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chapter6.aux
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\@writefile{toc}{\contentsline {chapter}{\numberline {VI.}\uppercase {Evolution of increased binding specificity in\newline S100A5}}{116}}
\@writefile{toc}{\contentsline {section}{ Author Contributions}{116}}
\@writefile{toc}{\contentsline {section}{ Abstract}{116}}
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\@writefile{toc}{\contentsline {section}{ Introduction}{117}}
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\@writefile{toc}{\contentsline {section}{ Results}{120}}
\@writefile{toc}{\contentsline {subsection}{ Estimating peptide interactions by phage display}{120}}
\@writefile{lof}{\contentsline {figure}{\numberline {19}{\ignorespaces Testing the increased specificity hypothesis requires extensive\newline sampling of targets}}{121}}
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\@writefile{lof}{\contentsline {figure}{\numberline {20}{\ignorespaces Set of binding peptides can be estimated using phage display.}}{123}}
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\@writefile{lof}{\contentsline {figure}{\numberline {21}{\ignorespaces A subpopulation of phage respond to addition of competitor}}{124}}
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\@writefile{toc}{\contentsline {subsection}{ Supervised machine learning allows prediction of binding}{124}}
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\@writefile{lot}{\contentsline {table}{\numberline {2}{\ignorespaces Protein binding model statistics}}{126}}
\@writefile{lof}{\contentsline {figure}{\numberline {22}{\ignorespaces Peptide binding can be predicted from amino acid sequence}}{127}}
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\@writefile{toc}{\contentsline {subsection}{ Venn diagrams can be estimated using MCMC}{129}}
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\@writefile{toc}{\contentsline {subsection}{ hA5 is more specific than hA6 or the ancestor}{130}}
\@writefile{lof}{\contentsline {figure}{\numberline {23}{\ignorespaces Changes in binding sets over time}}{131}}
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\@writefile{toc}{\contentsline {subsection}{ Re-evaluating the empirical support for the increasing specificity hypothesis}{133}}
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\@writefile{toc}{\contentsline {subsection}{ Quantifying the evolution of specificity informs S100 biology and biochemistry}{135}}
\@writefile{toc}{\contentsline {subsection}{ Future directions}{136}}
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\@writefile{toc}{\contentsline {subsection}{ Implications for protein engineering}{138}}
\@writefile{toc}{\contentsline {section}{ Conclusions}{138}}
\@writefile{toc}{\contentsline {section}{ Materials and Methods}{139}}
\@writefile{toc}{\contentsline {subsection}{ Molecular cloning, expression and purification in of S100 proteins}{139}}
\@writefile{toc}{\contentsline {subsection}{ Isothermal Titration Calorimetry}{140}}
\@writefile{toc}{\contentsline {subsection}{ Preparation of biotinylated proteins for phage display}{141}}
\@writefile{toc}{\contentsline {subsection}{ Phage display}{142}}
\@writefile{toc}{\contentsline {subsection}{ Preparation of deep sequencing libraries}{144}}
\@writefile{toc}{\contentsline {subsection}{ Phage display analysis pipeline}{144}}
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\@writefile{toc}{\contentsline {subsection}{ Identifying the read count cutoff}{146}}
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\@writefile{toc}{\contentsline {subsection}{ Measuring enrichment values}{147}}
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\@writefile{toc}{\contentsline {subsection}{ Principle Component Analysis}{149}}
\@writefile{toc}{\contentsline {subsection}{ Incorporating uncertainty into an estimate of a Venn diagram}{149}}
\@writefile{toc}{\contentsline {section}{ Bridge to Chapter VII}{152}}
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