Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins
Members of the human Zyxin family are LIM domain-containing proteins that perform critical cellular functions and are indispensable for cellular integrity. Despite their importance, not much is known about their structure, functions, interactions and dynamics. To provide insights into these, we used...
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MDPI AG
2021-03-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/22/5/2647 |
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| author | M. Quadir Siddiqui Maulik D. Badmalia Trushar R. Patel |
| author_facet | M. Quadir Siddiqui Maulik D. Badmalia Trushar R. Patel |
| author_sort | M. Quadir Siddiqui |
| collection | DOAJ |
| description | Members of the human Zyxin family are LIM domain-containing proteins that perform critical cellular functions and are indispensable for cellular integrity. Despite their importance, not much is known about their structure, functions, interactions and dynamics. To provide insights into these, we used a set of in-silico tools and databases and analyzed their amino acid sequence, phylogeny, post-translational modifications, structure-dynamics, molecular interactions, and functions. Our analysis revealed that zyxin members are ohnologs. Presence of a conserved nuclear export signal composed of LxxLxL/LxxxLxL consensus sequence, as well as a possible nuclear localization signal, suggesting that Zyxin family members may have nuclear and cytoplasmic roles. The molecular modeling and structural analysis indicated that Zyxin family LIM domains share similarities with transcriptional regulators and have positively charged electrostatic patches, which may indicate that they have previously unanticipated nucleic acid binding properties. Intrinsic dynamics analysis of Lim domains suggest that only Lim1 has similar internal dynamics properties, unlike Lim2/3. Furthermore, we analyzed protein expression and mutational frequency in various malignancies, as well as mapped protein-protein interaction networks they are involved in. Overall, our comprehensive bioinformatic analysis suggests that these proteins may play important roles in mediating protein-protein and protein-nucleic acid interactions. |
| first_indexed | 2024-03-09T05:16:30Z |
| format | Article |
| id | doaj.art-ed98be949f574ff090a5254145d52fc1 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T05:16:30Z |
| publishDate | 2021-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-ed98be949f574ff090a5254145d52fc12023-12-03T12:45:40ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-03-01225264710.3390/ijms22052647Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family ProteinsM. Quadir Siddiqui0Maulik D. Badmalia1Trushar R. Patel2Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, CanadaAlberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, CanadaAlberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, CanadaMembers of the human Zyxin family are LIM domain-containing proteins that perform critical cellular functions and are indispensable for cellular integrity. Despite their importance, not much is known about their structure, functions, interactions and dynamics. To provide insights into these, we used a set of in-silico tools and databases and analyzed their amino acid sequence, phylogeny, post-translational modifications, structure-dynamics, molecular interactions, and functions. Our analysis revealed that zyxin members are ohnologs. Presence of a conserved nuclear export signal composed of LxxLxL/LxxxLxL consensus sequence, as well as a possible nuclear localization signal, suggesting that Zyxin family members may have nuclear and cytoplasmic roles. The molecular modeling and structural analysis indicated that Zyxin family LIM domains share similarities with transcriptional regulators and have positively charged electrostatic patches, which may indicate that they have previously unanticipated nucleic acid binding properties. Intrinsic dynamics analysis of Lim domains suggest that only Lim1 has similar internal dynamics properties, unlike Lim2/3. Furthermore, we analyzed protein expression and mutational frequency in various malignancies, as well as mapped protein-protein interaction networks they are involved in. Overall, our comprehensive bioinformatic analysis suggests that these proteins may play important roles in mediating protein-protein and protein-nucleic acid interactions.https://www.mdpi.com/1422-0067/22/5/2647cancerZyxinlim domainsleucine rich motifsprotein bioinformatics |
| spellingShingle | M. Quadir Siddiqui Maulik D. Badmalia Trushar R. Patel Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins International Journal of Molecular Sciences cancer Zyxin lim domains leucine rich motifs protein bioinformatics |
| title | Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins |
| title_full | Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins |
| title_fullStr | Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins |
| title_full_unstemmed | Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins |
| title_short | Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins |
| title_sort | bioinformatic analysis of structure and function of lim domains of human zyxin family proteins |
| topic | cancer Zyxin lim domains leucine rich motifs protein bioinformatics |
| url | https://www.mdpi.com/1422-0067/22/5/2647 |
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