NDLI: Contributions of substitutions and indels to the structural variations in ancient protein superfamilies

Content Provider	Springer Nature : BioMed Central
Author	Zhang, Zheng Wang, Jinlan Gong, Ya Li, Yuezhong
Abstract	Background Quantitative evaluation of protein structural evolution is important for our understanding of protein biological functions and their evolutionary adaptation, and is useful in guiding protein engineering. However, compared to the models for sequence evolution, the quantitative models for protein structural evolution received less attention. Ancient protein superfamilies are often considered versatile, allowing genetic and functional diversifications during long-term evolution. In this study, we investigated the quantitative impacts of sequence variations on the structural evolution of homologues in 68 ancient protein superfamilies that exist widely in sequenced eukaryotic, bacterial and archaeal genomes. Results We found that the accumulated structural variations within ancient superfamilies could be explained largely by a bilinear model that simultaneously considers amino acid substitution and insertion/deletion (indel). Both substitutions and indels are essential for explaining the structural variations within ancient superfamilies. For those ancient superfamilies with high bilinear multiple correlation coefficients, the influence of each unit of substitution or indel on structural variations is almost constant within each superfamily, but varies greatly among different superfamilies. The influence of each unit indel on structural variations is always larger than that of each unit substitution within each superfamily, but the accumulated contributions of indels to structural variations are lower than those of substitutions in most superfamilies. The total contributions of sequence indels and substitutions (46% and 54%, respectively) to the structural variations that result from sequence variations are slightly different in ancient superfamilies. Conclusions Structural variations within ancient protein superfamilies accumulated under the significantly bilinear influence of amino acid substitutions and indels in sequences. Both substitutions and indels are essential for explaining the structural variations within ancient superfamilies. For those structural variations resulting from sequence variations, the total contribution of indels is slightly lower than that of amino acid substitutions. The regular clock exists not only in protein sequences, but also probably in protein structures.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-018-5178-8.pdf
Ending Page	9
Page Count	9
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-018-5178-8
Journal	BMC Genomics
Issue Number	1
Volume Number	19
Language	English
Publisher	BioMed Central
Publisher Date	2018-10-24
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Indel Substitution Genome Structural variations Ancient protein superfamilies
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	3.5/2023
5-Year Journal Impact Factor	4.1/2023

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

The development of ideal insertion and deletion (InDel) markers and initial indel map variation in cucumber using re-sequenced data

The distribution and mutagenesis of short coding INDELs from 1,128 whole exomes

Identification of genomic indels and structural variations using split reads

Screening of nucleotide variations in genomic sequences encoding charged protein regions in the human genome

Hepatitis C virus core protein substitutions affect the response to pegylated-interferon and ribavirin therapy

Populational landscape of INDELs affecting transcription factor-binding sites in humans

Minimum InDel pattern analysis of the Zika virus

Erratum to: inferring the global structure of chromosomes from structural variations

Retrocopy contributions to the evolution of the human genome

Contributions of substitutions and indels to the structural variations in ancient protein superfamilies

Similar Documents

The development of ideal insertion and deletion (InDel) markers and initial indel map variation in cucumber using re-sequenced data

The distribution and mutagenesis of short coding INDELs from 1,128 whole exomes

Identification of genomic indels and structural variations using split reads

Screening of nucleotide variations in genomic sequences encoding charged protein regions in the human genome

Hepatitis C virus core protein substitutions affect the response to pegylated-interferon and ribavirin therapy

Populational landscape of INDELs affecting transcription factor-binding sites in humans

Minimum InDel pattern analysis of the Zika virus

Erratum to: inferring the global structure of chromosomes from structural variations

Retrocopy contributions to the evolution of the human genome

Contributions of substitutions and indels to the structural variations in ancient protein superfamilies