5 - Lecture 5 Friday September 3 2010 Announcements 1 Quiz...

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Lecture 5 Friday, September 3, 2010 Announcements: 1. Quiz Wed 9/8. More info at the end of today's lecture PyMOL exercise next week (for second quiz): #2, Secondary Structure. 2. See the schedule of reviews and office hours in LG or Blackboard. PyMOL reviews on Sunday 9/5 and on Tu 9/7. 3. Today, Friday, Comstock B108 at 2:55PM: info session, “Did you find an undergrad research position? What is expected of a new, inexperienced researcher?” 4. First gen. body meeting of Cornell’s March of Dimes Collegiate Council, Tuesday 9/7 at 4:30PM in Rockefeller 185. E-mail with any questions to RLK45 Friday’s class : Role of the Mb heme group and the holoprotein What to do with an AA sequence without the 3-d structure? a. Compare the new AA sequence to a data bank of all previously-determined AA sequences, and look for matches with proteins of known function. b. Evolutionary relationships: Look at the big picture, how lifeforms are connected, by studying protein sequences. c. Special sequences: Find short stretches of AA sequence that match "special sequences" that have known function: e.g. target of a kinase; import into nucleus d. Predict protein folding? (some success for very small proteins, but not from "first principles" of chemistry and physics) e. History of x-ray diffraction Today's lecture: p.42 The X-ray diffraction experiment: An intense beam of x-rays strikes a protein crystal. Use a crystal of protein, since repeating arrays of aligned atoms are needed in order to yield x-ray diffraction spots. The atoms cannot be moving much, or the alignment would be lost. In fact, these days many (most?) structures are solved at liquid nitrogen temp of 77K. Some x-rays are scattered by the atoms in the protein crystal (most x-rays go directly through the crystal). In those particular scattering directions, the scattered x- rays reinforce each other (wave intensities can add together or subtract). The waves of scattered (diffracted) x-rays actually have all information needed to find the arrangement of atoms in the protein crystal. If we could get all info about this scattered wave, we could just calculate both the type of atom (C, N, O, S, etc
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but not H which scatters x-rays too weakly), and the position of each atom in the crystal. For these x-ray waves (or any waves): POSITION, INTENSITY, PHASE, and X-RAY WAVELENGTH are the “wave properties” of diffracted beams that are used to solve for the arrangement of “electron density” in the crystal that caused this diffraction pattern. In effect, this electron density in the crystal is the arrangement of matter in 3D that we seek to determine. But, OH NO! the phase information of each wave is missing! It is missing because waves produce the same spot on the detector no matter what their phase. This problem took 30 years to solve. Now we can find the phase info, but it can be difficult.
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