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BIOL 4030 (1)
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Department
Biology
Course Code
BIOL 4030
Professor
Logan Donaldson

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Proteomics
ldserver.bio.yorku.ca/biol4030
The Science of Proteomics
Proteomics is the study of protein structure and function at a large scale
The name is derived from genomics (the study of genomes)
Started in 1997
SNPS differences are extrememly old and can be used to look at migration patterns. Genomics looks at whats different among
people
proteome changes between cells and tissues unlike DNA so studying it gets even more difficult
Protein calledNotch, which makes a B-line for nucleus
Mass spectrometry is the main method of study to examine proteins
mRNA
a recent study showed that amount of mRNA in a cell does not reflect the amount of protein being made interestingly
enough
Post-translational modifications
simple phosphorylation: very good way of modifying protein activity
~2% of our proteome encodes kinases (~500 proteins)
serine, threonine and tyrosine are commonly phosphorylated
ophosphotyrosine: SH2 domain
extremely powerful signal because it calls upon other protein to cause chain reactions
ST1571 aka GLEEVEC: drug thats a hybrid protein. Works on domains of protein Bcr-Abl which is a tyrosine kinase
oExpensive drug that REALLY works for cancers like leukemia (covered in Canada)
Platforms for Proteomics and Functional Genomics
figure shows how complex proteomics is
topics prof will cover:
omass spectrometry
oGFP + FRET fluorescence
oProtein Arrays
oChemical Arrays
oAntibody Arrays
HERCEPTIN: drug that works on receptor kinases
Botulism toxin payload + Antibody
Array Based Proteomics
FRET (fluorescence resonance energy transfer): two fluorescently tagged molecules/proteins come together, detect
by shining light on one molecule which emits a certain wavelenth which is absorbed by the protein nearby which then
emits a different wavelength
How to tag a protein: GO after an animo acid that has a specific chemical reactivity. A popular method is looking at
cysteine which is rare on the surface on a protein.
oThiol groups: make disulfide bonds
oAmino groups (NH3+):
oLysine:
Structural Proteomics
X-ray crystollagraphy and NMR spectroscopy are the two main methods
oRIKEN is a company in Japan that has a factory that just find structure of proteins
Informatics
Clinical Proteomics
NMR of urine can have a thousand peaks but each persons pattern is different? Each peak ofcourse corresponds to a
certain protein or compound but theyre only interested in the pattern
Even if your sick, knowing your protein complement is important ex. Your doctor can change your prescription or
therapy based on it
1
www.notesolution.com
Lecture 2 – September 20, 2010
Levels of Protein Structure
Primary: just the sequence of the protein
Secondary: alpha helices (right-handed) and beta strands
Teritary: global fold of protein
Quatenary: bunch of proteins together
Amino Acids
generally two classes: hydrophobic, hydrophilic
oaliphatic
oaromatic
alpha carbon contains R-group
oR = H: glycerin
oR = methyl: alanine etc
Substition Chart shows what can be tolerated
Its more difficult to make a substitution for an interior amino acid than for an exterior. In general assume that when
you replace an a.a. itll be replaced by an a.a within its group eg. Aliphatic, hyrdrophobic for hydrophobic
To make or break peptide bond just add or substract water
oNot only are the planars flat but they have diploes as well
Torsion Angles: depending on which side of the Calpha youre at.
oProtein can be expressed simply as a table of phi and psy
Ramachandran Map
what are the allowable angles in a protein? He discovered them…certain angles aren’t allowed, in fact most aren’t only
certain angles shown in red dots, red brown is more common and brown is slightly common? Grey is forbidden
Profs Work
triangles are glyceins and assumes a lot more conformation so it can go almost anywhere on the map
Side Chain Torsion Angles
again you don’t see every angle, steric repulsion (where atoms bump into each other). 60, 180 and 300 degrees are the
most favourable ….especially for the big buly amino acids like phe follow those angles
“click the
Torsion angle dynamics: much more efficientnot sure why
Weak Forces
help protein fold and are broken easily
If you take a sequnces of a protein and let it fold, its important in the study of diseases like Mad Cow. Some times you have a
good form of a protein and sometimes it forms a bad form which serves as a nucleus to turn the good proteins to bad ones.
when proteins change structure they tend to stick together in odered fashion (oligermize) likein alzheimers. Aggregates
of protein can kill proteins around them.
proteins are always vibrating and are not static as shown in many pictures
main thing in proteins: slow motions in terms of millisecond to microsecond time scale, movements include loops
moving back and forth, protein looks like its breathing
protein folding can happen in less than a second, (tenths of a second being the max)
The Alpha Helix
hydrogen bonds play big role, they help stabilize the structure
I don’t get the deal with i and i+4 and something about affecting the width of the protein
Beta Strands
The Beta Turn
two H-bonds are formed in this turn
only come in certain shapes and show a.a preference for positions 2 and 3
Lecture 3 – September 22, 2010
2
www.notesolution.com
Play game to get 10% of your final!
The Beta Turn
Hs have to be 1.8 to 2.0 Angstroms to bond so adjacent Hs wont bond as theyre too far
Amino Acid Preference for Secondary Structures
Computer servers and algorihms help predict alpha helices and beta strands in a given protein sequence
Certain amino acids have a preference to be in a certain structure (add chart from slides)
oSome prefer alpha helices some prefer beta strands
o1.0 is no preference
owww.predictprotein.org a portal to software that allow you to predict protein structure
Richardson Diagram
shows two pics of 4 beta strand proteins and three hairpins
only shows protein backbone and doesnt include protein side-chains
Topology Cartoons
compares a given protein to all other proteins in the database
triangle is a beta strand etc.
instead of having to search through database you can search with the motif of the simple shapes
Prof worked on gpU (neck protein between capsid and tail).
The sequence of this strange protein is so unique it shows no similarity to any other species. It has no homologue!
DALI, SSM and VAST
ogpU is a hexomer and acts as a monomer and makes a polymer of six units
a)just shows accumulation of datathe more trials the more they should fit (if it doesnt fit its because of
protein motion skewing data slightly…it sampling many conformations)
b)shows one beta strand network (b1 and b2 are parellel to each other, a couple helices). When you search
the motif in the database you get the shapes shown under c
c)Nature likes the general shape of the protein structure?
Virus have gpV for body or tunnel of the virus (tail protein), gpH determines its length (tells gpV when to stop)
If you look at enough structure you can get different rules…a protein folding language developing
Helix Packing
a helix presents certain aa at certain places (he drew a diagram)
20’ and 50’ for packing tubes
just appreciate the fact that secondary structures interact with other secondary structure in different ways
Helices have thisnotching log characteristic (like a log cabin)
odone by having two glyceins
Coiled Coil (red and blue pic…rest were skipped)
coiled coil have some flexibility to them that are actually stable structures
otwo forms: antiparallel and parallel
Binary Coiled Coils
going around a helix there are 7 positions you have to consider and there are certain preferences of amino acid for each
point
If you have 2 helices close together you have hydrophobic reaction at the interface and that forms thenothch
You have ionic and Van der waals interactions to make a very stable structure
You can even form ahelix of helices”
Transcription factors COied Coil Complex
coiled complex are found in nature
fos/jun makes the particular motifleucine zipper that interacts with the major grooves in DNA (interactions
composed mostly of ionic forces)
MAIN POINT: SNARE COILED COIL PROTEINS
three different SNARE PROTEINS
3
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Description
Proteomics ldserver.bio.yorku.ca/biol4030 The Science of Proteomics Proteomics is the study of protein structure and function at a large scale The name is derived from genomics (the study of genomes) Started in 1997 SNPS differences are extrememly old and can be used to look at migration patterns. Genomics looks at whats different among people proteome changes between cells and tissues unlike DNA so studying it gets even more difficult Protein called Notch, which makes a B-line for nucleus Mass spectrometry is the main method of study to examine proteins mRNA a recent study showed that amount of mRNA in a cell does not reflect the amount of protein being made interestingly enough Post-translational modifications simple phosphorylation: very good way of modifying protein activity ~2% of our proteome encodes kinases (~500 proteins) serine, threonine and tyrosine are commonly phosphorylated o phosphotyrosine: SH2 domain extremely powerful signal because it calls upon other protein to cause chain reactions ST1571 aka GLEEVEC: drug thats a hybrid protein. Works on domains of protein Bcr-Abl which is a tyrosine kinase o Expensive drug that REALLY works for cancers like leukemia (covered in Canada) Platforms for Proteomics and Functional Genomics figure shows how complex proteomics is topics prof will cover: o mass spectrometry o GFP + FRET fluorescence o Protein Arrays o Chemical Arrays o Antibody Arrays HERCEPTIN: drug that works on receptor kinases Botulism toxin payload + Antibody Array Based Proteomics FRET (fluorescence resonance energy transfer): two fluorescently tagged molecules/proteins come together, detect by shining light on one molecule which emits a certain wavelenth which is absorbed by the protein nearby which then emits a different wavelength How to tag a protein: GO after an animo acid that has a specific chemical reactivity. A popular method is looking at cysteine which is rare on the surface on a protein. o Thiol groups: make disulfide bonds + o Amino groups (NH ):3 o Lysine: Structural Proteomics X-ray crystollagraphy and NMR spectroscopy are the two main methods o RIKEN is a company in Japan that has a factory that just find structure of proteins Informatics Clinical Proteomics NMR of urine can have a thousand peaks but each persons pattern is different? Each peak ofcourse corresponds to a certain protein or compound but theyre only interested in the pattern Even if your sick, knowing your protein complement is important ex. Your doctor can change your prescription or therapy based on it 1 www.notesolution.com Lecture 2 September 20, 2010 Levels of Protein Structure Primary: just the sequence of the protein Secondary: alpha helices (right-handed) and beta strands Teritary: global fold of protein Quatenary: bunch of proteins together Amino Acids generally two classes: hydrophobic, hydrophilic o aliphatic o aromatic alpha carbon contains R-group o R = H: glycerin o R = methyl: alanine etc Substition Chart shows what can be tolerated Its more difficult to make a substitution for an interior amino acid than for an exterior. In general assume that when you replace an a.a. itll be replaced by an a.a within its group eg. Aliphatic, hyrdrophobic for hydrophobic To make or break peptide bond just add or substract water o Not only are the planars flat but they have diploes as well Torsion Angles: depending on which side of the Calpha youre at. o Protein can be expressed simply as a table of phi and psy Ramachandran Map what are the allowable angles in a protein? He discovered themcertain angles arent allowed, in fact most arent only certain angles shown in red dots, red brown is more common and brown is slightly common? Grey is forbidden Profs Work triangles are glyceins and assumes a lot more conformation so it can go almost anywhere on the map Side Chain Torsion Angles again you dont seeevery angle, steric repulsion (where atoms bump into each other). 60, 180 and 300 degrees are the most favourable .especially for the big buly amino acids like phe follow those angles click the Torsion angle dynamics: much more efficientnot sure why Weak Forces help protein fold and are broken easily If you take a sequnces of a protein and let it fold, its important in the study of diseases like Mad Cow. Some times you have a good form of a protein and sometimes it forms a bad form which serves as a nucleus to turn the good proteins to bad ones. when proteins change structure they tend to stick together in odered fashion (oligermize) likein alzheimers. Aggregates of protein can kill proteins around them. proteins are always vibrating and are not static as shown in many pictures main thing in proteins: slow motions in terms of millisecond to microsecond time scale, movements include loops moving back and forth, protein looks like its breathing protein folding can happen in less than a second, (tenths of a second being the max) The Alpha Helix hydrogen bonds play big role, they help stabilize the structure I dont get the deal with i and i+4 and something about affecting the width of the protein Beta Strands The Beta Turn two H-bonds are formed in this turn only come in certain shapes and show a.a preference for positions 2 and 3 Lecture 3 September 22, 2010 2 www.notesolution.com Play game to get 10% of your final! The Beta Turn Hs have to be 1.8 to 2.0 Angstroms to bond so adjacent Hs wont bond as theyre too far Amino Acid Preference for Secondary Structures Computer servers and algorihms help predict alpha helices and beta strands in a given protein sequence Certain amino acids have a preference to be in a certain structure (add chart from slides) o Some prefer alpha helices some prefer beta strands o 1.0 is no preference o www.predictprotein.org a portal to software that allow you to predict protein structure Richardson Diagram shows two pics of 4 beta strand proteins and three hairpins only shows protein backbone and doesnt include protein side-chains Topology Cartoons compares a given protein to all other proteins in the database triangle is a beta strand etc. instead of having to search through database you can search with the motif of the simple shapes Prof worked on gpU (neck protein between capsid and tail). The sequence of this strange protein is so unique it shows no similarity to any other species. It has no homologue! DALI, SSM and VAST o gpU is a hexomer and acts as a monomer and makes a polymer of six units a) just shows accumulation of datathe more trials the more they should fit (if it doesnt fit its because of protein motion skewing data slightlyit sampling many conformations) b) shows one beta strand network (b1 and b2 are parellel to each other, a couple helices). When you search the motif in the database you get the shapes shown under c c) Nature likes the general shape of the protein structure? Virus have gpV for body or tunnel of the virus (tail protein), gpH determines its length (tells gpV when to stop) If you look at enough structure you can get different rulesa protein folding language developing Helix Packing a helix presents certain aa at certain places (he drew a diagram) 20 and 50 for packing tubes just appreciate the fact that secondary structures interact with other secondary structure in different ways Helices have this notching log characteristic (like a log cabin) o done by having two glyceins Coiled Coil (red and blue picrest were skipped) coiled coil have some flexibility to them that are actually stable structures o two forms: antiparallel and parallel Binary Coiled Coils going around a helix there are 7 positions you have to consider and there are certain preferences of amino acid for each point If you have 2 helices close together you have hydrophobic reaction at the interface and that forms the nothch You have ionic and Van der waals interactions to make a very stable structure You can even form a helix of helices Transcription factors COied Coil Complex coiled complex are found in nature fos/jun makes the particular motif leucine zipper that interacts with the major grooves in DNA (interactions composed mostly of ionic forces) MAIN POINT: SNARE COILED COIL PROTEINS three different SNARE PROTEINS 3 www.notesolution.com important infusing vesicles and membranes together at a certain point they snap and pull membranes apart illustrates that they have a function Greek Keys 4 beta strands lines up as shown and folded down you get a motif called a Greek Key some proteins use multiple greek keys and build on top of each other into more complex structures Crystall
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