From: W. Trevor King Date: Sat, 23 Oct 2010 16:39:32 +0000 (-0400) Subject: Added dates to carrion-vazques99* which swapped a <-> b. X-Git-Tag: v1.0~366 X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=0ac4440a540bbebfc606b6ad7c49384d33462f83;p=thesis.git Added dates to carrion-vazques99* which swapped a <-> b. --- diff --git a/tex/src/cantilever/methods.tex b/tex/src/cantilever/methods.tex index 373f045..5ac0c54 100644 --- a/tex/src/cantilever/methods.tex +++ b/tex/src/cantilever/methods.tex @@ -5,7 +5,7 @@ The experiments were carried out on octomers of I27 (\cref{fig:I27}). \nomenclature{I27}{Immunoglobulin-like domain 27 from human Titin}\index{I27} I27 is a model protein that has been used in mechanical unfolding experiments since the first use of synthetic -chains\citep{carrion-vazquez99b,TODO}. It was used here because it is +chains\citep{carrion-vazquez99a,TODO}. It was used here because it is both well characterized and readily available (% \href{http://www.athenaes.com/}{AthenaES}, Baltimore, MD, \href{http://www.athenaes.com/I27OAFMReferenceProtein.php}{0304}). diff --git a/tex/src/cantilever/theory.tex b/tex/src/cantilever/theory.tex index ae30cd9..7ab8b31 100644 --- a/tex/src/cantilever/theory.tex +++ b/tex/src/cantilever/theory.tex @@ -26,7 +26,7 @@ tension. The Bell-model unfolding rate is thus and stiffer linkers will increase the mean unfolding force. Unfolded I27 domains can be well-modeled as wormlike chains (WLCs, -\cref{sec:tension:wlc})\citep{carrion-vazquez99b}, where $p \approx +\cref{sec:tension:wlc})\citep{carrion-vazquez99a}, where $p \approx 4\U{\AA}$ is the persistence length, and $L \approx 28\U{nm}$ is the contour length of the unfolded domain. Obviously effective stiffness of an unfolded I27 domain is highly dependent on the unfolding force, diff --git a/tex/src/introduction/main.tex b/tex/src/introduction/main.tex index cd8e510..1ba7bef 100644 --- a/tex/src/introduction/main.tex +++ b/tex/src/introduction/main.tex @@ -116,7 +116,7 @@ microscopes\citep{halvorsen09}. Of these mechanical manipulation methods, AFM is the most widely used due to the availability of user-friendly commercial instruments. AFM has been employed on several types of biological macromolecules, mechanically unfolding -proteins\citep{carrion-vazquez99b} and forcing structural transitions +proteins\citep{carrion-vazquez99a} and forcing structural transitions in DNA\citep{rief99} and polysaccharides\citep{rief97b}. An AFM\index{AFM} uses a sharp tip integrated at the end of a cantilever to interact with the sample. Cantilever bending is measured by a @@ -162,7 +162,7 @@ interactions between the AFM tip and the substrate may be stronger than the forces required to unfold the protein when the surfaces are a few nanometers apart. To circumvent these difficulties, globular protein molecules are linked into polymers, which are then used in the -AFM studies\citep{carrion-vazquez99b,chyan04,carrion-vazquez03}. When +AFM studies\citep{carrion-vazquez99a,chyan04,carrion-vazquez03}. When such a polymer is pulled from its ends, each protein molecule feels the externally applied force, which increases the probability of unfolding by reducing the free energy barrier between the native and diff --git a/tex/src/root.bib b/tex/src/root.bib index 2203e0a..f04841d 100644 --- a/tex/src/root.bib +++ b/tex/src/root.bib @@ -1838,11 +1838,30 @@ } @article { carrion-vazquez99a, + author = MCarrionVazquez #" and "# AOberhauser #" and "# SFowler #" and "# + PMarszalek #" and "# SBroedel #" and "# JClarke #" and "# JFernandez, + title = "Mechanical and chemical unfolding of a single protein: A + comparison", + year = 1999, + month = mar, + day = 30, + journal = PNAS, + volume = 96, + number = 7, + pages = "3694--3699", + doi = "10.1073/pnas.96.7.3694", + eprint = "http://www.pnas.org/cgi/reprint/96/7/3694.pdf", + url = "http://www.pnas.org/cgi/content/abstract/96/7/3694" +} + +@article { carrion-vazquez99b, author = MCarrionVazquez #" and "# PMarszalek #" and "# AOberhauser #" and "# JFernandez, title = "Atomic force microscopy captures length phenotypes in single proteins", year = 1999, + month = sep, + day = 28, journal = PNAS, volume = 96, number = 20, @@ -1853,21 +1872,6 @@ abstract = "" } -@article { carrion-vazquez99b, - author = MCarrionVazquez #" and "# AOberhauser #" and "# SFowler #" and "# - PMarszalek #" and "# SBroedel #" and "# JClarke #" and "# JFernandez, - title = "Mechanical and chemical unfolding of a single protein: A - comparison", - year = 1999, - journal = PNAS, - volume = 96, - number = 7, - pages = "3694--3699", - doi = "10.1073/pnas.96.7.3694", - eprint = "http://www.pnas.org/cgi/reprint/96/7/3694.pdf", - url = "http://www.pnas.org/cgi/content/abstract/96/7/3694" -} - @article { chyan04, author = CLChyan #" and "# FCLin #" and "# HPeng #" and "# JMYuan #" and "# CHChang #" and "# SHLin #" and "# GYang, diff --git a/tex/src/sawsim/introduction.tex b/tex/src/sawsim/introduction.tex index a0522d9..aff4c47 100644 --- a/tex/src/sawsim/introduction.tex +++ b/tex/src/sawsim/introduction.tex @@ -23,7 +23,7 @@ as the distance from the native state to the transition state along the pulling direction. The Monte Carlo simulation method has been used since the first report of mechanical unfolding experiments using the AFM% -\citep{rief97b,rief97a,rief98,carrion-vazquez99b,best02,zinober02,jollymore09}, +\citep{rief97b,rief97a,rief98,carrion-vazquez99a,best02,zinober02,jollymore09}, but these previous implementations are neither fully described nor publicly available. diff --git a/tex/src/unfolding-distributions/review.tex b/tex/src/unfolding-distributions/review.tex index b561b05..5e45b19 100644 --- a/tex/src/unfolding-distributions/review.tex +++ b/tex/src/unfolding-distributions/review.tex @@ -5,7 +5,7 @@ There's not all that much information here, but it's a good place to go to get a big-picture overview before diving into the more technical papers. There are two main approaches to modeling protein domain unfolding under tension: Bell's and Kramers'\citep{schlierf06,dudko06,hummer03}. -Bell introduced his model in the context of cell adhesion\citep{bell78}, but it has been widely used to model mechanical unfolding in proteins\citep{rief97a,carrion-vazquez99b,schlierf06} due to it's simplicity and ease of use\citep{hummer03}. +Bell introduced his model in the context of cell adhesion\citep{bell78}, but it has been widely used to model mechanical unfolding in proteins\citep{rief97a,carrion-vazquez99a,schlierf06} due to it's simplicity and ease of use\citep{hummer03}. Kramers introduced his theory in the context of thermally activated barrier crossings, which is how we use it here. There is an excellent review of Kramers' theory in \citet{hanggi90}.