From 88d2ce49cf1cb863867c629ecc4f9a5e6f87281c Mon Sep 17 00:00:00 2001 From: "W. Trevor King" Date: Tue, 23 Feb 2010 11:19:24 -0500 Subject: [PATCH] Added Introduction \section{Thesis Outline}. Spellchecked introduction/main.tex. Changed title (again :p) to: "Temperature and cantilever dependent protein unfolding" --- tex/src/apparatus/main.tex | 1 + tex/src/cantilever-calib/main.tex | 2 + tex/src/cantilever/main.tex | 8 ++++ tex/src/contour-space/main.tex | 5 ++- tex/src/future/main.tex | 3 +- tex/src/introduction/main.tex | 30 ++++++++++++- tex/src/local_words | 15 +++++-- tex/src/root.bib | 57 ++++++++++++++++++++++++ tex/src/root.tex | 8 ++-- tex/src/temperature-theory/main.tex | 1 + tex/src/temperature/main.tex | 1 + tex/src/tension/main.tex | 1 + tex/src/unfolding-distributions/main.tex | 2 + tex/src/unfolding/main.tex | 1 + tex/src/viscocity/main.tex | 1 + 15 files changed, 125 insertions(+), 11 deletions(-) diff --git a/tex/src/apparatus/main.tex b/tex/src/apparatus/main.tex index 9416383..b14b075 100644 --- a/tex/src/apparatus/main.tex +++ b/tex/src/apparatus/main.tex @@ -1 +1,2 @@ \chapter{Apparatus} +\label{sec:apparatus} diff --git a/tex/src/cantilever-calib/main.tex b/tex/src/cantilever-calib/main.tex index 8a5555f..3c1486f 100644 --- a/tex/src/cantilever-calib/main.tex +++ b/tex/src/cantilever-calib/main.tex @@ -1,4 +1,6 @@ \chapter{Cantilever Calibration} +\label{sec:cantilever-calib} + \input{cantilever-calib/overview} \input{cantilever-calib/setup_general} \input{cantilever-calib/solve_highly_damped} diff --git a/tex/src/cantilever/main.tex b/tex/src/cantilever/main.tex index 652b193..b8da235 100644 --- a/tex/src/cantilever/main.tex +++ b/tex/src/cantilever/main.tex @@ -1 +1,9 @@ \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. + diff --git a/tex/src/contour-space/main.tex b/tex/src/contour-space/main.tex index 5a07ff2..9111f72 100644 --- a/tex/src/contour-space/main.tex +++ b/tex/src/contour-space/main.tex @@ -1 +1,4 @@ -\chapter{Contour space} +\chapter{Contour length space} +\label{sec:contour-space} + +TODO\citet{puchner08}. diff --git a/tex/src/future/main.tex b/tex/src/future/main.tex index 211dd41..0a46023 100644 --- a/tex/src/future/main.tex +++ b/tex/src/future/main.tex @@ -1 +1,2 @@ -\chapter{Conclusions} +\chapter{Conclusions and future work} +\label{sec:future} diff --git a/tex/src/introduction/main.tex b/tex/src/introduction/main.tex index 19f9004..adbfce1 100644 --- a/tex/src/introduction/main.tex +++ b/tex/src/introduction/main.tex @@ -46,7 +46,7 @@ remarkably difficult. 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} @@ -142,6 +142,9 @@ stimulated much effort in both experimental and theoretical research. \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 @@ -196,3 +199,28 @@ time, facilitating single molecule studies. \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. diff --git a/tex/src/local_words b/tex/src/local_words index f7b26b9..e03a47d 100644 --- a/tex/src/local_words +++ b/tex/src/local_words @@ -2,20 +2,24 @@ %% 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 @@ -23,3 +27,6 @@ %% Reference abbreviations % LocalWords: sec fig eq expt sim dep const prob hist hists + +%% Other +% Localwords: proven diff --git a/tex/src/root.bib b/tex/src/root.bib index 0b6d288..76752d4 100644 --- a/tex/src/root.bib +++ b/tex/src/root.bib @@ -142,6 +142,7 @@ @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."} @@ -235,6 +236,7 @@ @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"} @@ -7573,3 +7575,58 @@ url = "http://www.sciencedirect.com/science/article/B6WBK-4F5M7K3-3C/2/c94b612e0 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", +} diff --git a/tex/src/root.tex b/tex/src/root.tex index eb392b6..a40095a 100644 --- a/tex/src/root.tex +++ b/tex/src/root.tex @@ -19,7 +19,7 @@ % } \author{William Trevor King} -\title{Mechanical protein unfolding analysis} +\title{Temperature and cantilever dependent protein unfolding} \defmonth{July} \defyear{2010} \degree{Doctor of Philosophy} @@ -57,11 +57,11 @@ R01-GM071793. \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} diff --git a/tex/src/temperature-theory/main.tex b/tex/src/temperature-theory/main.tex index 5901bee..1980f0e 100644 --- a/tex/src/temperature-theory/main.tex +++ b/tex/src/temperature-theory/main.tex @@ -1,4 +1,5 @@ \chapter{Temperature dependent unfolding theory} +\label{sec:temperature-theory} \section{Energy landscape roughness} diff --git a/tex/src/temperature/main.tex b/tex/src/temperature/main.tex index accb47f..354d00c 100644 --- a/tex/src/temperature/main.tex +++ b/tex/src/temperature/main.tex @@ -1 +1,2 @@ \chapter{Temperature dependent unfolding experiments} +\label{sec:temperature} diff --git a/tex/src/tension/main.tex b/tex/src/tension/main.tex index 3d626d4..8d59ee2 100644 --- a/tex/src/tension/main.tex +++ b/tex/src/tension/main.tex @@ -1 +1,2 @@ \chapter{Chain Tension} +\label{sec:tension} diff --git a/tex/src/unfolding-distributions/main.tex b/tex/src/unfolding-distributions/main.tex index 411dd10..22481c6 100644 --- a/tex/src/unfolding-distributions/main.tex +++ b/tex/src/unfolding-distributions/main.tex @@ -1,4 +1,6 @@ \chapter{Theoretical unfolding force distributions} +\label{sec:unfolding-distributions} + \input{unfolding-distributions/overview} \input{unfolding-distributions/review} \input{unfolding-distributions/singledomain_constantloading} diff --git a/tex/src/unfolding/main.tex b/tex/src/unfolding/main.tex index 7b0e701..9cdc232 100644 --- a/tex/src/unfolding/main.tex +++ b/tex/src/unfolding/main.tex @@ -1 +1,2 @@ \chapter{Unfolding Theory} +\label{sec:unfolding} diff --git a/tex/src/viscocity/main.tex b/tex/src/viscocity/main.tex index d8d8cfb..8ec3c4f 100644 --- a/tex/src/viscocity/main.tex +++ b/tex/src/viscocity/main.tex @@ -1,4 +1,5 @@ \chapter{Hydrodynamic effects in fast AFM single-molecule force measurements} +\label{sec:viscocity} \begin{center} {\Large M\"uller notes} \\ -- 2.26.2