From fb89b559c36a44458cab9abe7e10bd5e7e3008af Mon Sep 17 00:00:00 2001 From: "W. Trevor King" Date: Mon, 22 Feb 2010 18:01:12 -0500 Subject: [PATCH] Added "Double T" folding pathway example --- tex/src/figures/main.bib | 2 +- tex/src/introduction/main.tex | 34 +++++++++++++++------ tex/src/packages.tex | 5 +++ tex/src/root.bib | 57 +++++++++++++++++++++++++++++++++++ 4 files changed, 88 insertions(+), 10 deletions(-) diff --git a/tex/src/figures/main.bib b/tex/src/figures/main.bib index 2b7e1a4..ea1c5c5 100644 --- 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 03164c8..6626ecb 100644 --- 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 077b8ac..49be2ba 100644 --- 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 eafe4c8..06f512c 100644 --- 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", +} -- 2.26.2