale = "Lehninger")
mw<-mw(seq, monoisotopic = FALSE)
pro<-cbind(ch,p.interaction,ampI,hy,pI,mw)
colnames(pro)<-c("CHARGE","P-
P","AMPIPHILLICITY","HYDRPHOBICITY","ISOELECTRIC","MOL WEIGHT")
p<-cbind(seq,pro)
colnames(p)<-c("AA","CHARGE","P-
P","AMPIPHILLICITY","HYDRPHOBICITY","ISOELECTRIC","MOL WEIGHT")
return(p)}
#Membrane protein
mem.p<-read.pdb("2jqy")
## PDB has ALT records, taking A only, rm.alt=TRUE
seq.mem.p<-pdbseq(mem.p)
mem.pr<-p.property(seq.mem.p)
pca.mem.p<-protein.pca(seq.mem.p)
par(mfrow=c(1,2))
biplot(pca.mem.p,main="PCA of 2jqy")
#Cytosolic protein
cyt.p<-read.pdb("3ibv")
seq.cyt.p<-pdbseq(cyt.p)
cyt.pr<-p.property(seq.cyt.p)
pca.cyt.p<-protein.pca(seq.cyt.p)
biplot(pca.cyt.p,main="PCA of 3ibv")
