Identification of post-translational modified amino acids

Tsiboli, Paraskevi; Konstantinidis, G.; Skendros, Y.; Katsani, A.; Choli‐Papadopoulou, Theodora

doi:10.1007/bf01373045

Cited by 5 publications

(5 citation statements)

References 25 publications

(16 reference statements)

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“…These are shown in the previous works within the subjects of H1N1 virus (Tambunan et al, 2012). The resulted best cyclic peptides, namely the threoninedominated CKTTC and lysine-dominated CKKTC could be affected by the posttranslational modification, if no cyclization is applied (Tsiboli et al, 1997). Threonine can undergo glycosylation while lysine can be hampered with methylation (Zhang et al, 2012).…”

Section: Discussionmentioning

confidence: 54%

Designing of Disulfide Cyclic Peptide for Inhibiting Polymerase A and B1 (PAC-PB1N) in H1N1 Virus using Molecular Simulation Approach

Tambunan¹,

Nasution²,

Parikesit³

et al. 2016

OnLine Journal of Biological Sciences

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Abstract:The drug resistance A/H1N1 flu virus is emerging rapidly. Therefore, looking for potential therapy is very important. PB2, PB and PA are subunits of viral RNA-dependent RNA polymerase (RdRp). They play an important role in viral replication. The PA and PB1 binding sites can be considered as potential targets for the development of new influenza drugs. The peptide inhibitors can be designed specifically due to their highpreferred activity. In this study, the cyclic peptide ligands were designed based on the crystal structure of PA C -PB1 N in the surface of the molecule, resulting 1728 cyclopentadienyl compounds. The MOE 2008.10 software was utilized for molecular docking and dynamics simulation approach, while Lipinski's Rules of Five were utilized to evaluate the feasibility of drug candidates. Thus, molecular dynamics simulation was applied, in order to facilitate the interaction between the ligand and enzyme. The simulations have successfully produced two cyclopentyl peptides, namely CKKTC and CKTTC, which results in both ligands providing a potent inhibitor of polymerase PA C -PB1 N of Influenza A/2009 (H1N1).

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Section: Discussionmentioning

confidence: 54%

Designing of Disulfide Cyclic Peptide for Inhibiting Polymerase A and B1 (PAC-PB1N) in H1N1 Virus using Molecular Simulation Approach

Tambunan¹,

Nasution²,

Parikesit³

et al. 2016

OnLine Journal of Biological Sciences

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“…[50][51][52][53][54][55][56][57][58][59][60] Amine reactive dimethylaminoazobenzene dyes, DABsyl and DAB-ITC, have been extensively used for labeling of biomolecules. [61][62][63][64][65][66][67] They have also been applied in the functionalization or tagging of soluble amino-polymers 68 and dendrimers 49,69 as well as in the surface modification of fused silica. 70 We investigated the preparation of dyed NPs in a similar way by reacting these orange-colored chromophores with amino-functionalized NPs.…”

Section: Resultsmentioning

confidence: 99%

A versatile preparation of azobenzene‐dye functionalized colored polymer nanoparticles by surface modification

Cannizzo

Amigoni

Frigoli

et al. 2008

J. Polym. Sci. A Polym. Chem.

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A series of stable and translucent colored nanolatex, that is, colloidal aqueous suspensions of dye-tagged polymer nanoparticles (NPs) in the 15-to 20-nm diameter range, have been prepared by covalent attachment of azobenzene chromophores to the surface of reactive NPs. Primary crosslinked NPs bearing chlorobenzyl groups were produced by microemulsion copolymerization of styrene and vinylbenzylchloride. Amine-functionalized NPs were obtained after a second functionalization step with polyamines (cyclam and polypropyleneimine dendrimers of first and third generations). Dye-doped particles were obtained by reacting pyridylazo-dimethylaminobenzene (PADA) with chlorobenzyl-NPs and by reacting amine-reactive dimethylaminoazobenzene dyes (DABsyl, DAB-ITC) as well as Disperse Red 1 acrylate with polyamine-coated NPs. Regardless the dye solubility, the grafting readily proceeded in aqueous suspensions at room temperature in the presence of a cationic surfactant without added solvent. Purple, red, and orange suspensions (maximum absorption around 550, 500, 430 nm), with dye loads ranging from 0.3 to 1.2 mmol/g, corresponding to 400-1800 azobenzene residues per NP, are obtained. The reported results indicate that functional polymer NPs, with remarkably accessible multiple anchoring sites, are useful building blocks. V

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“…Amino acids were identified after post‐column derivatization with o ‐phthaldialdehyde (OPA; Tsiboli et al, 1997). Separation of amino acids was done on a Shim‐pack ISC‐07/S1504 Na column (150 mm length × 4.0 mm diameter, Shimadzu) under gradient elution by using two sodium citrate buffers at a flow rate of 0.3 mL min −1 (Buffer A: 0.067 M sodium citrate in 4% ethanol solution, pH was adjusted to 3.2 by 60% perchloric acid; Buffer B: 0.2 M sodium citrate and 0.2 M orthoboric acid, pH was adjusted to 10.0 by 4 M NaOH solution).…”

Section: Methodsmentioning

confidence: 99%

Adsorption efficiency of a continuous trapping system and its use for the collection of root exudates from cucumber

Dong

Chu

et al. 2015

J. Plant Nutr. Soil Sci.

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Root exudates comprising soluble low-molecular-weight organic compounds (LMWOCs) play a crucial role in the rhizosphere processes. Therefore, accurate determination of the composition and quantity of these compounds is of importance. A continuous trapping system (CTS) with XAD-4 macroporous resin is widely used for collecting root exudates in hydroponics, and ion exchange resins are used in the separation of root exudates into neutral, acid and basic fractions. Here, we studied the adsorption equilibrium isotherms and dynamic adsorption properties of 27 standard LMWOCs on XAD-4 resin. The adsorption isotherms of most LMWOCs matched the Langmuir isotherm equations. Furthermore, we investigated the adsorption efficiency of the CTS for LMWOCs and the recovery ratios during fractionation by ion exchange resins. The adsorption capacities of the CTS for LMWOCs which are non-polar or having large non-polar moieties were higher. The recovery ratios of most LMWOCs were larger than 80% during fractionation. The overall recovery ratios of LMWOCs were ca. 10, 20, and 30% for sugars, organic acids, and amino acids, respectively. Using this collection method, we present the composition and quantity of root exudates of cucumber (Cumumis sativus L.) at four different growth stages. The major components of root exudates were similar to previous works, whereas the quantities were different. The various collection methods may be the main reason for these differences. Therefore, it is necessary to study the overall recovery ratios when the compositions of root exudates via different collection methods are compared.

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Identification of post-translational modified amino acids

Abstract: Summary. Methylated lysines (N Show more

Cited by 5 publications

References 25 publications

Designing of Disulfide Cyclic Peptide for Inhibiting Polymerase A and B1 (PA<sub>C</sub>-PB1<sub>N</sub>) in H1N1 Virus using Molecular Simulation Approach

Designing of Disulfide Cyclic Peptide for Inhibiting Polymerase A and B1 (PA<sub>C</sub>-PB1<sub>N</sub>) in H1N1 Virus using Molecular Simulation Approach

A versatile preparation of azobenzene‐dye functionalized colored polymer nanoparticles by surface modification

Adsorption efficiency of a continuous trapping system and its use for the collection of root exudates from cucumber

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