Bahnson Biochemistry Cume, April 8, 2006 The Structural Biology of Signal Transduction
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1 Name page 1 of 6 Bahnson Biochemistry Cume, April 8, 2006 The Structural Biology of Signal Transduction Part I. The ion Ca 2+ can function as a 2 nd messenger. Pick a specific signal transduction pathway that utilizes Ca 2+ in the signal. With this system, tell me what you know about what the overall function of the signaling pathway is. What aspects are specific? What aspects are general? For any of the proteins that are directly involved in the Ca 2+ signaling that you chose, do structural models exist? If not, why not? If so, describe generally the features of the specific structure(s) that make it well suited to help perform its signaling function (25 pts).
2 Name page 2 of 6 Part II. There are several phospholipase enzymes that are involved in signal transduction. As you did in part-i, pick one specific phospholipase enzyme that has been suggested to play a central role in signaling. With this system, tell me what you know about what the overall function of the signaling pathway is. What aspects are specific? What aspects are general? Do structural models of this phospholipase exist? If not, why not? If so, describe generally the features of this structure that make it well suited to help perform its signaling function. (25 pts).
3 Name page 3 of 6 Part III. In general, many protein kinases and protein phosphatases are key players in signal transduction pathways. Many researchers in academics and industry are interested in obtaining structural models as well as developing specific tight binding inhibitors. Describe some of the complications of a. getting structural models of each of the protein kinases and protein phosphatases, b. developing inhibitors that show high specificity for specific protein kinases or protein phosphatases (25 pts).
4 Name page 4 of 6 Part IV. G Protein Coupled Receptors (GPCR) make up a protein family that mediate a wide array of signal transduction pathways. The β-adrenergic receptor binds the hormone adrenaline from the outside of a cell and transmits a signal to the inside of the cell. The GPCR rhodopsin absorbs a photon of light and transmits a signal to the cytoplasm of the cell that it is located in. A. Compare and contrast the structures and functions of the two proteins by answering the questions: What do they have in common and how do they differ? Try to be as thorough as possible. You must explain your answers to get full credit, since there may be many correct answers. In answering the questions you should refer to the attached figures from the article [Crystal Structure of Rhodopsin: A G Protein-Coupled Receptor Palczewski et al., Science 289, (2000)] on the next two pages. (15 pts)
5 Name page 5 of 6 B. Does the structure of rhodopsin (PDB id 1F88) reported in the article represent a reliable model of the protein in its biologically significant form. Explain, what your concerns might be and any information you know that could support or diminish the significance of the model in this regard. (10 pts) Fig. 2a Fig. 3
6 Name page 6 of 6 SEQUENCE ALLIGNMENT footnote 22 of articl, Supplemental Figure 1. The length of transmembrane a helices and sequence alignment of rhodopsins, cone pigments, and β2-adrenegric receptor (βar). The sequences were obtained from GenBank for bovine rhodopsin (brho; P02699), human rhodopsin (hrho, P08100), frog rhodopsin (frho, P56515), human blue cone pigment (blue, P03999), human green cone pigment (green, P04001), human red cone pigment (red cone pigment, P04000), and human β2-adrenergic receptor (bar, P07550). Identical amino acids in all receptors are in white letters on black background, conservative replacement residues (T = S, E = D = Q = N, M = L = I = V, R = K, Y = F = W) are in white letters on blue background, conservative replacement residues among rhodopsins and cone pigments are shaded in green, conservative replacement residues among rhodopsins are shaded in yellow. Transmembrane helices (H-I to H-VII) are marked as a thick, colored bar and encompass residues H-I (Trp35-Gln64), H-II (Pro71-His100), H-III (Pro107-Val139), H- IV (Asn151-Val173), H-V (Asn200-Gln225), H-VI (Glu247-Thr277), and H-VII (Ile286- Tyr306). Four strands of β-sheet region and a short cytoplasmic helix VIII are also marked. Posttranslational modifications are: N-terminal acetylation, glycosylation (Asn2 and Asn15, indicated as numbers 1 and 2 above the sequences), Cys-Cys bridge (numbers 3 and 4), Lys296 that forms the Schiff base with the chromophore (number 5), and two palmitoylation sites (numbers 6 and 7). Rhodopsin kinase phosphorylation region is marked by a solid red line, and major determinates of the G-protein interaction is marked by a blue line.
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