HGP (Human Genome Project) HPP (Human Proteome Proyect)

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

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

3. Determination of Protein Structures 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 National Institutes of Health, USA

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

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

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

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 computedstructures 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 structureanalyses of biological macromolecules J.B. Fenn K. Tanaka K. Wüthrich for their development of soft desorptionionisation methods for massspectrometric analyses of biologicalmacromolecules for his development of nuclear magnetic resonancespectroscopy fordetermining the 3D structure of biologicalmacromolecules insolution"

10. Electrospray ionisation (John B. Fenn) Thebiomolecule starts out as an entity or complex, usually charged and dissolved in a water-richenvironment. At the end of the process the same biomolecule is represented and harvestedthrough 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- anddoubly 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 nuclearOverhauser enhancement (NOE) effect. This providesinformation about inter-atomic distancesbetween nuclei close in space. Different types of two-dimensional NMR spectra: a COSY spectrum, which gives crosspeaks between resonancesfrom protons bound to adjacent carbons or nitrogens, and a NOESY spectrum, which gives crosspeaks between resonancesfrom 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 athree-dimensional picture of the house. In the same way, by measuring a vastnumber of short distances in a protein it is possible to create a three-dimensionalpicture of its structure.

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

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 d - a a d + 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. b CONFORMACIÓN EN HOJA PLEGADA ANTIPARALELA C N O O H H O H H O H H O H H H O O H O O H O O O O H H N C 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. Protein StructureClassification The CATH Hierarchy C: Class A: Architecture T: Topology H: Homologous Superfamily CATH database of structural domains SCOP: Structural Classification of Proteins http://scop.mrc-lmb.cam.ac.uk/scop/

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

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

26. Divergent Evolution The Apoptosis Inducing Factor (AIF) 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

27. Apoptosis 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. H. Ye et al. (2002) Nature Struct Biol 9, 680

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

29. 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. H. Ye et al. (2002) Nature Struct Biol 9, 680

30. 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. H. Ye et al. (2002) Nature Struct Biol 9, 680

31. The Apoptosis Inducing Factor (AIF) The structure reveals the presence of a strong positive electrostatic potential at the AIF surface. H. Ye et al. (2002) Nature Struct Biol 9, 680

32. light b6f Fd PS I Pc Cyt c6 Convergent Evolution PSI-driven Electron Transfer

33. Bats Dragonfly 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).

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

35. Protein evolution: convergence or divergence? Six criteria for testing whether two proteins have evolved from a common precursor: Structure and Mechanism in Protein Science A. Fersht (1999) WH Freeman and Company, New York, USA 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 Recombination of beta-lactamases TEM-1 (gray line) and PSE-4 (black line) Voigtet al. (2002) Nature Struct Biol 9, 553

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

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

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

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

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 Neurosporacrassa isincredibly quick, moving along filamentous tracks called microtubules at speeds of 2.5 mm persecond — some five times faster than other conventionalkinesins

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 aresting length myosin head (c) or to a head bearing a load (b) results a change inconformation in the myosin head, causing a rapid,almost irreversible dissociation of themyosin head from actin (d). Following detachment from actin, the ATP is hydrolysed to ADPand Pi, both of which remain very tightly bound to the myosin head (e).

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

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

48. Protein mobility and enzyme mechanism 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. Structure and Mechanism in Protein Science A. Fersht (1999) WH Freeman and Company, New York, USA

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

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