Proteomics – l dserver.bio.yorku.ca / b iol4030
The Science of Proteomics Proteomics is the study of protein structure and funct ion at a la rge scale The name is der ived f rom genomics (the study of genomes) Sta rted i n 1997
SNPS – d ifferences are extrememly old and can be used to look at m igrat ion patterns. Genomics looks at whats d ifferent among people proteome changes between cells and t issues un l i ke DNA so studying i t gets even more d i ff icul t Protein cal led “Notch”, wh ich makes a B-l i ne for nucleus Mass spectrometry is the main method of study to examine proteins mRNA a recent study showed that amount of mRNA i n a cell does not ref lect the amount of protein being made i n terestingly enough
Post-t ranslat ional modi f icat ions simple phosphorylat ion: very good way of modifying protein activ i ty ~2% of our proteome encodes k inases (~500 proteins) serine, th reonine and tyrosine are commonly phosphorylated o phosphotyrosine: SH2 domain extremely powerfu l signal because i t cal ls upon other protein to cause chain reactions ST1571 a k a GLEE VEC: d rug that’s a hybr id protein. Works on domains of protein Bcr-Abl wh ich is a tyrosine k inase o Expensive d rug that REA LLY works for cancers l i ke leukemia (covered i n Canada)
Platforms for Proteomics and Funct ional Genomics f igure shows how complex proteomics is topics prof w i l l cover: o mass spectrometry o GFP + FRET f l uorescence o Protein A r rays o Chemical A r rays o Ant ibody Ar rays
H E RCE P T I N : d rug that works on receptor k inases
Botu l ism toxin payload + Ant ibody
Ar ray Based Proteomics F R E T ( f l uo rescence resonance energy t r a nsfer): two f l uorescently tagged molecules / p roteins come together, detect by shin ing l ight on one molecule wh ich emits a certain wavelenth wh ich is absorbed by the protein nearby wh ich then emits a d ifferent wavelength How to tag a protein: GO after an an imo acid that has a specif ic chemical reactiv i ty. A popula r method is looking at cysteine wh ich is ra re on the surface on a protein. o T h iol groups: make d isu lf ide bonds o Ami no groups ( N H 3+): o Lysine:
Structu ra l Proteomics X-r ay crystol l ag r aphy and N M R spect roscopy are the two ma in methods o R I K E N is a company i n Japan that has a factory that j ust f i nd structu re of proteins
I nformat ics
Cl in ica l Proteomics N MR of u r i ne can have a thousand peaks but each person’s pattern is d i fferent? Each peak ofcourse corresponds to a certain protein or compound but they’re only i n terested i n the pattern Even i f your sick, knowing your protein complement is i mportant ex. Your doctor can change your prescr ipt ion or therapy based on i t
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Lecture 2 – September 20, 2010
Levels of Protein Structure
Pr ima ry: just the sequence of the protein
Secondary: alpha hel ices (r ight-handed) and beta strands
Ter ita ry: global fold of protein
Quatena ry: bunch of proteins together
Am ino Acids generally two classes: hydrophobic, hydrophi l ic o al iphat ic o aromat ic alpha carbon contains R-group o R = H: glycerin o R = methyl: alan ine etc
Substi t ion Char t shows what can be tolerated
I ts more d i f f icu lt to make a substitut ion for an i n ter ior am ino acid than for an exterior. I n general assume that when you replace an a.a. i t’ l l be replaced by an a.a w ith in i ts group eg. Al iphat ic, hyrd rophobic for hydrophobic
To make or break peptide bond just add or substract water o Not only are the planars f lat but they have d ip loes as well
Torsion Angles: depending on wh ich side of the Calpha you’re at. o Protein can be expressed simply as a table of ph i and psy
Ramachand ran Map what are the al lowable angles i n a protein? He d iscovered them…certa in angles aren’t al lowed, i n fact most aren’t only certain angles shown i n red dots, red brown is more common
