1. HGP (Human Genome Project) HPP (Human Proteome Proyect) D:\SPLASH.EXE

2. ..\..\LINKS\Ho Nature(2002).pdf Ho et al. (2002) Nature 415, 180 Protein network in Saccharomyces cerevisiae

3. Determination of Protein Structures National Institutes of Health, USA The two most common methods used to investigate molecular structures are: 1. X-ray crystallography (also called X-ray diffraction) 2. Nuclear magnetic resonance (NMR) spectroscopy

4. X-ray crystallography National Institutes of Health, USA X-Ray Beam Scattered X-Rays CrystalDetector

5. The First X-Ray Structure: Myoglobin Kendrew (1959)

6. Why X-Rays? National Institutes of Health, USA Radio waves UltravioletMicrowavesInfrared X-Rays Visible Protein Water molecule Cell Tennis ball House Soccer field Period Wavelength (meters)

7. ESRF - The European Synchrotron Radiation Facility Grenoble, Francia National Institutes of Health, USA

8. One of the first three-dimensional NMR solution structures determined by Wüthrich, in 1985. a) A schematic view of the topology of the polypeptide backbone of BUSI IIA (bull seminal plasma proteinase inhibitor IIA). The structure represents an average of several computed structures that fulfil the structural constraints. b) A set of five backbone structures of BUSI IIA, calculated with distance geometry using the NOE distance constraints.

9. The Nobel Prize in Chemistry 2002 For the development of methods for identification and structure analyses of biological macromolecules for his development of nuclear magnetic resonance spectroscopy for determining the 3D structure of biological macromolecules in solution" for their development of soft desorption ionisation methods for mass spectrometric analyses of biological macromolecules J.B. FennK. TanakaK. Wüthrich

10. Electrospray ionisation (John B. Fenn) The biomolecule starts out as an entity or complex, usually charged and dissolved in a water-rich environment. At the end of the process the same biomolecule is represented and harvested through the orifice of a mass analyser as a series of ‘naked’ multicharged ions. In a vacuum, the biomolecular ions then are selectively analysed according to their mass/charge ratio.

11. Soft laser desorption (SLD) (Koishi Tanaka) Gaseous macromolecular ions can be formed using a low-energy (nitrogen) laser. The figure shows the signals from singly- and doubly charged molecular ions and a protein cluster-ion with a single charge.

12. NMR structure determination (Kurt Wüthrich) The most important parameter for structure determination based on NMR is the nuclear Overhauser enhancement (NOE) effect. This provides information about inter-atomic distances between nuclei close in space. Different types of two-dimensional NMR spectra: a COSY spectrum, which gives crosspeaks between resonances from protons bound to adjacent carbons or nitrogens, and a NOESY spectrum, which gives crosspeaks between resonances from protons close in space. Then paste together the upper half of a NOESY spectrum with the lower half of a COSY spectrum, so that they coincide in the diagonal, providing a connectivity diagram.

13. If one knows all the measurements of a house, one can draw a three- dimensional picture of the house. In the same way, by measuring a vast number of short distances in a protein it is possible to create a three- dimensional picture of its structure.

14. NMR Spectroscopy National Institutes of Health, USA Most NMR spectroscopists use magnets that are 500 megahertz to 800 megahertz. This magnet is 900 megahertz—the strongest one available.

15. Los Elementos y Moléculas de la Vida Losada, Vargas, Florencio y De la Rosa (1998-9) Editorial Rueda, Madrid

16. Los Elementos y Moléculas de la Vida Losada, Vargas, Florencio y De la Rosa (1998-9) Editorial Rueda, Madrid

17.     - + ESTRUCTURA PLANA DE LA UNIDAD PEPTÍDICA Los Elementos y Moléculas de la Vida Losada, Vargas, Florencio y De la Rosa (1998-9) Editorial Rueda, Madrid

18. Los Elementos y Moléculas de la Vida Losada, Vargas, Florencio y De la Rosa (1998-9) Editorial Rueda, Madrid

19. CONFORMACIÓN EN HOJA PLEGADA ANTIPARALELA OO OO OH HH HHHHH HH HH HO OO OOOOO N C C N  Los Elementos y Moléculas de la Vida Losada, Vargas, Florencio y De la Rosa (1998-9) Editorial Rueda, Madrid

20. ..\..\..\Mis documentos\webdpto\biomoleculas\biomodel\model1\INICIO.HTM

21. The CATH Hierarchy C: Class A: Architecture T: Topology H: Homologous Superfamily CATH database of structural domains Protein Structure Classification http://scop.mrc-lmb.cam.ac.uk/scop/ SCOP: Structural Classification of Proteins

22. Proteínas: Evolución a nivel molecular

23. A strict principle of economy: The same economy that reuses a few motifs to subserve different functions (divergent evolution) increased the chance of different biological systems coming up with different solutions to the same problem (convergent evolution).

24. Evolutionary tree showing how the globin protein family arose, starting from the most primitive oxygen-binding proteins, leghemoglobins, in plants. Divergent Evolution

25. Gomis et al. (2001) Nature 409, 637-641 Lateral view View along the 6-fold axis Divergent Evolution The bacterial conjugation protein TrwB resembles F1-ATPase

26. Left, Ribbon diagram of the structure of AIF. Right, Superposition of AIF and BphA4, a bacterial oxygenase-coupled NADH-dependent ferredoxin reductase (BphA4 in light blue). H. Ye et al. (2002) Nature Struct Biol 9, 680 The Apoptosis Inducing Factor (AIF) Divergent Evolution

27. H. Ye et al. (2002) Nature Struct Biol 9, 680 Apoptosis (or programmed cell death, PCD) is a highly organized multi- step process, with the induction of mitochondrial membrane permeabilization as a decisive event in the commitment to cell death. The execution of apoptosis comprises both caspase-dependent and caspase-independent processes. The Apoptosis Inducing Factor (AIF), a resident protein of the inter- mitochondrial space, has been implicated as a crucial early effector of caspase-independent apoptosis, acting before or in parallel with the onset of caspase-dependent processes. The ectopic presence of AIF in the extra-mitochondrial compartment suffices to kill cells. Apoptosis

28. S. Hunot and R.A. Flavel (2002) Science 292, 865 Apoptosis The caspase-dependent (right) and AIF- dependent (left) apoptotic pathways

29. H. Ye et al. (2002) Nature Struct Biol 9, 680 The Apoptosis Inducing Factor (AIF) Human AIF is synthesized as a precursor protein of 67 kDa and converted to mature AIF of 57 kDa upon mitochondrial import and removal of the N-terminal mitochondrial localization signal. Mature AIF is a flavoprotein with significant structural similarity to bacterial nicotinamide adenine dinucleotide (NAD)-dependent ferredoxin oxidoreductases (FNR). This suggests that AIF is a bifunctional protein with a mitochondrial resident function and an apoptogenic function. Because the flavin adenine dinucleotide (FAD) cofactor is dispensable for the apoptogenic function but required for the oxidoreductase activity of AIF, the structural bases for the mitochondrial and ectopic functions of AIF are probably entirely different.

30. H. Ye et al. (2002) Nature Struct Biol 9, 680 The Apoptosis Inducing Factor (AIF) When released from the mitochondria or added to purified nuclei, AIF enters the nucleus and induces chromatin condensation and large-scale DNA fragmentation to ca. 50 kilobases (kb) in a caspase-independent fashion. AIF induces chromatin condensation and initial DNA cleavage via an unknown molecular mechanism. DNA binding is required for the apoptogenic action of AIF, which interacts with DNA in a sequence-independent manner. The structure reveals the presence of a strong positive electrostatic potential at the AIF surface.

31. H. Ye et al. (2002) Nature Struct Biol 9, 680 The Apoptosis Inducing Factor (AIF)

32. Cyt c 6 Pc PS I b6fb6f PSI-driven Electron Transfer Fd light Convergent Evolution

33. A strict principle of economy: The same economy that reuses a few motifs to subserve different functions (divergent evolution) increased the chance of different biological systems coming up with different solutions to the same problem (convergent evolution). Dragonfly Bats

34. Pterosauria (pterosaurs) Chiroptera (bats)Aves (birds) The Three Solutions to Vertebrate Flight

35. Protein evolution: convergence or divergence? Structure and Mechanism in Protein Science A. Fersht (1999) WH Freeman and Company, New York, USA Six criteria for testing whether two proteins have evolved from a common precursor: 1. The DNA sequences of their genes are similar 2. Their amino acid sequences are similar 3. Their three-dimensional structures are similar 4.Their enzyme-substrate interactions are similar 5. Their catalytic mechanisms are similar 6. The segments of polypeptide chain essential for catalysis are in the same sequence (i.e., not transposed).

36. Protein building blocks preserved by recombination Voigt et al. (2002) Nature Struct Biol 9, 553 Recombination of beta- lactamases TEM-1 (gray line) and PSE-4 (black line)

37. Protein building blocks preserved by recombination Voigt et al. (2002) Nature Struct Biol 9, 553 Structures of the designed hybrids of  -lactamase TEM-1 (red) and PSE-4 (blue), shown in order of increasing disruption There exists a threshold in the amount of schema disruption that the hybrid protein can tolerate. To the extent that introns function to promote recombination within proteins, natural selection would serve to bias their locations to schema boundaries.

38. Dinámica Molecular de las Estructuras Proteicas La biología es inconcebible sin movimiento

39. http://www.life.uiuc.edu/crofts/bioph354/lect10.html ATP synthase Animation of the complete mechanism Lecture 10, ATP synthase

40. Schnitzer (2001) Nature 410, 878 - 881 Molecular machines They use ATP binding at one catalytic site to trigger a large conformational change and the release of ADP from another catalytic site.

41. Microtubule filament (left) with the bound motor domain of Neurospora crassa conventional kinesin Song, Y.-H. et al. (2001) EMBO J. 20, 6213-6225

42. The 'conventional' kinesin from the fungus Neurospora crassa is incredibly quick, moving along filamentous tracks called microtubules at speeds of 2.5  m per second — some five times faster than other conventional kinesins

43. Microtubule-motor protein interactions A. Hoenger, EMBL 2000 Research Reports

44. Myosin, a cellular motor protein It takes 37-nm steps by placing one “foot” after the other Cover - Science 27 June 2003

45. The Actomyosin Cross Bridge Cycle ATP binding to either a resting length myosin head (c) or to a head bearing a load (b) results a change in conformation in the myosin head, causing a rapid, almost irreversible dissociation of the myosin head from actin (d). Following detachment from actin, the ATP is hydrolysed to ADP and Pi, both of which remain very tightly bound to the myosin head (e).

46. The Actomyosin Cross Bridge Cycle http://www.mrc-lmb.cam.ac.uk/myosin/motility/XBcycle.html XBcycle

47. http://molmovdb.mbb.yale.edu/MolMovDB/cgi-bin/morph.cgi?ID=12221-32592 Myosin

48. A major question is: Are the modes of mobility observed in enzymes just incidental (...) or are they essential for catalysis? Flexibility could be useful in aiding the access of ligands to active sites. Protein mobility and enzyme mechanism Structure and Mechanism in Protein Science A. Fersht (1999) WH Freeman and Company, New York, USA

49. Untangling Protein Folding National Institutes of Health, USA Least Flexible Most Flexible Unfolded Partially folded Completely folded

50. E. Myshkin & G. Bullerjahn Bowling Green, Ohio,USA Dynamics of Plastocyanin The compact globular regions of proteins have structural fluctuations “Breathing” of proteins

51. Mioglobina

52. Hemoglobina

53. Domain movements: segment flexibility Structure and Mechanism in Protein Science A. Fersht (1999) WH Freeman and Company, New York, USA All domains movements may be constructucted from a combination of hinge and shear motions: Hinge motions, in which two elements of structure open and close as if connected by a hinge. Shear motions, in which one element of structure slides relative to the other.

54. Movimiento de bisagra Movimiento de deslizamiento Tipos de movimientos de las estructuras proteicas

55. Movimientos internos de las proteínas Empaquetamiento MantenidoNo mantenido de las interfases Empaquetamiento RestringidoLibre en la bisagra de la cadena principal Torsiones de la cadena Cambios pequeños Cambios grandes principal y numerosospero pocos Movimiento globalMovimientos localesIgual al de la bisagra pequeños y encadenados Movimiento en laParalelo al planoPerpendicular a interfasede la interfasela interfase EmpaquetamientoCierto empaquetamientoNuevos contactos en de las cadenas lateralesen las dos mitadesla base de la bisagra Torsiones de lasCambios pequeños Cambios grandes cadenas lateralesy numerosospero pocos CaracterísticasMecanismo deMecanismo de estructuralesdeslizamientobisagra

56. Transferrin Iron Transport Protein Database of Macromolecular Movements

57. Ca - ATPase

59. L-Alanina (Ala) : L-Glicina (Gly) : L-Valina (Val) : L-Leucina (Leu) : L-Metionina (Met) : L-Isoleucina (Ileu) : C C C C C C C C C C CC C C C S H H H H H H H H H H H HH H H H - - - - -- - - ---- 3 3 3 2 2 3 3 22 3 3 3 I. Grupos R no polares (a)

60. I. Grupos R no polares (b) L-Prolina (Pro) : L-Fenilalanina (Phe) : L-Triptofano (Trp) : C C C C C C H H N H H H H H - - - + 2 22 2 2 2 NH

61. II. Grupos R polares sin carga L-Serina (Ser) : L-Treonina (Thr) : L-Cisteína (Cys) : L-Asparragina (Asn) : L-Glutamina (Gln) : L-Tirosina (Tyr) : H C H O O N N C CO C C CC CH C C O H S H H H HH H H HH HO - -- - -- -- --- - 3 2 2 2 2 2 22 2

62. III. Grupos R con carga negativa L-Aspartato (Asp) : L-Glutamato (Glu) : C CC C C O O O O - - H HH - -- - - 2 22

63. IV. Grupos R con carga positiva L-Lisina (Lys) : L-Arginina (Arg) : L-Histidina (His) : C C N N N N H CC N C C C H H ) ) ( ( H H H H N H H H H - - - 2 2 4 3 3 2 2 + + + 2