ISSN: 0974-276X
Journal of Proteomics & Bioinformatics
Like us on:
Make the best use of Scientific Research and information from our 700+ peer reviewed, Open Access Journals that operates with the help of 50,000+ Editorial Board Members and esteemed reviewers and 1000+ Scientific associations in Medical, Clinical, Pharmaceutical, Engineering, Technology and Management Fields.
Meet Inspiring Speakers and Experts at our 3000+ Global Conferenceseries Events with over 600+ Conferences, 1200+ Symposiums and 1200+ Workshops on
Medical, Pharma, Engineering, Science, Technology and Business

Possible Single Nucleotide Polymorphism (SNP) in the Nucleic Sequence of A-kinase- anchoring Protein 9

Viroj Wiwanitkit*
Viroj Wiwanitkit House, 38/167 Soi Yim Prayoon, Bangkhae Bangkok Thailand 1016
Corresponding Author : Dr. Viroj Wiwanitkit
M.D.Wiwanitkit House
38/167 Soi Yim Prayoon
Bangkhae Bangkok Thailand 1016
E-mail :
Received June 25, 2008; Accepted July 16, 2008; July 17, 2008
Citation: Viroj W (2008) Possible Single Nucleotide Polymorphism (SNP) in the Nucleic Sequence of A-kinase-anchoring Protein 9. J Proteomics Bioinform 1:227-229. doi:10.4172/jpb.1000027
Copyright: © 2008 Viroj W. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Related article at
DownloadPubmed DownloadScholar Google

Visit for more related articles at Journal of Proteomics & Bioinformatics


In cardiac physiology, ion channel macromolecular complexes can be formed by the strong correlation of Akinase anchoring proteins, therefore, AKAP becomes an important antiarrhytmic target. Here, the author performed a bioinformatics analysis to study the possible single nucleotide polymorphism (SNP) in the amino acid sequence of AKAP9. In this work, the author could not identify any SNP with in AKAP9. This confirms that there is no report on SNP on this molecule.

A-kinase anchoring protein; Arrhythmia; Single nucleotide polymorphism
In normal cardiac physiology, sympathetic nervous system (SNS) regulation of cardiac action potential duration (APD), mediated by beta-adrenergic receptor (betaAR) activation, usually requires assembly of A-kinase anchoring protein (AKAP)9 (Yotiao) with the I(Ks) potassium channel alpha subunit (KCNQ1) (Chen et al., 2001). Ion channel macromolecular complexes can be formed by the strong correlation of AKAPs (Chen et al., 2006; Marx and Kurokawa, 2006). Therefore, AKAP becomes an important antiarrhytmic target (Marx and Kurokawa, 2006). Analysis on the AKAP in depth helps better understand the pathogenesis of this protein-relate arrythmic disorder. AKAP disorder can be seen in the recent reports (Lin et al., 1998; Tao et al., 2006), however, the prevalence of mutations in the AKAP is not well known. In addition, single nucleotide polymorphism (SNP) within AKAP has never been mentioned.
Importance of SNP study for AKAP and other AKAP targets for new therapeutic interventions should be mentioned. Burns-Hamuro et al., (2004) said that there had been considerable progress in understanding the structural features of this AKAP and its interaction with protein kinase A (Burns-Hamuro et al., 2004). Burns-Hamuro et al reported that comprehensive analysis of the PKA binding motif could lead to the development of novel peptides derived from DAKAP2 and could be useful tools in probing the function of this AKAP in cellular and animal models (Burns-Hamuro et al., 2004). However, there is limited reported on AKAP9. There was a paper by Rudd et al., (2006) describing the possible correlation of SNP for AKAP9 and lung cancer (Rudd et al., 2006). However, there was no proof from this work (Rudd et al., 2006). Here, the author performed a bioinformatics analysis to study the SNP in the amino acid sequence of AKAP9.
Materials and Methods
At first, the database Expert Protein Analysis System (ExPASY) (Gasteiger et al., 2003) was used for searching for the amino acid sequence of AKAP9. Then the derived sequences were used for further study for SNP. GENSNiP was further used for identification on SNP within the derived sequence. Briefly, GEN-SNiP help finds polymorphisms present in DNA sequences with respect to a standard reference sequence. This tool is selected because it is only one simple online access tool and is confirmed for its validity. The output lists substitutions, insertions and deletions. Since there is no other similar tool to GEN-SNiP, further comparative study to other tool cannot be performed.
In this work, AKAP9 (NG_007968) was used for further study. There is no identified SNP for this sequence.
Importance of SNP search for target drug discovery/ new therapeutic interventions should be mentioned in the present post-genomics era. The analysis of SNPs permits determining relationships between genotypic and phenotypic information as well as the identification of SNPs related to a disease, which can be useful for further drug development (Shah and Kusiak, 2004). The good examples are on antineoplastic (Mack et al., 2008) and cardiovascular drugs (Borgiani et al., 2007). There are numerous experimental and clinical data supporting the existence or variant AKAP proteins (Chen et al., 2001). However, the exact functions of variant AKAP proteins, either physiological or pathological, are still unclear, although roles for some AKAP variants in cardiac arrythmia progression might be consistent with the accumulated data (Chen et al., 2001; Saucerman et al., 2004). On one hand, AKAP polymorphism might connect with some rare syndromes of arrhythmic disorder and on other side it is the post-receptor modifications that very well explain the molecular pathogenesis of AKAP and arrythmia. Identification of the SNP within AKAP can be useful for further researches to understand the pathogenesis of AKAP disorder. In this work, the author could not identify any SNP with in AKAP9. This confirms that there is no report on SNP on this molecule although there is for other AKAPs (Burns-Hamuro et al., 2004; Frank et al., 2004).
Conclusions and Future Perspectives
In this work, the author used a novel bioinformatics tool to find possible SNP in the amino acid sequence of AKAP9 and found no SNP. This might imply that the AKAP9 might have no polymorphism. However, due to the limitation of the present tool, the conclusion cannot be reached. Future analysis by future available tool is suggested. In addition, a study on the probable mutated prone position, weak linkage analysis, is another in silico methods suitable for this AKAP protein.
Declaration on Conflict of Interest
The author hereby would like to declare for no confliction of interest in this work.

Select your language of interest to view the total content in your interested language
Share This Article
Relevant Topics
Disc Applications of Bioinformatics
Disc Bacterial transcriptome
Disc Bioinformatics Algorithms
Disc Bioinformatics Databases
Disc Bioinformatics Tools
Disc Cancer Pharmacogenomics
Disc Cancer Proteomics
Disc Clinical Pharmacogenomics
Disc Clinical Proteomics
Disc Cluster analysis
Disc Comparative genomics
Disc Comparative proteomics
Disc Comparative transcriptomics
Disc Computational drug design
Disc Current Proteomics
Disc Data algorithms
Disc Data mining applications in genomics
Disc Data mining applications in proteomics
Disc Data mining in drug discovery
Disc Data mining tools
Disc Data modelling and intellegence
Disc Data warehousing
Disc Drug Dosage Formulations
Disc Drug Toxicity and Efficacy
Disc Epigenetics
Disc Epigenomic studies
Disc Gene Expression profiling
Disc Gene polymorphism
Disc Genome annotation
Disc Genomic Targets
Disc Genomic data mining
Disc Genomic data warehousing
Disc Glycome
Disc Human Proteome Project Applications
Disc Immune Disorders
Disc Individualized Medicine
Disc Mapping of genomes
Disc Mass Spectrometry in Proteomics
Disc Meta genomics
Disc Metabolome
Disc Microarray
Disc Microarray Proteomics
Disc Molecular and Cellular Proteomics
Disc Mouse transcriptome
Disc Non coding MRNA
Disc Personalized Medicine Studies
Disc Pharmacoeconomics in Drug Development
Disc Pharmacogenetics
Disc Pharmacogenomic Biomarker
Disc Pharmacogenomics Applications
Disc Pharmacogenomics Future Medicine
Disc Pharmacogenomics and Personalized Medicine
Disc Pharmacogenomics for Patient Care
Disc Pharmacoproteomics in Drug development
Disc Profiling
Disc Protein Sequence Analysis
Disc Protein engineering
Disc Proteogenomics
Disc Proteome
Disc Proteome Profiling
Disc Proteomic Analysis
Disc Proteomic Biomarkers
Disc Proteomics Clinical Applications
Disc Proteomics Research
Disc Proteomics Science
Disc Proteomics and Pharmacodynamics
Disc Proteomics data warehousing
Disc Python for Bioinformatics
Disc Quantitative Proteomics
Disc RNA sequencing
Disc RNA sequencing and analysis
Disc Sequencing
Disc Small RNA Sequencing
Disc Statistical data mining
Disc Transcripotme
Disc Transcriptional Attenuation
Disc Transcriptional Regulation
Disc Transcriptome analysis
Disc Translational Medicine
Recommended Journals
Disc Transcriptomics Journal
Disc Pharmacogenomics Journal
Disc Data Mining Journal
  View More»
Recommended Conferences
Disc 6th Bioinformatics Conference
August 22-23, 2016 Philadelphia, Pennsylvania, USA
Disc 7th International Conference and Expo on Proteomics
October 24-26, 2016 Rome, Italy
View More»
Article Tools
Disc Export citation
Disc Share/Blog this article
Article usage
  Total views: 11225
  [From(publication date):
July-2008 - Jul 01, 2016]
  Breakdown by view type
  HTML page views : 7492
  PDF downloads :3733

Post your comment

captcha   Reload  Can't read the image? click here to refresh

OMICS International Journals
Make the best use of Scientific Research and information from our 700 + peer reviewed, Open Access Journals
OMICS International Conferences 2016-17
Meet Inspiring Speakers and Experts at our 3000+ Global Annual Meetings

Contact Us

Agri, Food, Aqua and Veterinary Science Journals

Dr. Krish

1-702-714-7001 Extn: 9040

Clinical and Biochemistry Journals

Datta A

1-702-714-7001Extn: 9037

Business & Management Journals


1-702-714-7001Extn: 9042

Chemical Engineering and Chemistry Journals

Gabriel Shaw

1-702-714-7001 Extn: 9040

Earth & Environmental Sciences

Katie Wilson

1-702-714-7001Extn: 9042

Engineering Journals

James Franklin

1-702-714-7001Extn: 9042

General Science and Health care Journals

Andrea Jason

1-702-714-7001Extn: 9043

Genetics and Molecular Biology Journals

Anna Melissa

1-702-714-7001 Extn: 9006

Immunology & Microbiology Journals

David Gorantl

1-702-714-7001Extn: 9014

Informatics Journals

Stephanie Skinner

1-702-714-7001Extn: 9039

Material Sciences Journals

Rachle Green

1-702-714-7001Extn: 9039

Mathematics and Physics Journals

Jim Willison

1-702-714-7001 Extn: 9042

Medical Journals

Nimmi Anna

1-702-714-7001 Extn: 9038

Neuroscience & Psychology Journals

Nathan T

1-702-714-7001Extn: 9041

Pharmaceutical Sciences Journals

John Behannon

1-702-714-7001Extn: 9007

Social & Political Science Journals

Steve Harry

1-702-714-7001 Extn: 9042

© 2008-2016 OMICS International - Open Access Publisher. Best viewed in Mozilla Firefox | Google Chrome | Above IE 7.0 version