From: W. Trevor King <wking@tremily.us>
Date: Sat, 18 May 2013 13:51:54 +0000 (-0400)
Subject: sawsim/discussion.tex: Clean up history of simulations section
X-Git-Tag: v1.0~167
X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=862681249440093de5ac6daff8365604f6cdf9d9;p=thesis.git

sawsim/discussion.tex: Clean up history of simulations section

Mom pointed out that MD wasn't in the nomenclature.
---

diff --git a/src/root.bib b/src/root.bib
index 19e6e3c..8c30e07 100644
--- a/src/root.bib
+++ b/src/root.bib
@@ -982,6 +982,7 @@
 @string{PTalkner = "Talkner, Peter"}
 @string{RTampe = "Tamp{\'e}, Robert"}
 @string{JTang = "Tang, Jianyong"}
+@string{PTavan = "Tavan, P."}
 @string{BNTaylor = "Taylor, Barry N."}
 @string{THEMath = "Technische Hogeschool Eindhoven, Nederland,
   Onderafdeling der Wiskunde"}
@@ -4032,6 +4033,55 @@
         verified experimentally but appears physically reasonable."
 }
 
+@article{ grubmuller96,
+  author = HGrubmuller #" and "# BHeymann #" and "# PTavan,
+  title = {Ligand binding: molecular mechanics calculation of the
+    streptavidin-biotin rupture force.},
+  year = 1996,
+  month = feb,
+  day = 16,
+  address = {Theoretische Biophysik, Institut f{\"u}r Medizinische
+             Optik, Ludwig- Maximilians-Universit{\"a}t M{\"u}nchen,
+             Germany. Helmut.Grubmueller@ Physik.uni-muenchen.de},
+  journal = SCI,
+  volume = 271,
+  number = 5251,
+  pages = {997--999},
+  issn = {0036-8075},
+  url = {http://www.ncbi.nlm.nih.gov/pubmed/8584939},
+  eprint = {http://pubman.mpdl.mpg.de/pubman/item/escidoc:1690312:2/component/escidoc:1690313/1690312.pdf},
+  language = {eng},
+  keywords = {Bacterial Proteins},
+  keywords = {Biotin},
+  keywords = {Chemistry, Physical},
+  keywords = {Computer Simulation},
+  keywords = {Hydrogen Bonding},
+  keywords = {Ligands},
+  keywords = {Microscopy, Atomic Force},
+  keywords = {Models, Chemical},
+  keywords = {Molecular Conformation},
+  keywords = {Physicochemical Phenomena},
+  keywords = {Protein Conformation},
+  keywords = {Streptavidin},
+  keywords = {Thermodynamics},
+  abstract = {The force required to rupture the streptavidin-biotin
+                 complex was calculated here by computer simulations.
+                 The computed force agrees well with that obtained by
+                 recent single molecule atomic force microscope
+                 experiments. These simulations suggest a detailed
+                 multiple-pathway rupture mechanism involving five major
+                 unbinding steps. Binding forces and specificity are
+                 attributed to a hydrogen bond network between the
+                 biotin ligand and residues within the binding pocket of
+                 streptavidin. During rupture, additional water bridges
+                 substantially enhance the stability of the complex and
+                 even dominate the binding interactions. In contrast,
+                 steric restraints do not appear to contribute to the
+                 binding forces, although conformational motions were
+                 observed.},
+}
+
+
 @article { izrailev97,
     author = SIzrailev #" and "# SStepaniants #" and "# MBalsera #" and "#
         YOono #" and "# KSchulten,
diff --git a/src/sawsim/discussion.tex b/src/sawsim/discussion.tex
index 6c0178f..3d3a167 100644
--- a/src/sawsim/discussion.tex
+++ b/src/sawsim/discussion.tex
@@ -614,8 +614,20 @@ There have been some tangential attempts towards even fancier models.
 
 \subsection{History of simulations}
 
-Early molecular dynamics (MD) work on receptor-ligand breakage by Grubmuller 1996 and Izrailev 1997 (according to Evans 1997).
-\citet{evans97} introduce a smart Monte Carlo (SMC) Kramers' simulation.
+There is a long history of protein unfolding and unbinding
+simulations.  Early work by \citet{grubmuller96} and
+\citet{izrailev97} focused on molecular dynamics (MD) simulations of
+receptor-ligand breakage.  Around the same time, \citet{evans97}
+introduced a Monte Carlo Kramers' simulation in the context of
+receptor-ligand breakage.  The approach pioneered by \citet{evans97}
+was used as the basis for analysis of the initial protein unfolding
+experiments\citep{rief97a}.  However, none of these earlier
+implementations were open source, which made it difficult to reuse or
+validate their results.
+%
+\nomenclature{MD}{Molecular dynamics simulation.  Simulate the
+  physical motion of atoms and molecules by numerically solving
+  Newton's equations.}
 
 \subsection{History of experimental AFM unfolding experiments}