Quantitative elucidation of associations between nucleotide identity and physicochemical properties of amino acids and the functional insight

Jin, Yan-Ting; Jin, Tian-Yue; Zhang, Zhi-Li; Ye, Yuan-Nong; Deng, Zixin; Ju, Wang; Guo, Feng‐Biao

doi:10.1016/j.csbj.2021.07.012

Cited by 3 publications

(2 citation statements)

References 41 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Two SNPs rs1463893698 and rs140630557 reduced stability of mutated proteins to greater extent. GRAVY indicates the polarity level of proteins [ 45 ]. In cases of both the ESR1 and ESR2 genes, the negative values of GRAVY indicate that all the mutated proteins are hydrophilic just like the normal one.…”

Section: Discussionmentioning

confidence: 99%

Exploring the association of ESR1 and ESR2 gene SNPs with polycystic ovary syndrome in human females: a comprehensive association study

Muccee,

Ashraf,

Razak

et al. 2024

J Ovarian Res

View full text Add to dashboard Cite

Background Polycystic Ovary Syndrome (PCOS) affects a significant proportion of human females worldwide and is characterized by hormonal, metabolic, and reproductive dysfunctions, including infertility, irregular menstrual cycles, acanthosis nigricans, and hirsutism. Mutations in the estrogen receptor genes ESR1 and ESR2, involved in normal follicular development and ovulation, can contribute to development of the PCOS. The present study focuses on investigating the potential correlation between single nucleotide polymorphisms (SNPs) of ESR1 and ESR2 genes and the incidence of this syndrome. Methods For this study, SNPs in ESR1 and ESR2 genes were retrieved from the ENSEMBL database and analyzed for their effect on mutated proteins using different bioinformatics tools including SIFT, PolyPhen, CADD, REVEL, MetaLR, I-Mutant, CELLO2GO, ProtParam, SOPMA, SWISS-MODEL and HDDOCK. Results All the SNPs documented in the present study were deleterious. All the SNPs except rs1583384537, rs1450198518, and rs78255744 decreased protein stability. Two variants rs1463893698 and rs766843910 in the ESR2 gene altered the localization of mutated proteins i.e. in addition to the nucleus, proteins were also found in mitochondria and extracellular, respectively. SNPs rs104893956 in ESR1 and rs140630557, rs140630557, rs1596423459, rs766843910, rs1596405923, rs762454979 and rs1384121511 in ESR2 gene significantly changed the secondary structure of proteins (2D). SNPs that markedly changed 3D configuration included rs1554259481, rs188957694 and rs755667747 in ESR1 gene and rs1463893698, rs140630557, rs1596423459, rs766843910, rs1596405923, rs762454979 and rs1384121511 in ESR2 gene. Variants rs1467954450 (ESR1) and rs140630557 (ESR2) were identified to reduce the binding tendency of ESRα and β receptors with estradiol as reflected by the docking scores i.e. -164.97 and -173.23, respectively. Conclusion Due to the significant impact on the encoded proteins, these variants might be proposed as biomarkers to predict the likelihood of developing PCOS in the future and for diagnostic purposes.

show abstract

Section: Discussionmentioning

confidence: 99%

Exploring the association of ESR1 and ESR2 gene SNPs with polycystic ovary syndrome in human females: a comprehensive association study

Muccee,

Ashraf,

Razak

et al. 2024

J Ovarian Res

View full text Add to dashboard Cite

show abstract

“…The protein's higher aliphatic index value of 89.69 indicates increased thermos-stability over a wide temperature range, which is a favorable factor [42,43]. The GRAVY index value of −0.212 suggested the protein's hydrophilic character and, hence, the prospect of more water interaction [44,45].…”

Section: Identification Of the Physicochemical Properties Of The Proteinmentioning

confidence: 99%

In-Silico Approaches for Molecular Characterization and Structure-Based Functional Annotation of the Matrix Protein from Nipah henipavirus

Saikat

Paul

Dey

et al. 2022

The 26th International Electronic Conference on Synthetic Organic Chemistry

View full text Add to dashboard Cite

show abstract

Graphene-based Nanocomposites for Amino Acid Sensing

Manoj,

Rajendran,

Murphy

et al. 2023

Graphene-Based Nanocomposite Sensors

View full text Add to dashboard Cite

Thanks to the intriguing thermal, electrical and mechanical properties offered by graphene by which the potential applications now extend over a wide range, from electronic devices to wearable patches. For biosensor development, in particular, various graphene-based composites have been fruitfully used in different forms, e.g. as electrode substrates, molecular hybrids, patterned films and biocompatible platforms. In the past couple of years, a significant number of reports have been devoted to graphene-based nanocomposites for electrochemical sensing of small biomolecules such as amino acids. Because of its outstanding conductivity, hydrophilicity, abundant functional groups, large surface area, and high chemical and thermal stability, graphene-based nanocomposites as electrode supports can act as a conductive platform for signal improvement for single amino acids or for two or more amino acids simultaneously. Therefore, it is essential for researchers to acknowledge the recent design and developments of graphene-based nanocomposites for sensing amino acids and derived neurotransmitters. The present chapter aims to highlight the importance of amino acids and their role in the human body and the various analytical methods employed for their effective detection. We will also highlight the reports on various graphene-based nanocomposites as electrode materials for the sensing of various amino acids such as cysteine, tryptophan and tyrosine. Finally, we will also conclude the chapter with remarks and perspectives for future development of smart sensing devices.

show abstract

Quantitative elucidation of associations between nucleotide identity and physicochemical properties of amino acids and the functional insight

Abstract: Graphical abstract

Cited by 3 publications

References 41 publications

Exploring the association of ESR1 and ESR2 gene SNPs with polycystic ovary syndrome in human females: a comprehensive association study

Exploring the association of ESR1 and ESR2 gene SNPs with polycystic ovary syndrome in human females: a comprehensive association study

In-Silico Approaches for Molecular Characterization and Structure-Based Functional Annotation of the Matrix Protein from Nipah henipavirus

Graphene-based Nanocomposites for Amino Acid Sensing

Contact Info

Product

Resources

About