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="Conclusion", ax=ax)
ax1 = Template1.add_figure_border(figure, [-.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(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="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(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=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
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, "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",
]
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.",
]
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"""
# $\bf{Summary:}$
# - Members of the Src family of kinases (SFK) share well-conserved sequence
# features involving aromatic residues in their Unique domains.
# - SFK's UD sequences encodes specificity to input signals.
# - Shared mechanism among SFK's connecting disordered and structured domains
# and SFK's kinase activity.
# """
text_ = r"""
$\bf{Evolutionary\ conservation\ of\ implicit\ features\ in}$
$\bf{SFKs\ Unique\ Domain}$
- specificity to input signals
- Proline - Phenylalanine combination
"""
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",
]
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.",
]
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"""
# $\bf{Summary:}$
# - UD investigation via Real-Time NMR.
# - Phosphorylation of Src's Unique Domain at different Serie redidues.
# - Unique Domain as signaling hub between phosphorilative pathways and
# Src's activity.
# """
text_ = r"""
$\bf{Unique\ Domain\ as\ signaling\ hub\ between\ phosphorilative}$
$\bf{pathways\ and\ Src's\ activity}$
- UD-phosphorylation via Real-Time NMR.
- Phosphorylation at different Serie redidues.
"""
ax.text(x=0.45, y=0.55, s=text_, **Template1.text_box)
return figure, ax