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Struttura primaria Struttura secondaria (alfa-elica, filamento beta, turn) Struttura supersecondaria (motivi strutturali) fold dominio classe subunità

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Presentazione sul tema: "Struttura primaria Struttura secondaria (alfa-elica, filamento beta, turn) Struttura supersecondaria (motivi strutturali) fold dominio classe subunità"— Transcript della presentazione:

1 Struttura primaria Struttura secondaria (alfa-elica, filamento beta, turn) Struttura supersecondaria (motivi strutturali) fold dominio classe subunità Struttura terziaria Struttura quaternaria All alpha All beta Alpha and beta Alpha + beta

2 All- topologies

3 The lone helix There are a number of examples of small proteins (or peptides) which consist of little more than a single helix. A striking example is alamethicin, a transmembrane voltage gated ion channel, acting as a peptide antibiotic.

4 The helix-turn-helix motif The simplest packing arrangement of a domain of two helices is for them to lie antiparallel, connected by a short loop. This constitutes the structure of the small (63 residue) RNA-binding protein Rop, which is found in certain plasmids (small circular molecules of double-stranded DNA occurring in bacteria and yeast) and involved in their replication. There is a slight twist in the arrangement as shown.

5 Catene laterali idrofobe Catene laterali idrofile FASCIO DI QUATTRO ELICHE

6 Cytochrome c1 ferritin

7 cytokines

8 Fascio di 4 eliche antiparallele 2 coppie di eliche parallele unite in modo antiparallelo

9 domains which bind DNA A three-helix bundle forms the basis of a DNA-binding domain which occurs in a number of proteins

10 globins

11 Strutture all alpha elica solitaria elica-turn-elica Fascio di 4 eliche Globine (fascio di 8 eliche) Domini ad alfa elica di grandi dimensioni

12 All- topologies

13 The Greek Key topology The Greek Key topology, named after a pattern that was common on Greek pottery, is shown below. Three up-and-down -strands connected by hairpins are followed by a longer connection to the fourth strand, which lies adjacent to the first.


15 Ipotetica modalità di ripiegamento di una struttura a forcina per formare la struttura a chiave greca. I filamenti 2 e 3 si ripiegano sugli altri due in modo che il filamento 2 viene ad essere allineato e antiparallelo al filamento 1.

16 Gamma-crystallin has two domains each of which is an eight- stranded -barrel-type structure composed of two Greek keys. In fact, the structure is more accurately described as consisting of two -sheets, one consisting of strands 2,1,4,7 (white) and the other of strands 6,5,8,3 (red) as indicated in the diagram. Gamma-crystallin

17 Aligned and orthogonal sandwiches

18 Diagram of this -sheet arrangement in the Lipocalin family, which binds small molecules between the sheets of the sandwich.

19 barrels

20 Strutture alfa/beta

21 / topologies The most regular and common domain structures consist of repeating - - supersecondary units, such that the outer layer of the structure is composed of helices packing against a central core of parallel -sheets. These folds are called /, or wound. Many enzymes, including all those involved in glycolysis, are / structures. Most / proteins are cytosolic. The - - is always right-handed. In / structures, there is a repetition of this arrangement, giving a - - -.....etc sequence. The strands are parallel and hydrogen bonded to each other, while the helices are all parallel to each other, and are antiparallel to the strands. Thus the helices form a layer packing against the sheet. The - - - - subunit, often present in nucleotide-binding proteins, is named the Rossman Fold, after Michael Rossman (Rao and Rossman,1973).

22 Beta-alfa-beta destrorsaBeta-alfa-beta sinistrorsa

23 Alfa-eliche sul medesimo piano del foglietto beta Alfa-eliche su piani opposti del foglietto beta Elica di collegamento

24 / barrels Consider a sequence of eight - motifs If the first strand hydrogen bonds to the last, then the structure closes on itself forming a barrel-like structure.


26 Enzima triosofosfato isomerasi Struttura a TIM barrel Enzima lattato deidrogenasi Rossman Fold


28 In tutte le strutture / a botte il sito attivo si trova in una tasca formata dalle regioni loop che collegano le estremità carbossiliche dei filamenti beta con le adiacenti alfa eliche.

29 Nei domini con struttura / aperta ruotata il sito attivo si trova in una fessura localizzata esternamente allestremità carbossilica del filamenti. Questa fessura è formata da due regioni loop adiacenti che collegano i due filamenti con eliche presenti su facce opposte del foglietto

30 Adenilato chinasiflavodossina Punti di inversione topologica (topological switch points)

31 Strutture alfa/beta I) TIM barrel II) a)Struttura / aperta e ruotata (di tipo parallelo o misto) - b) Rossmann fold III) / horseshoe (ferro di cavallo)

32 Alpha+Beta Topologies Ribonuclease-H

33 Structural Classification of Proteins (SCOP) Authors. Alexey G. Murzin, Loredana Lo Conte, Bartlett G. Ailey, Steven E. Brenner, Tim J. P. Hubbard, and Cyrus Chothia. Reference: Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540. Classes: 1.All alpha proteins (151) 2.All beta proteins (111) 3.Alpha and beta proteins (a/b) (117) Mainly parallel beta sheets (beta-alpha-beta units) 4.Alpha and beta proteins (a+b) (212) Mainly antiparallel beta sheets (segregated alpha and beta regions) 5.Multi-domain proteins (alpha and beta) (39) Folds consisting of two or more domains belonging to different classes 6.Membrane and cell surface proteins and peptides (12) Does not include proteins in the immune system 7.Small proteins (59) Usually dominated by metal ligand, heme, and/or disulfide bridges 8.Coiled coil proteins (5) Not a true class 9.Low resolution protein structures (17) Not a true class 10.Peptides (95) Peptides and fragments. Not a true class 11.Designed proteins (36) Experimental structures of proteins with essentially non-natural sequences. Not a true class


35 Membrane protein topology


37 Paradosso di Levinthal Proteina di 100 residui Due gradi di liberta torsionali/residuo (phi,psi) 3 conformazioni accessibili per ogni grado di liberta torsionale 3 2x100 possibili conformazioni @ 10 13 conformazioni esplorate/sec Tempo richiesto per esplorare tutte le conformazioni: t = 20 x 10 9 anni ! Le proteine si devono ripiegare seguendo un cammino definito, caratterizzato da conformazioni via via piu stabili (diminuizione di G)

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