Padova, 16 Ottobre 2007

IL MISTERO DELLEPROTEINEFlavioFlavio SenoSeno

Dipartimento di Fisica – Universita’di Padova

Istituto Nazionale Fisica Nucleare (INFN)

Consorzio Nazionale Interuniversitario per la Struttura della Materia (CNISM)

M5P SEMINARS

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

BiofisicaBiofisica : Applicazione di principi e metodi fisici per lo studio della strutturadegli organismi viventi e per la comprensione dei meccanismi vitali

FisicaFisica ee BiologiaBiologia

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

FisicaFisica BiologicaBiologica ( Biologically motivated Physics)( Biologically motivated Physics)

ModelliModelli sonosono giocattoligiocattoli mentalimentali cheche possonopossono guidareguidare ilil nostronostromodomodo didi pensarepensare ee didi comprenderecomprendere

Molte delle principali scoperte in meccanica statistica derivano da semplificazioni chepotrebbero sembrare irrealistiche a prima vista: particelle rappresentate da sfereperfette con ogni dettaglio atomico dimenticato, trascurando la presenza di altreparticelle, 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 thecoagulation 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: 12106240 ONHC

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: 1285436 ONHC

Von Liebig (working with casein) purified to small molecules:

first amino-acids: leucine and tyrosine

20 KIND OF AMINO-ACIDS

C COOHNH

H

R

2

Amino groupCarboxylic acid group

Protein Structure

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

Alanine

Valine

Glycine

Serine

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 isthermodynamically stableand reachable from differentstarting conditions.

• Only few sequences areproteins

• Only few conformationsare native states

• The folding time is veryrapid (0.01-100 sec)

The Inverse Folding Problem• Given a desired structure to

find an aminoacid sequencethat folds on it

• Protein functionality iscontrolled by its nativeconformation

• Powerful DNA-recombinationtechniques allow to modifythe sequence of amino-acids

• To solve the problem wouldallow to design new proteinswith new functionality

(drug design)

?

Protein folding is complex

• 20 type of amino acids with distinct sidechains

• 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 rulesan all atoms model (protein+solvent)

Blue Gene:IBM challenge

Many results are corroborating the existence of a few , effective mechanisms which are the relevantones for the folding process:

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

Physcists’ Challenge…

Very interesting fact

~ 100.000 sequences exist and only~ 1.000 folds

� mapping many to one

Compactness-Hydrophobicity

HH PP

SolventSolvent

Connessioni con la Fisica Teorica

•Catene lineari: polimeri, fenomeni critici,modello O(n), universalitàgruppo di rinormalizzazione

•Dinamica: free energy landscape, modelli frustrati,vetri di spin, processi di ottimizzazione

•Simulazioni: Dinamica molecolare e Monte-Carlo,Enumerazioni esatte

COARSE-GRAINEDMODELS

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. )αC

Effective interactions between these “amino-acids” are postulated toarise on integrating out the other degrees of freedom

HP ModelOnly two kinds of aminoacids: H Hydrophobic

P Polar

Tk

E

B

1−

0

0

08−=E

2

1 3

45

66

77

8

PROTEIN DESIGN

*C

Target

PROTEIN DESIGN

Solution*S

5− 4−

TEST N. 2TEST N. 2

TEST N. 2TEST N. 2

TEST N. 2TEST N. 2Right

Left

Forward

Backward

Up

Down

10/10 successes

TEST N. 3TEST N. 3

3rn3

124 aa

74 %

PRE-SCULPTED ENERGY

Very interesting fact

Protein sequences have undergone evolutionbut folds have not…. they seem immutable

~ 100.000 sequences exist and only~ 1.000 folds

� mapping many to one

Is it possibile to develop anunifying framework thatcan explain the stability ofthese Platonic folds?

Can we use this frameworkto understand more aboutproteins?

1 Step:

Which are the reallyimportant leading forces andrules that drive to these folds?

Thick Homopolymers

• Chain directionality breaks rotational symmetry ofthe tethered objects.

Optimal Helix

Pieranski

-5 -4 -3 -2 -1 0 +1 +2 +3 +4

eW

4

3

2

1

0

eR

Ground State Phase Diagram

ew = water mediated hydrophobic interaction

No sequence specificity: HOMOPOLYMER

eR = curvature - Ramachandran

StructurelessCompact Swollen

?

Ground State Phase Diagram

-5 -4 -3 -2 -1 0 +1 +2 +3 +4

eW

4

3

2

1

0

eR

SwollenStructurelessCompact

bend

ing

ener

gy

attraction energy

HOMOPOLYMER

Ground State Phase Diagram

All Minima In The Vicinity Of theSwollen Phase

48 beads

Alzheimer disease and hereditary cerebral hemmorhage with amylodosis.

Conjectured Amyloid Fiber

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

Single Chain versus multiple chains

…amyloid formation arises primarly from main chaininteractions (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 EnzymeCatalysis 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)

seno@pd.infn.it

Fisica BiologicaProblemi 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

BiofisicaFondamenti di Biologia Cellulare e Biochimica

Laboratorio di ElettronicaMicroscopia 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):Sensory and signal transductionin the inner ear (sperimentale)

Venetian Institute of Molecular Medicine (VIMM)-Via Orus

Theory (Dipartimento - CNISM )

Amos Maritan Flavio Seno Antonio Trovato