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Gene & Protein in Disease Bioinformatics study of PCNP

congenital disorders . PTMs refer to amino acid side chain recommended to perform functional assays in cell lines as
[49]
modifications in some proteins after their biosynthesis. well as crystallographic analysis to fully understand the
Disruption in PTMs can cause malfunctioning of vital PCNP structure and its binding abilities.
biological processes and, hence, lead to various diseases .
[50]
Therefore, considering the DPM1 and PCNP coexpression 4. Conclusion
as synchronization of PCNP functions, there is an urgent Our study presents an in silico structural and functional
need to predict PTMs in this least explored protein, which interpretation of the PCNP by employing various
will provide a clear picture of PCNP functions, especially bioinformatics tools. We identified the phylogenetic
in cancer onset. Based on these already published findings relationship of PCNP and then performed structural
and the predicted outcomes of the present study, it can be and functional analysis. Overall, PCNP is slightly acidic,
deduced that PCNP might have diverse functions, although hydrophilic in nature, and a thermostable protein. The
many of which remain unreported. protein secondary structure has a dominant random coil

3.6. Phylogenetic analysis region followed by beta turns and an alpha helix. Through
the coexpression and PPI analyses, we discovered that the
The phylogenetic neighbor-joining tree presented in PCNP gene is expressed with MORF4LI and RSL24D1
this study reveals many interesting characteristics of genes and has close interactions with TRAM1, PSMC6,
the candidate protein in vertebrates. The human PCNP SRP9, PRKRIR, UHRF2, and BMI1 proteins. The GO
protein phylogenetic tree revealed remarkable similarities results are consistent with the previously reported studies
to Pan troglodytes and Bos taurus. The results indicate and endorse PCNP’s involvement in vital cell functions,
a close relationship with both species but that they have such as cell cycle and cancer progression as an oncogenic
ancestor linkage in a distinguished clade. The generated protein. Among the four different 3D structure generation
phylogenetic tree of PCNP is presented in Figure 6A. tools, I-TASSER generated a model that had the highest
Besides, the evolutionary tree shows that the ancestry of quality factor score, which was further validated through
PCNP protein is closer to the Bovidae family but far away MDS. To date, this is the first comprehensive study to
from other primates like Mus musculus. The tree also shows elucidate the structural outlook and functional details
that in the PCNP phylogeny, Gallus gallus is an out-group. of PCNP. This computational work, therefore, provides
Moreover, based on the pairwise sequence identity, the an essential perspective of PCNP, which can be useful
PCNP protein from the Bovidae family could be clustered for proteomics or genomic research involving extensive
as one subgroup. The pair-wise identity matrix of PCNP in vivo experimental work on this vital NP, and helps
sequences and its eight orthologs in various vertebrates deepen our understanding regarding the function of
is demarcated in Figure 6B. These findings additionally PCNP in the nucleus and its potential role as a diagnostic
support the phylogenetic tree that presents an indication and therapeutic target in cancer biology discipline.
of the molecular kinship of PCNP proteins belonging
to diverse mammalian species. Overall, the in silico Acknowledgments
results reveal many hidden functional, structural, and
evolutionary characteristics of the human PCNP protein. We acknowledged all the database websites tools and
servers for providing a platform of knowledge and data
3.7. Scope and limitations of the study interpretation as well. We also thankfully acknowledged
Mr. Abbas Khan for helping us with the editing of this
Doubtlessly, the in silico study presented here provides manuscript. The authors thank the expert reviewers
a critical, quick, and low-cost structure prediction and for taking their time to kindly review the manuscript
functional elucidation of PCNP, and it will add more
literature and understanding of PCNP for the future and provide their valuable suggestions to improve the
studies. However, there are some limitations to this study, manuscript. Nazeer Hussain Khan pays countless thanks to
such as the fact that it is a computational study. A study his Lala for his presence and support in the journey of PhD.
based on the results that were retrieved from public data- Funding
tools has no affirmation from a wet laboratory study.
Results generated from software implementation of This work was financially supported by the National
the data have high false positive or false negative rates, Natural Science Foundation of China (No. 81670088 and
which restrict us from being fully confident in the results. No. 81602708).
Furthermore, PCNP is the least explored protein, so
there is a lack of data to validate the molecular dynamics Conflict of interest
experiments and structural stability. Therefore, it is highly All the authors declare no conflict of interest.

Volume 1 Issue 1 (2022) 9 https://doi.org/10.36922/gpd.v1i1.65