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Galvanization.lyx
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#LyX 2.3 created this file. For more info see http://www.lyx.org/
\lyxformat 544
\begin_document
\begin_header
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\origin unavailable
\textclass classicthesis
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\begin_body
\begin_layout Chapter
Galvanization of Protein–Protein Interactions in a Dynamic Zinc Interactome
\end_layout
\begin_layout Standard
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
chaptermark{
\backslash
protect
\backslash
parbox{0.9
\backslash
linewidth}{Galvanization of Protein-Protein Interactions in a Dynamic Zinc
Interactome}}
\end_layout
\end_inset
\end_layout
\begin_layout Standard
\begin_inset CommandInset label
LatexCommand label
name "chap:Galvanization-of-Protein-Protein"
\end_inset
\end_layout
\begin_layout Standard
\shape smallcaps
Anna Kocyła, Józef Ba Tran and Artur Krężel
\shape default
\begin_inset Newline newline
\end_inset
\begin_inset Flex CT - Spaced Low Small Caps
status open
\begin_layout Plain Layout
Department of Chemical Biology, Faculty of Biotechnology, University of
Wrocław, F.
Joliot-Curie 14a, 50-383 Wrocław, Poland
\end_layout
\end_inset
\begin_inset Newline newline
\end_inset
\shape italic
Trends in Biochemical Sciences
\shape default
\size small
\size default
2021 46(1), 64–79.
\begin_inset VSpace medskip
\end_inset
\end_layout
\begin_layout Section
Brief history and bibliometric data
\end_layout
\begin_layout Standard
The first chapters presenting published work of mine (
\begin_inset Flex CT - auto cross-reference
status open
\begin_layout Plain Layout
\begin_inset CommandInset ref
LatexCommand labelonly
reference "chap:Galvanization-of-Protein-Protein"
plural "false"
caps "false"
noprefix "false"
\end_inset
\end_layout
\end_inset
and
\begin_inset Flex CT - auto cross-reference
status open
\begin_layout Plain Layout
\begin_inset CommandInset ref
LatexCommand labelonly
reference "chap:InterMetalDB"
plural "false"
caps "false"
noprefix "false"
\end_inset
\end_layout
\end_inset
) focus mostly on
\emph on
in silico
\emph default
endeavors to systematically describe, and characterize metal-involved
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
glspl{ppi}
\end_layout
\end_inset
.
My contribution in neither of the articles would not be possible without
involvement in the wet lab experiments from the very beginning of my master's
and doctoral studies.
My ongoing journey with computer programming began as a mere way to make
my laboratory work easier.
Producing countless amounts of data, I had to prepare scripts to pre-process
the raw data or workflows to facilitate data analysis, some of those scripts
were made at the request of my coworkers (e.g.
the script that was part of the fluorescence lifetime analysis workflow),
some already may solve the problems of the researchers on the other continents.
\begin_inset Foot
status open
\begin_layout Plain Layout
Allowing for batch export of the data from
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
gls{cd}
\end_layout
\end_inset
like
\begin_inset CommandInset href
LatexCommand href
name "jws2txt"
target "https://github.com/jzftran/jws2txt"
literal "false"
\end_inset
, mentioned at:
\begin_inset Flex URL
status open
\begin_layout Plain Layout
https://www.researchgate.net/post/Batch_export_processing_of_Jasco_interval_data_f
iles_jwb_to_csv
\end_layout
\end_inset
.
\begin_inset Note Note
status open
\begin_layout Plain Layout
, or adding the multiple-binding sites model for the open
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
gls{code}
\end_layout
\end_inset
program for
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
gls{itc}
\end_layout
\end_inset
analysis.
\begin_inset Note Note
status open
\begin_layout Plain Layout
need to be done
\end_layout
\end_inset
\end_layout
\end_inset
\end_layout
\end_inset
My interest in programming led to a collaboration with Anna Kocyła on the
\begin_inset CommandInset citation
LatexCommand citetitle
key "Kocyla2021"
literal "true"
\end_inset
, where I was able to use my skills in preparing a structural data set of
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
glspl{zppi}
\end_layout
\end_inset
.
After the few years I have been back to scripts written for our publication,
I am pleased with how much I have grown in terms of writing clear and efficient
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
gls{code}
\end_layout
\end_inset
.
And though the
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
gls{code}
\end_layout
\end_inset
I have written at the time was not beautiful, to say, it worked and was
one of the reasons why we were able to select around 150 examples of the
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
gls{zppi}
\end_layout
\end_inset
deposited in the
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
gls{rcsb}
\end_layout
\end_inset
and publish our results in a well-renowned journal
\shape italic
Trends in Biochemical Sciences
\emph on
, the
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
gls{if}
\end_layout
\end_inset
of 14.264 (as of March 6, 2023).
\shape default
\emph default
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
begin{pycode}[sessionA]
\end_layout
\begin_layout Plain Layout
from scholarly import scholarly
\end_layout
\begin_layout Plain Layout
\end_layout
\begin_layout Plain Layout
num2words = {1: 'one',
\end_layout
\begin_layout Plain Layout
2: 'two',
\end_layout
\begin_layout Plain Layout
3: 'three',
\end_layout
\begin_layout Plain Layout
4: 'four',
\end_layout
\begin_layout Plain Layout
5: 'five',
\end_layout
\begin_layout Plain Layout
6: 'six',
\end_layout
\begin_layout Plain Layout
7: 'seven',
\end_layout
\begin_layout Plain Layout
8: 'eight',
\end_layout
\begin_layout Plain Layout
9: 'nine',
\end_layout
\begin_layout Plain Layout
10: 'ten',
\end_layout
\begin_layout Plain Layout
11: 'eleven',
\end_layout
\begin_layout Plain Layout
12: 'twelve',
\end_layout
\begin_layout Plain Layout
13: 'thirteen',
\end_layout
\begin_layout Plain Layout
14: 'fourteen',
\end_layout
\begin_layout Plain Layout
15: 'fifteen',
\end_layout
\begin_layout Plain Layout
16: 'sixteen',
\end_layout
\begin_layout Plain Layout
17: 'seventeen',
\end_layout
\begin_layout Plain Layout
18: 'eighteen',
\end_layout
\begin_layout Plain Layout
19: 'nineteen',
\end_layout
\begin_layout Plain Layout
20: 'twenty',
\end_layout
\begin_layout Plain Layout
30: 'thirty',
\end_layout
\begin_layout Plain Layout
40: 'forty',
\end_layout
\begin_layout Plain Layout
50: 'fifty',
\end_layout
\begin_layout Plain Layout
60: 'sixty',
\end_layout
\begin_layout Plain Layout
70: 'seventy',
\end_layout
\begin_layout Plain Layout
80: 'eighty',
\end_layout
\begin_layout Plain Layout
90: 'ninety',
\end_layout
\begin_layout Plain Layout
0: 'zero'}
\end_layout
\begin_layout Plain Layout
\end_layout
\begin_layout Plain Layout
\end_layout
\begin_layout Plain Layout
def n2w(n):
\end_layout
\begin_layout Plain Layout
try:
\end_layout
\begin_layout Plain Layout
return (num2words[n])
\end_layout
\begin_layout Plain Layout
except KeyError:
\end_layout
\begin_layout Plain Layout
try:
\end_layout
\begin_layout Plain Layout
return ((num2words[n-n % 10]) + ' ' + (num2words[n % 10].lower()))
\end_layout
\begin_layout Plain Layout
except KeyError:
\end_layout
\begin_layout Plain Layout
return ('Number out of range')
\end_layout
\begin_layout Plain Layout
\end_layout
\begin_layout Plain Layout
\end_layout
\begin_layout Plain Layout
search_query = scholarly.search_single_pub(
\end_layout
\begin_layout Plain Layout
'Galvanization of Protein-Protein Interactions in a Dynamic Zinc Interactome
')
\end_layout
\begin_layout Plain Layout
\end_layout
\begin_layout Plain Layout
num_citations = search_query['num_citations']
\end_layout
\begin_layout Plain Layout
\end_layout
\begin_layout Plain Layout
if num_citations <= 10:
\end_layout
\begin_layout Plain Layout
print(f'The article was warmly received in the scientific community
and was cited by {n2w(num_citations)} other articles so far (as of
\backslash
\backslash
today).')
\end_layout
\begin_layout Plain Layout
else:
\end_layout
\begin_layout Plain Layout
print(f'The article was warmly received in the scientific community
and was cited by {num_citations} other articles so far (as of
\backslash
\backslash
today).')
\end_layout
\begin_layout Plain Layout
\backslash
end{pycode}
\end_layout
\begin_layout Plain Layout
\end_layout
\end_inset
\begin_inset Foot
status open
\begin_layout Plain Layout
\begin_inset Flex URL
status open
\begin_layout Plain Layout
https://scholar.google.com/
\end_layout
\end_inset
\end_layout
\end_inset
\end_layout
\begin_layout Section
Summary
\end_layout
\begin_layout Standard
The functions that are performed by macromolecules in the cell are dependent
on the interaction with their partners.
The role of the macromolecule depends on what the interaction partner is.
For example, in the case of glucose-6-phosphate isomerase, one of the interacti
on partners for the enzyme is glucose 6-phosphate, which is interconverted
into fructose-6-phosphate.
\begin_inset CommandInset citation
LatexCommand citep
key "Berg2007"
literal "true"
\end_inset
Other proteins interact with lipids, nucleic acid, and other proteins.
It is not an exaggeration to state that virtually every protein has to
interact, transiently or permanently, with other macromolecules to realize
its function in the organism.
The holistic knowledge
\begin_inset Note Note
status open
\begin_layout Plain Layout
nie wiem czy tutaj dobrze używam holistyczny
\end_layout
\end_inset
about these interactions is used to plot the map of the interactions, which
in turn can identify the functions of the proteins and their interdependence
leading to understanding the cellular function.
\begin_inset CommandInset citation
LatexCommand citep
key "Cafarelli2017"
literal "true"
\end_inset
From this network of interactions,
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
glspl{ppi}
\end_layout
\end_inset
are crucial to gain comprehension of the functional relationships between
proteins.
Over the last decades, the development of
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
gls{hts}
\end_layout
\end_inset
methods e.g.
peptide phage display ,
\begin_inset CommandInset citation
LatexCommand citep
key "Sundell2014"
literal "true"
\end_inset
yeast surface display,
\begin_inset CommandInset citation
LatexCommand citep
key "Boder1997"
literal "true"
\end_inset
yeast-two-hybrid system,
\begin_inset CommandInset citation
LatexCommand citep
key "Fields1989"
literal "true"
\end_inset
and others lead to heaping amount of data.
Together with huge amount of data a large number of databases have been
founded to curate and annotate the
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
glspl{ppi}
\end_layout
\end_inset
.
\begin_inset CommandInset citation
LatexCommand citep
key "Patil2018"
literal "true"
\end_inset
\end_layout
\begin_layout Standard
However, none of the vast interaction networks presents a full landscape,
as interactions induced by small ligands as well as caused by metal ions
may be missing from the picture.
What is worth mentioning here, is the rough projection of how many proteins
associate with metal ions – it is estimated that roughly 30-40% of all
proteins interact with metal ions.
\begin_inset CommandInset citation
LatexCommand citep
key "Andreini2008,Andreini2013,Waldron2009"
literal "true"
\end_inset
Taking into account that bioinformatic analyses estimate that in human
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
gls{proteome}
\end_layout
\end_inset
every tenth protein is a zinc-binding protein
\begin_inset CommandInset citation
LatexCommand citep
key "Andreini2009,Bertini2010"
literal "true"
\end_inset
, and the fact that most of the
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
gls{hts}
\end_layout
\end_inset
methods do not even consider the presence of another actor (i.e.
Zn(II)) in the interaction, thus causing such interactions to be overlooked,
makes a substantial amount of interactions not fully resolved.
\begin_inset Note Note
status open
\begin_layout Plain Layout
nie wiem czy resolved jest dobrym słowem tutaj.
\end_layout
\begin_layout Plain Layout
W ogóle to zdanie jest średnie i może wymagać zmiany
\end_layout
\end_inset
Although metal ions, compared to macromolecules, are small in both mass
and size, they have a significant impact on protein structure, which implies
consequences for the stability and function of proteins and protein complexes.
Though the impact of various metal ions on living organisms has been studied
for a while, and the effects of deficit or surplus of some microelements
are known, the mechanism of action of those elements may be still vague.
As has been described in
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Zn(II) can be found in various architectures.
The studies of how the architecture translates into function led to the
identification of catalytic and structural zinc-binding sites, however,
the fact that Zn(II) can be located on the
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is often overlooked.
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W tym paragrafie szybko opisać dlaczego cynk.
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Our goal in this report was to provide a comprehensive description of
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