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Integrative Investigation and Modeling of Macromolecular Complexes

Ihms, Elihu Carl
http://rave.ohiolink.edu/etdc/view?acc_num=osu1429547886

Abstract Details

2015, Doctor of Philosophy, Ohio State University, Biophysics.
Many processes in biological systems are dependent upon complex regulatory schemes, often arranged in scale-free networks. Because of the difficulties in studying the nuanced behavior of such complicated systems, understanding the interactions between the individual nodes is essential to grasp the system as a whole. A highly productive example is the mechanism controlling tryptophan biosynthesis in Bacillus species. Thirty years of investigation into this system has resulted in paradigmatic examples of biosensors, response-amplification schemes, and closed-loop control. Despite this thorough inquest, many important processes within the TRAP system are still poorly understood; several are investigated with a variety of experimental techniques and analytical approaches in this work. One is the feedback rescue mechanism provided by the protein Anti-TRAP (AT) – although a crystal structure of a TRAP-AT complex is available, this static representation has proved to be misleading. Here, we show that the TRAP-Anti-TRAP interaction is actually quite complex, because the components the polydentate nature of each component leads to the formation of large heteropolymers at physiological ratios. These complexes are studied extensively with a broad range of structural, thermodynamic, and kinetic experiments. In addition to the complicated behavior they display in combination, the individual components themselves display fascinating properties that are tied to their regulatory function. Because TRAP is a homopolymer of eleven identical subunits, its activation by binding up to eleven tryptophans provides an unparalleled opportunity to examine binding cooperativity. The nature of this thermodynamic coupling mechanism is investigated in this work, leading to the realization that the presence of just a few bound tryptophan molecules causes profound changes in TRAP long before a majority of its active sites are occupied. AT, which also exists as a homopolymer of three identical subunits, can self-associate with an important effect on its regulatory properties. The assembly of AT subunits and their configurational dynamics are investigated in detail in this work, providing insight into not just the behavior of TRAP and Anti-TRAP, but oligomeric proteins as a whole. The exceptional complexity and quality of data provided by this system has necessitated the development and validation of new tools, as existing methods have often found to be inadequate. One of tbhe new tools described here, MESMER, provides a powerful and fully integrated analysis of heterogenous structural data, and has already started to find use in the scientific community.
Mark Foster, Ph.D (Advisor)
Venkat Gopalan, Ph.D (Committee Member)
Richard Swenson, Ph.D (Committee Member)
Charles Bell, Ph.D (Committee Member)
209 p.
Biochemistry; Biophysics; Molecular Physics; Molecules; Polymers
Macromolecular complexes; Integrative modeling; Computational biophysics; Reversible oligomerization; Quantitative modeling; Gene regulation networks; Macromolecule structure and configurational dynamics

Recommended Citations

Citations

  • Ihms, E. C. (2015). Integrative Investigation and Modeling of Macromolecular Complexes [Doctoral dissertation, Ohio State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=osu1429547886

    APA Style (7th edition)

  • Ihms, Elihu. Integrative Investigation and Modeling of Macromolecular Complexes. 2015. Ohio State University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=osu1429547886.

    MLA Style (8th edition)

  • Ihms, Elihu. "Integrative Investigation and Modeling of Macromolecular Complexes." Doctoral dissertation, Ohio State University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=osu1429547886

    Chicago Manual of Style (17th edition)

osu1429547886
77
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This open access ETD is published by The Ohio State University and OhioLINK.