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
