Application of FTTP to alpha-helix or beta-strand motifs

Yang, Jie; Dong, Xiao; Leng, Yao

doi:10.1016/j.jtbi.2006.02.014

Cited by 5 publications

(6 citation statements)

References 43 publications

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“…Besides the common C subunit, along with CBD-A domain and the inhibitor sequence of RIIa subunit similar to those of RIa subunit, RIIa-C complex also contains the D/D domain and CBD-B. The "neck" of RIIa includes an acidic sequence (73-84), a free loop (58)(59)(60)(61)(62)(63)(64)(65)(66)(67)(68)(69)(70)(71)(72) and a turn (107-109) besides the inhibitor sequence above. In comparison with human KAP3 (RIIb), CBDs of RIIa and RIa have also two eight-strand "beta-barrel" regions, each consisting of an eight-stranded antiparallel six-residue sheet.…”

Section: Discussionmentioning

confidence: 99%

“…These acidic side-chains could form a negatively charged face, proposed to provide protein-protein contact sites for RNA polymerase II on several mammalian transcription activation factors by hydrogen bonding between acidic and hydroxylated amino acids. The acidic region (73-87, DAKGDSESEEDEDLE) of KAP2 is similar to the above-mentioned acidic cluster (68)(69)(70)(71)(72)(73)(74)(75)(76)(77)(78)(79)(80)(81)(82). Consequently, the anchoring protein receptor is immediately adjacent to the autoinhibitor domain in RII [3].…”

Section: Discussionmentioning

confidence: 99%

“…The unique right-handed twisting of beta-sheets is one of the most characteristic structural patterns of globular proteins. The structures of the parallel or antiparallel beta-barrel are related to that of the beta-sheet from which they are formed [72]. The eight-stranded antiparallel beta-barrels composed of six-residue strands.…”

Section: Structural Models Of Human Kap2 (The Regulatory Subunit Riiamentioning

confidence: 99%

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Molecular Modeling of Human Hepatocyte PKA (cAMP-Dependent Protein Kinase Type-II) and Its Structure Analysis

Yang

2010

PPL

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Two binary complexes (KAP2-C subunit and cAMP-bound KAP2) were built, to investigate molecular interaction. The binding sites of KAP2 include the acidic sequence motif (Asp73-Glu87), the inhibitor peptide/linker region (Arg93-Val118), and beta barrel of cAMP-binding domains (CBD-A/B). The binding surface on the C subunit anchoring KAP2 extends to the inhibitor binding site at the active site cleft (Glu127-Glu230), Pro243-Ser252 helix and the phosphorylated activation loop (Arg194-Thr201) of the large lobe besides some sites in the small lobe. KAP2 undergoes major conformational changes in comparison of the two complexes above, especially the linker region and Met251 at Arg234-Phe252 helix as an inflexion point of the turnaround. Additionally, the interaction between KAP2 and cAMP concentrates on two catalytic motifs (FGELAL and PRAA) of phosphate binding cassette regions and the cyclic-monophosphate and ribose of cAMP. On the other hand, WAVE1 of BAD complex maybe interacts with the D/D domain of KAP2 by each of three helical motifs (Asn24-Lys46, Pro492-Val514, and Glu525-Glu547). This is helpful for our research of molecular mechanism of PKA and further analysis of BAD complex how to modulate glycolysis and apoptosis.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Structural Models Of Human Kap2 (The Regulatory Subunit Riiamentioning

confidence: 99%

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Molecular Modeling of Human Hepatocyte PKA (cAMP-Dependent Protein Kinase Type-II) and Its Structure Analysis

Yang

2010

PPL

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“…We estimated codon frequencies from the observed codon counts of these protein-coding sequences mentioned above. 64 codons are obtained using the sliding window method one by one from 5'-terminal of protein-coding sequences to 3'-teminal: a sequence of n residues gives rise to 3 n units [32]. The accumulative times   l M of each codon in 211 DRPs and 223 GMRPs were analysized and calculated 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

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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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“…According to the set theory of mathematics [42], the GPCRs chosen above consist of different training sets…”

Section: Test Setsmentioning

confidence: 99%

Discovery and validation of potential drug targets based on the phylogenetic evolution of GPCRs

Yang¹,

Li²,

Zhu³

et al. 2012

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Target identification is a critical step following the discovery of small molecules that elicit a biological phenotype. G-protein coupled recaptors (GPCRs) are among the most important drug targets for the pharmaceutical industry. The present work seeks to provide an in silico model of known GPCR protein fishing technologies in order to rapidly fish out potential drug targets on the basis of amino acid sequences and seven transmembrane regions (TMs) of GPCRs. Some scoring matrices were trained on 22 groups of GPCRs in the GPCRDB database. These models were employed to predict the GPCR proteins in two groups of test sets. On average, the mean correct rate of each TM of 38 GPCRs from two test sets ( and ) was found 62% and 57.5%, respectively, using training set 18 ( ); the mean hit rate of each TM of 38 GPCRs from and S 24 was found 68.1% and 64.7%, respectively. Based on the scoring matrices of PreMod, the mean correct rate of each TM of GPCRs from and was found 62% and 62.04%, respectively; the mean hit rate of each TM of GPCRs from and was found 67.7% and 68.0%, respectively. The means of GPCRs in based on is close to those based on PreMod; whereas the means of GPCRs in 24 based on D S 18 is less than those based on PreMod. Moreover, the accuracy ("2") and validity ("2 + 1") rates of prediction all seven TMs of 38 GPCRs by the scoring matrices of PreMod are more than those by ,

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Application of FTTP to alpha-helix or beta-strand motifs

Cited by 5 publications

References 43 publications

Molecular Modeling of Human Hepatocyte PKA (cAMP-Dependent Protein Kinase Type-II) and Its Structure Analysis

Molecular Modeling of Human Hepatocyte PKA (cAMP-Dependent Protein Kinase Type-II) and Its Structure Analysis

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

Discovery and validation of potential drug targets based on the phylogenetic evolution of GPCRs

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