From: W. Trevor King Date: Thu, 18 Nov 2010 18:10:29 +0000 (-0500) Subject: Add force spectroscopy and research posts. X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=caf7a4a6e4c300fc75d5252eb550d5bb017a4032;p=blog.git Add force spectroscopy and research posts. --- diff --git a/posts/Force_spectroscopy.mdwn b/posts/Force_spectroscopy.mdwn new file mode 100644 index 0000000..afa48f7 --- /dev/null +++ b/posts/Force_spectroscopy.mdwn @@ -0,0 +1,41 @@ +[Force spectroscopy][fs] is the process of extracting information +about the unfolding (or unbinding) characteristics of a protein (or +ligand-receptor pair) by measuring force vs. extension curves while +gradually ripping the protein (or pair) apart. Consider this cartoon +representation of the procedure + +[[!img afm_protein_pulling_cartoon.jpg class="scaled" + alt="Protein unfolding cartoon" + title="Protein unfolding cartoon"]] + +The AFM tip is pulling a protein chain away from the substrate, +causing one of the protein domains to uncoil. + +The procedure yields 'force curves' like this + +[[!img force_curve_regions.png class="scaled" + alt="Protein unfolding force curve" + title="Protein unfolding force curve"]] + +To interpret the force curve, let us examine it piece-by-piece as the +AFM tip gradually pulls away from the substrate. + +1. The linear 'contact' region demonstrates the Hooke's law behavior + of the AFM cantilever, with force ∝ displacement. +2. The high force 'bulge' linking the contact region to the sawtooth + comes from the AFM tip pulling free of the surface and associated + protein 'mat' (the cartoon being excessively pretty, and our sample + having too high a protein concentration :p). +3. The characteristic 'sawtooth' comes from several identical domains + unfolding one after the other. +4. After the last of the protein domains unfolds the protein snaps off + of the AFM tip (or the substrate), and the deflection of the + now-free cantilever ceases to depend on distance. + +[[!img force_curve_regions_cantilever.png class="scaled" + alt="Force curve cantilever positions" + title="Force curve cantilever positions"]] + +[fs]: http://en.wikipedia.org/wiki/Force_spectroscopy + +[[!tag tags/theory]] diff --git a/posts/Force_spectroscopy/afm_protein_pulling_cartoon.jpg b/posts/Force_spectroscopy/afm_protein_pulling_cartoon.jpg new file mode 100644 index 0000000..babc3be Binary files /dev/null and b/posts/Force_spectroscopy/afm_protein_pulling_cartoon.jpg differ diff --git a/posts/Force_spectroscopy/force_curve_regions.png b/posts/Force_spectroscopy/force_curve_regions.png new file mode 100644 index 0000000..2b74dd3 Binary files /dev/null and b/posts/Force_spectroscopy/force_curve_regions.png differ diff --git a/posts/Force_spectroscopy/force_curve_regions_cantilever.png b/posts/Force_spectroscopy/force_curve_regions_cantilever.png new file mode 100644 index 0000000..b1fd863 Binary files /dev/null and b/posts/Force_spectroscopy/force_curve_regions_cantilever.png differ diff --git a/posts/Gentoo_overlay.mdwn b/posts/Gentoo_overlay.mdwn index b0d9d3e..a3a5c3a 100644 --- a/posts/Gentoo_overlay.mdwn +++ b/posts/Gentoo_overlay.mdwn @@ -23,7 +23,7 @@ personal `layman.xml`). The overlay is a fairly strange mix: ([Gentoo 76017](http://bugs.gentoo.org/76017), also in the [Sunrise overlay][]) - sci-physics/hooke - (my branch of the [[Hooke]] force spectroscopy analyzer) + (my branch of the [[Hooke]] [[force spectroscopy]] analyzer) - sci-physics/sawsim (my [[sawsim]] force spectroscopy simulator) diff --git a/posts/Hooke.mdwn b/posts/Hooke.mdwn index 38d5d52..97af0c5 100644 --- a/posts/Hooke.mdwn +++ b/posts/Hooke.mdwn @@ -1,11 +1,11 @@ [[!template id=hgrepo repo=hooke]] -[Hooke][] is a force spectroscopy data analysis package. For example, -Hooke can extract unfolding forces from your experimental data. You -can then fit the unfolding forces to models using my [[sawsim]] -simulator. Of course, some experiments (e.g. force clamp) need no -Monte Carlo analysis, so for those, Hooke alone provides a complete -analysis package. +[Hooke][] is a [[force spectroscopy]] data analysis package. For +example, Hooke can extract unfolding forces from your experimental +data. You can then fit the unfolding forces to models using my +[[sawsim]] simulator. Of course, some experiments (e.g. force clamp) +need no Monte Carlo analysis, so for those, Hooke alone provides a +complete analysis package. Getting started =============== diff --git a/posts/Research.mdwn b/posts/Research.mdwn new file mode 100644 index 0000000..1c15be3 --- /dev/null +++ b/posts/Research.mdwn @@ -0,0 +1,20 @@ +My current work for [Prof. Yang][GY] involves unfolding proteins using +an Atomic Force Microscope (AFM) at different temperatures to estimate +the roughness of their free energy landscape. For a brief overview of +force spectroscopy, see my [[two second +summary|Force_spectroscopy]]. For more detail, you can look at some of +my [[papers|tags/papers]]. + +I've written some [[experimental control software|unfold_protein]], a +Monte Carlo simulation program ([[sawsim]]) for analyzing the +unfolding sawtooth curves, as well as software for calibrating AFM +cantilevers via the thermal tune method ([[calibcant]]), scaling the +unfolding data, selecting good curves, and fitting those curves with +wormlike chains ([[Hooke]]). + +Along the way I've had to learn way too much about the internal +workings of our [[MultiMode]] AFM. + +I've also posted my notes for our [[Debian cluster|Abax]]. + +[GY]: http://www.physics.drexel.edu/~gyang/ diff --git a/posts/sawsim.mdwn b/posts/sawsim.mdwn index fdb2b61..15882ae 100644 --- a/posts/sawsim.mdwn +++ b/posts/sawsim.mdwn @@ -4,7 +4,7 @@ Introduction ============ My [[thesis]] project investigates protein unfolding via the -experimental technique of [force spectroscopy][fs]. In force +experimental technique of [[force spectroscopy]]. In force spectroscopy, we mechanically stretch chains of proteins, usually by pulling one end of the chain away from a surface with an [AFM][]. @@ -27,7 +27,6 @@ actually going on behind the scenes. Sawsim is my ([published][]!) tool for simulating force spectroscopy experiments and matching the simulations to experimental results. -[fs]: http://en.wikipedia.org/wiki/Force_spectroscopy [AFM]: http://en.wikipedia.org/wiki/Atomic_force_microscopy [published]: http://dx.doi.org/10.1016/j.ijbiomac.2009.12.001