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Consensus, Correlation And Combinatorics Based Approaches In Engineering And Exploring Triosephosphate Isomerase Stability

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2017, Doctor of Philosophy, Ohio State University, Biophysics.
Proteins represent the most diverse class of molecules that form the biochemical basis of life, and are products of the innumerable ways in which the 20 canonical amino acids link to each other. The specific sequences of amino acids are the sole determinants of the 3-dimensional properties and functions of proteins. While it is imperative that we develop a holistic model to comprehend and predict the effects of amino acids and changes in protein sequences, our current understanding tends to be context-sensitive and limited to only a few properties over which we have exerted very little control. The structural homology of proteins is an outcome of natural evolution and forms the basis for our classification of these molecules. Parsing these 'families' of proteins has yielded interesting knowledge that has enabled us to make ascribe due importance to specific positions and their amino acid identities in determining many biophysical characteristics, such as thermodynamic stability, solubility, catalysis, and binding. Of the many approaches that aim to supplement our knowledge of this sequence-structure-function relationship, we have used statistical methods that rely on protein multiple-sequence alignments to uncover the underlying evolutionary mechanisms of amino acid interactions in the 3-dimensional context of a model protein, Triosephosphate Isomerase (TIM). Positions that are relatively invariant across a family of homologous proteins are said to be conserved across a fold. On the other hand, positions that co-vary with each other are said to be correlated. In the extreme cases where one can ascribe a 'consensus' amino acid to a position in a protein family, one can interrogate the roles of such positions and amino acids. In some cases, such patterns are obvious, but in many situations, the subtle effects of poorly conserved and correlated positions are more challenging to demonstrate, obfuscating their biological importance. Two key TIM variants from the Magliery Lab have created a 'sandbox' where the outcomes from the statistical design are investigated in the context of protein stability and reported in this dissertation. One outcome of this investigation was an empirical approach to engineer protein stability in specific target proteins (including those outside the TIM-family) using the information-theory metrics of Relative Entropy and Mutual Information to determine mutational windows that draw on extant knowledge of the effects of consensus and correlations. We have employed rational and combinatorial approaches to explore the mutational and fitness landscape between the 2 TIM sequences 'cTIM' and 'ccTIM', and report findings that justify the idea that protein stability has complex and global sequence dependencies, displaying an emergent-property like behavior. The work presented here highlights the need for more nuanced methodologies to probe the roles of conserved and co-varying residues.
Thomas Magliery (Advisor)
William Ray (Committee Member)
Richard Swenson (Committee Member)
204 p.

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Citations

  • Mohan, S. (2017). Consensus, Correlation And Combinatorics Based Approaches In Engineering And Exploring Triosephosphate Isomerase Stability [Doctoral dissertation, Ohio State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=osu1503054678218166

    APA Style (7th edition)

  • Mohan, Sidharth. Consensus, Correlation And Combinatorics Based Approaches In Engineering And Exploring Triosephosphate Isomerase Stability. 2017. Ohio State University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=osu1503054678218166.

    MLA Style (8th edition)

  • Mohan, Sidharth. "Consensus, Correlation And Combinatorics Based Approaches In Engineering And Exploring Triosephosphate Isomerase Stability." Doctoral dissertation, Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu1503054678218166

    Chicago Manual of Style (17th edition)