Conformation biases of amino acids based on tripeptide microenvironment from PDB database

Yang, Jie; Dong, Xiao; Leng, Yao

doi:10.1016/j.jtbi.2005.09.025

Cited by 9 publications

(8 citation statements)

References 35 publications

(28 reference statements)

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“…Similarly, codon usage biases in AD and other neurodegenerative diseases indicated that GCrich codons are mainly in charge of forming contracted conformation, especially the first nucleotide of codons plays a dominant role in translating the genomic GC signature into protein sequences and structures [11]. Our previous research has revealed that conformation biases of amino acids are present in natural proteins and the corresponding biases of codons show an evident tendency in protein folding [26].…”

Section: Discussionmentioning

confidence: 97%

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Systematic analysis of diabetes- and glucose metabolism-related proteins and its application to Alzheimer’s disease

Yang¹,

Li²,

Liu³

2013

JBiSE

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Alzheimer disease has been defined as Type 3 Diabetes due to their shared metabolic profiles. Like our previously research, results of Alzheimer's disease and other neurodegenerative diseases, systematic analysis of diabetes-and glucose metabolism-related proteins also provides help in the treatment of Alzheimer's patients. Some interesting results indicate that diabetes-related proteins (DRPs) are rich in Lys and the content of Trp can distinguish between type 1 and type 2 diabetes mellitus in particular, while glucose metabolism-related proteins (GMRPs) possess Leurich and Trp-poor character. Moreover, the usage biases of codons depend on GC contents to a great extent, in concord with all codons of the highly expressed genes with the terminal of C/G. Especially, the deficit of CpG dinucleotides is largely attributed to the hypermutability of methylated CpGs to UpGs by the mutational pressure. Besides a common node insulin receptor, there are some similar node proteins, such as glucose transporter member, protein tyrosine phosphatase, and adipose metabolism signal protein. The sharing proteins involve glucagon, amylin, insulin, PPARγ, angiopoietin, PC-1/ENPP1, and adiponectin mediated signal pathway. Meanwhile, the gene sequences of node proteins contained the binding sites of 37 transcription factors divide into four kinds of superclasses. Additionally, BAD complex can integrate pathways of glucose metabolism and apoptosis by BH3 domain of BAD directly interacting with GK as well as GK binding with the consensus motif [G]-[1]-[K]-[2]-[S/T] or [L/M]-[R/K]-[2]-[T] of PP1 orWAVE1. This facilitates the therapies for diabetes mellitus as well as Alzheimer's disease. Science and Engineering 6 (2013) 615-644 616 portions, because of an increased number of elderly people, and a greater prevalence of obesity and sedentary lifestyles [8,9]. Diabetes mellitus is associated with decreased body insulin production than required (type 1) and impaired insulin signaling (type 2/T2DM). Diabetes especially T2DM and AD follow the same pathological mechanisms resulting in misfolded proteins, insulin impairment, abnormal glucose metabolism, abnormal fatty acid metabolism, mitochondrial dysfunction, and high oxidative stress [1]. These shared metabolic profiles and diabetes as extreme risk factor for AD lead to the assumption that AD may reflect type-3 diabetes.We have previously finished construction of cell model for screening Alzheimer's drugs [10], codon usage biases in AD and other neurodegenerative diseases [11], and protein-protein interactions related to AD based on complex network [12]. Similarly, we are to propose a computational analysis on codon biases of some proteins related to diabetes and glucose metabolism, hoping that the findings might be useful for developing new therapeutic treatment for diabetes as well as AD. Moreover, the proteins related to diabetes are located at signal transduction pathway [13,14], gene control pathway [15,16], glucose metabolic pathway [17,18], etc. A large number of research work on t...

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Section: Discussionmentioning

confidence: 97%

“…According to our methods [26,27], the accumulative times   i c and the percentage of each amino acid in 211 known DRPs, 100 hGMRPs and 123 mGMRPs ( Table 1) were analysized and calculated by symbolic statistic method as follows:…”

Section: Amino Acid Compositionmentioning

confidence: 99%

Systematic analysis of diabetes- and glucose metabolism-related proteins and its application to Alzheimer’s disease

Yang¹,

Li²,

Liu³

2013

JBiSE

Self Cite

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show abstract

“…Similarly, SCUB in AD and other neurodegenerative diseases indicated that GC-rich codons are mainly in charge of forming contracted conformation, especially the first nucleotide of codons plays a dominant role in translating the genomic GC signature into protein sequences and structures . Our previous research has revealed that conformation biases of amino acids are present in natural proteins and the corresponding biases of codons show an evident tendency in protein folding (Yang et al, 2006).…”

Section: Discussionmentioning

confidence: 99%

System analysis of synonymous codon usage biases in archaeal virus genomes

Yang

2014

Journal of Theoretical Biology

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Recent studies of geothermally heated aquatic ecosystems have found widely divergent viruses with unusual morphotypes. Archaeal viruses isolated from these hot habitats usually have double-stranded DNA genomes, linear or circular, and can infect members of the Archaea domain. In this study, the synonymous codon usage bias (SCUB) and dinucleotide composition in the available complete archaeal virus genome sequences have been investigated. It was found that there is a significant variation in SCUB among different Archaeal virus species, which is mainly determined by the base composition. The outcome of correspondence analysis (COA) and Spearman׳s rank correlation analysis shows that codon usage of selected archaeal virus genes depends mainly on GC richness of genome, and the gene׳s function, albeit with smaller effects, also contributes to codon usage in this virus. Furthermore, this investigation reveals that aromaticity of each protein is also critical in affecting SCUB of these viral genes although it was less important than that of the mutational bias. Especially, mutational pressure may influence SCUB in SIRV1, SIRV2, ARV1, AFV1, and PhiCh1 viruses, whereas translational selection could play a leading role in HRPV1׳s SCUB. These conclusions not only can offer an insight into the codon usage biases of archaeal virus and subsequently the possible relationship between archaeal viruses and their host, but also may help in understanding the evolution of archaeal viruses and their gene classification, and more helpful to explore the origin of life and the evolution of biology.

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“…And it helps for the following statistic analysis and further matrix comparison. According to our methods [17,18], the accumulative times ( k c ) and the percentage ( k P ) of each herbal medicine in 233…”

Section: Database Of Diabetes Mellitus Proved Recipes and Statistic Amentioning

confidence: 99%

Systematical Analysis of the Application of Chinese Traditional Medicine Informatics to Diabetes Proved Recipesw

Yang¹

2012

J Diab Res Clin Met

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Chinese medicinal materials that originate from animal, mineral and plant have thousands years for diabetes therapy and accumulate a great deal of valuable clinical experience. The rapidly increasing diabetes mellitus is becoming a serious threat to mankind health in all parts of the world. Currently, bioinformatics has already impenetrate biology, medicine, genomics, clinical pharmacology, botany, and other subjects. This paper mainly expatiates the actual application of information technology to traditional Chinese medicinal materials, especially build a database of diabetes mellitus proved recipe (DMPR) by Microsoft Access 2000; analyze and find complexity information of DMPR viz matrix alignment. Our research results reveal that there is not linearity relationship between P value and clinical activities of DMPR that show diversity and complexity; and t-test results show that P1 value of simple score matrix and P2 value of complex score matrix present significantly difference and the latter is more rational than the former because the secondary score matrix plays a complementary role to the first score matrix so that enhance the reliability and the veracity of prediction. Therefore, bioinformatics at many scales and many levels should be spread for Chinese traditional medicine proved recipe possessing complexity, diversity, and non-linearity. This will greatly change the research actuality of Chinese traditional medicine, improve the research level of Chinese traditional medicine informatics, and accelerate the research step of modernization of Chinese traditional medicine.

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Conformation biases of amino acids based on tripeptide microenvironment from PDB database

Cited by 9 publications

References 35 publications

Systematic analysis of diabetes- and glucose metabolism-related proteins and its application to Alzheimer’s disease

Systematic analysis of diabetes- and glucose metabolism-related proteins and its application to Alzheimer’s disease

System analysis of synonymous codon usage biases in archaeal virus genomes

Systematical Analysis of the Application of Chinese Traditional Medicine Informatics to Diabetes Proved Recipesw

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