salt/main.tex: Start to summarize my salt experiments

diff --git a/src/local_cmmds.tex b/src/local_cmmds.tex
index a8562fd61d98b8c93727fa6d1cd415e00118eb18..ae2975194732ac3670a4062869bce48a1781222a 100644 (file)
--- a/src/local_cmmds.tex
+++ b/src/local_cmmds.tex
@@ -144,10 +144,13 @@
 % Chemicals
 \newcommand{\Ca}{Ca\textsuperscript{2+}}
 \newcommand{\CaCl}{CaCl\textsubscript{2}}
+\newcommand{\Cl}{Cl\textsuperscript{-}}
+\newcommand{\HCl}{HCl}
 \newcommand{\Na}{Na\textsuperscript{+}}
 \newcommand{\NaCl}{NaCl}
 \newcommand{\diNaHPO}{Na\textsubscript{2}HPO\textsubscript{4}}
 \newcommand{\NadiHPO}{NaH\textsubscript{2}PO\textsubscript{4}}
+\newcommand{\NaOH}{NaOH}
 
 % Workaround for inline minted markup
 %   http://code.google.com/p/minted/issues/detail?id=15

diff --git a/src/root.tex b/src/root.tex
index 8de670fca888c441da95077621ed196bbb54f696..a461de1c8426985df21913f47b076d82d9ed315e 100644 (file)
--- a/src/root.tex
+++ b/src/root.tex
@@ -70,6 +70,7 @@ defaultpen(fontsize(10));  // match drexel-thesis's default 10pt font size
 \include{hooke/main}
 %\include{temperature/main}
 %\include{cantilever/main}
+\include{salt/main}
 \include{future/main}
 \end{thesis}
 
@@ -80,6 +81,7 @@ defaultpen(fontsize(10));  // match drexel-thesis's default 10pt font size
   pyafm/main,%
   calibcant/main,%
   hooke/main,%
+  salt/main,%
   packaging/main,%
   figures/main,%
   root}

diff --git a/src/salt/main.tex b/src/salt/main.tex
new file mode 100644 (file)
index 0000000..2445512
--- /dev/null
+++ b/src/salt/main.tex
@@ -0,0 +1,91 @@
+\chapter{The effect of ions on unfolding force}
+\label{sec:salt}
+
+With the tools in place, it's time to do some science!  As a simple
+experiment to demonstrate the utility of the new stack, I ran a series
+of velocity clamp unfolding experiments on I27 octomers in PBS
+(\cref{sec:sample-preparation}).  After a series of pulls in the
+standard buffer, a buffer with additional sodium (from
+\NaCl\citep{bdh-NaCl}) or calcium (from \CaCl\citep{fisher-CaCl})
+was flushed into the fluid cell.  After the new buffer equilibrated,
+unfolding experiments were continued.
+
+Previous research on the effect of ions on unfolding forces is small,
+although earlier experimental work on Amyloid $\beta$ shows decreased
+fibrillation with even small
+\Ca\ concentrations\citep{chauhan97,itkin11}.  The mechanism behind
+this weaker bonding is unclear\citep{chauhan97,zhang06}, although
+aspartic and glutamic acid groups tend to have a strong affinity for
+cations while argenine has a strong affinity for the
+\Cl\ anion\citep{friedman11}.  Of these amino acids, only glutamic
+acid occurs in the key hydrogen bond regions responsible for I27
+unfolding\citep{lu00b}.  \NaCl\ has also been shown to decrease
+hydrogen bonding\citep{zidar11}.
+
+We added $0.5\U{M}$ \CaCl\ to our standard PBS
+(\cref{sec:sample-preparation}), which is much larger than
+extracellular \Ca\ levels on the order of
+$2\U{mM}$\citep{isaacs06,itkin11}.  After mixing, both buffers were
+adjusted with drops of \HCl\ and \NaOH\ as needed to reach a pH around
+7.5 (7.42 for the PBS, and 7.60 for the \Ca-enhanced PBS).
+
+Unfolding experiments carried out on 2013-03-04 using our usual
+procedure (\cref{sec:procedure}) yielded an unusual density of clean
+unfolding curves\footnote{
+  Experiments carried out using the same procedures throughout
+  February were much less successful.
+},
+with 105 successful pulls concentrated in a two hour window.  Of these
+pulls, 37 were in the standard PBS and 68 were in the enhanced
+\Ca\ buffer.  Histograms of unfolding forces show decreased
+unfolding forces in the \Ca\ buffer (\cref{fig:calcium:histogram}),
+which is what we expect due to destabilized hydrogen bonding.
+
+\begin{figure}
+  \begin{center}
+    \includegraphics[width=0.9\textwidth]{figures/salt/2013-03-04-CaCl2}
+    \caption{I27 runs from 2013-03-04 with (red) and without (blue) an
+      extra $0.5\U{m}$ \Ca.  Clockwise from the upper left, we have
+      the distance (in nm) between peaks, the unfolding force (in pN),
+      and example force curve, and a scatter plot of unfolding force
+      (in pN) versus the distance between peaks.  All of the pulls
+      were taken with the same Olympus TR400-PSA cantilever with a
+      pulling speed of $1\U{$\mu$m/s}$.  The green histogram drawn
+      over the unfolding force histograms is I27 unfolding data in PBS
+      with $5\U{mM}$ DTT from \citet{carrion-vazquez99b}, rescaled by
+      a factor of $\frac{1}{2}$ because they had more unfolding
+      events.\label{fig:calcium:histogram}}
+  \end{center}
+\end{figure}
+%
+\nomenclature{DTT}{Dithiothreitol
+  (C\textsubscript{4}H\textsubscript{10}O\textsubscript{2}S\textsubscript{2}),
+  also known as Cleland's reagent\citep{cleland64}.  It can be used to
+  reduce disulfide bonding in proteins.}
+
+Modeling I27 as a Bell-model unfolder, we can use \sawsim\ to find the
+Bell parameters that best fit these experimental unfolding histograms
+(\cref{sec:sawsim:rate:bell,sec:sawsim:results:fitting}).  The results
+in \cref{fig:calcium:valley} show that the best fit for standard PBS
+was with $\Delta x_u = TODO\U{nm}$ and $k_{u0}=TODO\U{s$^{-1}$}$.  In
+the \Ca\ buffer, the best fit was with $\Delta x_u = TODO\U{nm}$ and
+$k_{u0}=TODO\U{s$^{-1}$}$.
+
+\begin{figure}
+  \begin{center}
+    \subfloat[][]{%
+      \includegraphics[width=0.45\textwidth]{figures/salt/valley-PBS}%
+      \label{fig:calcium:valley:pbs}}
+    \subfloat[][]{%
+      \includegraphics[width=0.45\textwidth]{figures/salt/valley-PBS-CaCl2}%
+      \label{fig:calcium:valley:pbs-calcium}}
+    \caption{\protect\subref{fig:calcium:valley:pbs} Model fit quality
+      for the standard PBS unfolding histogram data shown in
+      \cref{fig:calcium:histogram}.
+      \protect\subref{fig:calcium:valley:pbs-calcium} Model fit
+      quality for the \Ca-enhanced PBS unfolding histogram data.  The
+      best fit parameters occur when the Jensen--Shannon divergence is
+      minimized (at the bottom of these valleys,
+      \cref{sec:sawsim:results:fitting}).\label{fig:calcium:valley}}
+  \end{center}
+\end{figure}