From: W. Trevor King Date: Sat, 23 Oct 2010 16:49:18 +0000 (-0400) Subject: Added dates to rief97* which swapped a <-> b. X-Git-Tag: v1.0~365 X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=4c32843dfed54c01dc31c3ab77a968f72bedc8ce;p=thesis.git Added dates to rief97* which swapped a <-> b. --- diff --git a/tex/src/introduction/main.tex b/tex/src/introduction/main.tex index 1ba7bef..3abb644 100644 --- a/tex/src/introduction/main.tex +++ b/tex/src/introduction/main.tex @@ -117,7 +117,7 @@ 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-vazquez99a} and forcing structural transitions -in DNA\citep{rief99} and polysaccharides\citep{rief97b}. An +in DNA\citep{rief99} and polysaccharides\citep{rief97a}. 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 laser reflected off the cantilever and incident on a position diff --git a/tex/src/root.bib b/tex/src/root.bib index f04841d..889fd8b 100644 --- a/tex/src/root.bib +++ b/tex/src/root.bib @@ -1213,6 +1213,8 @@ title = "A simple method for probing the mechanical unfolding pathway of proteins in detail", year = 2002, + month = sep, + day = 17, journal = PNAS, volume = 99, number = 19, @@ -5557,27 +5559,6 @@ } @article { rief97a, - author = MRief #" and "# MGautel #" and "# FOesterhelt #" and "# JFernandez - #" and "# HEGaub, - title = "Reversible Unfolding of Individual Titin Immunoglobulin Domains by - {AFM}", - year = 1997, - journal = SCI, - volume = 276, - number = 5315, - pages = "1109--1112", - doi = "10.1126/science.276.5315.1109", - eprint = "http://www.sciencemag.org/cgi/reprint/276/5315/1109.pdf", - url = "http://www.sciencemag.org/cgi/content/abstract/276/5315/1109", - note = "Seminal paper for force spectroscopy on Titin. Cited by - \citet{dietz04} (ref 9) as an example of how unfolding large proteins - is easily interpreted (vs.\ confusing unfolding in bulk), but Titin is - a rather simple example of that, because of its globular-chain - structure.", - project = "Energy Landscape Roughness" -} - -@article { rief97b, author = MRief #" and "# FOesterhelt #" and "# BHeymann #" and "# HEGaub, title = "Single Molecule Force Spectroscopy on Polysaccharides by Atomic Force Microscopy", @@ -5606,6 +5587,29 @@ reversible and was corroborated by molecular dynamics calculations." } +@article { rief97b, + author = MRief #" and "# MGautel #" and "# FOesterhelt #" and "# JFernandez + #" and "# HEGaub, + title = "Reversible Unfolding of Individual Titin Immunoglobulin Domains by + {AFM}", + year = 1997, + month = may, + day = 16, + journal = SCI, + volume = 276, + number = 5315, + pages = "1109--1112", + doi = "10.1126/science.276.5315.1109", + eprint = "http://www.sciencemag.org/cgi/reprint/276/5315/1109.pdf", + url = "http://www.sciencemag.org/cgi/content/abstract/276/5315/1109", + note = "Seminal paper for force spectroscopy on Titin. Cited by + \citet{dietz04} (ref 9) as an example of how unfolding large proteins + is easily interpreted (vs.\ confusing unfolding in bulk), but Titin is + a rather simple example of that, because of its globular-chain + structure.", + project = "Energy Landscape Roughness" +} + @article { rief98, author = MRief #" and "# JFernandez #" and "# HEGaub, title = "Elastically Coupled Two-Level Systems as a Model for Biopolymer diff --git a/tex/src/sawsim/introduction.tex b/tex/src/sawsim/introduction.tex index aff4c47..474df66 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-vazquez99a,best02,zinober02,jollymore09}, +\citep{rief97a,rief97b,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 5e45b19..42b2540 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-vazquez99a,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{rief97b,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}. @@ -59,7 +59,7 @@ or laser-tweezers based \subsection{Evolution of unfolding modeling} Evans introduced the saddle-point Kramers' approximation in a protein unfolding context 1997 (\citet{evans97} Eqn.~3). -However, early work on mechanical unfolding focused on the simper Bell model\citep{rief97a}.%TODO +However, early work on mechanical unfolding focused on the simper Bell model\citep{rief97b}.%TODO In the early `00's, the saddle-point/steepest-descent approximation to Kramer's model (\citet{hanggi90} Eqn.~4.56c) was introduced into our field\citep{dudko03,hyeon03}.%TODO By the mid `00's, the full-blown double-integral form of Kramer's model (\citet{hanggi90} Eqn.~4.56b) was in use\citep{schlierf06}.%TODO @@ -75,7 +75,7 @@ Early molecular dynamics (MD) work on receptor-ligand breakage by Grubmuller 199 \subsection{History of experimental AFM unfolding experiments} \begin{itemize} - \item \citet{rief97a}: + \item \citet{rief97b}: \end{itemize} \subsection{History of experimental laser tweezer unfolding experiments}