Biochemistry Online: An Approach Based on Chemical Logic

Biochemistry Online





Learning Goals/Objectives for Chapter 5C:  After class and this reading, students will be able to

  • explain the similarities and differences in structure between myoglobin and hemoglobin in the deoxy and oxy states
  • state structural features of Hb that stabilizes the deoxystate and the oxystate
  • draw graphs of fractional saturation Y vs L (or pO2) for Mb and Hb  (at different pHs and in the presence of CO2 for Hb) and explain their apparent similarities and differences
  • draw a thermodynamic cycle for the interactions of O2, CO2 and H+ with deoxy-Hb and oxy-Hb
  • explain how Hill Plot analysis can account for cooperative binding curves for Hb.
  • give a simple explanation of the MWC model and draw cartoon representations of Hb in the T and R state, describing the characteristics of those states
  • given definitions of the MWC parameters (L, KT, KR, c, and α) and the assumptions of the model, explain how this model accounts for cooperative sigmoidal binding curves for Hb and dioxygen.
  • draw cartoon models and explain differences in lock and key, induced fit, and conformational selection as mechanisms for ligand bind.
  • Explain biological advantages elicited on ligand binding by intrinsically disordered proteins

C13.  Links and  References

  1. David W. Sanders and Clifford P. Brangwynn, RNA repeats put a freeze on cells.  Nature, 546, 215 (2017) 
  2. Ankur Jain & Ronald D. Vale. RNA phase transitions in repeat expansion disorders. Nature, 546, 243 (2017) .doi:10.1038/nature22386
  3. Allyson M. Rice and Michael K. Rosen.  ATP controls the crowd.  Science, 356, 701 (2017)
  4. ATP as a biological hydrotrope By Avinash Patel, Liliana Malinovska, Shambaditya Saha, Jie Wang, Simon Alberti, Yamuna Krishnan, Anthony A. Hyman Science, 356, 753 (2017)
  5. Anthony A. Hyman,1 Christoph A.Weber, and Frank Ju(umlaut)licher. Liquid-Liquid Phase Separation in Biology. Annu. Rev. Cell Dev. Biol. 2014. 30:39–58. Doi: 10.1146/annurev-cellbio-100913-013325
  6. Vacic, V. et al. Characterization of Molecular Recognition Features, MoRFs, and Their Binding Partners.  Journal of Proteome Research 6, 2351 (2007)  DOI: 10.1021/pr0701411
  7. Mohan, A. et al Analysis  of molecular recognition features (MoRFs). J Mol Biol. 362, 1043 (2006)
  8. Junker, J et al.  Science 323, pp. 633-637 (2009)
  9. Lee, J. et al. Surface Sites for Engineering of Allosteric Control in Proteins. Science 322, 438 (2008)
  10. Rea, A. et al. Mechanism of Ligand-Induced Folding of a Natively Unfolded Helixless Variant of Rabbit I-BABP.  Biochemistry, 48, 7556 (2009)
  11. Boehr, D. and Wright, P.  How Do Proteins Interact.  Science 320, 1429 (2008)
  12. Lange, O.  . Science 320: 1471 (2008)
  13. Greuninger, D. et al.  Designed Protein-Protein Association.  Science. 319, pg 206 (2008)
  14. Chen, B. et al. Structure of an unliganded simian immunodeficiency virus gp120 core. Nature. 433, pg 834 (2005)
  15. Koshland, D. and Hamadani, K. Proteomic and Models for Enzyme Cooperativity. J. Biol. Chem. 277, pg 46841 (2002)
  16. Schotte, F. et al. Watching a protein as it functions with 50 ps time-resolved X-ray crystallography.  Science, 300, pg 1944 (2003)
  17. James, L. et al. Antibody Multispecificity Mediated by Conformational Diversity. Science. 299, pg 1362 (2003)
  18. Chueh, P. et al. Molecular Cloning and Characterizatio of a Tumor-Associated, Growth-Related, and Time-Keeping  Hydroquinone (NADH) Oxidase (tNOX) of the HeLa Cell Surface.  Biochemistry. 41, pg 3732 (2002)
  19. Morre et al. Biochemical Basis for the Biological Clock. Biochemistry, 41, pg 11941 (2002)
  20. Lipton et al. Nitric Oxide and Respiration. (about role of Hb in carrying NO).   Nature. 413, pg 118, 171 (2001)
  21. Volkman et al. Two State Allosteric Behavior in a single-domain signaling protein. Science. 291, pg 2329, 2429 (2001)


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