DASAR-DASAR

STRUKTUR PROTEIN

Traditional Architecture

Wood, brick, nails, glass

Temperature, earthquakes

How many people?

Form
fits
function

Materials
Environmental Factors
Population Factors

How many doors and windows?

Portals

Spanish, Victorian,
1950's blocky science building

Motifs/Styles

Julia Morgan

Architect

Molecular Architecture

Amino acids,cofactors

Temperature, solubility

# partner proteins, # reactants

Passages forsubstratesand reactants

Conserved domains or protein folds

Evolution

Tingkatan Struktur Protein

Struktur Primer= urutan asam

amino pada rantai protein

Anatomi asam amino

Asam amino Non-polar

Asam amino Polar, tak bermuatan

Asam amino Bermuatan Negatif

Asam amino bermuatan Positif

Gugus R bermuatan dan polar

cenderung memetakan permukaan
protein

Gugus R Non-polar cenderung

terbenam pada sumbu protein
Myoglobin
Blue = non-polar
R-group
Red = Heme

Beberapa gugus R dapat diionisasi

The HendersonHasselbalch
equation allows
calculation of the
ratio of a weak acid
and its conjugate
base at any pH

Nilai-nilai pK protein
ApproximatepK'
Group
InaTypicalProtein
carboxyl(free)
3(Cterminalonly)
carboxyl(Asp)
4
carboxyl(Glu)
4
imidazole(His)
6
sulfhydryl(Cys)
8
1amino(free)
8(Nterminalonly)
amino(Lys)
10
hydroxyl(Tyr)
10
2amino(Pro)(free) 9(Nterminalonly)
guanido(Arg)
12

Beberapa gugus R dapat dimodifikasi

Asam Amino dihubungkan melalui

ikatan Peptida
- -carboxyl dari suatu asam amino dihubungkan
dengan -amino dari asam amino kedua (dengan
mengeluarkan air)
- Hanya gugus -carboxyl dan gugus -amino yang
digunakan, bukan gugus carboxyl atau gugus amino
R

Pembentukan ikatan peptida

Ikatan peptida planar

This resonance
restricts the number
of conformations in
proteins -- main
chain rotations are
restricted to and

Urutan Primer, petunjuk penting

tentang suatu protein
Evolution conserves amino acids that are important to protein
structure and function across species. Sequence comparison
of multiple homologs of a particular protein reveals highly
conserved regions that are important for function.
Clusters of conserved residues are called motifs -- motifs
carry out a particular function or form a particular structure that
is important for the conserved protein.
motif

DnaGE.coli
small hydrophobic
DnaGS.typ
large hydrophobic
DnaGB.subt
polar
gp4T3
positive charge
gp4
negative
T7
charge

...EPNRLLVVEGYMDVVAL...
...EPQRLLVVEGYMDVVAL...
...KQERAVLFEGFADVYTA...
...GGKKIVVTEGEIDMLTV...
...GGKKIVVTEGEIDALTV...
: : : :

* *

Struktur Sekunder = pelipatan lokal

residu menjadi pola regular

-helix
In the -helix, the carbonyl
oxygen of residue i forms a
hydrogen bond with the
amide of residue i+4.
Although each hydrogen
bond is relatively weak in
isolation, the sum of the
hydrogen bonds in a helix
makes it quite stable.
The propensity of a peptide
for forming an -helix also
depends on its sequence.

-sheet
In a -sheet, carbonyl
oxygens and amides form
hydrogen bonds.
These secondary
structures can be either
antiparallel (as shown) or
parallel and need not be
planar (as shown) but can be
twisted.
The propensity of a peptide
for forming -sheet also
depends on its sequence.

 turns

-turns allow the protein backbone to make abrupt turns.

Again, the propensity of a peptide for forming -turns depends
on its sequence.

Residu mana yang umum bagi

unsur -helix, -sheet,dan -turn?

Ramachandran plot menunjukkan sudut

dan untuk struktur sekunder

Struktur Tersier = pelipatan global

rantai protein

Struktur Tersier agak bervariasi

Struktur Quaterner = Penyusunan

protein dengan keteraturan tinggi

Contoh struktur tersier dan

quaterner - 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.

Contoh struktur quaterner yang lain

Tetramer

SSB
Allows coordinated
DNA binding

Hexamer

Filament

DNA helicase
Recombinase
Allows coordinated DNA binding
Allows complete
and ATP hydrolysis
coverage of an
extended molecule

Kelas-kelas protein
Definisi Fungsional :
Enzim:
Mempercepat reaksi-reaksi biokimia
Struktural:

Membentuk struktur biologis

Transport:

Membawa zat-zat yang penting secara biokimia

Pertahanan:

Melindungi tubuh dari serangan benda asing

Definisi Struktural :
Globular:
Pelipatan kompleks, struktur tersier yang tidak teratur
Fibrous:

Pelipatan sederhana, memanjang protein struktural

Definisi Lokalisasi selular:

Membran:
Bersentuhan langsung dengan membran; umumnya tidak
larut dalam air
Dapat larut:

Larut dalam air; dapat di mana saja dalam sel.

TERIMA KASIH