PROTEIN ARCHITECTURE

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OBJECTIVE
You should be able to explain protein architecture and how it generally folds.

CONTENT
Primary structure of protein Secondary structure of protein Tertiary structure of protein Quaternary structure of protein Introduction to protein folding

PROTEIN PRIMARY STRUCTURE

All protein have similar backbone Primary Structure

Only peptide bonds to form polypeptide chain

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) Bend dan Loop

NHO=C

Peptide bond resonance

C=O partially negative NH partially positive Most of peptide bonds are in trans configuration.

Resonance arranges peptide bonds in planar form

Phi () = rotation angle at N-C bond Psi () = rotation angle at C C bond

-helix
About one third of protein secondary structure is in the form of -helix. Each amide hydrogen and carbonyl oxygen form hydrogen bond, except at N1, N2, N3, C3, C2 dan C1

-helix

SIDE VIEW

-helix
TOP VIEW

310-helix dan -helix

- sheets
NH-CO hydrogen bonds between close polypeptide chains.

-sheets

- sheets
Example: silk fibroin composed mainly by Gly and Ala.

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.

Hairpin Loop

Hairpin loops connect anti paralel -strand structures. Type I is 2-3 X more likely than type II.

Amino acid preferences in secondary structures

Ramachandran Plot

Parameters of protein secondary structures

Secondary structural motif

Secondary structures form supersecondary structure (motif) Example:
motif -helix loop -helix motif -sheet loop -sheet motif -sheet loop -helix - -sheet

Secondary structural motif

PROTEIN TERTIARY STRUCTURE

Formed trough intramolecular interactions of side chains in the same polypeptide chain, giving a stable 3D structure: Ionic bond (salt bridge) interaction between amino acids with + and - charges. Hydrogen bond interaction between R groups of polar amino acids. Hidrofobik interaction interaction between R groups of non polar amino acids. Disulfide bond interaction between Cys.

PROTEIN TERTIARY STRUCTURE

Tertiary structural motif All

Tertiary structural motif All

Tertiary structural motif +

Tertiary structural motif /

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

PROTEIN QUARTERNARY STRUCTURE

Example: 4 polipeptide chain with 2 prosthetic group

PROTEIN QUARTERNARY STRUCTURE

Proteins are synthesized as linear polymers

Ribosome

But proteins fold into compact 3D shapes

What determines fold? The Anfinsen paradigm

Ribonuclease A

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

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!

The Levinthal paradox

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

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

a random search of conformational space for the native fold. 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.

The Levinthal paradox

Typically, proteins fold by structures. progressive formation of native-like

Folding energy surface is highly connected with

many different routes to

final folded state.

Folding landscapes and the Levinthal paradox

Flat landscape (Levinthal paradox)

Tunnel landscape (discrete pathways)

Realistic landscape (folding funnel)

PROTEIN UNFOLDING
Denaturation the breakdown of protein native structure due to: Extrem pH or temperature Addition of denaturant

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

PROTEIN UNFOLDING
Denaturasi Protein

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

Mutations may cause part or entire protein to unfold

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.

Morphology of amyloid fibrils

Amyloid is formed by partially folded intermediates

fibrils

Amyloid disease can be infectious

The seeding model for prion transmission

Nobel Prize for Protein Misfolding

Stanley B. Prusiner 1997 Nobel Prize in Medicine or Physiology

SUMMARY OF PROTEIN STRUCTURES

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.