From 518345149384fbb491f51f28c365b0dfda6d8cae Mon Sep 17 00:00:00 2001 From: "W. Trevor King" Date: Thu, 13 Jun 2013 11:23:11 -0400 Subject: [PATCH] salt/main.tex: Add 1TIT-hbond figure based on lu00b --- src/figures/i27/1TIT-hbond.pml | 131 +++++++++++++++++++++++++++++++++ src/salt/main.tex | 16 +++- 2 files changed, 145 insertions(+), 2 deletions(-) create mode 100644 src/figures/i27/1TIT-hbond.pml diff --git a/src/figures/i27/1TIT-hbond.pml b/src/figures/i27/1TIT-hbond.pml new file mode 100644 index 0000000..6771d05 --- /dev/null +++ b/src/figures/i27/1TIT-hbond.pml @@ -0,0 +1,131 @@ +load 1TIT.pdb + +# opaque white background with lots of fog +set ray_opaque_background, on +set transparency, 0 +bg_color white +set depth_cue, 1 +set ray_trace_fog, 1 +set fog_start, 0 +set fog, -1000 + +# max performance (slower) +util.performance(0) +# printable CMYK colors +cmd.space('cmyk') + +# ball and stick display style +#set_bond stick_color, white, (all), (all) +#set_bond stick_radius, 0.14, (all), (all) +#set sphere_scale, 0.25, (all) + +# stick-only display style +set_bond stick_radius, 0.2, (all), (all) +# but still use sphere for backbone-bound hydrogens +set sphere_scale, 0.25, (all) + +# add hydrogens to protein +h_add (all) + +# Setup selection groups + +select backbone, name C+O+N+CA +select backbone_h, (elem H and neighbor name N) + +# N-terminus +select n_term, resi 1 +# C-terminus +select c_term, resi 89 + +# sheet A +select sheet_a, resi 3-6 +# sheet A' +select sheet_ap, resi 9-15 +# sheet B (last few residues) +select sheet_b, resi 24-26 +# sheet G (last few residues) +select sheet_g, resi 83-87 +# tip and tail +select early, resi 1-29 +select late, resi 80-89 + +# anything in the interesting chains +select front, (sheet_a or sheet_ap or sheet_b or sheet_g) +select interesting, (front or late or early) + +# Ca-sensitive residues +select ca_res, resn asp+glu +select hot, (ca_res and front) + +# don't show anything except the backbone +hide everything, all +#show sticks, backbone +#show spheres, backbone + +# draw hydrogen bonds +#dist hbond, front, all, mode=2 +#dist hbond, all, front, mode=2 +#dist hbond, all, all, mode=2 +#dist hbond, front, front, mode=2 +# manually match lu00 +distance hbond_a, (resi 3 and name O), (resi 26 and backbone_h), mode=0 +distance hbond_b, (resi 6 and backbone_h), (resi 24 and name O), mode=0 +distance hbond_c, (resi 6 and name O), (resi 24 and backbone_h), mode=0 +distance hbond_d, (resi 9 and name O), (resi 83 and backbone_h), mode=0 +distance hbond_e, (resi 11 and backbone_h), (resi 83 and name O), mode=0 +distance hbond_f, (resi 13 and backbone_h), (resi 85 and name O), mode=0 +distance hbond_g, (resi 13 and name O), (resi 87 and backbone_h), mode=0 +distance hbond_h, (resi 15 and backbone_h), (resi 87 and name O), mode=0 +# but don't label the distances +hide labels + +# decorate selections +show sticks, backbone +set_bond stick_radius, 0.05, (all), (all) +set_bond stick_radius, 0.2, (interesting), (interesting) +#show spheres, (backbone and interesting) +show spheres, (front and backbone_h) +color white, all +color lightblue, early +color lightpink, late +color brown, n_term +color cyan, c_term +color br0, sheet_a +color br2, sheet_ap +color br4, sheet_b +color br6, sheet_g +color red, (hot and resn asp) +color green, (hot and resn glu) +color yellow, hbond_a +color yellow, hbond_b +color yellow, hbond_c +color yellow, hbond_d +color yellow, hbond_e +color yellow, hbond_f +color yellow, hbond_g +color yellow, hbond_h + +# zoom so molecule fills window +set_view (\ + 1.000000000, 0.000000000, 0.000000000,\ + 0.000000000, 0.087155743, 0.996194698,\ + 0.000000000, -0.996194698, -0.087155743,\ + 0.000000000, -5.000000000, -40.000000000,\ + 0.043053962, 0.000000000, 4.578000069,\ + 20.000000000, 60.000000000, 45.000000000 ) +# view matrix (from pymol.viewing.get_view) +# 3x3 matrix rotating model space to camera space +# 1x3 origin of rotation relative to camera in camera space +# 1x3 origin of rotation relative to camera in model space +# 1x1 front plane distance from the camera +# 1x1 rear plane distance from the camera +# 1x1 orthoscopic flag (+/-) and field of view (if abs(value) > 1) +# The camera always looks down -Z with its +X left and its +Y down. +# Therefore, in the default view, model +X is to the observer\'s +# right, +Y is upward, and +Z points toward the observer. +# +# To zoom, tweak the field-of-view setting, decreasing to zoom in. + +# render with 640 pixel width +png 1TIT-hbond.png, width=640 +quit diff --git a/src/salt/main.tex b/src/salt/main.tex index 135b80b..a6ff6e8 100644 --- a/src/salt/main.tex +++ b/src/salt/main.tex @@ -19,8 +19,20 @@ aspartic and glutamic acid groups tend to have a strong affinity for cations while argenine has a strong affinity for the \Cl\ anion\citep{friedman11}. Of these amino acids, only glutamic acid occurs in the key hydrogen bond regions responsible for I27 -unfolding\citep{lu00b}. \NaCl\ has also been shown to decrease -hydrogen bonding\citep{zidar11}. +unfolding\citep{lu00b} (\cref{fig:I27:H-bonds}). \NaCl\ has also been +shown to decrease hydrogen bonding\citep{zidar11}. + +\begin{figure} + \begin{center} + \includegraphics[width=0.5\textwidth]{figures/i27/1TIT-hbond} + \caption{The backbone of I27 showing the eight key hydogen bonds + responsible for the critical unfolding force. Glutamic acids + are highlighted in green. Based on \xref{lu00b}{figure}{1b}. + For a ribbon diagram of I27 showing the $\beta$-sheets, see + \cref{fig:I27}. This figure was also generated with + \citetalias{pymol}.\label{fig:I27:H-bonds}} + \end{center} +\end{figure} We added $0.5\U{M}$ \CaCl\ to our standard PBS (\cref{sec:sample-preparation}), which is much larger than -- 2.26.2