Presentation on theme: "What determines the structure of the native folds of proteins?"— Presentation transcript:
1 What determines the structure of the native folds of proteins? Antonio TrovatoINFMUniversità di Padova
2 Outline Protein folding problem: native sequences vs. structures - sequences are many and selected by evolution- folds are few and conservedSimple physical model capturing of main folding driving forces: hydrophobicity, sterics, hydrogen bondsProtein energy landscape is presculpted by the generalphysical-chemical properties of the polypeptide backbone
3 Protein Folding Problem Central Dogma of Molecular Biology:DNA RNA Amino Acid Sequence (primary structure) Native conformation (tertiary structure) Biological FunctionAnfinsen experiment: small globular proteins fold reversibly in vitro to a unique native state free energy minimumWhich Hamiltonian?Which structure?Levinthal paradox: how does a protein always find its nativestate in ms-s time?
4 Protein folding is complex 20 type of amino acids with distinct side chainshuge number of degrees of freedompolymer chain constraintsteric constraints (excluded volume)crucial role of the aqueous solventquantum chemistry (hydrogen bond)
5 How to tackle the problem? All atom models: remarkable results for short peptidesbut problems for longer proteins:time constraint, stability of force fieldsKnowledge-based models: learn parameters from PDB;ok for structure prediction,but general or selected properties?Coarse-grained models: how to learn correctly the mainrules in the game?In all cases: sequence by sequence approach
6 Energy landscape paradygm (from cubic lattice models) Levinthal paradox: how to reconcile the uniqueness ofthe native state with itskinetic accessibility?Principle of minimal frustration Energy-entropy relationship is carving a funnel for designed sequences in the energy landscapeEnergyConformationsEnergyConformations
7 Funnel determined by native topology? Practical recipe (for off-lattice models): use Go model- a priori knowledge of the native conformation- folding mechanism (to some extent) depends onlyon the topology of the native state
8 However Only a Limited Number of Fold Topology Exists Protein sequences have undergone evolution but folds have not…. they seem immutable- M. Denton &C. Marshall, Nature 410, 417 (2001).- C. Chotia & A.V. Finkelstein, Annu. Rev. Biochem. 59, 1007 (1990).C. Chotia, Nature 357, 543 (1992).C. P. Pointing & R.R. Russel, Annu. Rev. Biophys. Biomol. Struct. 31, 45 (2002).A.V. Finkelstein, A.M. Gutun & A.Y. Badretdinov, FEBS Lett. 325, 23 (1993).
10 Most common superfolds the same fold can house many different sequences and perform several biological functionscan the emergence of a rich yet limited number of foldsbe explained by means of simple physical arguments?
12 Compact Phases of Standard Polymers: String and beads modelrall pairsCompact disordered phaseCrystalline phase: Hamiltonian walksTSwollen
13 Is compactness alone driving secondary structure formation? K.A. Dill & H.S. Chan, Origin of structures in globular proteins, PNAS 87, (1990).D.P. Yee, H.S. Chan, T.F. Havel & K.A. Dill, Does compactness induce secondary structure in proteins? – A study of poly-alanine chains computed by distance geometry, JMB 241, (1994).N.D. Socci, W.S. Bialek, & J.N. Onuchic, Properties and origins of secondary structure, PRE 49, (1994)Conclusion: compactness alone (in the absenceof hydrogen bonding) does not drivesecondary structure formation.
14 Secondary structures Linus Pauling: motifs. and with consistent is bondHydrogenbaL. Pauling & R.B. Corey, Conformations of polypeptides chains with favored orientations aroundsingle bonds: two new plated sheets, PNAS 37, (1951); ibid with H.R. Branson
15 Steric constraintsRamachandran plot: Only certain regions in the phi-psi plane are allowedfor most of the a.a.; constraints are specificG.N. Ramachandran & Sasisekharan, Conformations of polypeptides and proteins, Adv. Protein. Chem. 23, (1968).
16 Strong Hint Both hydrogen bonding and steric interaction encourage secondary structure
17 Thick Homopolymers Features & Motivations Chain directionality breaks rotational symmetry of the tethered objects.Need for a three body interaction.Continuum limit without singular interaction potentials 2-body interaction must be discarded.Nearby objects due to chain constraint do not necessarily interact.Compact phase of relatively short thick polymers are different from the compact phase of the standard string and beads model.O. Gonzalez & J.H. Maddocks, PNAS 96, 4769 (1999).J.R. Banavar, O. Gonzalez, J.H. Maddocks & A. Maritan, J. Stat. Phys.110,35(2003).A. Maritan, C.Micheletti, A. Trovato & J.R. Banavar, Nature 406, 287 (2000) .J.R. Banavar, A. Maritan, C. Micheletti & A. Trovato, Proteins. 47, 315 (2002).J.R. Banavar, A. Flammini, D. Marenduzzo, A. Maritan & A. Trovato, ComPlexUs 1, 8 (2003).
18 Optimal packing of short tubes leads to the emergence of secondary structures Nearly parallel placement ofdifferent nearby portions ofthe tubeOptimal helix (pitch/radius= ):generalization of Kepler problemfor hard spheres
20 Previous Attempts with H-bonds N.G. Hunt, L.M. Gregoret & F.E. Cohen, The origin of protein secondary structure: Effects of packing density and hydrogen bonding studied by a fast conformational search, J. Mol. Biol. 241, (1994).J.P. Kemp & Z.Y. Chen, Formation of helical structures in wormlike polymers, Phys. Rev. Lett. 81, (1998).A. Trovato, J. Ferkinghoff-Borg & M.H. Jensen, Compact phases of polymers with hydrogen bonding, Phys. Rev. E67, (2003).Conclusion: Secondary structures formation isenhanced by hydrogen bonding, but no particularresemblance with native-like tertiary arrangementsof secondary motifs.
21 Formulation of the Model RepresentaC-aTube Constraint (three-body constraint)Hydrogen bonding geometric constraintHydrophobic interaction: eWLocal bending penalty: eR
22 Formulation of the Model: Rules. H-Bond From 600 proteins in the PDB rijbinormals at the j-th and i-th residuesii+1j+1jj-1
23 How Many Parameters? Hydrogen bonding Local i – i+3 eH = -1 Non-Local i – i+5, i+6,… eH = -0.7Cooperativity ecoop = -0.3Remark: no H-bond between i – i+4 !
24 Formulation of the Model: Rules. Thickness - Steric Curvature-StericRamachandranRVcReR
25 Formulation of the Model: Rules Formulation of the Model: Rules. Hydrophobicity From 600 proteins in the PDBklVew
26 Ground State Phase Diagram eR = bending penaltyew = water mediated hydrophobic interactionNo sequence specificity: HOMOPOLYMEReW4321eRStructurelessCompactSwollen?
27 Ground State Phase Diagram bending energyattraction energyeW4321eRSwollenStructurelessCompact
29 All Minima In The Vicinity Of the Swollen Phase (Marginally Compact)
30 Similar structures for longer chains (48 residues)
31 Pre-sculpted energy landscape Sequence selection is easy!
32 Free Energy Landscape At Non Zero T Extended conformationis entropically favored:implication for aggregationin amyloid fibrils?length = 24
33 Aggregation of short peptides Jimenez et al., EMBO J. 18, (1999)Aggregation in amyloid fibrils is a universalfeature of the polypeptide backbone chain
34 CONCLUSIONS Homopolymer with: hydrogen bondinghydrophobic interactionthickness + steric interaction + curvaturePhase diagram where in the vicinity of the swollenphase marginally compact structures emerges:Huge reduction in the ground state degeneracy few folds (menu)!Marginally compact tertiary structures biological function (disordered proteins)Pre-sculpted free energy landscape Specific protein sequence chooses the native state from a fixed menu of possible foldsLarge basin of attraction mutation stability & easier foldingevolution of protein-protein interactions!
35 ConclusionsSimple physical model capturing geometry and symmetry of main folding driving forces: hydrophobicity, sterics, hydrogen bondsProteinlike conformations emerge as coexisting energy minima for an isolated homopolymer in a marginally compact phase flexibility ; aggregation in amyloid fibrils is promoted increasing chain concentrationThe energy landscape is presculpted by the physical-chemical properties of the polypeptide backbone;- design for folding is “easy”: neutral evolution- evolutionary pressure for optimizing protein-protein interaction(active sites, binding sites) and against aggregation
36 Acknowledgments Jayanth R. Banavar (Penn State) Alessandro Flammini (SISSA Trieste)Trinh Xuan Hoang (Hanoi)Davide Marenduzzo (Oxford)Amos Maritan (INFM Padova)Cristian Micheletti (SISSA Trieste)Flavio Seno (INFM Padova)