Prediction of protein structural classes by Chou's pseudo amino acid composition: approached using continuous wavelet transform and principal component analysis.

Abstract:

:A prior knowledge of protein structural classes can provide useful information about its overall structure, so it is very important for quick and accurate determination of protein structural class with computation method in protein science. One of the key for computation method is accurate protein sample representation. Here, based on the concept of Chou's pseudo-amino acid composition (AAC, Chou, Proteins: structure, function, and genetics, 43:246-255, 2001), a novel method of feature extraction that combined continuous wavelet transform (CWT) with principal component analysis (PCA) was introduced for the prediction of protein structural classes. Firstly, the digital signal was obtained by mapping each amino acid according to various physicochemical properties. Secondly, CWT was utilized to extract new feature vector based on wavelet power spectrum (WPS), which contains more abundant information of sequence order in frequency domain and time domain, and PCA was then used to reorganize the feature vector to decrease information redundancy and computational complexity. Finally, a pseudo-amino acid composition feature vector was further formed to represent primary sequence by coupling AAC vector with a set of new feature vector of WPS in an orthogonal space by PCA. As a showcase, the rigorous jackknife cross-validation test was performed on the working datasets. The results indicated that prediction quality has been improved, and the current approach of protein representation may serve as a useful complementary vehicle in classifying other attributes of proteins, such as enzyme family class, subcellular localization, membrane protein types and protein secondary structure, etc.

journal_name

Amino Acids

journal_title

Amino acids

authors

Li ZC,Zhou XB,Dai Z,Zou XY

doi

10.1007/s00726-008-0170-2

subject

Has Abstract

pub_date

2009-07-01 00:00:00

pages

415-25

issue

2

eissn

0939-4451

issn

1438-2199

journal_volume

37

pub_type

杂志文章
  • Brassinolide enhances cold stress tolerance of fruit by regulating plasma membrane proteins and lipids.

    abstract::How to enhance fruit tolerance to cold stress is an important biological interest. In this paper, we found that mango (Mangifera indica L.) fruit treated with 10 μM brassinolide (BL) showed a higher tolerance to cold temperature of 5 °C. Further, we compared the changes in expression profiles of plasma membrane (PM) p...

    journal_title:Amino acids

    pub_type: 杂志文章

    doi:10.1007/s00726-012-1327-6

    authors: Li B,Zhang C,Cao B,Qin G,Wang W,Tian S

    更新日期:2012-12-01 00:00:00

  • D-Aspartyl residue in a peptide can be liberated and metabolized by pig kidney enzymes.

    abstract::The presence of an enzyme activity which hydrolyzes glycyl-D-aspartate was found in the homogenates of pig kidney cortex. The activity was inhibited by metal chelating agents and cilastatin, suggesting that the enzyme was a cilastatin-sensitive metallo-peptidase. Of the two hydrolysis products,D-aspartate was found to...

    journal_title:Amino acids

    pub_type: 杂志文章

    doi:10.1007/BF00806591

    authors: Kera Y,Funabashi K,Matsumoto T,Watanabe T,Nagasaki H,Yamada R

    更新日期:1996-06-01 00:00:00

  • Attenuation by dietary taurine of dextran sulfate sodium-induced colitis in mice and of THP-1-induced damage to intestinal Caco-2 cell monolayers.

    abstract::The effects of dietary taurine on the experimental colitis induced by dextran sulfate sodium (DSS) in mice were evaluated. C57BL/6 female mice were given 3% DSS in drinking water for 5 d to induce acute colitis. Taurine at 2% was added to the drinking water 5 d before and during the DSS-treatment to investigate its pr...

    journal_title:Amino acids

    pub_type: 杂志文章

    doi:10.1007/s00726-007-0562-8

    authors: Zhao Z,Satsu H,Fujisawa M,Hori M,Ishimoto Y,Totsuka M,Nambu A,Kakuta S,Ozaki H,Shimizu M

    更新日期:2008-06-01 00:00:00

  • Dakin-West reaction on 1-thyminyl acetic acid for the synthesis of 1,3-bis(1-thyminyl)-2-propanone, a heteroaromatic compound with nucleopeptide-binding properties.

    abstract::This work deals with the Dakin-West synthesis, starting from the nucleoamino acid 1-thyminyl acetic acid, as well the NMR, ESI MS, and X-ray characterization of a heteroaromatic compound denominated by us T(2)CO, comprising two thymine moieties anchored to a 2-propanonic unit, the spectroscopic properties of which wer...

    journal_title:Amino acids

    pub_type: 杂志文章

    doi:10.1007/s00726-012-1237-7

    authors: Roviello GN,Roviello G,Musumeci D,Bucci EM,Pedone C

    更新日期:2012-10-01 00:00:00

  • Evidence for the involvement of D-aspartic acid in learning and memory of rat.

    abstract::D-Aspartic acid (D-Asp) is an endogenous amino acid present in neuroendocrine systems. Here, we report evidence that D-Asp in the rat is involved in learning and memory processes. Oral administration of sodium D-aspartate (40 mM) for 12-16 days improved the rats' cognitive capability to find a hidden platform in the M...

    journal_title:Amino acids

    pub_type: 杂志文章

    doi:10.1007/s00726-009-0369-x

    authors: Topo E,Soricelli A,Di Maio A,D'Aniello E,Di Fiore MM,D'Aniello A

    更新日期:2010-05-01 00:00:00

  • Spectroscopic and structural elucidation of amino acid derivatives and small peptides: experimental and theoretical tools.

    abstract::This mini review deals with the modern aspects of the spectroscopy and structural elucidation of amino acid derivatives and small biologically active compounds. Free peptide bond rotation in these systems yields various conformers, which possess differing biological activities. Another phenomenon is the intermolecular...

    journal_title:Amino acids

    pub_type: 杂志文章,评审

    doi:10.1007/s00726-008-0220-9

    authors: Kolev T,Spiteller M,Koleva B

    更新日期:2010-01-01 00:00:00

  • Regulation of xCT expression and system x (c) (-) function in neuronal cells.

    abstract::The glutamate/cystine antiporter system x(c)(-) transports cystine into cells in exchange for glutamate at a ratio of 1:1. It is composed of a specific light chain, xCT, and a heavy chain, 4F2, linked by a disulfide bridge. Intracellularly, cystine is reduced into cysteine, the rate-limiting precursor of glutathione (...

    journal_title:Amino acids

    pub_type: 杂志文章,评审

    doi:10.1007/s00726-011-0862-x

    authors: Lewerenz J,Maher P,Methner A

    更新日期:2012-01-01 00:00:00

  • Microwave-assisted solid-phase peptide synthesis of the 60-110 domain of human pleiotrophin on 2-chlorotrityl resin.

    abstract::A fast and efficient microwave-assisted solid phase peptide synthesis (MW-SPPS) of a 51mer peptide, the main heparin-binding site (60-110) of human pleiotrophin (hPTN), using 2-chlorotrityl chloride resin (CLTR-Cl) following the 9-fluorenylmethyloxycarbonyl/tert-butyl (Fmoc/tBu) methodology and with the standard N,N'-...

    journal_title:Amino acids

    pub_type: 杂志文章

    doi:10.1007/s00726-010-0753-6

    authors: Friligou I,Papadimitriou E,Gatos D,Matsoukas J,Tselios T

    更新日期:2011-05-01 00:00:00

  • High plasma guanidinoacetate-to-homoarginine ratio is associated with high all-cause and cardiovascular mortality rate in adult renal transplant recipients.

    abstract::L-Arginine:glycine amidinotransferase (AGAT) is the main producer of the creatine precursor, guanidinoacetate (GAA), and L-homoarginine (hArg). We and others previously reported lower levels of circulating and urinary hArg in renal transplant recipients (RTR) compared to healthy subjects. In adults, hArg emerged as a ...

    journal_title:Amino acids

    pub_type: 杂志文章

    doi:10.1007/s00726-019-02783-6

    authors: Hanff E,Said MY,Kayacelebi AA,Post A,Minovic I,van den Berg E,de Borst MH,van Goor H,Bakker SJL,Tsikas D

    更新日期:2019-11-01 00:00:00

  • Nucleobase-containing peptides: an overview of their characteristic features and applications.

    abstract::Reports on nucleobase-containing chiral peptides (both natural and artificial) and achiral pseudopeptides are reviewed. Their synthesis, structural features, DNA and RNA-binding ability, as well as some other interesting applications which make them promising diagnostic/therapeutic agents of great importance in many a...

    journal_title:Amino acids

    pub_type: 杂志文章,评审

    doi:10.1007/s00726-010-0567-6

    authors: Roviello GN,Benedetti E,Pedone C,Bucci EM

    更新日期:2010-06-01 00:00:00

  • Transglutaminases: future perspectives.

    abstract::This is the third special issue focused on "Transglutaminases" that is now available on this journal and dedicated to one of the pioneers of these enzymes, John Edward Folk, who died December 2010 [see in this issue Beninati et al. 2012a]. The first edition, "Polyamines and Transglutaminases" was published in Amino Ac...

    journal_title:Amino acids

    pub_type: 社论

    doi:10.1007/s00726-012-1431-7

    authors: Beninati S,Facchiano F,Piacentini M

    更新日期:2013-01-01 00:00:00

  • Asymmetric synthesis of quaternary α-amino acid derivatives and their fluorinated analogues.

    abstract::In this work, we describe the asymmetric synthesis of a series of fluorinated and non-fluorinated quaternary α-amino acid derivatives. This methodology involves the diastereoselective addition of chiral 2-p-tolylsulfinyl benzylcarbanions to either imines containing a 2-furyl moiety or trifluoromethyl α-imino esters. S...

    journal_title:Amino acids

    pub_type: 杂志文章

    doi:10.1007/s00726-011-0881-7

    authors: Fustero S,Sánchez-Roselló M,Báez C,Del Pozo C,García Ruano JL,Alemán J,Marzo L,Parra A

    更新日期:2011-08-01 00:00:00

  • Enhancing effect of macroporous adsorption resin on gamma-aminobutyric acid production by Enterococcus faecium in whole-cell biotransformation system.

    abstract::Gamma-aminobutyric acid (GABA) biosynthesis depended to a great extent on the biotransformation characterization of glutamate decarboxylase (GAD) and process conditions. In this paper, the enhancing effect of D101 macroporous adsorption resin (MAR) on the GABA production was investigated based on the whole-cell biotra...

    journal_title:Amino acids

    pub_type: 杂志文章

    doi:10.1007/s00726-020-02850-3

    authors: Yang SY,Liu SM,Jiang M,Wang BS,Peng LH,Zeng C

    更新日期:2020-05-01 00:00:00

  • Mitomycin C modulates DNA-double strand break repair genes in cervical carcinoma cells.

    abstract::In a previous study, we elucidated the apoptotic mechanism mediated via Fas/FasL-dependent pathway in mitomycin C-treated cervical carcinoma cells. In this study, 2-D and MALDI-TOF analyses were performed in order to search mitomycin C-induced modulators in cervical carcinoma cells. Some protein spots down- or up-regu...

    journal_title:Amino acids

    pub_type: 杂志文章

    doi:10.1007/s00726-010-0568-5

    authors: Kang YH,Lee KA,Kim JH,Park SG,Yoon DY

    更新日期:2010-11-01 00:00:00

  • The gastro-intestinal tract as the major site of biological action of dietary melanoidins.

    abstract::Emerging evidence from laboratory researches has highlighted the bioactivity of food melanoidins and melanoproteins. Whilst such studies have been carried out with different in vitro systems, information about melanoidins absorption and bio-availability are scarce. However, they are generally considered as poorly abso...

    journal_title:Amino acids

    pub_type: 杂志文章,评审

    doi:10.1007/s00726-015-1951-z

    authors: Tagliazucchi D,Bellesia A

    更新日期:2015-06-01 00:00:00

  • Preclinical evaluation of a 64Cu-labeled disintegrin for PET imaging of prostate cancer.

    abstract::A novel recombinant disintegrin, vicrostatin (VCN), displays high binding affinity to a broad range of human integrins in substantial competitive biological advantage over other integrin-based antagonists. In this study, we synthesized a new 64Cu-labeled VCN probe and evaluated its imaging properties for prostate canc...

    journal_title:Amino acids

    pub_type: 杂志文章

    doi:10.1007/s00726-019-02794-3

    authors: Jadvar H,Chen K,Park R,Yap LP,Vorobyova I,Swenson S,Markland FS

    更新日期:2019-11-01 00:00:00

  • In sickness and in health: the widespread application of creatine supplementation.

    abstract::There is an extensive and still growing body of the literature supporting the efficacy of creatine (Cr) supplementation. In sports, creatine has been recognized as the most effective nutritional supplement in enhancing exercise tolerance, muscle strength and lean body mass. From a clinical perspective, the application...

    journal_title:Amino acids

    pub_type: 杂志文章,评审

    doi:10.1007/s00726-011-1132-7

    authors: Gualano B,Roschel H,Lancha AH Jr,Brightbill CE,Rawson ES

    更新日期:2012-08-01 00:00:00

  • Diastereoselective Michael reaction of chiral nickel(II) glycinate with nitroalkenes for asymmetric synthesis of β-substituted α,γ-diaminobutyric acid derivatives in water.

    abstract::We have developed the first operationally simple and environmentally benign protocol for the aqueous asymmetric Michael addition reaction of chiral nickel(II) glycinate with nitroalkenes. The reactions proceeded smoothly in the presence of TBAB (tetrabutyl ammonium bromide) in neat water at room temperature and provid...

    journal_title:Amino acids

    pub_type: 杂志文章

    doi:10.1007/s00726-011-0870-x

    authors: Wang J,Ji X,Shi J,Sun H,Jiang H,Liu H

    更新日期:2012-05-01 00:00:00

  • Synthesis and characterization of aspartic acid complexes of antimony and bismuth triiodide.

    abstract::New bioinorganic complexes of the aspartic acid with the antimony or bismuth triiodide were synthesized by a direct solid-solid reaction at room temperature. The formula of the complex is MI(3)[OOCCH(2)CH(NH(2))CO](2.5) x 2.5H(2)O (M = Sb, Bi). The complex may be a dimer with bridge structure. The crystal structure of...

    journal_title:Amino acids

    pub_type: 杂志文章

    doi:10.1007/s00726-005-0210-0

    authors: Jia RR,Wu CP,Wu S,Yang YX,Chen YR,Jia YQ

    更新日期:2006-07-01 00:00:00

  • The role of substance P in stress and anxiety responses.

    abstract::Substance P (SP) is one of the most abundant peptides in the central nervous system and has been implicated in a variety of physiological and pathophysiological processes including stress regulation, as well as affective and anxiety-related behaviour. Consistent with these functions, SP and its preferred neurokinin 1 ...

    journal_title:Amino acids

    pub_type: 杂志文章,评审

    doi:10.1007/s00726-006-0335-9

    authors: Ebner K,Singewald N

    更新日期:2006-10-01 00:00:00

  • Conservation of the basic pattern of cellular amino acid composition during biological evolution in plants.

    abstract::The cellular amino acid composition of plant cells was analyzed. The callus of carrot (Daucus carota), leaves of Torenia fournieri and protocomb-like body of Cymbidium, s.p. were examined as examples of plant cells. The cellular amino acid compositions differed in the plant cells, but their basic patterns were quite s...

    journal_title:Amino acids

    pub_type: 杂志文章

    doi:10.1007/s007260050016

    authors: Sorimachi K,Okayasu T,Akimoto K,Niwa A

    更新日期:2000-01-01 00:00:00

  • Ethynylglycine synthon, a useful precursor for the synthesis of biologically active compounds: an update: part I: preparations of ethynylglycine synthon.

    abstract::The ethynylglycine synthon {(R)-2,2-dimethyl-3-(tert-butoxycarbonyl)-4-ethynyloxazolidine} is a chiral compound with valuable synthetic interest. An update on the different routes for its synthesis is reviewed and discussed. ...

    journal_title:Amino acids

    pub_type: 杂志文章,评审

    doi:10.1007/s00726-014-1902-0

    authors: Benfodda Z,Bénimélis D,Reginato G,Meffre P

    更新日期:2015-02-01 00:00:00

  • Synthesis, characteristics and biological activity of pentacoordinated spirophosphoranes derived from amino acids.

    abstract::The reactions of phosphorus trichloride with various amino acids afford the pentacoordinated spirophosphoranes. The reaction procedures were traced by (31)P NMR spectra techniques. A new crystal structure of alanine derivative was characterized, which is a slightly distorted TBP structure. Besides, this kind of spirop...

    journal_title:Amino acids

    pub_type: 杂志文章

    doi:10.1007/s00726-005-0207-8

    authors: Yu L,Liu Z,Fang H,Zeng QL,Zhao YF

    更新日期:2005-06-01 00:00:00

  • Oxygen radical induced fluorescence in proteins; identification of the fluorescent tryptophan metabolite, N-formyl kynurenine, as a biological index of radical damage.

    abstract::The effect of oxygen derived free radicals (OFR) on aromatic and sulphur containing amino acids has been investigated, both in their free form and within protein backbones. Aerated amino acids and proteins in solution were exposed to three discrete OFR generating systems; (1) gamma radiation in the presence or absence...

    journal_title:Amino acids

    pub_type: 杂志文章

    doi:10.1007/BF00806783

    authors: Griffiths HR,Lunec J,Blake DR

    更新日期:1992-06-01 00:00:00

  • Age-related salivary polyamine increase in adolescents wearing orthodontic Ni-Ti archwires.

    abstract::Until now information about the influence of puberty on gingival tissue responses to Ni-Ti alloy haven't been available. Since our previous researches have demonstrated that Ni-Ti appliances have an influence on hyperplastic gingivopathy and data has pointed out a possible hormonal influence on the susceptibility of g...

    journal_title:Amino acids

    pub_type: 杂志文章

    doi:10.1007/s007260200001

    authors: Venza M,Visalli M,Ruggeri P,Cicciù D,Teti D

    更新日期:2002-01-01 00:00:00

  • Metabolism and function in animal tissues of agmatine, a biogenic amine formed from arginine.

    abstract::Recently agmatine, decarboxylated arginine, has been shown to be an important biological compound in several animal tissues. This paper summarizes the known information regarding the transport of arginine, its decarboxylation and the effects of the agmatine formed mainly on NO and polyamine synthesis. ...

    journal_title:Amino acids

    pub_type: 杂志文章,评审

    doi:10.1007/s00726-003-0030-z

    authors: Grillo MA,Colombatto S

    更新日期:2004-02-01 00:00:00

  • Chronic treatment with zinc and antidepressants induces enhancement of presynaptic/extracellular zinc concentration in the rat prefrontal cortex.

    abstract::Zinc exhibits antidepressant-like activity in preclinical tests/models. Moreover, zinc homeostasis is implicated in the pathophysiology of affective disorders. The aim of the present study was to examine the effect of chronic zinc, citalopram and imipramine intraperitoneal administration on the presynaptic and extrace...

    journal_title:Amino acids

    pub_type: 杂志文章

    doi:10.1007/s00726-010-0641-0

    authors: Sowa-Kućma M,Kowalska M,Szlósarczyk M,Gołembiowska K,Opoka W,Baś B,Pilc A,Nowak G

    更新日期:2011-01-01 00:00:00

  • Piceatannol attenuates homocysteine-induced endoplasmic reticulum stress and endothelial cell damage via heme oxygenase-1 expression.

    abstract::A growing body of evidence implicates endoplasmic reticulum (ER)-induced cellular dysfunction and apoptosis as important factors to a variety of diseases. In endothelial cells (ECs), the sulfur-containing amino acid homocysteine (Hcy) causes EC apoptosis and reactive oxygen species (ROS) generation through induction o...

    journal_title:Amino acids

    pub_type: 杂志文章

    doi:10.1007/s00726-016-2375-0

    authors: Kil JS,Jeong SO,Chung HT,Pae HO

    更新日期:2017-04-01 00:00:00

  • Enzyme promiscuity in earthworm serine protease: substrate versatility and therapeutic potential.

    abstract::Enzymes are the most versatile molecules in the biological world. These amazing molecules play an integral role in the regulation of various metabolic pathways and physiology subsequently. Promiscuity of an enzyme is the capacity to catalyze additional biochemical reactions besides their native one. Catalytic promiscu...

    journal_title:Amino acids

    pub_type: 杂志文章,评审

    doi:10.1007/s00726-015-2162-3

    authors: Verma MK,Pulicherla KK

    更新日期:2016-04-01 00:00:00

  • Effect of taurine chloramine, the product of activated neutrophils, on the development of collagen-induced arthritis in DBA 1/J mice.

    abstract::Taurine chloramine (TauCl), a product of neutrophil myeloperoxidase - halide system, formed by a reaction of taurine with HOCl, is known as an anti-microbial and anti-inflammatory long-lived oxidant. We previously reported that TauCl inhibits in vitro the production of proinflammatory cytokines (IL-6, IL-8) by RA syno...

    journal_title:Amino acids

    pub_type: 杂志文章

    doi:10.1007/s00726-002-0207-x

    authors: Kwaśny-Krochin B,Bobek M,Kontny E,Gluszko P,Biedroń R,Chain BM,Maśliński W,Marcinkiewicz J

    更新日期:2002-01-01 00:00:00