From 0032855addfa26ce6e826308ddb3d3397f2a1529 Mon Sep 17 00:00:00 2001 From: "W. Trevor King" Date: Wed, 15 May 2013 20:11:50 -0400 Subject: [PATCH] Fix 'timescales' -> 'time scales', and other assorted typos As pointed out by Granddaddy: * "because it takes a quite a bit": The first "a" is redundant * "timescales": this is awkward: "time-scales" is more logical than "timescales." I suggest you hyphenate this word. * "unfolding experiment, they observed ...": "the" is a typo I went with "time scale" which we see in abstracts for evans97, lu99, evans01, msli06, mickler07. "timescale" shows up in dietz04, but I agree with Graddaddy that it's awkward. I imagine the shortening comes from writing too much software and/or speaking German ;). I fixed some other things I noticed along the way. --- src/apparatus/polymer-synthesis.tex | 4 +-- src/calibcant/discussion.tex | 2 +- src/introduction/main.tex | 15 +++++---- src/root.bib | 48 +++++++++++++++-------------- src/sawsim/methods.tex | 4 +-- 5 files changed, 37 insertions(+), 36 deletions(-) diff --git a/src/apparatus/polymer-synthesis.tex b/src/apparatus/polymer-synthesis.tex index 5ac5814..ecb511b 100644 --- a/src/apparatus/polymer-synthesis.tex +++ b/src/apparatus/polymer-synthesis.tex @@ -10,8 +10,8 @@ a muscle protein involved in passive elasticity the effect of mechanical force\citep{labeit95}. Titin is also interesting because, while it is one of the largest known proteins, it is composed of a series of globular domains. When \citet{rief97a} -carried out their seminal unfolding experiment, the observed a very -charachteristic sawtooth as the domains unfolded (see +carried out their seminal unfolding experiment, they observed a very +characteristic sawtooth as the domains unfolded (see \cref{sec:procedure} for a discussion of these sawteeth). \begin{figure} diff --git a/src/calibcant/discussion.tex b/src/calibcant/discussion.tex index 2b6672c..cb186dd 100644 --- a/src/calibcant/discussion.tex +++ b/src/calibcant/discussion.tex @@ -77,7 +77,7 @@ thermal vibrations) several times, we can estimate the statistical uncertainty in each parameter (\cref{fig:calibcant:statistics}). Values for $\sigma_p$ and $\avg{V_p^2}$ are quite sensitive to the location of the laser spot on the cantilever, so they can vary over -large timescales as the microscope alignment drifts (e.g.~due to +large time scales as the microscope alignment drifts (e.g.~due to thermal expansion as the room warms up). However TODO For example, on a recent calibration run\footnote{2013-02-07T08-20-46} diff --git a/src/introduction/main.tex b/src/introduction/main.tex index 8d0b107..34650ab 100644 --- a/src/introduction/main.tex +++ b/src/introduction/main.tex @@ -146,14 +146,13 @@ Single molecule techniques provide an opportunity to study protein folding and unfolding at the level of a single molecule, where the distinction between the pathway model and funnel model is clearer. They also provide a convenient benchmark for verifying molecular -dynamics simulations, because it takes a quite a bit of computing -power to simulate even one biopolymer with anything close to atomic -resolution over experimental timescales. Even with significant -computing resources, comparing molecular dynamics results with -experimental data remains elusive. For example, experimental pulling -speeds are on the order of \bareU{$\mu$m/s}, while simulation pulling -speeds are on the order of -\bareU{m/s}\citep{lu98,lu99,rief02,zhao06,berkemeier11}. +dynamics simulations, because it takes lots of computing power to +simulate even one biopolymer with anything close to atomic resolution +over experimental time scales. Even with significant computing +resources, comparing molecular dynamics results with experimental data +remains elusive. For example, experimental pulling speeds are on the +order of \bareU{$\mu$m/s}, while simulation pulling speeds are on the +order of \bareU{m/s}\citep{lu98,lu99,rief02,zhao06,berkemeier11}. % why AFM & what an AFM is Single molecule techniques for manipulating biopolymers include diff --git a/src/root.bib b/src/root.bib index 8d04f80..d93800e 100644 --- a/src/root.bib +++ b/src/root.bib @@ -2512,25 +2512,28 @@ doi = "10.1073/pnas.0404549101", eprint = "http://www.pnas.org/cgi/reprint/101/46/16192.pdf", url = "http://www.pnas.org/cgi/content/abstract/101/46/16192", - abstract = "We use single-molecule force spectroscopy to drive single GFP - molecules from the native state through their complex energy landscape - into the completely unfolded state. Unlike many smaller proteins, - mechanical GFP unfolding proceeds by means of two subsequent - intermediate states. The transition from the native state to the first - intermediate state occurs near thermal equilibrium at {approx}35 pN and + abstract = "We use single-molecule force spectroscopy to drive + single GFP molecules from the native state through their + complex energy landscape into the completely unfolded + state. Unlike many smaller proteins, mechanical GFP unfolding + proceeds by means of two subsequent intermediate states. The + transition from the native state to the first intermediate + state occurs near thermal equilibrium at $\approx35\U{pN}$ and is characterized by detachment of a seven-residue N-terminal - {alpha}-helix from the beta barrel. We measure the equilibrium free - energy cost associated with this transition as 22 kBT. Detachment of - this small {alpha}-helix completely destabilizes GFP thermodynamically - even though the {beta}-barrel is still intact and can bear load. - Mechanical stability of the protein on the millisecond timescale, - however, is determined by the activation barrier of unfolding the - {beta}-barrel out of this thermodynamically unstable intermediate - state. High bandwidth, time-resolved measurements of the cantilever - relaxation phase upon unfolding of the {beta}-barrel revealed a second - metastable mechanical intermediate with one complete {beta}-strand - detached from the barrel. Quantitative analysis of force distributions - and lifetimes lead to a detailed picture of the complex mechanical + $\alpha$-helix from the beta barrel. We measure the + equilibrium free energy cost associated with this transition + as 22 kBT. Detachment of this small $\alpha$-helix completely + destabilizes GFP thermodynamically even though the + $\beta$-barrel is still intact and can bear load. Mechanical + stability of the protein on the millisecond timescale, + however, is determined by the activation barrier of unfolding + the $\beta$-barrel out of this thermodynamically unstable + intermediate state. High bandwidth, time-resolved measurements + of the cantilever relaxation phase upon unfolding of the + $\beta$-barrel revealed a second metastable mechanical + intermediate with one complete $\beta$-strand detached from + the barrel. Quantitative analysis of force distributions and + lifetimes lead to a detailed picture of the complex mechanical unfolding pathway through a rough energy landscape.", note = "Nice energy-landscape-to-one-dimension compression graphic. Unfolding Green Flourescent Protein (GFP) towards using it as an @@ -2884,8 +2887,7 @@ pages = "105--128", issn = "1056-8700", doi = "10.1146/annurev.biophys.30.1.105", - url = "http://arjournals.annualreviews.org/doi/abs/10.1146%2Fannurev.biophy - s.30.1.105", + url = "http://arjournals.annualreviews.org/doi/abs/10.1146%2Fannurev.biophys.30.1.105", keywords = "Biophysics;Kinetics;Microscopy, Atomic Force;Models, Chemical;Protein Binding;Spectrum Analysis;Time Factors", abstract = "On laboratory time scales, the energy landscape of a weak bond @@ -4383,7 +4385,7 @@ protein) for all 20 structures deposited in the Protein Data Bank. Our approach suggests a natural way to measure the phase diagram in the (f,C) plane, where C is the concentration of denaturants.", - note = "Simulated unfolding timescales for Ig27-like S1 and S2 domains" + note = {Simulated unfolding time scales for Ig27-like S1 and S2 domains.}, } @article { klimov99, @@ -5579,8 +5581,8 @@ including a characterization of the structures, albeit at a coarse- grained level, of the three metastable intermediates.", note = {Hiccup in unfolding leg corresponds to unfolding - intermediate (\fref{figure}{2}). The unfolding timescale in GFP - is about $6\U{ms}.} + intermediate (\fref{figure}{2}). The unfolding time scale in GFP + is about $6\U{ms}$.}, } @article { nevo03, diff --git a/src/sawsim/methods.tex b/src/sawsim/methods.tex index 733b39b..8f9c8ea 100644 --- a/src/sawsim/methods.tex +++ b/src/sawsim/methods.tex @@ -328,12 +328,12 @@ one sawtooth in the force curve. As the pulling continues and more domains unfold, force curves with a series of sawteeth are generated (\cref{fig:sawsim:sim-sawtooth}). -\subsubsection{Equlibration timescales} +\subsubsection{Equlibration time scales} \label{sec:sawsim:timescales} The tension calculation assumes an equilibrated chain, so consideration must be given to the chain's relaxation time, which -should be short compared to the loading timescale. The relaxation +should be short compared to the loading time scale. The relaxation time for a WLC\index{WLC!relaxation time} is given by \begin{equation} \tau \approx \eta \frac{k_BT p}{F^2} -- 2.26.2