modul - protein structure

7/30/2019 Modul - Protein Structure

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PROTEIN ARCHITECTURE

www.elearning.unsyiah.ac.id

Biokimia I

pw: biokimia
http://www.elearning.unsyiah.ac.id/http://www.elearning.unsyiah.ac.id/


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OBJECTIVE

You should be able to explain protein

architecture and how it generally folds.


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CONTENT

Primary structure of protein

Secondary structure of protein

Tertiary structure of protein Quaternary structure of protein

Introduction to protein folding


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PROTEIN PRIMARY STRUCTURE

Only peptide bonds to form polypeptide chain

All protein have similar backbone Primary Structure


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PROTEIN SECONDARY STRUCTURE

Formed through the formation of hydrogen bond between

C=O carbonyl and NH amide of the polypeptide chain.

Protein secondary structure:

Helix (, 310, ) -sheet (paralel dan anti paralel)

Benddan Loop

N H O = C


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Peptide bond resonance

C=O partially negative

NH partially positive

Most of peptide bonds are in trans configuration.


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Resonance arranges peptide bonds in planar

form


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Phi () = rotation angle at N-C bond

Psi () = rotation angle at CC bond


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-helix

About one third of protein

secondary structure is in

the form of -helix.

Each amide hydrogen andcarbonyl oxygen form

hydrogen bond, except at

N1, N2, N3, C3, C2 dan C1


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-helix

SIDE VIEW


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-helix

TOP VIEW


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310-helix dan -helix


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- sheets

NH-CO hydrogen bonds between close

polypeptide chains.


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-sheets


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- sheets

Example: silk fibroin composed mainly by Gly

and Ala.


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Bends dan Loops

Bend 4 residues

Conecting secondary structures (-helix, -

sheet).

Loop 6-16 residues

Continuous segment of a polypeptide chain

Bend dan loop function as connectors.


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Hairpin Loop

Hairpin loops connect anti paralel -strand structures.

Type I is 2-3 X more likely than type II.


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Amino acid preferences in secondary

structures


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Ramachandran Plot


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Parameters of protein secondary structures


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Secondary structural motif

Secondary structures form supersecondary

structure (motif)

Example:

motif-helix loop-helix

motif-sheet loop-sheet

motif-sheet loop-helix - -sheet


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Secondary structural motif


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PROTEIN TERTIARY STRUCTURE

Formed trough intramolecular interactions of sidechains in the same polypeptide chain, giving a stable 3Dstructure:

Ionic bond (salt bridge) interaction betweenamino acids with + and - charges.

Hydrogen bond interaction between R groupsof polar amino acids.

Hidrofobik interaction interaction between Rgroups of non polar amino acids.

Disulfide bond interaction between Cys.


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PROTEIN TERTIARY STRUCTURE


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Tertiary structural motifAll


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Tertiary structural motifAll


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Tertiary structural motif+


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Tertiary structural motif/


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PROTEIN QUARTERNARY STRUCTURE

Formed trough intermolecular interactions of side

chains of different polypeptide chains or interaction

between tertiary structures:

Ionic bond (salt bridge)

Hydrogen bond

Hidrofobik interaction

Disulfida bond


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Example: 4

polipeptide chainwith 2prosthetic

group


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Proteins are synthesized as linear polymers

Ribosome


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But proteins fold into compact 3D shapes


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What determines fold? The Anfinsen paradigm

Anfinsen paradigm: the information required for correct folding of the protein is

contained within the amino acid sequence

Christian Anfinsen was awarded the Nobel Prize in 1972

Ribonuclease A


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Anfinsens Experiment

Refolding bovine pancreatic ribonuclease

Consist of 8 Cys (4 pairs of disulfide

bonds).

Native RNase + urea +mercaptoethanol = denaturation.

Reoxidation produces 105

possibilities of S-S pairs. Enzyme

inactive!

Dialisis (-Urea, -mercaptoethanol),

activity is back to normal.

AMINO ACID SEQUENCE DETERMINE THE 3D

STRUCTURE!


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The Levinthal paradox

Cyrus Levinthal tried to estimate how long it would take a protein to do

a random search of conformational space for the native fold.

Many proteins fold in seconds or less: how is this possible?

Imagine a 100-residue protein with three possible conformations per

residue. Thus, the number of possible folds = 3100 = 5 x 1047.

Let us assume that protein can explore new conformations at the same

rate that bonds can reorient (1013 structures/second).

Thus, the time to explore all of conformational space = 5 x 1047/1013 = 5

x 1034 seconds = 1.6 x 1027 years >> age of universe

In fact, protein fold in seconds. This is known as the Levinthal paradox.


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The Levinthal paradox

Typically, proteins fold

by progressive

formation of native-like

structures.

Folding energy surface is

highly connected with

many different routes to

final folded state.


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Folding landscapes and the Levinthal paradox

Flat landscape

(Levinthal paradox)

Tunnel landscape

(discrete pathways)

Realistic landscape

(folding funnel)


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PROTEIN UNFOLDING

Denaturation the breakdown of protein nativestructure due to:

Extrem pH or temperature

Addition of denaturant

Protein will lose its biological functions.Example: Coagulation, fried egg.


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PROTEIN UNFOLDING

Denaturasi Protein


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Protein folding diseases

Protein unfolding/enhanced proteolysis

p16/p53 mutations in cancer

DF508 mutation in cystic fibrosis

Aggregation/formation of amyloids

Alzheimer amyloid

Parkinsons -synuclein

Mad cow disease Prpc

Familial amyloidotic polyneuropathy transthyretin


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Mutations may cause part or entire protein to unfold


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Amyloid diseases

Protein aggregates deposit in brain, heart, liver, or kidney.

About 20 proteins can form amyloid under physiological

conditions.

More proteins can be induced to form amyloid under

laboratory conditions.

The origin of tissue toxicity is unclear.


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Morphology of amyloid fibrils


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Amyloid is formed by partially folded intermediates

fibrils


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Amyloid disease can be infectious

The seeding model for prion transmission


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Nobel Prize for Protein Misfolding

Stanley B. Prusiner1997 Nobel Prize in Medicine or Physiology


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SUMMARY OF PROTEIN STRUCTURES


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SUMMARY OF PROTEIN FOLDING

Central dogma of protein folding: Primary

structures determine the 3D native structure

Anfinsens Experiment.

Denaturation causes the collapse of the

proteins structure and thus remove their

biological functions.

modul - protein structure

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