TY  - JOUR
AU  - Perović, Vladimir R.
AU  - Šumonja, Neven
AU  - Marsh, Lindsey A.
AU  - Radovanović, Sandro
AU  - Vukićević, Milan
AU  - Roberts, Stefan G. E.
AU  - Veljković, Nevena V.
PY  - 2018
UR  - http://www.nature.com/articles/s41598-018-28815-x
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/7811
AB  - Intrinsically disordered proteins (IDPs) are characterized by the lack of a fixed tertiary structure and are involved in the regulation of key biological processes via binding to multiple protein partners. IDPs are malleable, adapting to structurally different partners, and this flexibility stems from features encoded in the primary structure. The assumption that universal sequence information will facilitate coverage of the sparse zones of the human interactome motivated us to explore the possibility of predicting protein-protein interactions (PPIs) that involve IDPs based on sequence characteristics. We developed a method that relies on features of the interacting and non-interacting protein pairs and utilizes machine learning to classify and predict IDP PPIs. Consideration of both sequence determinants specific for conformational organizations and the multiplicity of IDP interactions in the training phase ensured a reliable approach that is superior to current state-of-the-art methods. By applying a strict evaluation procedure, we confirm that our method predicts interactions of the IDP of interest even on the proteome-scale. This service is provided as a web tool to expedite the discovery of new interactions and IDP functions with enhanced efficiency. © 2018 The Author(s).
T2  - Scientific Reports
T1  - IDPpi: Protein-Protein Interaction Analyses of Human Intrinsically Disordered Proteins
VL  - 8
IS  - 1
SP  - 10563
DO  - 10.1038/s41598-018-28815-x
ER  - 

@article{
author = "Perović, Vladimir R. and Šumonja, Neven and Marsh, Lindsey A. and Radovanović, Sandro and Vukićević, Milan and Roberts, Stefan G. E. and Veljković, Nevena V.",
year = "2018",
abstract = "Intrinsically disordered proteins (IDPs) are characterized by the lack of a fixed tertiary structure and are involved in the regulation of key biological processes via binding to multiple protein partners. IDPs are malleable, adapting to structurally different partners, and this flexibility stems from features encoded in the primary structure. The assumption that universal sequence information will facilitate coverage of the sparse zones of the human interactome motivated us to explore the possibility of predicting protein-protein interactions (PPIs) that involve IDPs based on sequence characteristics. We developed a method that relies on features of the interacting and non-interacting protein pairs and utilizes machine learning to classify and predict IDP PPIs. Consideration of both sequence determinants specific for conformational organizations and the multiplicity of IDP interactions in the training phase ensured a reliable approach that is superior to current state-of-the-art methods. By applying a strict evaluation procedure, we confirm that our method predicts interactions of the IDP of interest even on the proteome-scale. This service is provided as a web tool to expedite the discovery of new interactions and IDP functions with enhanced efficiency. © 2018 The Author(s).",
journal = "Scientific Reports",
title = "IDPpi: Protein-Protein Interaction Analyses of Human Intrinsically Disordered Proteins",
volume = "8",
number = "1",
pages = "10563",
doi = "10.1038/s41598-018-28815-x"
}

Perović, V. R., Šumonja, N., Marsh, L. A., Radovanović, S., Vukićević, M., Roberts, S. G. E.,& Veljković, N. V.. (2018). IDPpi: Protein-Protein Interaction Analyses of Human Intrinsically Disordered Proteins. in Scientific Reports, 8(1), 10563.
https://doi.org/10.1038/s41598-018-28815-x

Perović VR, Šumonja N, Marsh LA, Radovanović S, Vukićević M, Roberts SGE, Veljković NV. IDPpi: Protein-Protein Interaction Analyses of Human Intrinsically Disordered Proteins. in Scientific Reports. 2018;8(1):10563.
doi:10.1038/s41598-018-28815-x .

Perović, Vladimir R., Šumonja, Neven, Marsh, Lindsey A., Radovanović, Sandro, Vukićević, Milan, Roberts, Stefan G. E., Veljković, Nevena V., "IDPpi: Protein-Protein Interaction Analyses of Human Intrinsically Disordered Proteins" in Scientific Reports, 8, no. 1 (2018):10563,
https://doi.org/10.1038/s41598-018-28815-x . .

TY  - JOUR
AU  - Bogojević, Jelena
AU  - Nikolić, Miloš
AU  - Marković, Tatjana
AU  - Ćirić, Ana
AU  - Marković, Dejan
PY  - 2016
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/11675
AB  - Twenty one essential oils (EOs) documented their significant antimicrobial effect with regard to our pre-set criterion of the Minimal Inhibitory Concentration (MIC ≤ 200 μL / mL) of EOs towards Enterococcus faecalis (ATCC 29212 and or clinical isolates); the best effect MIC 0.4 μL / mL (approx. 0.26 μg / mL) achieved Satureja horvatii L. EO, while the EOs with the lowest antimicrobial efficacy were Rosmarinus officinalis L. and Achilea milefolium L., both with MIC s160.0 μg / mL. Analysis of the MIC values within the groups revealed that ATCC strain of E. faecalis is generally lower, ranging from 0.26 to 156 μg / mL, in comparison to those for clinical isolateswhich ranged from 10 to 160 μg / mL. Twelve 12 components that are common in EOs whith MIC s ≤ 200 μg / mL in testings towards both, the clinical and referent strains are given in descending order according to number of oils they are present in: trans-β-caryophyllene (13) > myrcene (8) > α-pinene (8) > linalool (7) > p-cymene (7) > borneol (7) > geraniol (6) > camphene (6) > limonene (5) > 1,8- cineol (5) > γ -terpinene (5) > α- terpinene (4). Comparison of EO constituents reviled that only, geraniol and 1,8-cineol, contributed with ≥ 10 % to more than one EO (MIC 0.3-200 μg / mL) efficient against both E. faecalis strains. Thirteen components in 11 EOs with MIC ≤ 200 μg / mL towards ATCC 29212 were representative based on their contents in EOs: eugenol 82.9 % > thymol 63.7 % > hexadecanoic acid 47.8 % > menthol 46.6 % > cis-b-ocimene 44.2 % > geranial 42.1 % > trans-β-caryophyllene 40.8 % > citronellal 36.7 % > α-pinene 31.2 % > neral 30.5 % > α-eudesmol 22.4 % > citronellol 13.1 % > menthone 11.3 %. Following seven components, representative in 10 EOs with MIC ≤ 200 μg / mL towards clinical isolates, are presented in order of their contribution to EOs: phenylethyl alcohol 57.7 % > geranial 32.9 % > neral 22.2 % > p- cymene 20 % > carvacrol 14 % > α-pinene 11.5 % > linalool 11.4 %. Out of 21 highly efficient EOs selected in this study, six EOs proved to be the most efficient (MIC ≤ 30 μg / mL ); three oils in control of E.faecalis ATCC strain (Satureja horvatii, Mentha pulegium and Rosmarinus officinalis) and other three in control of E. faecalis clinical isolates (Leptospermum petersonii, Thymus algeriensis, Thymus serpyllum). Thymol is a major component in three out of the six aforementioned most efficient EOs. The aim of our study was to investigate differences in efficacy of selected EOs that proved to possess great antimicrobial activity, towards the referent strain ATCC 29212 and clinical isolates of E. faecalis on, and to estimate which of their constituents might contribute to desired activity, as 'markers compunds'.
T2  - Lekovite sirovine
T1  - Analysis of chemical composition of the most efficient essential oils towards Enterococcus faecalis referent strain ATCC 29212 and clinical isolates
IS  - 36
SP  - 3
EP  - 25
DO  - 10.5937/leksir1636003B
ER  - 

@article{
author = "Bogojević, Jelena and Nikolić, Miloš and Marković, Tatjana and Ćirić, Ana and Marković, Dejan",
year = "2016",
abstract = "Twenty one essential oils (EOs) documented their significant antimicrobial effect with regard to our pre-set criterion of the Minimal Inhibitory Concentration (MIC ≤ 200 μL / mL) of EOs towards Enterococcus faecalis (ATCC 29212 and or clinical isolates); the best effect MIC 0.4 μL / mL (approx. 0.26 μg / mL) achieved Satureja horvatii L. EO, while the EOs with the lowest antimicrobial efficacy were Rosmarinus officinalis L. and Achilea milefolium L., both with MIC s160.0 μg / mL. Analysis of the MIC values within the groups revealed that ATCC strain of E. faecalis is generally lower, ranging from 0.26 to 156 μg / mL, in comparison to those for clinical isolateswhich ranged from 10 to 160 μg / mL. Twelve 12 components that are common in EOs whith MIC s ≤ 200 μg / mL in testings towards both, the clinical and referent strains are given in descending order according to number of oils they are present in: trans-β-caryophyllene (13) > myrcene (8) > α-pinene (8) > linalool (7) > p-cymene (7) > borneol (7) > geraniol (6) > camphene (6) > limonene (5) > 1,8- cineol (5) > γ -terpinene (5) > α- terpinene (4). Comparison of EO constituents reviled that only, geraniol and 1,8-cineol, contributed with ≥ 10 % to more than one EO (MIC 0.3-200 μg / mL) efficient against both E. faecalis strains. Thirteen components in 11 EOs with MIC ≤ 200 μg / mL towards ATCC 29212 were representative based on their contents in EOs: eugenol 82.9 % > thymol 63.7 % > hexadecanoic acid 47.8 % > menthol 46.6 % > cis-b-ocimene 44.2 % > geranial 42.1 % > trans-β-caryophyllene 40.8 % > citronellal 36.7 % > α-pinene 31.2 % > neral 30.5 % > α-eudesmol 22.4 % > citronellol 13.1 % > menthone 11.3 %. Following seven components, representative in 10 EOs with MIC ≤ 200 μg / mL towards clinical isolates, are presented in order of their contribution to EOs: phenylethyl alcohol 57.7 % > geranial 32.9 % > neral 22.2 % > p- cymene 20 % > carvacrol 14 % > α-pinene 11.5 % > linalool 11.4 %. Out of 21 highly efficient EOs selected in this study, six EOs proved to be the most efficient (MIC ≤ 30 μg / mL ); three oils in control of E.faecalis ATCC strain (Satureja horvatii, Mentha pulegium and Rosmarinus officinalis) and other three in control of E. faecalis clinical isolates (Leptospermum petersonii, Thymus algeriensis, Thymus serpyllum). Thymol is a major component in three out of the six aforementioned most efficient EOs. The aim of our study was to investigate differences in efficacy of selected EOs that proved to possess great antimicrobial activity, towards the referent strain ATCC 29212 and clinical isolates of E. faecalis on, and to estimate which of their constituents might contribute to desired activity, as 'markers compunds'.",
journal = "Lekovite sirovine",
title = "Analysis of chemical composition of the most efficient essential oils towards Enterococcus faecalis referent strain ATCC 29212 and clinical isolates",
number = "36",
pages = "3-25",
doi = "10.5937/leksir1636003B"
}

Bogojević, J., Nikolić, M., Marković, T., Ćirić, A.,& Marković, D.. (2016). Analysis of chemical composition of the most efficient essential oils towards Enterococcus faecalis referent strain ATCC 29212 and clinical isolates. in Lekovite sirovine(36), 3-25.
https://doi.org/10.5937/leksir1636003B

Bogojević J, Nikolić M, Marković T, Ćirić A, Marković D. Analysis of chemical composition of the most efficient essential oils towards Enterococcus faecalis referent strain ATCC 29212 and clinical isolates. in Lekovite sirovine. 2016;(36):3-25.
doi:10.5937/leksir1636003B .

Bogojević, Jelena, Nikolić, Miloš, Marković, Tatjana, Ćirić, Ana, Marković, Dejan, "Analysis of chemical composition of the most efficient essential oils towards Enterococcus faecalis referent strain ATCC 29212 and clinical isolates" in Lekovite sirovine, no. 36 (2016):3-25,
https://doi.org/10.5937/leksir1636003B . .