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Classificazione dei livelli strutturali in proteine 1.

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Presentazione sul tema: "Classificazione dei livelli strutturali in proteine 1."— Transcript della presentazione:

1 Classificazione dei livelli strutturali in proteine 1

2 Struttura primaria (sequenza amminoacidica) 2

3 Struttura primaria (sequenza amminoacidica) 3

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5 struttura secondaria: la forma della catena principale della proteina (protein backbone) 5

6 DIAGRAMMA DI RAMACHANDRAN Gopalasamudram Narayana Iyer Ramachandran 8 October April

7 DIAGRAMMA DI RAMACHANDRAN Gopalasamudram Narayana Iyer Ramachandran 8 October April 2001 Journal of Molecular Biology


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11 Conformazione delle catene laterali 11

12 eliche α An α-helix in ultra-high-resolution electron density contours, with O atoms in red, N atoms in blue, and hydrogen bonds as green dotted lines (PDB file 2NRL, 17-32). in α-helix hydrogen bonds between carbonyl i and amide i+4 12

13 Folding mechanism of alpha helices 13

14 φ ψ eliche α, ma non solo 14

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24 anse 24

25 a:  b: ripiegamento a forcina a: motivo  d: barile  e: barile  (e) Strutture supersecondarie o motivi (elementi di struttura secondaria uguali o diversi si combinano) 25

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36 Domini strutturali (subunità avente stabilità strutturale ed una propria funzione) gliceraldeide-3-fosfato deidrogenasi dominio che lega il NAD + dominio che lega il gliceraldeide-3-fosfato 36

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38 Piruvato chinasi Enzima bifunzionale PRA-isomerasi IGP-sintetasi 38

39 Struttura quaternaria Eteromultimeri Omomultimeri 39

40 The Increase in the Number of PubMed Hits Dealing with Intrinsically Unstructured Proteins Set of keywords used: Natively denatured Natively unfolded Intrinsically unstructured Intrinsically disordered Intrinsically Unstructured Proteins (IUPs) 40

41 The natively unstructured state is a simple and elegant solution adopted by evolution to avoid large protein, genome and cell sizes Implications… Schematic representation of dimers (a) unstable (disordered) and (b) stable (ordered) monomers. Although in both cases the interface area between the monomers is the same, the size of the ordered monomer is much larger compared with the disordered example TiBS, 2003, 28, 81 Cell size constraints? 41

42 Some Structural Features Combination of low overall hydrophobicity and relative high net charge under physiological conditions Blue squares=275folded Red circle=91 IUPs Green circles=130 Predicted IUPs Cyan circle=242 Homologues of IUPs Proteins, 2000, 41,415 A combination of low mean hydrophobicity and high net charge preclude the formation of a hydrophobic cluster and promote an extended conformation 42

43 IUPs are enriched in S,P,E,K (disorder promoting) and depleted in W, Y,F,C,I, L, N (order promoting) IUPs have a distinctive aa composition Table 2 Aminoacid Frequencies of Ordered and Disordered Proteins TiBS, 2002, 527 Some Structural Features… 43

44 Linnaeus [5] Linnaeus [5] (1735) 2 kingdoms Haeckel [6] Haeckel [6] (1866) 3 kingdoms Chatton [7] Chatton [7] (1925) 2 groups Copeland [8] Copeland [8] (1938) 4 kingdoms Whittaker [2] Whittaker [2] (1969) 5 kingdoms WoeseWoese [9][10] (1977,1990) 3 domains [9][10] Animalia Eukaryote Animalia Eukarya VegetabiliaPlantae Protoctista Fungi (not treated)Protista ProcaryoteMonera Archaea Bacteria Taxonomy is the practice and science of classification 44

45 Phylogenetic Tree of All Life 45

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48 estimated number of protein folds: ~ 2000 (?) This three-dimensional map of the protein universe shows the distribution in space of the 500 most common protein folds as represented by spheres. The spheres, which are colored according to classification, reveal four distinct classes. From It is conceivable that, of the primordial peptides, those containing fragments with high helix and/or strand propensity found their way to fold into small alpha, beta, and alpha plus beta structures," Kim says. "The alpha slash beta fold structures do not appear until proteins of sufficient size rose through evolution and the formation of supersecondary structural units became possible. 48

49 Statistics of new folds in PDB 49

50 Top Folds in Yeast Transcriptome 50

51 TIM barrel nelle strutture depositate nel PDB 51

52 ENERGIA TOTALE CONFORMAZIONALE E=E a +E r +E es +E l +E t +E  +E H +E H  E a attrazione E r repulsione E es potenziale elettrostatico E l variazione di lunghezze di legame E t variazione di angoli di legame E  potenziale torsionale E H legame ad idrogeno Eh  interazione idrofobica 52

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54 Ipotetico meccanismo di ripiegamento di una proteina con due domini: formazione di elementi di struttura secondaria locali con formazione dei domini e loro assemblaggio finale. La struttura terziaria è raggiunta in pochi secondi. Nel paradosso di Levinthal una proteina di 100 residui raggiungerebbe la struttura nativa attraverso una ricerca casuale nello spazio conformazionale in s. Ogni aa con tre possibilità di  e  : conformazioni diverse. Tempo minimo di interconversione s / circa s 54

55 This is the E. coli major cold shock protein, CspA. This folding pathway is completely fictitious. The structure of CspA was solved by Hermann Schindelin and coworkers (PNAS, 91: , 1994). The coordinates for the cold shock protein (ID code "1mjc") may be retrieved from the Brookhaven Protein Data Bank. Below is a step by step presentation. 55

56 Chaperone-assisted protein folding The unfolded polypeptide enters the central cavity of chaperonin, where it folds. The hydrolysis of several ATP molecules is required for chaperonin function. The three dimensional proteins structure is shown in Figure. The lines on the chaperonin cylinder are to represent the 7 identical GroEL subunits that make up each ring. Not shown is the end cap composed of GroES subunits. 56

57 E. coli chaperonin (GroE) The core structure of chaperonin consists of two identical rings composed of seven GroEL subunits. Unfolded prteins bind to the central cavity. Bound ATP molecules can be identified by their red oxygen atoms (spacefill). The quaternary structure is shown from (a) the side, and (b) the top. [PDB 1DER] (c) During folding, the size of the central cavity of one of the rings increases and the end is capped by a protein containing seven GroES subunits. [PDB 1AON]. Highlighted in green is one of the GroEL subunits. 57

58 Christian P. Schultz Illuminating folding intermediates Nature Structural Biology 7, (2000) Schematic of the folding energy landscape of a protein molecule where the energy of the protein is displayed as a function of the topological arrangements of the atoms. The multiple states of the unfolded protein located at the top fall into a folding funnel consisting of an almost infinite number of local minima, each of which describes possible folding arrangements in the protein. Most of these states represent transient folding intermediates in the process of attaining the correct native fold. Some of these intermediates retain a more stable structure such as the molten globule, whereas other local minima act as folding traps irreversibly capturing the protein in a misfolded state. 58

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60 The ability of proteins to change conformation is the essence of the amyloidoses — in these diseases, the proteins have converted into the ‘primordial’ structure rather than remaining in their evolved states. Dobson, C. M., Ellis, R. J. & Fersht, A. R. (eds) Phil.Trans. R. Soc. Lond. B335, 129–227 (2001). Solomon, B., Taraboulos, A. & Katchalski-Katzir, E.(eds) Conformational Diseases: A Compendium (Karger, Tunbridge Wells, UK, 2001).Csermely, P. Trends Genom.17, 701–704 (2001). Ellis, R. J. & Pinheiro, T. J. T. Nature416, 483–484 (2002). Iverson, L. Nature417, 231–233 (2002). Ferguson, N. M. et al. Nature415, 420–423 (2002). 60

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63 Proposed three-dimensional structure (a) PrP C and (b) PrP Sc The structure of the normal prion protein, PrP C, is characterised by four -helices. Conversion of PrP C to the disease-associated form of PrP Sc results in the loss of two of the helical structures (shown shaded in brown), which are converted to linear structures known as -sheets. It is this conversion that is associated with the aquisition of prion infectivity. 63

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67 mutazione E/V in posizione 6 nella emoglobina Anemia falciforme 67

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