Asam Amino dan Protein

 Protein adaalah makromolekul yang terdapat

dalam sel (50% dr berat sel)
 Dalam satu sel terdapat ratusan jenis protein
 Protein mempunyai peranan biologis karena
protein merupakan instrument yang
mengekspresikan informasi genetik
 Protein dibangun dari rangkaian dasar dari 20
jenis asam amino yang berikatan kovalen dalam
berbagi kombinasi dan urutan menghasilkan
beberapa sifat protein dan kombinasi yang
berbeda
 Seperti enzim, hormon, lensa protein pada mata,
bulu ayam, kulit kura kura, protein susu bergizi
dll
Asam Amino

 merupakan unit penyusun

protein
 Struktur:
satu atom C sentral yang
mengikat secara kovalent:
 gugus amino,
R
 gugus karboksil,
I
 satu atom H dan

 rantai samping (gugus R)

H2N—C —COOH
I
H
• Gugus R  rantai samping yang berbeda-beda pada
setiap jenis asam amino
• Gugus R yang berbeda-beda tersebut menentukan:
-. Struktur
-. Ukuran
-. Muatan elektrik
-. Sifat kelarutan di dalam air
Asam amino standar
 Asam amino yang menyusun
protein organisme ada 20
macam disebut sebagai asam
amino standar
 Diketahui asam amino ke 21
disebut selenosistein (jarang
ditemukan) Terdapat di
beberapa enzim seperti
gluthatione peroxidase
 Selenenosistein mempy kode
genetik: UGA  biasa utk stop
kodon  tjd pd mRNA dgn
struktur 2nd yg banyak.
Asam Amino Essensial

 10 asam amino yang tidak dapat disintesis

oleh tubuh yi : arg, his, ile, leu, lys, met,
phe, thr, trp, val
 Must obtain from the diet
 All in diary products
 1 or more missing in grains
and vegetables

8
Sifat asam-basa dari asam Amino

 Ionisasi dari –NH2 dan gugus –COOH

 Zwitterion mempunyai muatan (+) & (–)

+
NH2–CH2–COOH H3N–CH2–COO–
glisin Zwitterion dari glisin

9
pH dan ionisasi

H+ OH–

+ +
H3N–CH2–COOH H3N–CH2–COO– H2N–CH2–
COO–
Positive ion zwitterion Negative ion
Low pH neutral pH High pH

10
Sifat Amfoter AA
R CH COOH
NH2

R CH COO- R CH COO-
- -
R CH COOH +OH +OH

NH3+ +H+ NH3+ +H+ NH2

pH<pI pH=pI pH>pI

kation amfoteri anion

Perhatikan struktur kedua asam
amino berikut
CH3 CH3
+
H3N–CH–COOH H2N–CH2–COO–
(1) (2)
Perhatikan kedua struktur tersebut
A. Alanine bersifat basa ?
B. Alanine bersifat asam ?

12
Jawab ; AA2

CH3 CH3
+
H3N–CH–COOH H2N–CH2–COO–
(1) (2)

A. (2) Alanine in base.

B. (1) Alanine in acid.

13
Ikatan Peptida

ikatan amid terbentuk oleh gugus –COOH dari suatu

asam amino dan –NH2 dari asam amino linnya
O CH3
+ || + |
NH3–CH2–COH + H3N–CH–COO–
O CH3
+ || |
NH3–CH2–C – N–CH–COO–
| ikatan peptida
H
14
Peptida

 Amino acids linked by amide (peptide) bonds

Gly Lys Phe Arg Ser

H2N- -
COOH
end Peptide bonds end

Glisil-lisil-fenilalanil-arginil-serin
Chemistry of peptide bond formation
Ikatan peptida planar
Soal AA3

Apakah mungkin tripeptida terbentuk dari

suatu leusin, glisin dan alanin ?

Tripeptides possible from one each of

leucine, glycine, and alanine
Leu-Gly-Ala
Leu-Ala-Gly
Ala-Leu-Gly
Ala-Gly-Leu
Gly-Ala-Leu
Gly-Leu-Ala
 Contoh soal; AA4

Tuliskan nama tetra peptida berikut :

CH3
CH3 S
CH CH3 SH CH2
CH3 O CH O CH2 O CH2 O
-
H3N CH C N CH C N CH C N CH C O
H H H

19
Solution AA4

CH3
CH3 S
CH CH3 SH CH2
CH3 O CH O CH2 O CH2 O
-
H3N CH C N CH C N CH C N CH C O H
H H H

Ala-Leu-Cys-Metionin

20
Klasifikasi Asam amino
 Diklasifikasikan berdasar gugus R (rantai samping)
 Biasanya sifat-sifat seperti: hidrofobik/hidrofilik, polar/non
polar, ada/tidaknya gugus terionisasi

AROMATIK
NON
POLAR POLAR
Asam amino

BASIC (+) ACIDIC (-)

Asam amino non polar
 Memiliki gugus R alifatik
 Glisin, alanin, valin, leusin, isoleusin dan prolin
 Bersifat hidrofobik. Semakin hidrofobik suatu a.a spt
Ile (I)  biasa terdapat di bagian dlm protein.
 Prolin berbeda dgn a.a  siklis. Tapi mempunyai
byk kesamaan sifat dgn kelompok alifatis ini.
 Umum terdapat pada protein yang berinteraksi
dengan lipid
Asam amino polar
 Memiliki gugus R yang tidak bermuatan
 Serin , threonin, sistein, metionin, asparagin,
glutamin
 Bersifat hidrofilik  mudah larut dalam air
 Cenderung terdapat di bagian luar protein
 Sistein berbeda dgn yg lain, karena ggs R
terionisasi pada pH tinggi (pH = 8.3) sehingga dapat
mengalami oksidasi dengan sistein membentuk
ikatan disulfide
 (-S-S-)  sistin (tdk tmsk dlm a.a. standar karena
selalu tjd dari 2 buah molekul sistein dan tidak
dikode oleh DNA)
Basic AAs
 R groups have one -NH2.
 R groups are positively charged at
neutral pH (=7.0).
 AAs are highly hydrophilic.
Acidic AAs

 R groups have –COOH.

 R groups are negatively charged at
physiological pH (=7.4).
 AAs are soluble in H2O.
Aspartic acid glutamic acid
(Asp or D) (Glu or E)
Asam amino dengan gugus R bermuatan positif
 Lisin, arginin, dan histidin
 Mempunyai gugus yg bsft basa pd rantai
sampingnya
 Bersifat polar  terletak di permukaan protein dapat
mengikat air.
 Histidin mempunyai muatan mendekati netral (pd
gugus imidazol) dibanding
 lisin  gugus amino
 arginin  gugus guanidino
 Krn histidin dpt terionisasi pada pH mendekati pH
fisioligis  sering berperan dlm reaksi ensimatis yg
melibatkan pertukaran proton
Asam amino dengan gugus R
bermuatan negatif
 Aspartat dan glutamat
 Mempunyai gugus karboksil pada rantai
sampingnya  bermuatan (-) / acid pada pH 7
Asam amino non standar
 Merupakan asam amino
diluar 20 mcm as. Amino
standar
 Terjadi karena modifikasi
yang terjadi setelah suatu
asam amino standar
menjadi protein.
 Kurang lebih 300 asam
amino non standar modifikasi serin yang
dijumpai pada sel mengalami fosforilasi
oleh protein kinase
• modifikasi prolin  dlm proses
modifikasi posttranslasi, oleh
prokolagen prolin hidroksilase.

• Ditemukan pada kolagen untuk

menstabilkan struktur

• Dari modifikasi Glu oleh vit K.

•  karboksi glutamat mampu
mengikat Ca  penting utk
penjendalan darah.
• Ditemukan pd protein protombin
• Modifikasi lisin. Terdapat di kolagen dan miosin (protein
kontraksi pd otot) dan berperan untuk sisi terikatnya
polisakarida
• Beberapa ditemukan asam amino nonstandar yang tidak
menyusun protein  merupakan senyawa antara
metabolisme (biosintesis arginin dan urea)
 20 asam amino sebagian besar disintesis
dari intermediet siklus asam sitrat atau asam
piruvat
Asam amino yang berhubungan
dengan intermediet siklus TCA
Metabolisme Glu, Asp, Ala, Gln, Asn
 Biosintesis dan degradasi menggunakan
transaminasi NH , NADPH, Glu dehidr-
3
genase NH ,ATP, Gln sintetase
3
 Ala, peruvat
-ketoglutarat
transminase glutamat glutamin

NH3
Gln, NADPH, Glu sintase H2O, glutaminase

NH3, NADPH, Asn sintetase -ketoglutarat, transaminase

asparagin aspartat
oksaloasetat
glutamin

NH3 H2O, asparatase

H2O, asparaginase fumarat + NH3
Arginin
dan Prolin
 Met,
 Thr,
 Lys
Asam amino yang berhubungan
dengan piruvat
Val, Isoleu,
Leu
Asam amino dari PG
dan asam amino dengan
unsur S

 Ser
 Gly
Cys
 Di mamalia metionin
merupakan sumber
sistein
Asam amino
aromatis (Jalur
asam shikimat)
Triptofan
Phe dan Tyr
Asam amino dari Glukosa 6P (His)
Protein
 Molekul yg sangat vital untuk
organisme  terdapt di semua sel
 Polimer  disusun oleh 20 mcm
asam amino standar
 Rantai asam amino dihubungkan dg
iktn kovalen yg spesifik
 Struktur & fungsi ditentukan oleh
kombinasi, jumlah dan urutan asam
amino
 Sifat fisik dan kimiawi  dipengaruhi
oleh asam amino penyusunnya
Fungsi Protein

 Reaksi kimia  enzymes

 Immune system  antibodies
 Mechanical structure  tendons
 Generation of force  muscles
 Nerve conduction  ion channels
 Vision  eye lens
 . . . and much more!
Proteins diklasifikasikan dalam 3 group:

A. Globular protein
 Polypeptide folded into globular shape
 Contain more than 1 type of secondary structure

Soluble in water

B. Fibrous proteins
 Polypeptide chain arranged in sheets or strands
 Contain single type of secondary structure
 Insoluble in water

C. Membrane proteins
• Later….
Structur primer dari insulin

Two peptides of 21 and 30 AAs

Two inter-chain -S-S- bonds
One intra-chain -S-S- bond
Primary structure = order of amino
acids in the protein chain
Secondary structure = local folding
of residues into regular patterns
Tertiary structure = global folding of
a protein chain
Tertiary structures are quite varied
Quaternary structure = Higher-order
assembly of proteins
 Example of tertiary and quaternary
structure - PriB homodimer

QuickTime™ and a
Cinepak decompressor
are needed to see this picture.

Example is PriB replication protein solved at UW: Lopper, Holton, and Keck
(2004) Structure 12, 1967-75.
Example of tertiary and quaternary
structure - Sir1/Orc1 heterodimer

Example is Sir1/Orc1 complex solved at UW: Hou, Bernstein, Fox, and Keck
(2005) Proc. Natl. Acad. Sci. 102, 8489-94.
 Examples of other quaternary
structures
Tetramer Hexamer Filament

SSB DNA helicase Recombinase

Allows coordinated Allows coordinated DNA binding Allows complete
DNA binding and ATP hydrolysis coverage of an
extended molecule
 Classes of proteins
Functional definition:
Enzymes: Accelerate biochemical reactions

Structural: Form biological structures

Transport: Carry biochemically important substances

Defense: Protect the body from foreign invaders

Structural definition:
Globular: Complex folds, irregularly shaped tertiary structures

Fibrous: Extended, simple folds -- generally structural proteins

Cellular localization definition:

Membrane: In direct physical contact with a membrane; generally
water insoluble.

Soluble: Water soluble; can be anywhere in the cell.

Protein crystals

X-ray crystallography can

be used to get structure,
if you have crystals.

Protein structure
 NMR can be used to get structure,
if your protein is relatively small (<30kD)

• Solution structure
• No need for
protein crystals
•Sometimes
domains of larger
proteins can be
studied
Page 243

The NMR structure of a 64-residue polypeptide comprising

the Src protein SH3 domain
Tertiary structure of sperm whale myoglobin

8  helix
Some bends which are  turns

From Lehninger
Principles of Biochemistry
Tertiary structure of sperm whale myoglobin

Hydophobic
residues
(buried)

From Lehninger
Principles of Biochemistry
Table 6-2. Hydropathy Scale for Amino Acid Side Chains

Side Hydropathy Hydrophobic forces are a major

Chain influence in causing proteins to fold into
their native conformations.
Ile 4.5
Val 4.2
Leu 3.8
Phe 2.8
Cys 2.5
Met 1.9
Ala 1.8
Gly -0.4
Thr -0.7
Ser -0.8
Trp -0.9
Tyr -1.3
Pro -1.6
His -3.2
Glu -3.5
Gln -3.5
Asp -3.5
Asn -3.5
Lys -3.9
Arg -4.5

Source: Kyte, J. and Doolittle, R.F.,

J. Mol. Biol. 157, 110 (1982).
The greater the hydropathy, the
more likely that the residue will be
buried inside the folded protein.
Polypeptides with more than a few
hundred amino acids tend to fold
into two or more stable globular
units called domains From Lehninger
Principles of Biochemistry
Fibrous Proteins

From Lehninger
Principles of Biochemistry
A hair is an array of many -keratin filaments

From Lehninger
Principles of Biochemistry
 Structure of hair
(right-handed  helix)
Higher order structures

From Lehninger
Principles of Biochemistry
Collagen has a distinct tertiary and quaternary structure

• Collagen is
35% Gly
11% Ala
21% Pro and Hyp
(Hyp is 4-hydroxyproline)

•Repeating tripeptide sequence

Gly-X-Y, where X is often Pro and
Y is often Hyp

•Unique secondary structure

distinct from  helix

•Adopts a left-handed helical

structure with three residues per
turn

•Forms a three-stranded
 The amino acid sequence at the C-terminal end of the triple
helical region of the bovine 1(I) collagen chain
Page 234
X-Ray structure of the triple helical collagen
model peptide (Pro-Hyp-Gly)10 in which the
fifth Gly is replaced by Ala

(a) Ball and

stick
representation

(b) View
along
helix axis
Structure of silk Each chain of fibroin is made
Silk or spider web up of multiple repeats of the
sequence
made up of the (Gly-Ser-Gly-Ala-Gly-Ala)n.
protein fibroin

Small R
groups
allow close
packing

Layers of
antiparallel 
sheet
Reductive denaturation & oxidative renaturation of RNase A

Proteins can be
reversibly
denatured
Renaturation – The
return of 3D structure after
it has been removed by
heat or chemicals.

Christian Anfinsen showed

that protein polypeptides
contain all the information
needed to return to their
native 3D structure.
Hypothetical
protein folding
pathway
Much of secondary
structure is present
No tertiary structure
-- Molten globule

Hydrophobic collapsed
state is known as
molten globule

Linear pathway
for folding a two-
domain protein
 Hierarchical organization of globular proteins
Page 279
A simulated protein folding pathway

Short stretches
of secondary
Unfolded
structure
Has many possible
conformations

Folded
Native conformation
 PROBLEM

If proteins fold by trial and error method to get the native structure:

For a 100 amino acid residue long protein,

it will take 1087 seconds--- too long!

t h e i r
l d i n to
t h e y fo l e s s
e a l it y t i o n i n
In r f o rm a
e c o n d s
na t i v se c o n
a f e w
t h a n
 Free-energy funnel description of
the protein folding pathway
 Folding funnels

dealized funnel landscape Rugged energy surface

Misfolded Proteins in Neurodegenerative Diseases

Taylor JP, Hardy J, Fischbeck KH. (2002)

 Pictured below are two conformations of the prion protein

PrPSC is a very stable

isoform of the prion protein
and is associated with the
mad-cow disease

PrPSC has high

thermodynamic
stability and is highly
resistant to heat
denaturation (it can
be heated to ashing
temperatures and it
Normal cellular conformer still maintains its
structure enough to
remain pathogenic).
Folding Accesory Proteins: C. Molecular chaperones

A. Protein disulfide isomerases PDI

B. Proline isomerases

QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
 Reaction cycle of the GroEL/ES chaperonin system in
protein folding
Page 296
Molecular dynamics of
Myoglobin
Several snapshots of the
protein calculated at
intervals of 5 x 10-12 s are
superimposed.

Proteins have some

conformational flexibility
that results in small
molecular motions

Backbone is blue, the heme group is yellow, and the His

side chain linking the heme to the protein is orange.
Eksplorasi Protein
Isolation dan purification

 Homogenization and centrifugation

 Dialysis
 Precipitation
 Chromatography
 Electrophoresis
§6.1.a Homogenization

 Rupture the plasma membrane to release

the intracellular components into the
buffered solution

 Sonication, French pressure, mechanical

grinding,
 Chemical reagents, lysozymes
 Centrifugation
 Because of the differences in size and
shape, proteins will sediment gradually
under the centrifugal force until the
sedimentation force and buoyant force
reach the balance.
 The sedimentation behavior is described in
sedimentation coefficient (S) which is
proportional to the molecular weight.
Differential centrifugation
Differential centrifugation
homogenate

600 g，3 min

Pellet supernatant
(nuclei)
6,000 g，8 min

Pellet supernatant
(mitochondria, chloroplasts,
lysosomes, peroxisomes) 40,000 g，30 min

Pellet
supernatant
(plasma membrane,
fragments of Golgi and ER)
100,000 g，90 min

Pellet supernatant
(ribosomal subunits) (cytosol)
Rate-zone centrifugation
§6.1.b Dialysis
 Proteins, as macromolecules, cannot pass
through the semipermeable membrane
containing pores of smaller than protein
dimension, thus large proteins and small
molecules can be separated.
 Dialysis can be used for protein
purification, desalting, and condensation.
§6.1.c Precipitation

 Adding a large quantity of salts, such as

Ammonia sulfate, into the protein solution will
neutralize the surface charges and the
destruct the hydration shell of proteins,
causing them to precipitate.
 Acetone has the similar function.
 An efficient way to concentrate proteins.
6.1.d Chromatography

When a protein solution (called as mobile

phase) passes through a stationary phase,
proteins can interact with the stationary
phase due to the differences in size, charge,
and affinity, making the different proteins flow
through the stationary phase at different
speeds.
 Elution
buffer
Protein mixture

Solid
phase
capable
of
reacting
with
proteins
to be
separated

Protein 1 Protein 2
OD280nm

Elution volume
Type of chromatography

 Ion exchange: based on the ionic

interactions
 Affinity: based on the binding strengths
 Filtration: based on the protein sizes
 Hydrophobicity: based on the hydrophobic
forces
Ion-exchange chromatography
More negatively charged
proteins bind to the solid
phase tightly, and stronger
elution buffer is needed to
elute them out the column

＝ －
＝ －
－ ＋ ＋
＝
＋ ＋ ＝ ＋ ＋
＝ － ＝
＋ ＋ ＝ ＋ ＋
＝ －
＋ ＋ ＋ ＋
＝ ＝
＋ ＋
＝
－ ＝
－
－
－
－ Ionic exchange
column with
Less negatively charged positive charge
proteins bind to the solid
phase loosely, and weak
elution buffer can be used to
elute them out the column
Affinity chromatography
Exchange column
with the ligands
for binding
special proteins

Proteins having Proteins having

weak binding strong binding
affinity with the affinity with the
ligads ligads
Gel filtration
Proteins are separated based on their sizes
and shapes. The stationary phase is of semi-
uniform pores. When the protein solution
flows through porous beads, smaller proteins
can enter the pores and stay there for a
longer period, but larger proteins flow directly
through the column, resulting in the
separation of proteins. It is also called
molecular sieve or size exclusion.
Gel filtration
Small proteins can
enter the porous
beads, and have a
longer stationary
time

Porous beads
Large proteins that
allow the small
are unable to enter
proteins enter
the porous beads will
pass by and flow out
directly
§6.2 Electrophoresis Analysis
Used mainly for determination of
proteins

SDS-PAGE = Sodium dodecyl sulfate

polyacrylamide gel electrophoresis
IEF = isoelectric focusing electrophoresis
2D = two dimensional electrophoresis
§6.2.a SDS-PAGE

Sodium dodecyl sulfate is a kind of

detergent to denature the proteins
Anionic SDS bind to protein in the ratio of 1
SDS per 2 AAs.
The protein-SDS complex is roughly
charged proportional to the mass.
The smaller the protein, the faster the
moving speed in the electric field.
 The gel polymer material for protein
discrimination is composed of
methylenebisacrylamide and acrylamide.
 The pore size can be controlled by
changing the concentration of cross-linking
reagent.
 The gel with different concentration of
cross-linking reagent can be used for
different size proteins.
§ 6.2.b Isoelectric focusing

Depend upon the electric properties of

proteins
The charged proteins, either positively or
negatively, will migrate in the electric
field.
The proteins having net zero charges stop
moving in the electric field.
 Principle of IFE

Stable pH Proteins with

gradient different pI
gel medium

＋－－
－ －
＋－－
－ － pH 7.0 pH 7.0
Proteins of
－ － － ＋
－ －
large pI show
zero net
changes
＋－＋
－ －
＋ ＋
－

＋－＋
－ －
Proteins of
＋ ＋
－
small pI show
pH 3.0 pH 3.0 zero net
changes
§6.2.c 2D electrophoresis

 1st dimension: isoelectric focusing

electrophoresis
 2nd dimension: SDS-PAGE
 A high throughput approach to identify
proteins
§6.3 Composition and Sequence
 Composition
 Determination of terminal residues
 Edman degradation
 Sequencing strategy
 Mass spectroscopy
 Deduction form DNA sequences
§6.3.a Composition analysis

 Hydrolyzing the purified protein samples in

an evacuated and sealed tube by heating it
in 6 M HCl at 100°C
 Analyzing the AA components using
chromatography
 (Alaa, Argb, Asnc, Aspd, … Valz)
Chromatography of AA
§6.3.b Terminal residues

 The amino-terminal residue reacts with

fluorodinitrobenzene or dabsyl chloride to
form a stable product which can be
analyzed using chromatography.
 The carboxyl-terminal residue can react
with fluorodinitrobenzene or dabsyl
chloride to form a stable product.
N-terminal reaction
 §6.3.c Edman degradation
1. Labeling the N-terminal residue with a
fluorophore.
2. Cleaving the labeled residue without
breaking the peptide bonds of the rest part
of the peptide.
3. Determining the N-terminal residue with
chromatography.
4. Repeating the same procedure to the rest
peptide until the whole sequence is
determined.
First cycle of Edman degradation
H O H O
N C S H2N C C N C C

R1 H R2
phenyl
isothiocyanate labeling

H S H H O H O

N C N C C N C C
R1 H R2

releasing

S H O H O

N C H2N C C N C C

R2 H R3
C N H
O
C

H R1
Edman degradation
 §6.3.d Overlapping approach
1. Cleaving a protein into small peptides by
chemical or enzymatic methods, and purify
these peptides.
2. Sequencing each peptide using Edman
degradation approach.
3. Overlapping peptide fragments to arrange
them in a right order, and accomplishing the
AA sequencing.
Cleavage of peptides

Cleavage reagent Cleavage site

Cyanogen bromide Met (C)

O-Iodosobenzoate Try (C)

Hydroxylamine Asp-Gly

Trypsin Lys and Arg (C)

Clostripain Arg (C)

Staphylococcal protease Asp and Glu (C)

Thrombin Arg (C)

 Overlapping approach
1. Tryptic cleavage generates two peptides
Gly-Phe-Val-Glu-Arg, Val-Phe-Asp-Lys

2. Chymotryptic cleavage generates three

peptides
Val-Phe, Val-Glu-Arg, Asp-Lys-Gly-Phe

3. Overlapping the sequenced peptides

 Tryptic pe ptide Tryptic pe ptide

Va l - P he - As p - Lys - Gly - P he - Va l - Glu - Arg

Chymotryptic pe ptide
§6.3.e Mass spectroscopy

 Newly developed approach applied to

biology and medicine areas
 Revolutionized bioanalytical technique
 Offering a fast, high accuracy, and high
throughput determination for analyzing
peptides and proteins.
Matrix-aided ionization

1. Deposit samples
on a plate.
2. Introduce a beam
of laser.
3. Ionize samples.
4. Analyze ionized
molecules.
5. Determine the AA
sequence.
Fragmentation of peptide
xn+3
yn+3

xn+2
yn+2
xn+1
yn+1
O O O O O
—N—C—C —N—C—C—N—C—C —N—C—C —N—C—C
H Ri H Ri+1 H Ri+2 H Ri+3 H Ri+4
a i+1
bi+1

a i+2
bi+2

a i+3
bi+3
From MS to AA sequence
§6.3.f Deduction from DNA sequence
Isolate the genes encoding the protein

DNA sequencing

mRNA sequencing

Determine the AA sequence according to the 3-

letter genetic codons
§5.4 Structure Determination
 Circular dichroism spectroscopy
 X-ray crystallography
 Nuclear magnetic resonance spectroscopy
 Prediction based on the protein sequence
homology
 Computer simulation
 Section 7
Proteomics:
A New Frontier
Proteomics

a comprehensive knowledge
about all the proteins of a cell at a
specific given time.
Objectives
 Biological process
 The overall process toward which this
protein contributes
 Molecular function
 The biological activity the protein
accomplishes
 Cellular component
 The location of protein activity
Proteomics approaches

 Separation
 Sequence determination
 3D-structure
 Functionality
 Expression regulation
 Post-translation modification
Protein chips
 Incorrect conformation and diseases
 Proteins synthesis, post-translation
modification and maturation is a very
complex process.
 Only the correct folding process leads to the
correct conformation and the proper functions
of proteins.
 Incorrect folding process may lead to
diseases.
 Structures of Cytochrome C

Rice Yeast Bacterium

Phylogenetic tree of cytochrome C
Human,
Chimpanzee
Horse, Macaque
Debaryomyces Zebra
Candida Monkey Penguin
kloeckeri
krusei Rabbit
Pig, cow, sheep Turkey, chicken
Dog Kangaroo Duck
Pigeon
Gray whale Turtle
Tuna
Shark Bullfrog Alligator
Baker’s
Carp Bonito Bacteria
yeast
Silk moth Fruit fly
Pacific
Neurospora Hornworm Screwworm lamprey
crassa moth fly

Mung-
bean
Pumpkin
Wheat

Tomato

Sunflower
Homology comparison