Added "Double T" folding pathway example

diff --git a/tex/src/figures/main.bib b/tex/src/figures/main.bib
index 2b7e1a4fac9209b7cc7071d21ffcf446c5fcca22..ea1c5c5c51f90292b24dcf0f693005da350e0abd 100644 (file)
--- a/tex/src/figures/main.bib
+++ b/tex/src/figures/main.bib
@@ -1,6 +1,6 @@
 @Misc{pymol,
   author = "DeLano, W. L.",
-  title = "The PyMOL Molecular Graphics System",
+  title = "The {PyMOL} Molecular Graphics System",
   url = "http://www.pymol.org",
   year = 2002,
   note = "Version 1.2.1.",

diff --git a/tex/src/introduction/main.tex b/tex/src/introduction/main.tex
index 03164c88bb7500b1b8a2d5afceb9ffad8718d473..6626ecbbf3c59bb1808f7d7096456d826908c707 100644 (file)
--- a/tex/src/introduction/main.tex
+++ b/tex/src/introduction/main.tex
@@ -66,18 +66,34 @@ explaining the folding mechanism.  For a number of years, the
 
 \begin{figure}
   \begin{center}
-  \subfloat[][]{\includegraphics[width=2in]{figures/schematic/pathway}%
-    \label{fig:folding:pathway}}
+  \subfloat[][]{
+    \begin{tikzpicture}[->,node distance=1.5cm]
+      \tikzstyle{every state}=[draw=white]
+      \node[state] (U)                 {$U$};
+      \node[state] (I1)  [right of=U]  {$I_1$};
+      \node[state] (I1X) [below of=I1] {$I_1^X$};
+      \node[state] (I2)  [right of=I1] {$I_2$};
+      \node[state] (I2X) [below of=I2] {$I_2^X$};
+      \node[state] (N)   [right of=I2] {$N$};
+    
+      \path[<->] (U)  edge (I1)
+                 (I1) edge (I1X)
+                 (I1) edge (I2)
+                 (I2) edge (I2X)
+                 (I2) edge (N);
+    \end{tikzpicture}\label{fig:folding:pathway}}
   % \hspace{.25in}%
   \subfloat[][]{\includegraphics[width=2in]{figures/schematic/dill97-fig4}%
     \label{fig:folding:landscape}}
-  \caption{(a) The pathway model of protein folding, in which the
-    protein proceeds through a well defined series of metastable
-    transition states.  Reproduced from \citet{TODO}.  (b) The landscape
-    model of protein folding, in which the protein diffuses through a
-    multi-dimensional free energy landscape.  Separate folding
-    attempts may take many distinct routes through this landscape on
-    the way to the folded state.  Reproduced from \citet{dill97}.
+  \caption{(a) A ``double T'' example of the pathway model of protein
+    folding, in which the protein proceeds through a series of
+    metastable transition states $I_1$ and $I_2$ with two ``dead end''
+    states $I_1^X$ and $I_2^X$.  Adapted from \citet{bedard08}.  (b)
+    The landscape model of protein folding, in which the protein
+    diffuses through a multi-dimensional free energy landscape.
+    Separate folding attempts may take many distinct routes through
+    this landscape on the way to the folded state.  Reproduced from
+    \citet{dill97}.
     \label{fig:folding}}
   \end{center}
 \end{figure}

diff --git a/tex/src/packages.tex b/tex/src/packages.tex
index 077b8ac6a01caee18deb4edeed9a3aa20da61020..49be2ba98e7fb40366b8eda5c056d7d3b44eacc7 100644 (file)
--- a/tex/src/packages.tex
+++ b/tex/src/packages.tex
@@ -30,5 +30,10 @@
 % so ensure line numbering is off for the tables.
 \usepackage{lineno}
 
+\usepackage{pgf}          % Fancy graphics
+\usepackage{tikz}         % A nice, inline PGF frontend
+\usetikzlibrary{automata} % Graph-theory library
+
+
 \usepackage{wtk_cmmds}  % common personal macros, in ~/texmf/tex/latex/
 \input{local_cmmds}

diff --git a/tex/src/root.bib b/tex/src/root.bib
index eafe4c82ed4f8a6008f79483b2ccb0125d4eda2f..06f512c476b9cf5f59ed3b16365241beabce8ccd 100644 (file)
--- a/tex/src/root.bib
+++ b/tex/src/root.bib
@@ -7515,3 +7515,60 @@ url = "http://www.sciencedirect.com/science/article/B6WBK-4F5M7K3-3C/2/c94b612e0
   eprint = "http://www.nature.com/nsmb/journal/v4/n1/pdf/nsb0197-10.pdf",
   note = "Pretty folding funnel figures.",
 }
+
+@Article{bedard08,
+  author =       "Sabrina B{\'e}dard and Mallela M. G. Krishna and
+                 Leland Mayne and S. Walter Englander",
+  title =        "Protein folding: independent unrelated pathways or
+                 predetermined pathway with optional errors.",
+  journal =      PNAS,
+  year =         2008,
+  month =        may,
+  day =          20,
+  volume =       105,
+  number =       20,
+  pages =        "7182--7187",
+  keywords =     "Biochemistry",
+  keywords =     "Guanidine",
+  keywords =     "Kinetics",
+  keywords =     "Micrococcal Nuclease",
+  keywords =     "Models, Biological",
+  keywords =     "Models, Chemical",
+  keywords =     "Models, Theoretical",
+  keywords =     "Protein Conformation",
+  keywords =     "Protein Denaturation",
+  keywords =     "Protein Folding",
+  keywords =     "Protein Structure, Secondary",
+  keywords =     "Proteins",
+  keywords =     "Proteomics",
+  keywords =     "Reproducibility of Results",
+  keywords =     "Thermodynamics",
+  abstract =     "The observation of heterogeneous protein folding
+                 kinetics has been widely interpreted in terms of
+                 multiple independent unrelated pathways (IUP model),
+                 both experimentally and in theoretical calculations.
+                 However, direct structural information on folding
+                 intermediates and their properties now indicates that
+                 all of a protein population folds through essentially
+                 the same stepwise pathway, determined by cooperative
+                 native-like foldon units and the way that the foldons
+                 fit together in the native protein. It is essential to
+                 decide between these fundamentally different folding
+                 mechanisms. This article shows, contrary to previous
+                 supposition, that the heterogeneous folding kinetics
+                 observed for the staphylococcal nuclease protein
+                 (SNase) does not require alternative parallel pathways.
+                 SNase folding kinetics can be fit equally well by a
+                 single predetermined pathway that allows for optional
+                 misfolding errors, which are known to occur
+                 ubiquitously in protein folding. Structural, kinetic,
+                 and thermodynamic information for the folding
+                 intermediates and pathways of many proteins is
+                 consistent with the predetermined pathway-optional
+                 error (PPOE) model but contrary to the properties
+                 implied in IUP models.",
+  ISSN =         "1091-6490",
+  doi =          "10.1073/pnas.0801864105",
+  url = "http://www.pnas.org/content/105/20/7182.full",
+  eprint = "http://www.pnas.org/content/105/20/7182.full.pdf",
+}