Proteins - INFN - Sezione di Padova

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degli organismi viventi e per la comprensione dei meccanismi vitali .... C. Branden e J. Tooze, Introduzione alla struttura delle proteine, Zanichelli. (1993). 3.

Padova, 16 Ottobre 2007

M5P SEMINARS

IL MISTERO DELLE PROTEINE Flavio Seno Dipartimento di Fisica – Universita’di Padova Istituto Nazionale Fisica Nucleare (INFN) Consorzio Nazionale Interuniversitario per la Struttura della Materia (CNISM)

Fisica e Biologia Biofisica : Applicazione di principi e metodi fisici per lo studio della struttura degli organismi viventi e per la comprensione dei meccanismi vitali

X-rays Diffraction of Lysozyme crystals obtained at -30°.

Leo Slizard: “Physicist bring to biology not any skills acquired in physics, but rather an attitude: the convinction which few biologist have that mysteries can be solved”

Fisica Biologica ( Biologically motivated Physics) Modelli sono giocattoli mentali che possono guidare il nostro modo di pensare e di comprendere Molte delle principali scoperte in meccanica statistica derivano da semplificazioni che potrebbero sembrare irrealistiche a prima vista: particelle rappresentate da sfere perfette con ogni dettaglio atomico dimenticato, trascurando la presenza di altre particelle, momenti magnetici trattati come frecce ….

PROTEINS

Proteins: why are so important? From the Greek: “Being of Primary Importance” No better world could have been chosen !!!!!! Enzymatic catalysis Transport and Storage Movement Immunitary Defense Transmission of nervous signals Hormon activity Forming tissues

Berzelius,1838

Albuminoids: these materials were identified (1800) in natural processes as the coagulation of egg white by heat, the curdling of milk with acid or the spontaneous clotting of blood

Gerardus Mulder (1802-1880) proposed a molecular form: C40 H 62 N10O12

+ S Justus von Liebig(1803-1873): We cannot isolate the particular substance described by Mr. Moulder. And so, it is a source of despair, after so much has been prattled and written about “protein”, to have to say there is no such thing. Mulder again:

C36 H 54 N 8O12

Von Liebig (working with casein) purified to small molecules: first amino-acids: leucine and tyrosine

20 KIND OF AMINO-ACIDS

R NH Amino group

2

C H

COOH Carboxylic acid group

Protein Structure Carbon alpha, Carbon’, Nitrogen, Oxigen …. Hydrogen omitted

Serine

Valine

Alanine

Glycine

Adenina Guanina Citosina Uracile

Integrin

Cell Adhesion Protein

184 Aminoacids

1491 Atoms

Integrin

Cell Adhesion Protein

184 Aminoacids

1491 Atoms

Integrin

Cell Adhesion Protein

184 Aminoacids

1491 Atoms

PROTEIN FOLDING

The Protein Folding Problem • The native state is uniquely determined by the sequence • The native state is thermodynamically stable and reachable from different starting conditions. • Only few sequences are proteins • Only few conformations are native states • The folding time is very rapid (0.01-100 sec)

The Inverse Folding Problem • Given a desired structure to find an aminoacid sequence that folds on it • Protein functionality is controlled by its native conformation

?

• Powerful DNA-recombination techniques allow to modify the sequence of amino-acids • To solve the problem would allow to design new proteins with new functionality (drug design)

Protein folding is complex • 20 type of amino acids with distinct side chains • huge number of degrees of freedom • polymer chain constraint (length 50-1000) • steric constraints (excluded volume) • role of the aqueous solvent • quantum chemistry

Current level of computational resources rules an all atoms model (protein+solvent) Blue Gene: IBM challenge Physcists’ Challenge… Many results are corroborating the existence of a few , effective mechanisms which are the relevant ones for the folding process:

•Many amino-acids sequences fold into the same structure •Hydrophobic effect as leading force for the folding

Very interesting fact ~ 100.000 sequences exist and only ~ 1.000 folds

mapping many to one

Compactness-Hydrophobicity H

P

Solvent

Connessioni con la Fisica Teorica •Catene lineari: polimeri, fenomeni critici, modello O(n), universalità gruppo di rinormalizzazione •Dinamica: free energy landscape, modelli frustrati, vetri di spin, processi di ottimizzazione •Simulazioni: Dinamica molecolare e Monte-Carlo, Enumerazioni esatte

COARSE-GRAINED MODELS

Coarse grained representation Too many details can obscure , rather than illuminate physical principles To consider just few degrees of freedom for each amino-acid (e.g.C ) Effective interactions between these “amino-acids” are postulated to arise on integrating out the other degrees of freedom

HP Model Only two kinds of aminoacids:

H Hydrophobic P Polar

E k BT

1

0 0 0

2 1

8 77

5

3 4

66

E= 8

PROTEIN DESIGN

Target

C

*

PROTEIN DESIGN

S

Solution

*

5

4

TEST N. 2

TEST N. 2

TEST N. 2 Right Left Forward Backward Up Down

10/10 successes

TEST N. 3

3rn3 124 aa 74 %

PRE-SCULPTED ENERGY

Very interesting fact ~ 100.000 sequences exist and only ~ 1.000 folds

mapping many to one

Protein sequences have undergone evolution but folds have not…. they seem immutable

Is it possibile to develop an unifying framework that can explain the stability of these Platonic folds?

Can we use this framework to understand more about proteins?

1 Step: Which are the really important leading forces and rules that drive to these folds?

Thick Homopolymers • Chain directionality breaks rotational symmetry of the tethered objects.

Optimal Helix

Pieranski

Ground State Phase Diagram eR = curvature - Ramachandran ew = water mediated hydrophobic interaction No sequence specificity: HOMOPOLYMER 4 3

eR

2 Structureless 1

Swollen

Compact

?

0 -5 -4 -3 -2

-1

0

eW

+1 +2 +3 +4

HOMOPOLYMER

bending energy

Ground State Phase Diagram

4 3 eR

2

Structureless Compact

1

Swollen

0 -5

-4

-3

-2

-1

0

eW

+1 +2 +3 +4

attraction energy

Ground State Phase Diagram

All Minima In The Vicinity Of the Swollen Phase

48 beads

Alzheimer disease and hereditary cerebral hemmorhage with amylodosis.

Proteins tend to misfold and to aggregate (in several diseases, but not only)

Conjectured Amyloid Fiber

Single Chain versus multiple chains

…amyloid formation arises primarly from main chain interactions (Fandrich-Dobson EMBO J. 21, 5892 (2002))

Human amyloid beta-peptide 1-40 (Alzheimer disease)

Qualche lettura:

1. E. Boncinelli, Prima lezione di biologia, Universale Laterza (2001) 2. C. Branden e J. Tooze, Introduzione alla struttura delle proteine, Zanichelli (1993) 3. M. Gross, Travels to the Nanoworld, Perseus Publishing (2001) 4. D. Dressler and H. Potter, Discovering enzymes, Scientific American Library (1991) 5. K. Huang, Statistical Physics and Protein Folding, World Scientific (2005) 6. A.R. Fersht, Structure and Mechanism in Protein Scienc: A guide to Enzyme Catalysis and Protein Folding, W.H. Freeman and Company (1999) 7. A.V. Finkelstein and O. Ptistyn, Protein physics: a course of lectures, Academic Press (2002)

[email protected]

Fisica Biologica Problemi fondamentali: universalità,interazioni competitive, proprietà topologiche, ottimizzazione Problemi applicativi con impatto bio-medico: disegno di nuovi farmaci, guida a terapie genetiche,prevenzione di malattie

Forte connessione quotidiana: Teoria-Esperimento

Cosa studiare (Laurea Specialistica): PERCORSO DI FISICA BIOLOGICA Biofisica Fondamenti di Biologia Cellulare e Biochimica Laboratorio di Elettronica Microscopia Ottica – Fisica dei Sistemi Complessi PERCORSO DI FISICA DELLA MATERIA Complementari: Biofisica-Fondamenti-Microscopia Ottica (Sperimentale) Complementari: Fisica dei Sistemi Complessi-Biofisica-Fondamenti (Teorica)

PERCORSO TEORICO: Complementari: Fisica dei Sistemi Complessi-Biofisica-Fondamenti (Teorica)

Con chi lavorare (Fare la Tesi): Venetian Institute of Molecular Medicine (VIMM)-Via Orus

Sensory and signal transduction in the inner ear (sperimentale)

Theory (Dipartimento - CNISM )

Amos Maritan

Flavio Seno

Antonio Trovato