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Molecular Biophysics

Molecular Biophysics. 12824 BCHS 6297 Lecturers held Tuesday and Thursday 10 AM – 12 Noon 402B-HSC. Aims of Course. Understand role of physics in protein structure Overview of the Electronic Spectroscopies

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Molecular Biophysics

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  1. Molecular Biophysics 12824 BCHS 6297 Lecturers held Tuesday and Thursday 10 AM – 12 Noon 402B-HSC

  2. Aims of Course • Understand role of physics in protein structure • Overview of the Electronic Spectroscopies • Understand the application of kinetics and thermodynamics to study enzyme catalysis and protein folding • Basics of NMR and X-ray crystallography

  3. Suggested texts • Principles of Physical Biochemistry, van Holde • Structure and Mechanism in Protein Science, Fersht • On-line resourses • Understanding NMR spectroscopy, by James Keeler http://www-keeler.ch.cam.ac.uk/lectures/ • Principles of Protein Structure Using the Internet, http://www.cryst.bbk.ac.uk/PPS2/course/index.html

  4. Structural Biology of the HIV proteome

  5. Molecular Forces in Protein Structure • Interactions, forces and energies • Covalent Interactions • Non-bonded Interactions • Electrostatic interactions: salt bridges, hydrogen bonds, partial charges and induction • The Lennard-Jones potential and van der Waals Radii • The effect of solvent and hydrophobic interactions • Dielectric effects • The hydrophobic effect

  6. Covalent bond The force holding two atoms together by the sharing of a pair of electrons. H + H  H:H or H-H The force: Attraction between two positively charged nuclei and a pair of negatively charged electrons. Orbital: a space where electrons move around. Electron can act as a wave, with a frequency, and putting a standing wave around a sphere yields only discrete areas by which the wave will be in phase all around. i.e different orbitals.

  7. Polarity of Bonds H | d+ d- CH3OH H—C—OH C O | H or even stronger polarity H d+d- d+d- H C O C O O> N> C, H electronegativity d-d+d+d-d+d- O H C N C O

  8. Geometry also determines polarity • d+d- • while CCl is polar carbon tetrachloride is not. The sum of the vectors equals zero and it is therefore a nonpolar molecule mCCl4 = m1+m2+m3+m4 = 0

  9. Electrostatic interactions by coulombs law F= kq1q2 q are charges r2D r is radius D = dielectric of the media, a shielding of charge. And k =8.99 x109Jm/C2 D = 1 in a vacuum D = 2-3 in grease D = 80 in water Responsible for ionic bonds, salt bridges or ion pairs,optimal electrostatic attraction is 2.8Å

  10. Dielectric effect D hexane 1.9 benzene 2.3 diethyl ether 4.3 CHCl3 5.1 acetone 21.4 Ethanol 24 methanol 33 H2O 80 HCN 116 H2O is an excellent solvent and dissolves a large array of polar molecules. However, it also weakens ionic and hydrogen bonds Therefore, biological systems sometimes exclude H2O to form maximal strength bonds!!

  11. Hydrogen bonds O-H N N-H O 2.88 Å 3.04 Å H bond donor or an H bond acceptor NHOC 3-7 kcal/mole or 12-28 kJ/mole very strong angle dependence

  12. A hydrogen bond between two water molecules

  13. . • van der Waals attraction • Non-specific attractions 3-4 Å in distance (dipole-dipole attractions) • Contact Distance • Å • H 1.2 1.0 kcal/mol • C 2.0 4.1 kJ/mol • N 1.5 weak interactions • O 1.4 important when many atoms • S 1.85 come in contact • P 1.9 • Can only happen if shapes of molecules match

  14. Hydrophobic interactions Non-polar groups cluster together DG = DH - TDS The most important parameter for determining a biomolecule’s shape!!! Entropy order-disorder. Nature prefers to maximize entropy “maximum disorder”. Enthalpy How can structures form if they are unstable? Structures are driven by the molecular interactions of the water!

  15. STRUCTURED WATER A cage of water molecules surrounding the non-polar molecule This cage has more structure than the surrounding bulk media. DG = DH -TDS Entropy decreases!! Not favorable! Nature needs to be more disorganized. A driving force. SO To minimize the structure of water the hydrophobic molecules cluster together minimizing the surface area. Thus water is more disordered but as a consequence the hydrophobic molecules become ordered!!!

  16. Proton and hydroxide mobility is large compared to other ions • H3O+ : 362.4 x 10-5 cm2•V-1•s-1 • Na+: 51.9 x 10-5 • Hydronium ion migration; hops by switching partners at 1012 per second.

  17. Free energy of transfer for hydrocarbons form water to organic solvent Process DH -TDS DG CH4 in H2O  CH4 in C6H6 11.7 -22.6 -10.9 CH4 in H2O  CH4 in CCl4 10.5 -22.6 -12.1 C2H6 in H2O  C2H6 in C6H6 9.2 -25.1 -15.9

  18. Amphiphiles form micelles, membrane bilayes and vesicles • A single amphiphile is surrounded by water, which forms structured “cage” water. To minimize the highly ordered state of water the amphiphile is forced into a structure to maximize entropy DG = DH -TDS driven by TDS

  19. Amino Acids:The building blocks of proteins pK1 pK2 a amino acids because of the a carboxylic and a amino groups pK1 and pK2 respectively pKR is for R group pK’s pK1 2.2 while pK2  9.4 In the physiological pH range, both carboxylic and amino groups are completely ionized

  20. Amino acids are Ampholytes They can act as either an acid or a base They are Zwitterions or molecules that have both a positive and a negative charge Because of their ionic nature they have extremely high melting temperatures

  21. Amino acids can form peptide bonds Amino acid residue peptide units dipeptides tripeptides oligopeptides polypeptides Proteins are molecules that consist of one or more polypeptide chains Peptides are linear polymers that range from 8 to 4000 amino acid residues There are twenty (20) different naturally occurring amino acids

  22. Characteristics of Amino Acids There are three main physical categories to describe amino acids: 1) Non polar “hydrophobic” nine in all Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Proline, Phenylalanine and Tryptophan 2) Uncharged polar, six in all Serine, Threonine, Asparagine, Glutamine Tyrosine, Cysteine 3) Charged polar, five in all Lysine, Arginine, Glutamic acid, Aspartic acid, and Histidine

  23. Amino Acids You must know: Their names Their structure Their three letter code Their one letter code Tyrosine, Tyr, Y, aromatic, hydroxyl

  24. Cystine consists of two disulfide-linked cysteine residues

  25. Acid - Base properties of amino acids Isoelectric point: the pH where a protein carries no net electrical charge For a mono amino-mono carboxylic residue pKi = pK1 and pKj = pK2 ; for D and E, pKi = pK1 and pKj - pKR ; For R, H and K, pKi = KR and pKj = pK2

  26. The tetra peptide Ala-Tyr-Asp-Gly or AYDG Greek lettering used to identify atoms in lysine or glutamate

  27. Optical activity - The ability to rotate plane - polarized light Asymmetric carbon atom Chirality - Not superimposable Mirror image - enantiomers (+) Dextrorotatory - right - clockwise (-) Levorotatory - left counterclockwise Na D Line passed through polarizing filters. Operational definition only cannot predict absolute configurations }

  28. The Fischer Convention Absolute configuration about an asymmetric carbon related to glyceraldehyde (+) = D-Glyceraldehyde (-) = L-Glyceraldehyde

  29. In the Fischer projection all bonds in the horizontal direction is coming out of the plane if the paper, while the vertical bonds project behind the plane of the paper All naturally occurring amino acids that make up proteins are in the L conformation The CORN method for L isomers: put the hydrogen towards you and read off CO R N clockwise around the Ca This works for all amino acids.

  30. An example of an amino acid with two asymmetric carbons

  31. Structural hierarchy in proteins

  32. Color conventions

  33. Protein Geometry CORN LAW amino acid with L configuration

  34. Greek alphabet

  35. The Polypeptide Chain

  36. Polypeptide geometry • Pauling and Corey

  37. Peptide bond • C-N bond displays partial double bond character

  38. Peptide bonds generally adopt a trans configuration

  39. Peptide Torsion Angles Torsion angles determine flexibility of backbone structure

  40. Steric hindrance limits backbone flexibility

  41. Rammachandran plot for L amino acids Indicates energetically favorable f/y backbone rotamers

  42. Regular Secondary StructurePauling and Corey Helix Sheet

  43. alpha helix

  44. Properties of the a helix • 3.6 amino acids per turn • Pitch of 5.4 Å • O(i) to N(i+4) hydrogen bonding • Helix dipole • Negative f and y angles, • Typically f = -60 º and y = -50 º

  45. Distortions of alpha-helices • The packing of buried helices against other secondary structure elements in the core of the protein. • Proline residues induce distortions of around 20 degrees in the direction of the helix axis. (causes two H-bonds in the helix to be broken) • Solvent. Exposed helices are often bent away from the solvent region. This is because the exposed C=O groups tend to point towards solvent to maximize their H-bonding capacity

  46. Top view along helix axis

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