Spellchecked introduction/main.tex.
Changed title (again :p) to:
"Temperature and cantilever dependent protein unfolding"
\chapter{Apparatus}
+\label{sec:apparatus}
\chapter{Cantilever Calibration}
+\label{sec:cantilever-calib}
+
\input{cantilever-calib/overview}
\input{cantilever-calib/setup_general}
\input{cantilever-calib/solve_highly_damped}
\chapter{Cantilever dependent unfolding experiments}
+\label{sec:cantilever}
+
+TODO...immunoglobulin-like domain 27 from human Titin (I27). I27 is a
+model protein that has been used in mechanical unfolding experiments
+since the first use of synthetic chains\cite{carrion-vazquez99b,TODO}.
+We use it here because it is both extremly well characterized and
+readily available.
+
-\chapter{Contour space}
+\chapter{Contour length space}
+\label{sec:contour-space}
+
+TODO\citet{puchner08}.
-\chapter{Conclusions}
+\chapter{Conclusions and future work}
+\label{sec:future}
ligand-receptor pair isolated from the bacterium
\species{Streptomyces avidinii}. Streptavidin binds to cell
surfaces, and bound biotin increases streptavidin's binding
- afinity\citep{alon90}.
+ affinity\citep{alon90}.
Figure generated with \citetalias{pymol}.
\label{fig:ligand-receptor}}
\end{center}
\end{center}
\end{figure}
+
+\section{Mechanical unfolding experiments}
+
% AFM unfolding procedure
In a mechanical unfolding experiment, a protein polymer is tethered
between two surfaces: a flat substrate and an AFM tip. The polymer is
\end{center}
\end{figure}
+
+\section{Thesis Outline}
+
+\Cref{sec:unfolding} of this thesis discusses the theory of protein
+unfolding for single domains. \Cref{sec:tension} discusses linker
+tension modeling. \Cref{sec:unfolding-distributions} pulls
+\cref{sec:unfolding,sec:tension} together to discuss the theory of
+mechanical unfolding experiments. This theory makes straightforward
+analysis of unfolding results difficult, so \cref{sec:sawsim} presents
+a Monte Carlo simulation approach to fitting unfolding parameters, and
+\cref{sec:contour-space} presents the contour-length space approach to
+fingerprinting unfolding pathways. \Cref{sec:temperature-theory}
+wraps up the theory section by extending the analysis in
+\cref{sec:unfolding,sec:unfolding-distributions} to multiple
+temperatures.
+
+\Cref{sec:apparatus} describes our experimental apparatus and methods,
+as well as calibration procedures. With both the theory and procedure
+taken care of, \cref{sec:cantilever,sec:temperature}
+present and analyze AFM cantilever- and temperature-dependent
+unfolding behavior of the immunoglobulin-like domain 27 from human
+Titin (I27).
+
+We close with \cref{sec:future}, which presents our conclusions and
+discusses possible directions for future work.
%% Science words
% LocalWords: polysaccharides polypeptide biomembrane biopolymers photodetector
-% LocalWords: piconewtons nanonewtons nanometers vt timesteps timestep
-% LocalWords: ubiquitin titin sawteeth octamer octameric
+% LocalWords: piconewtons nanonewtons nanometers vt tetramer timesteps timestep
+% LocalWords: ubiquitin titin immunoglobulin sawteeth octamer octameric multi
% LocalWords: unstretched undeflected unfoldings underdamped
% LocalWords: rebalances nonspecific equilibrated
+% LocalWords: Streptomyces avidinii streptavidin streptavidin's
%% Abbreviations:
-% LocalWords: Tel AFM afm WLC wlc FJC fjc PACS MSC pN nm MC ddFLN
+% LocalWords: Tel AFM AFMs afm WLC wlc FJC fjc PACS MSC pN nm MC ddFLN
+% LocalWords: PDB SWE
%% Names and related
% LocalWords: Hookean hooke Kramers kramers Mascheroni Kullback Leibler
% LocalWords: Markovian msu Meihong Su gyang Guoliang CSIRO Drexel
% LocalWords: bustamante forde smith merkel carrion vazquez rief levy fernandez
% LocalWords: chyan lu klimov li zinober jollymore marko sims evans schlierf
-% LocalWords: janshoff granzier linke verdier dicola lin
+% LocalWords: janshoff granzier linke verdier dicola lin wolfsberg mcpherson
+% LocalWords: collins claverie venter freitag alon levinthal bedard halvorsen
+% LocalWords: pymol sawsim
%% LaTeX and related
% LocalWords: documentclass elsarticle pt tnoteref tnotetext fnref fntext
%% Reference abbreviations
% LocalWords: sec fig eq expt sim dep const prob hist hists
+
+%% Other
+% Localwords: proven
@String{HErickson = "Erickson, Harold P."}
@String{MEsaki = "Esaki, Masatoshi"}
@String{JFernandez = "Fernandez, Julio M."}
+@String{GFranzen = "Franzen, Gereon"}
@String{ELFlorin = "Florin, Ernst-Ludwig"}
@String{SFossey = "Fossey, S. A."}
@String{SFowler = "Fowler, Susan B."}
@String{QPeng = "Peng, Qing"}
@String{OPerisic = "Perisic, Ognjen"}
@String{CPeterson = "Peterson, Craig L."}
+@String{EPuchner = "Puchner, Elias M."}
@String{LRandles = "Randles, Lucy G."}
@String{SRedick = "Redick, Sambra D."}
@String{ZReich = "Reich, Ziv"}
url = "http://www.pnas.org/content/105/20/7182.full",
eprint = "http://www.pnas.org/content/105/20/7182.full.pdf",
}
+
+@Article{puchner08,
+ author = EPuchner #" and "# GFranzen #" and "# MGautel #" and "# HGaub,
+ title = "Comparing proteins by their unfolding pattern.",
+ journal = BPJ,
+ year = 2008,
+ month = jul,
+ volume = 95,
+ number = 1,
+ pages = "426--434",
+ keywords = "Algorithms",
+ keywords = "Computer Simulation",
+ keywords = "Microscopy, Atomic Force",
+ keywords = "Models, Chemical",
+ keywords = "Models, Molecular",
+ keywords = "Protein Denaturation",
+ keywords = "Protein Folding",
+ keywords = "Proteins",
+ abstract = "Single molecule force spectroscopy has evolved into an
+ important and extremely powerful technique for
+ investigating the folding potentials of biomolecules.
+ Mechanical tension is applied to individual molecules,
+ and the subsequent, often stepwise unfolding is
+ recorded in force extension traces. However, because
+ the energy barriers of the folding potentials are often
+ close to the thermal energy, both the extensions and
+ the forces at which these barriers are overcome are
+ subject to marked fluctuations. Therefore, force
+ extension traces are an inadequate representation
+ despite widespread use particularly when large
+ populations of proteins need to be compared and
+ analyzed. We show in this article that contour length,
+ which is independent of fluctuations and alterable
+ experimental parameters, is a more appropriate variable
+ than extension. By transforming force extension traces
+ into contour length space, histograms are obtained that
+ directly represent the energy barriers. In contrast to
+ force extension traces, such barrier position
+ histograms can be averaged to investigate details of
+ the unfolding potential. The cross-superposition of
+ barrier position histograms allows us to detect and
+ visualize the order of unfolding events. We show with
+ this approach that in contrast to the sequential
+ unfolding of bacteriorhodopsin, two main steps in the
+ unfolding of the enzyme titin kinase are independent of
+ each other. The potential of this new method for
+ accurate and automated analysis of force spectroscopy
+ data and for novel automated screening techniques is
+ shown with bacteriorhodopsin and with protein
+ constructs containing GFP and titin kinase.",
+ ISSN = "1542-0086",
+ doi = "10.1529/biophysj.108.129999",
+ url = "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2426622/",
+ eprint = "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2426622/pdf/426.pdf",
+}
% }
\author{William Trevor King}
-\title{Mechanical protein unfolding analysis}
+\title{Temperature and cantilever dependent protein unfolding}
\defmonth{July}
\defyear{2010}
\degree{Doctor of Philosophy}
\include{tension/main}
\include{unfolding-distributions/main}
\include{sawsim/main}
-\include{contour-space} % TODO: conventional name?
-\include{apparatus/main}
+\include{contour-space/main}
\include{temperature-theory/main}
-\include{temperature/main}
+\include{apparatus/main}
\include{cantilever/main}
+\include{temperature/main}
\include{future/main}
\end{thesis}
\chapter{Temperature dependent unfolding theory}
+\label{sec:temperature-theory}
\section{Energy landscape roughness}
\chapter{Temperature dependent unfolding experiments}
+\label{sec:temperature}
\chapter{Chain Tension}
+\label{sec:tension}
\chapter{Theoretical unfolding force distributions}
+\label{sec:unfolding-distributions}
+
\input{unfolding-distributions/overview}
\input{unfolding-distributions/review}
\input{unfolding-distributions/singledomain_constantloading}
\chapter{Unfolding Theory}
+\label{sec:unfolding}
\chapter{Hydrodynamic effects in fast AFM single-molecule force measurements}
+\label{sec:viscocity}
\begin{center}
{\Large M\"uller notes} \\
projects / thesis.git / commitdiff