def slide(page_number, figure=None, ax=None, title="", **kwargs):
Template1.add_suptitle(s="Lyn's isoforms NMR assignment", ax=ax)
ax1 = Template1.add_figure(figure, [0.01, 0.3, 0.36, 1],
"figs/Lyn_family_and_constructs_lined.png")
ax2 = Template1.add_figure(figure, [0.42, 0.25, 0.56, 1],
"figs/assignment_SH3.png")
ax3 = Template1.add_figure(figure, [0.42, -0.25, 0.56, 1],
"figs/assignment_USH3.png")
text_ = r"""$\bf{Collaborators:}$
- Szymon Zerko and Dr. Wiktor Kozminski
University of Warsaw, Poland.
$\bf{Techniques:}$
- 278K (UD) and 298K (UD-SH3)
- temperature curve for assignment transfer
Pons' Lab:
- Combination of 3D BEST-TROSY (NUS) experiments
Kozminski's Lab:
- Combination of 3D and 5D NUS experiments
"""
ax.text(x=0.02, y=0.6, s=text_, **Template1.text_box)
return figure, ax
def slide(page_number, figure=None, ax=None, title="", **kwargs):
Template1.add_suptitle(s="Lyn UD·SH3 interaction: view from SH3", ax=ax)
ax1 = Template1.add_figure(figure, [0.01, 0.38, 0.36, 1], "figs/Lyn_constructs_AB_USH3_vs_SH3.png")
ax2 = Template1.add_figure(figure, [0.065, 0.44, 0.02, 1], "figs/eyes.png")
ax2.set_zorder(3)
list_of_figs = [
"figs/USH4-SH3_LynA.png",
"figs/USH4-SH3_LynB.png",
]
x_pos = np.linspace(0.01, 0.65, 3)
list_of_figures = []
for xx, fig_path in zip(x_pos, list_of_figs):
list_of_figures.append(
Template1.add_figure(figure, [xx, -0.08, 0.27, 1], fig_path)
)
list_of_figures[-1].set_zorder(1)
ax.set_zorder(2)
return figure, ax
def slide(page_number, figure=None, ax=None, title="", **kwargs):
Template1.add_suptitle(s="Conclusion", ax=ax)
# ax1 = Template1.add_figure_border(figure, [0.1, 0.1, 0.8, 0.8], "figs/lyn_graphical_abs.png")
return figure, ax
def slide(page_number, figure=None, ax=None, title="", **kwargs):
Template1.add_suptitle(ax, "Src's Unique Domain")
#ax1 = Template1.add_figure(figure, [0.2, 0.2, 0.6, 0.6], "figs/src_scheme.png")
ax1 = Template1.add_figure(figure, [-0.05, 0.15, 1, 0.7],
"figs/SRC_inkspace_classical.png")
rect = mpatches.Rectangle((0.04, 0.04),
0.9,
0.9,
ec="none",
facecolor="white",
alpha=0.8)
ax.add_artist(rect)
#ax2 = Template1.add_axis(figure, [0.1, 0.1, 0.8, 0.8])
#rect = mpatches.Rectangle((0.1, 0.1), 0.8, 0.8, ec="none", zorder=10)
#patches = [rect]
#collection = PatchCollection(patches, alpha=0.9, color="white")
#ax2.add_collection(collection)
ax1.set_zorder(1)
ax.set_zorder(2)
return figure, ax
def slide(page_number, figure=None, ax=None, title="", **kwargs):
Template1.add_suptitle(s="Lyn UD·SH3 interaction: view from UDs", ax=ax)
ax1 = Template1.add_figure(figure, [0.01, 0.38 - .15, 0.5, 1],
"figs/lynA-UD_vs_LynAUSH3.png")
ax2 = Template1.add_figure(figure, [0.01, 0.2 - .15, 0.68, 1],
"figs/Lyn_UD_LynA_CSPs.png")
# ax3 = Template1.add_figure(figure, [0.01, 0.38 - .55, 0.5, 1], "figs/LynB-USH3_vs_LynAUSH3_constructs.png")
# ax4 = Template1.add_figure(figure, [0.01, 0.2 - .55, 0.68, 1], "figs/Lyn_UD_LynB_CSPs.png")
ax5 = Template1.add_figure(figure, [0.04, 0.77 - .5, 0.02, 1],
"figs/eyes.png")
# ax6 = Template1.add_figure(figure, [0.03, 0.37 - .5, 0.02, 1], "figs/eyes.png")
# conclusions
text_ = r"""
$\bf{Conclusions:}$
- In contrast to what was found for Src,
the initial 18 residues (SH4+) are not
affected by the presence of the SH3,
for both LynA and B.
- Only the UD interacts with the SH3.
- The most affected region is that absent
in LynB (alternative-splicing).
"""
ax.text(x=0.7, y=0.85, s=text_, **Template1.text_box)
return figure, ax
def slide(page_number, figure=None, ax=None, title="", **kwargs):
Template1.add_suptitle(s="Experimental approach", ax=ax)
ax1 = Template1.add_figure_border(figure, [-0.05, 0.2, 0.6, 0.6],
"figs/lyn_graphical_abs.png")
ax2 = Template1.add_figure(figure, [0.47, 0.2, 0.5, 1],
"figs/Lyn_family_and_constructs.png")
text_ = """
- NMR assignment of USH3 Lyn A and B
- Chemical Shift Perturbations (CSPs)
- Paramagnetic Relaxation Enhancements (PREs)
"""
ax.text(x=0.5,
y=0.45,
s=text_,
**{
**Template1.text_box,
**{
"fontsize": 16
}
})
return figure, ax
def slide(page_number, figure=None, ax=None, title="", **kwargs):
Template1.add_suptitle(s="Lyn's isoforms NMR assignment", ax=ax)
ax1 = Template1.add_figure(figure, [0.01, 0.3, 0.36, 1],
"figs/Lyn_family_and_constructs_lined.png")
return figure, ax
def slide(page_number, figure=None, ax=None, title="", **kwargs):
Template1.add_suptitle(ax, "SFKs and their Unique Domain")
ax1 = Template1.add_figure(figure, [0.2, 0.2, 0.6, 0.6],
"figs/src_scheme_canonical.png")
return figure, ax
def slide(page_number, figure=None, ax=None, title="", **kwargs):
Template1.add_suptitle(ax=ax, s="The Lyn case")
list_of_figures = [
Template1.add_figure(figure, [0, 0.6, 0.3, 0.3], "figs/SFKs_tree.png"),
]
return figure, ax
def slide(page_number, figure=None, ax=None, title="", **kwargs):
text_ = """What about other SFKs?
The Lyn case.
"""
Template1.add_maintitle(s=text_, ax=ax)
return figure, ax
def slide(page_number, figure=None, ax=None, title="", **kwargs):
Template1.add_suptitle(s="Experimental approach", ax=ax)
ax1 = Template1.add_figure_border(figure, [-0.05, 0.2, 0.6, 0.6],
"figs/lyn_graphical_abs.png")
ax2 = Template1.add_figure(figure, [0.47, 0.2, 0.5, 1],
"figs/Lyn_family_and_constructs.png")
return figure, ax
def slide(page_number, figure=None, ax=None, title="", **kwargs):
Template1.add_suptitle(s="Src Family Kinases", ax=ax)
# text_ = r"""$\bf{Brief\ on\ SFKs:}$
# - SFK: Src Family Kinases
# - $\bf{Src}$, Yes, Fyn, Fgr, $\bf{Lyn}$, Hck, Lck, Blk
# - $\bf{Membrane - associated}$, $\bf{non - receptor}$ tyrosine kinases
# - Signaling intermediaries: cell proliferation, differentiation, apoptosis,
# migration, and metabolism.
# - v-Src one of the first proteins associated with
# oncogenesis (Rous sarcome virus).
# - Yet, we still lack complete understanding of c-Src role in
# tumor development.
# """
# ax.text(x=0.01, y=0.95, s=text_, **Template1.text_box)
# text_ = r"""$\bf{Structural\ features\ of\ SFKs:}$
# - All SFKs share the same motif:
# - Disordered region
# - SH3 domain (regulatory)
# - SH2 domain (regulatory)
# - SH1 domain (kinase)
# - High homology in SH1-SH3 domains
# - Very low sequence homology in Unique Domains
# - Activation / Inhibition:
# - Phosphorylation of Tyr-530 triggers inter-domain compaction
# """
# ax.text(x=0.51, y=0.95, s=text_, **Template1.text_box)
ax1 = Template1.add_figure(figure, [-0.05, 0.15, 1, 0.7],
"figs/SRC_inkspace_UD.png")
# ax1.set_zorder(1)
# ax.set_zorder(2)
#circle1 = mpatches.Ellipse((0.6, 0.64), 0.15, 0.2, color='r', alpha=0.3)
#ax.add_artist(circle1)
return figure, ax
def slide(page_number, figure=None, ax=None, title="", **kwargs):
Template1.add_suptitle(s="SFKs and their Unique Domain", ax=ax)
text_ = r"""$\bf{Brief\ on\ SFKs:}$
- SFK: Src Family Kinases
- $\bf{Src}$, Yes, Fyn, Fgr, $\bf{Lyn}$, Hck, Lck, Blk
- $\bf{Membrane - associated}$, $\bf{non - receptor}$ tyrosine kinases
- Signaling intermediaries: cell proliferation, differentiation, apoptosis,
migration, and metabolism.
- v-Src one of the first proteins associated with
oncogenesis (Rous sarcome virus).
- Yet, we still lack complete understanding of c-Src role in
tumor development.
"""
ax.text(x=0.01, y=0.95, s=text_, **Template1.text_box)
text_ = r"""$\bf{Structural\ features\ of\ SFKs:}$
- All SFKs share the same motif:
- Disordered region
- SH3 domain (regulatory)
- SH2 domain (regulatory)
- SH1 domain (kinase)
- High homology in SH1-SH3 domains
- Very low sequence homology in Unique Domains
- Activation / Inhibition:
- Phosphorylation of Tyr-530 triggers inter-domain compaction
"""
ax.text(x=0.51, y=0.95, s=text_, **Template1.text_box)
ax1 = Template1.add_figure(figure, [0.2, -0.04, 0.6, 0.6],
"figs/src_scheme_canonical.png")
ax1.set_zorder(1)
ax.set_zorder(2)
return figure, ax
def slide(page_number, figure=None, ax=None, title="", **kwargs):
Template1.add_suptitle(ax=ax, s="The Lyn case")
list_of_figures = [
Template1.add_figure(figure, [0, 0.6, 0.3, 0.3], "figs/SFKs_tree.png"),
Template1.add_figure(figure, [0.37, 0.39, 0.6, 1],
"figs/SFKs_general_construct.png"),
]
ax.text(x=0.1,
y=0.4,
va="center",
ha="center",
s="LynA",
color=Template1.color,
fontsize=20,
zorder=1)
ax.text(x=0.24,
y=0.4,
va="center",
ha="center",
s="LynB",
color="red",
fontsize=20,
zorder=1)
ax.arrow(x=0.165,
y=0.6,
dx=-0.05,
dy=-0.15,
head_length=0.015,
head_width=0.01,
color="black")
ax.arrow(x=0.165,
y=0.6,
dx=0.05,
dy=-0.15,
head_length=0.015,
head_width=0.01,
color="black")
# rect = mpatches.Rectangle((0.54, 0.5), 0.45, 0.2, ec="none", facecolor="white", alpha=0.7)
# ax.add_artist(rect)
# ax.set_zorder(2)
return figure, ax
def slide(page_number, figure=None, ax=None, title="", **kwargs):
Template1.add_suptitle(s="Lyn UD·SH3 interaction: view from SH3", ax=ax)
ax1 = Template1.add_figure(figure, [0.01, 0.38, 0.36, 1],
"figs/Lyn_constructs_AB_USH3_vs_SH3.png")
ax2 = Template1.add_figure(figure, [0.065, 0.44, 0.02, 1], "figs/eyes.png")
list_of_figs = [
"figs/USH4-SH3_LynA.png",
"figs/USH4-SH3_LynB.png",
"figs/USH4-SH3_LynA-LynB.png",
]
x_pos = np.linspace(0.01, 0.44, 3)
list_of_figures = []
for xx, fig_path in zip(x_pos, list_of_figs):
list_of_figures.append(
Template1.add_figure(figure, [xx, -0.05, 0.22, 1], fig_path))
text_ = r"""
$\bf{Conclusions:}$
- Perturbations far from the connecting
residues indicate interdomain interactions
- Retained low $^1$H dispersion in SH4-UD confirm
these regions remain disordered upon binding.
- Largest perturbations found in $\beta_2$ and
$\beta_3$ strands and the connecting n-Src
loop.
- LynA additionally interacts with RT loop.
- Interaction with nSrc and 3$_{10}$ regions
is very similar in both isoforms.
"""
ax.text(x=0.67, y=0.8, s=text_, **Template1.text_box)
return figure, ax
def slide(page_number, figure=None, ax=None, **kwargs):
Template1.add_suptitle(s="Lyn USH3 vs PPP", ax=ax)
ax1 = Template1.add_figure(figure, [0.01, 0.42, 0.35, 1],
"figs/Lyn_constructs_AB_USH3_PPP.png")
# ax3 = Template1.add_figure(
# figure,
# [0.01, 0.19, 0.5, 1],
# "figs/LynAB_vs_PPP_CSPs.png"
# )
ax1.set_zorder(3)
# ax3.set_zorder(1)
# ax2 = Template1.add_figure(figure, [0.01, -0.06, 0.35, 1], "figs/Lyn_constructs_AB_USH3_PPP_vs_SH3-PPP.png")
# ax4 = Template1.add_figure(figure, [0.01, -0.29, 0.5, 1], "figs/USH3_SH3_vs_PPP_CSPs.png")
# ax2.set_zorder(1)
# ax4.set_zorder(1)
ax.set_zorder(2)
# text_ = r"""$\bf{Conclusions:}$
# - Binding of PPP affects the regions where
# UD binds the SH3 domain.
# - As expected, PPP displaces the Unique Domain
# from the interation.
# - However, UD-SH3 interaction is partially maintained
# for both LynA and LynB in the nSrc and 3$_10$ region.
# - Interaction between UD and the RT loop is completely
# abolished.
# - In the presence of saturating conditions of PPP
# LynA and LynB behave the same.
# """
# ax.text(x=0.6, y=0.8, s=text_, **Template1.text_box)
return figure, ax
def slide(page_number, figure=None, ax=None, **kwargs):
Template1.add_maintitle(
ax=ax, s=("Lyn's is a member of the Src Family Kinases..."))
sig = r"""$\bf{João\ M.C.\ Teixeira}$
http://bit.ly/joaomcteixeira"""
ax.text(
x=0.01,
y=0.02,
s=sig,
fontname=Template1.font,
color=Template1.color,
fontsize=12,
)
return figure, ax
def slide(page_number, figure=None, ax=None, title="", **kwargs):
Template1.add_suptitle(ax=ax, s="The Lyn case")
list_of_figures = [
Template1.add_figure(figure, [0, 0.6, 0.3, 0.3], "figs/SFKs_tree.png"),
Template1.add_figure(figure, [0.37, 0.39, 0.6, 1],
"figs/LynAB_general_construct.png"),
]
ax.text(x=0.1,
y=0.4,
va="center",
ha="center",
s="LynA",
color=Template1.color,
fontsize=20,
zorder=1)
ax.text(x=0.24,
y=0.4,
va="center",
ha="center",
s="LynB",
color="red",
fontsize=20,
zorder=1)
ax.arrow(x=0.165,
y=0.6,
dx=-0.05,
dy=-0.15,
head_length=0.015,
head_width=0.01,
color="black")
ax.arrow(x=0.165,
y=0.6,
dx=0.05,
dy=-0.15,
head_length=0.015,
head_width=0.01,
color="black")
return figure, ax
def slide(page_number, figure=None, ax=None, title="", **kwargs):
Template1.add_suptitle(s="Experimental approach", ax=ax)
ax1 = Template1.add_figure(figure, [-0.05, 0.2, 0.6, 0.6],
"figs/lyn_graphical_abs.png")
ax1.axis("on")
ax1.tick_params(
axis='both',
which='both',
bottom=False,
left=False,
labelbottom=False,
labelleft=False,
)
return figure, ax
def slide(page_number, figure=None, ax=None, title="", **kwargs):
Template1.add_suptitle(s="Conclusion", ax=ax)
ax1 = Template1.add_figure_border(figure, [-0.1, 0.1, 0.8, 0.8],
"figs/Graphical_Abstract.png")
text_ = r"""$\bf{Conclusions}$
- Lyn's Unique Domain interaction with SH3 domain
displays characteristics of a fuzzy interaction as in Src.
- This interaction differs between Lyn's natural isoforms.
- Both Lyn A and B share UD·SH3 interaction at nSrc loop
and 3$_{10}$ region (perturbations).
- Lyn A has additional interactions with RT Loop.
- Contrary to Src, the SH4 domain does NOT interact with
the SH3 domain.
- Lyn B Unique Domain is more compact than that of Lyn A.
- PPP displaces interactions at the RT loop, yet iterations
at the nSrc loop are partially maintained.
"""
ax.text(x=0.6, y=0.9, s=text_, **Template1.text_box)
ref = "Teixeira, J. M. C., et.al. (2018). Molecules, 23(11)"
ax.text(x=0.64,
y=0.1,
s=ref,
**{
**Template1.text_box,
**{
"color": Template1.color
}
})
return figure, ax
def slide(page_number, figure=None, ax=None, title="", **kwargs):
Template1.add_suptitle(s="Lyn UD·SH3 interaction: view from UDs", ax=ax)
ax1 = Template1.add_figure(figure, [0.01, 0.38 - .15, 0.5, 1], "figs/lynA-UD_vs_LynAUSH3.png")
ax2 = Template1.add_figure(figure, [0.01, 0.2 - .15, 0.68, 1], "figs/Lyn_UD_LynA_CSPs.png")
# ax3 = Template1.add_figure(figure, [0.01, 0.38 - .55, 0.5, 1], "figs/LynB-USH3_vs_LynAUSH3_constructs.png")
# ax4 = Template1.add_figure(figure, [0.01, 0.2 - .55, 0.68, 1], "figs/Lyn_UD_LynB_CSPs.png")
ax5 = Template1.add_figure(figure, [0.04, 0.77 - .5, 0.02, 1], "figs/eyes.png")
# ax6 = Template1.add_figure(figure, [0.03, 0.37 - .5, 0.02, 1], "figs/eyes.png")
# # conclusions
# text_ = r"""
# $\bf{Conclusions:}$
# - In contrast to what was found for Src,
# the initial 18 residues (SH4+) are not
# affected by the presence of the SH3,
# for both LynA and B.
# - Only the UD interacts with the SH3.
# - The most affected region is that absent
# in LynB (alternative-splicing).
# - The last 16 residues of the UD interact
# with the nSrc and 3$_10$ loops in SH3.
# - LynA region 23-43 interacts with RT loop.
# - Reg. 23-43 perturns interactions with nSrc
# loop and 3$_10$ region.
# """
# ax.text(x=0.7, y=0.85, s=text_, **Template1.text_box)
return figure, ax
def slide(page_number, figure=None, ax=None, **kwargs):
Template1.add_suptitle(s="Lyn C3-MTSL in USH3 constructs", ax=ax)
ax1 = Template1.add_figure(
figure, [0.5, 0.4, 0.5, 1],
"figs/Lyn_constructs_AB_USH3_vs_SH3_para_vs_dia.png")
#ax2 = Template1.add_figure(figure, [0.09, 0.42, 0.02, 1], "figs/eyes.png")
ax3 = Template1.add_figure(figure, [-.025, 0.2, 0.6, 1],
"figs/LynAB_PRE_UD.png")
ax4 = Template1.add_figure(figure, [-.025, -0.25, 0.6, 1],
"figs/LynAB_PRE_SH3.png")
ax.set_zorder(4)
ax1.set_zorder(3)
ax3.set_zorder(2)
ax4.set_zorder(1)
text_ = r"""$\bf{Conclusions:}$
- SH4-Unique Domains show relaxation enhancement
higher than expected for a random-coil model.
- Disordered regions are in a more compacted state.
- There are no clear differences between the PRE
profiles in the SH3 domain for both LynA and LynB.
- Confirms that SH4 does not interact with the SH3
domain and scans the domain's surface equally
in both isoforms.
"""
ax.text(x=0.6, y=0.7, s=text_, **Template1.text_box)
return figure, ax
def slide(page_number, figure=None, ax=None, **kwargs):
Template1.add_maintitle(
ax=ax,
s=(
"Lyn's natural isoforms display different fuzzy "
"complexes in UD-SH3 interaction"
)
)
sig = r"""$\bf{João\ M.C.\ Teixeira}$
http://bit.ly/joaomcteixeira"""
ax.text(
x=0.01,
y=0.02,
s=sig,
fontname=Template1.font,
color=Template1.color,
fontsize=12,
)
return figure, ax
def slide(page_number, figure=None, ax=None, **kwargs):
Template1.add_suptitle(s="Acknowledgements", ax=ax)
path = "figs/photo_mpons.png"
ax1 = Template1.add_figure(figure, [0.4, 0.35, 0.1, 1], path)
path = "figs/UB_logo_home_nou.png"
ax3 = Template1.add_figure(figure, [0.14, 0.8, 1, 0.1], path)
path = "figs/photo_wiktor.png"
ax2 = Template1.add_figure(figure, [0.4, 0.1, 0.1, 1], path)
path = "figs/wiktor_group.png"
ax4 = Template1.add_figure(figure, [0.18, 0.56, 1, 0.07], path)
text_ = r"""$\bf{Miquel\ Pons'\ Lab:}$
- Héctor Fuentes (Msc.)
- Stase Bielskute (Visiting Student)
- Marga Gairi (NMR Facility)
- Miquel Pons
$\bf{Kozminski's\ Lab:}$
- Disordered Region assignments
- Szymon Zerko
- Wiktor Kozminski
"""
ax.text(x=0.1, y=0.9, s=text_, **Template1.text_box)
text_ = r"""$\bf{Some\ data:}$
- +100 NMR experiments, including assignment and
interaction assays.
"""
ax.text(x=0.1, y=0.4, s=text_, **Template1.text_box)
return figure, ax
def slide(page_number, figure=None, ax=None, title="", **kwargs):
Template1.add_suptitle(ax=ax, s="The Lyn case")
return figure, ax
def slide(page_number, figure=None, ax=None, title="", **kwargs):
Template1.add_suptitle(ax, "Brief highligh on Src's Unique Domain")
path = "figs/photo_mpons.png"
ax0 = Template1.add_figure(figure, [0.88, 0.35, 0.1, 1], path)
ax1 = Template1.add_figure(figure, [-0.05, 0.15, 1, 0.7],
"figs/SRC_inkspace_classical.png")
rect = mpatches.Rectangle((0.04, 0.04),
0.9,
0.9,
ec="none",
facecolor="white",
alpha=0.95)
ax.add_artist(rect)
ax0.set_zorder(10)
ax1.set_zorder(1)
ax.set_zorder(2)
# add titulares
list_of_fig_paths = [
"figs/paper_2009.png",
"figs/paper_2013_1.png",
]
y_pos_array = np.linspace(0.3, -0.2, 6)
list_of_figures = []
for y_pos, fig_path in zip(y_pos_array, list_of_fig_paths):
list_of_figures.append(
Template1.add_figure_border(figure, [0.03, y_pos, 0.4, 1],
fig_path))
for layer_level, ax_i in enumerate(list_of_figures, start=3):
# ax_i.axis("on")
# ax_i.tick_params(
# axis='both',
# which='both',
# bottom=False,
# left=False,
# labelbottom=False,
# labelleft=False,
# )
ax_i.set_zorder(layer_level)
# adds reference list
list_of_references = [
"· Pérez, Y., et.al (2009). Journal of Molecular Biology, 391(1), 136–148.",
"· Pérez, Y., et.al. (2013). Scientific Reports, 3, 1295.",
]
bullet_count = np.linspace(0.94, 0.6, 10)
for y_pos, ref in zip(bullet_count, list_of_references):
ax.text(y=y_pos, x=0.46, s=ref, **Template1.references_props)
# add text box
# rect2 = mpatches.FancyBboxPatch((0.5, 0.1), 0.45, 0.5, boxstyle=mpatches.BoxStyle("Round", pad=0.02))
# patches = [rect2]
# collection = PatchCollection(patches, facecolor="white", edgecolor="black", linewidth=1)
# ax.add_collection(collection)
# text_ = r"""
# $\bf{Summary:}$
# - Interactions between Unique and SH3 domains reported for the first time.
# - UD and SH3 lipid binding -> Unique Lipid Binding Region.
# - UD/SH3 lipid binding regulated by phosphorylation and CaM.
# - Mutations in ULBR change metastatic phenotype $\mathit{in vivo}$.
# - Disordered UD as new regulatory layer.
# """
text_ = r"""
$\bf{Disordered\ domain\ (UD)\ as\ a\ new\ Src\ regulatory\ layer}$
- UD·SH3 interactions reported
- UD's Unique Lipid Binding Region
- Modulations by phosphorylation
- UD affects metastatic phenotype
"""
ax.text(x=0.45, y=0.55, s=text_, **Template1.text_box)
return figure, ax
def slide(page_number, figure=None, ax=None, title="", **kwargs):
Template1.add_suptitle(ax, "Brief highligh on Src's Unique Domain")
path = "figs/photo_mpons.png"
ax0 = Template1.add_figure(figure, [0.88, 0.35, 0.1, 1], path)
ax1 = Template1.add_figure(figure, [-0.05, 0.15, 1, 0.7],
"figs/SRC_inkspace_classical.png")
rect = mpatches.Rectangle((0.04, 0.04),
0.9,
0.9,
ec="none",
facecolor="white",
alpha=0.95)
ax.add_artist(rect)
ax0.set_zorder(10)
ax1.set_zorder(1)
ax.set_zorder(2)
ax.patch.set_facecolor('none')
# add titulares
list_of_fig_paths = [
"figs/paper_2009.png",
]
y_pos_array = np.linspace(0.3, -0.2, 6)
list_of_figures = []
for y_pos, fig_path in zip(y_pos_array, list_of_fig_paths):
list_of_figures.append(
Template1.add_figure_border(figure, [0.03, y_pos, 0.4, 1],
fig_path))
for layer_level, ax_i in enumerate(list_of_figures, start=3):
# ax_i.axis("on")
# ax_i.tick_params(
# axis='both',
# which='both',
# bottom=False,
# left=False,
# labelbottom=False,
# labelleft=False,
# )
ax_i.set_zorder(layer_level)
# adds reference list
list_of_references = [
"· Pérez, Y., et.al (2009). Journal of Molecular Biology, 391(1), 136–148.",
]
bullet_count = np.linspace(0.94, 0.6, 10)
for y_pos, ref in zip(bullet_count, list_of_references):
ax.text(y=y_pos, x=0.46, s=ref, **Template1.references_props)
# add text box
# rect2 = mpatches.FancyBboxPatch((0.5, 0.1), 0.45, 0.5, boxstyle=mpatches.BoxStyle("Round", pad=0.02))
# patches = [rect2]
# collection = PatchCollection(patches, facecolor="white", edgecolor="black", linewidth=1)
# ax.add_collection(collection)
# text_ = r"""
# $\bf{Summary:}$
# - First structural characterization by NMR of the isolated Src's DISORDERED
# SH4 and Unique Domains.
# - NMR assignment, and charactization via CSPs and RDCs.
# - Identification of particular region deviating from random-coil, later known
# as Unique Lipid Binding Region (ULBR).
# - Initial assessment of phosphorilation effects on overall structure.
# """
text_ = r"""
$\bf{First\ structural\ characterization\ of\ the\ isolated\ Src's}$
$\bf{N-terminal\ DISORDERED\ region\ by\ NMR}$
- CSPs, RDCs and simulations
- SH4 and Unique Domains.
"""
ax.text(x=0.45, y=0.55, s=text_, **Template1.text_box)
return figure, ax
def slide(page_number, figure=None, ax=None, title="", **kwargs):
Template1.add_suptitle(ax=ax, s="The Lyn case")
list_of_figures = [
Template1.add_figure(figure, [0, 0.6, 0.3, 0.3], "figs/SFKs_tree.png"),
Template1.add_figure(figure, [0.37, 0.39, 0.6, 1],
"figs/LynAB_general_construct.png"),
Template1.add_figure(figure, [0.04, -.1, 0.9, 0.4],
"figs/Lyn_FASTA_2.png"),
]
ax.text(x=0.1,
y=0.4,
va="center",
ha="center",
s="LynA",
color=Template1.color,
fontsize=20,
zorder=1)
ax.text(x=0.24,
y=0.4,
va="center",
ha="center",
s="LynB",
color="red",
fontsize=20,
zorder=1)
ax.arrow(x=0.165,
y=0.6,
dx=-0.05,
dy=-0.15,
head_length=0.015,
head_width=0.01,
color="black")
ax.arrow(x=0.165,
y=0.6,
dx=0.05,
dy=-0.15,
head_length=0.015,
head_width=0.01,
color="black")
# rect = mpatches.Rectangle((0.54, 0.5), 0.45, 0.2, ec="none", facecolor="white", alpha=0.7)
# ax.add_artist(rect)
# ax.set_zorder(2)
list_of_figures[1].set_zorder(1)
text_ = r"""$\bf{Known\ Biological\ Implications:}$
- Lyn mainly expressed in hematopoietic cells
- Direct relation with immunological responses
- LynB -> alternative splicing
- 21 a.a. insert at UD
- Correct LynA::LynB ratio required for normalized responses.
- ONLY LynA promotes invasion in Breast Cancer (overexpression)
- STRUCTURAL origin remains obscure.
"""
ax.text(x=0.4,
y=0.74,
s=text_,
color="black",
fontname=Template1.font,
linespacing=2,
va="top",
ha="left",
fontsize=14,
zorder=1)
ax.text(
x=0.4,
y=0.24,
s=("Alvarez-Errico, D., et.al. (2010). The Journal of Immunology, 184(9), 5000–5008.\n"
"Tornillo, G., et. al. (2018). Cell Reports, 3674–3692."),
zorder=1,
**Template1.references_props)
for i in list_of_figures:
i.set_zorder(1)
rect = mpatches.Rectangle(
(0.01, 0.03),
0.98,
0.94,
facecolor="white",
ec="none",
alpha=0.8,
zorder=2,
)
ax.add_artist(rect)
ax_abs = Template1.add_figure_border(figure, [0.1, 0.1, 0.8, 0.8],
"figs/lyn_graphical_abs.png")
ax.set_zorder(2)
ax_abs.set_zorder(3)
return figure, ax
def slide(page_number, figure=None, ax=None, title="", **kwargs):
Template1.add_suptitle(ax, "Brief highligh on Src's Unique Domain")
path = "figs/photo_mpons.png"
ax0 = Template1.add_figure(figure, [0.88, 0.35, 0.1, 1], path)
ax1 = Template1.add_figure(figure, [-0.05, 0.15, 1, 0.7],
"figs/SRC_inkspace_classical.png")
rect = mpatches.Rectangle((0.04, 0.04),
0.9,
0.9,
ec="none",
facecolor="white",
alpha=0.95)
ax.add_artist(rect)
ax0.set_zorder(10)
ax1.set_zorder(1)
ax.set_zorder(2)
# add titulares
list_of_fig_paths = [
"figs/paper_2009.png",
"figs/paper_2013_1.png",
"figs/paper_2013_2.png",
"figs/paper_2015.png",
]
y_pos_array = np.linspace(0.3, -0.2, 6)
list_of_figures = []
for y_pos, fig_path in zip(y_pos_array, list_of_fig_paths):
list_of_figures.append(
Template1.add_figure_border(figure, [0.03, y_pos, 0.4, 1],
fig_path))
for layer_level, ax_i in enumerate(list_of_figures, start=3):
# ax_i.axis("on")
# ax_i.tick_params(
# axis='both',
# which='both',
# bottom=False,
# left=False,
# labelbottom=False,
# labelleft=False,
# )
ax_i.set_zorder(layer_level)
# adds reference list
list_of_references = [
"· Pérez, Y., et.al (2009). Journal of Molecular Biology, 391(1), 136–148.",
"· Pérez, Y., et.al. (2013). Scientific Reports, 3, 1295.",
"· Amata, I., et.al. (2013). Chembiochem, 14(14), 1820–1827.",
"· Maffei, M., et. al. (2015). Structure, 893–902.",
]
bullet_count = np.linspace(0.94, 0.6, 10)
for y_pos, ref in zip(bullet_count, list_of_references):
ax.text(y=y_pos, x=0.46, s=ref, **Template1.references_props)
# add text box
# rect2 = mpatches.FancyBboxPatch((0.5, 0.1), 0.45, 0.5, boxstyle=mpatches.BoxStyle("Round", pad=0.02))
# patches = [rect2]
# collection = PatchCollection(patches, facecolor="white", edgecolor="black", linewidth=1)
# ax.add_collection(collection)
# text_ = r"""
# $\bf{Summary:}$
# - Disordered SH4-UD interaction with folded SH3 domain.
# - Unique·SH3 interaction modulated via PolyProline peptide inhibitor.
# - SH3 domain suggested as scafold between UD mediated signaling
# and Src kinase activity.
# """
text_ = r"""
$\bf{SH3\ domain\ suggested\ as\ scafold\ between\ UD\ mediated}$
$\bf{signaling\ and\ Src\ kinase\ activity}$
- UD·SH3·Polyproline peptide allostery
"""
ax.text(x=0.45, y=0.55, s=text_, **Template1.text_box)
return figure, ax
def slide(page_number, figure=None, ax=None, title="", **kwargs):
Template1.add_suptitle(ax, "Brief highligh on Src's Unique Domain")
path = "figs/photo_mpons.png"
ax0 = Template1.add_figure(figure, [0.88, 0.35, 0.1, 1], path)
ax1 = Template1.add_figure(figure, [-0.05, 0.15, 1, 0.7], "figs/SRC_inkspace_classical.png")
rect = mpatches.Rectangle((0.04, 0.04), 0.9, 0.9, ec="none",
facecolor="white", alpha=0.95)
ax.add_artist(rect)
ax0.set_zorder(10)
ax1.set_zorder(1)
ax.set_zorder(2)
# add titulares
list_of_fig_paths = [
"figs/paper_2009.png",
"figs/paper_2013_1.png",
"figs/paper_2013_2.png",
"figs/paper_2015.png",
"figs/paper_2017.png",
"figs/paper_2019_2.png",
]
y_pos_array = np.linspace(0.3, -0.2, 6)
list_of_figures = []
for y_pos, fig_path in zip(y_pos_array, list_of_fig_paths):
list_of_figures.append(
Template1.add_figure_border(figure, [0.03, y_pos, 0.4, 1], fig_path)
)
for layer_level, ax_i in enumerate(list_of_figures, start=3):
# ax_i.axis("on")
# ax_i.tick_params(
# axis='both',
# which='both',
# bottom=False,
# left=False,
# labelbottom=False,
# labelleft=False,
# )
ax_i.set_zorder(layer_level)
# adds reference list
list_of_references = [
"· Pérez, Y., et.al (2009). Journal of Molecular Biology, 391(1), 136–148.",
"· Pérez, Y., et.al. (2013). Scientific Reports, 3, 1295.",
"· Amata, I., et.al. (2013). Chembiochem, 14(14), 1820–1827.",
"· Maffei, M., et. al. (2015). Structure, 893–902.",
"· Arbesú, M., et.al. (2017). Structure, 25(4), 630–640.e4.",
"· Le Roux, A.L., et.al. (2019). iScience, Accepted.",
"",
"Additional reviews:",
"· Amata, I., et. al. (2014). Frontiers in Genetics, 5(June), 1–6.",
"· Arbesú, M., et.al. (2018). Frontiers in Molecular Biosciences, 5(April), 1–7.",
]
bullet_count = np.linspace(0.94, 0.6, 10)
for y_pos, ref in zip(bullet_count, list_of_references):
ax.text(y=y_pos, x=0.46, s=ref, **Template1.references_props)
# add text box
# rect2 = mpatches.FancyBboxPatch((0.5, 0.1), 0.45, 0.5, boxstyle=mpatches.BoxStyle("Round", pad=0.02))
# patches = [rect2]
# collection = PatchCollection(patches, facecolor="white", edgecolor="black", linewidth=1)
# ax.add_collection(collection)
# text_ = r"""
# $\bf{Summary:}$
# - The N-terminal myristoyl group binds to the SH3 domain in the
# proximity of the RT loop in cytosolic Src.
# - Residues in the Unique Lipid Binding Region modulate this interaction.
# - The fuzzy complex between SH4-UD and SH3 domain is retained in the
# membrane bound form.
# - UD drives SH3 domain close to the membrane surface and restricting
# its orientation.
# """
text_ = r"""
$\bf{Network\ of\ interactions\ UD·SH3\ regulated\ by\ myristoylation}$
- The N-terminal myristoyl group binds to the SH3 domain.
- Modulated by lipid binding (ULBR).
- The UD·SH3 fuzzy complex retained in the membrane bound form.
"""
ax.text(x=0.45, y=0.55, s=text_, **Template1.text_box)
return figure, ax
