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The study of physicochemical and biochemical processes in living environment that have impacts on pollution and the investigation of possibilities for minimizing the consequences

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info:eu-repo/grantAgreement/MESTD/Basic Research (BR or ON)/172001/RS//

The study of physicochemical and biochemical processes in living environment that have impacts on pollution and the investigation of possibilities for minimizing the consequences (en)
Проучавање физичкохемијских и биохемијских процеса у животној средини који утичу на загађење и истраживање могућности за минимизирање последица (sr)
Proučavanje fizičkohemijskih i biohemijskih procesa u životnoj sredini koji utiču na zagađenje i istraživanje mogućnosti za minimiziranje posledica (sr_RS)
Authors

Publications

Short Intramolecular O···O Contact in Some o -Dialkoxybenzene Derivatives Generates Efficient Hydrogen Bonding Acceptor Area

Bogdanović, Goran A.; Ostojić, Bojana D.; Novaković, Slađana B.

(2018)

TY  - JOUR
AU  - Bogdanović, Goran A.
AU  - Ostojić, Bojana D.
AU  - Novaković, Slađana B.
PY  - 2018
UR  - http://pubs.acs.org/doi/10.1021/acs.cgd.7b00914
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/7659
AB  - Statistical analysis of data extracted from the Cambridge Structural Database (CSD) has been used to investigate the crystal structure properties of odialkoxybenzene derivatives, compounds containing two ether oxygen acceptors in ortho positions of benzene ring. It has been shown that in more than 90% of cases, the fragment has predictable geometrical characteristics where the two ether oxygens form short interatomic O center dot center dot center dot O contact (2.57 A in average), while O-substitutents take trans position, both approximately coplanar with the benzene ring. Such arrangement of oxygen acceptors produces a large and uniform area of the negative electrostatic potential suitable for multiple hydrogen bonding. The acceptor abilities of the O center dot center dot center dot O system have been investigated by the statistical CSD analysis. The ab initio estimation of the interaction energy in the dimer of o-dimethoxybenzene (DMB) and H2O, employed as a model system, is achieved via high-level electron correlation CCSD(T) calculation with the complete basis set extrapolation. The interaction energy is estimated to be 6.5 kcal/mol. The results indicate the existence of a very flat potential the region between methoxy oxygens and that DMB water is a highly flexible system. The structural role of the O center dot center dot center dot O acceptor system is particularly interesting considering its ability to form multiple hydrogen bonding
T2  - Crystal Growth & Design
T1  - Short Intramolecular O···O Contact in Some o -Dialkoxybenzene Derivatives Generates Efficient Hydrogen Bonding Acceptor Area
VL  - 18
IS  - 3
SP  - 1303
EP  - 1314
DO  - 10.1021/acs.cgd.7b00914
ER  - 
@article{
author = "Bogdanović, Goran A. and Ostojić, Bojana D. and Novaković, Slađana B.",
year = "2018",
url = "http://pubs.acs.org/doi/10.1021/acs.cgd.7b00914, http://vinar.vin.bg.ac.rs/handle/123456789/7659",
abstract = "Statistical analysis of data extracted from the Cambridge Structural Database (CSD) has been used to investigate the crystal structure properties of odialkoxybenzene derivatives, compounds containing two ether oxygen acceptors in ortho positions of benzene ring. It has been shown that in more than 90% of cases, the fragment has predictable geometrical characteristics where the two ether oxygens form short interatomic O center dot center dot center dot O contact (2.57 A in average), while O-substitutents take trans position, both approximately coplanar with the benzene ring. Such arrangement of oxygen acceptors produces a large and uniform area of the negative electrostatic potential suitable for multiple hydrogen bonding. The acceptor abilities of the O center dot center dot center dot O system have been investigated by the statistical CSD analysis. The ab initio estimation of the interaction energy in the dimer of o-dimethoxybenzene (DMB) and H2O, employed as a model system, is achieved via high-level electron correlation CCSD(T) calculation with the complete basis set extrapolation. The interaction energy is estimated to be 6.5 kcal/mol. The results indicate the existence of a very flat potential the region between methoxy oxygens and that DMB water is a highly flexible system. The structural role of the O center dot center dot center dot O acceptor system is particularly interesting considering its ability to form multiple hydrogen bonding",
journal = "Crystal Growth & Design",
title = "Short Intramolecular O···O Contact in Some o -Dialkoxybenzene Derivatives Generates Efficient Hydrogen Bonding Acceptor Area",
volume = "18",
number = "3",
pages = "1303-1314",
doi = "10.1021/acs.cgd.7b00914"
}
2
3
2

Study of the effect of Mg(II) addition and the annealing conditions on the structure of mesoporous aluminum oxide using Plackett-Burman design

Novaković, Tatjana B.; Rozic, Ljiljana S.; Petrović, Srđan P.; Vuković, Zorica M.; Mitrić, Miodrag

(2015)

TY  - JOUR
AU  - Novaković, Tatjana B.
AU  - Rozic, Ljiljana S.
AU  - Petrović, Srđan P.
AU  - Vuković, Zorica M.
AU  - Mitrić, Miodrag
PY  - 2015
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/869
AB  - A statistical design was used to investigate the effect of various processing conditions on the structure of sol-gel derived Mg(II) doped alumina. Six process variables were selected based on the Plackett-Burman design: concentration of magnesium nitrate, time and temperature of alcohol evaporation, temperature and time of annealing and heating rate were changed at two levels. For every set of conditions, samples with different specific surface area and degree of crystallinity were obtained. Analysis of the results showed that the annealing temperature, heating rate and concentration of magnesium nitrate were the main factors affecting the average crystallite size of the predominant alumina phase. In the case of the specific surface area, two of selected six variables had pronounced effects; however, the temperature of annealing was more effective than others. The present results showed that the proposed model that uses crystallite size as a response variable is preferable to other research.
T2  - Journal of the Serbian Chemical Society
T1  - Study of the effect of Mg(II) addition and the annealing conditions on the structure of mesoporous aluminum oxide using Plackett-Burman design
VL  - 80
IS  - 12
SP  - 1529
EP  - 1540
DO  - 10.2298/JSC141113056N
ER  - 
@article{
author = "Novaković, Tatjana B. and Rozic, Ljiljana S. and Petrović, Srđan P. and Vuković, Zorica M. and Mitrić, Miodrag",
year = "2015",
url = "http://vinar.vin.bg.ac.rs/handle/123456789/869",
abstract = "A statistical design was used to investigate the effect of various processing conditions on the structure of sol-gel derived Mg(II) doped alumina. Six process variables were selected based on the Plackett-Burman design: concentration of magnesium nitrate, time and temperature of alcohol evaporation, temperature and time of annealing and heating rate were changed at two levels. For every set of conditions, samples with different specific surface area and degree of crystallinity were obtained. Analysis of the results showed that the annealing temperature, heating rate and concentration of magnesium nitrate were the main factors affecting the average crystallite size of the predominant alumina phase. In the case of the specific surface area, two of selected six variables had pronounced effects; however, the temperature of annealing was more effective than others. The present results showed that the proposed model that uses crystallite size as a response variable is preferable to other research.",
journal = "Journal of the Serbian Chemical Society",
title = "Study of the effect of Mg(II) addition and the annealing conditions on the structure of mesoporous aluminum oxide using Plackett-Burman design",
volume = "80",
number = "12",
pages = "1529-1540",
doi = "10.2298/JSC141113056N"
}
3
3
2

Electronic features and hydrogen bonding capacity of the sulfur acceptor in thioureido-based compounds. Part 2. Further insight by theoretical charge density study

Francuski, Bojana; Novaković, Slađana B.; Ostojić, Bojana D.; Francuski, Đorđe D.; Bogdanović, Goran A.

(2015)

TY  - JOUR
AU  - Francuski, Bojana
AU  - Novaković, Slađana B.
AU  - Ostojić, Bojana D.
AU  - Francuski, Đorđe D.
AU  - Bogdanović, Goran A.
PY  - 2015
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/671
AB  - Theoretical charge density analysis of the thioureido based compound 4-methyl-3-thiosemicarbazide (MeTSC) is used in this study with the aim to provide additional insight into electronic features of the thioureido sulfur acceptor and the corresponding D-H...S hydrogen bonding (D=N, C). The present work is motivated by our earlier experimental charge density study on the same compound that pointed out to a great flexibility of the thioureido S acceptor and its ability to adjust the lone pair electron density to the donor groups in simultaneous hydrogen bonding. Through the additional theoretical approach we were able to single out different fragments of MeTSC crystal and to carefully follow the changes in electron density properties of the S acceptors belonging to: isolated MeTSC monomers (i.e. two crystallographically independent molecules), eight D-H...S bonded dimers and MeTSC molecules placed in full crystal environment, where each S atom engages in four hydrogen bonds. Deformation density of the sulfurs lone electron pair, topological properties of D-H...S interactions and electrostatic potential are here examined in order to comprehend the mutual influence and potential cooperative effects of the four simultaneously formed interactions to each of the S acceptors. The hydrogen bonding involving thioureido S acceptor is also investigated in terms of the energetic properties of the eight real MeTSC dimers existing in the crystal structure, and additional systems MeTSC/MeOH and acetone/MeOH. The latter systems are designed with the purpose of direct comparison and ranking of interactions involving thioureido S to those involving more conventional, carbonyl O acceptor. Energetic features were thoroughly studied through electrostatic interactions energies (XD2006), cohesive energies (CRYSTAL09) and ab initio approach employing the coupled-cluster single S and doubles augmented by a perturbational correction for connected triple excitations (CCSD(T)) method. (C) 2015 Elsevier B.V. All rights reserved.
T2  - Computational and Theoretical Chemistry
T1  - Electronic features and hydrogen bonding capacity of the sulfur acceptor in thioureido-based compounds. Part 2. Further insight by theoretical charge density study
VL  - 1067
SP  - 93
EP  - 102
DO  - 10.1016/j.comptc.2015.05.024
ER  - 
@article{
author = "Francuski, Bojana and Novaković, Slađana B. and Ostojić, Bojana D. and Francuski, Đorđe D. and Bogdanović, Goran A.",
year = "2015",
url = "http://vinar.vin.bg.ac.rs/handle/123456789/671",
abstract = "Theoretical charge density analysis of the thioureido based compound 4-methyl-3-thiosemicarbazide (MeTSC) is used in this study with the aim to provide additional insight into electronic features of the thioureido sulfur acceptor and the corresponding D-H...S hydrogen bonding (D=N, C). The present work is motivated by our earlier experimental charge density study on the same compound that pointed out to a great flexibility of the thioureido S acceptor and its ability to adjust the lone pair electron density to the donor groups in simultaneous hydrogen bonding. Through the additional theoretical approach we were able to single out different fragments of MeTSC crystal and to carefully follow the changes in electron density properties of the S acceptors belonging to: isolated MeTSC monomers (i.e. two crystallographically independent molecules), eight D-H...S bonded dimers and MeTSC molecules placed in full crystal environment, where each S atom engages in four hydrogen bonds. Deformation density of the sulfurs lone electron pair, topological properties of D-H...S interactions and electrostatic potential are here examined in order to comprehend the mutual influence and potential cooperative effects of the four simultaneously formed interactions to each of the S acceptors. The hydrogen bonding involving thioureido S acceptor is also investigated in terms of the energetic properties of the eight real MeTSC dimers existing in the crystal structure, and additional systems MeTSC/MeOH and acetone/MeOH. The latter systems are designed with the purpose of direct comparison and ranking of interactions involving thioureido S to those involving more conventional, carbonyl O acceptor. Energetic features were thoroughly studied through electrostatic interactions energies (XD2006), cohesive energies (CRYSTAL09) and ab initio approach employing the coupled-cluster single S and doubles augmented by a perturbational correction for connected triple excitations (CCSD(T)) method. (C) 2015 Elsevier B.V. All rights reserved.",
journal = "Computational and Theoretical Chemistry",
title = "Electronic features and hydrogen bonding capacity of the sulfur acceptor in thioureido-based compounds. Part 2. Further insight by theoretical charge density study",
volume = "1067",
pages = "93-102",
doi = "10.1016/j.comptc.2015.05.024"
}
1
2
2

Kopolimeri dobijeni kalemljenjem vinilnih monomera na skrob - uticaj amina na sintezu i procesi degradacije u životnoj sredini

Nikolić, Vladimir M.

(Универзитет у Београду, Хемијски факултет, 2013)

@phdthesis{
author = "Nikolić, Vladimir M.",
year = "2013",
url = "http://eteze.bg.ac.rs/application/showtheses?thesesId=906, https://fedorabg.bg.ac.rs/fedora/get/o:7424/bdef:Content/download, http://vbs.rs/scripts/cobiss?command=DISPLAY&base=70036&RID=44745743, http://nardus.mpn.gov.rs/123456789/3478, http://vinar.vin.bg.ac.rs/handle/123456789/7269",
abstract = "U prvom delu ove doktorske disertacije sintetisani su kalemljeni kopolimeri polistirena i skroba emulzionom polimerizacijom u vodi uz korišćenje natrijum-laurilsulfata kao emulgatora. Ispitivan je uticaj različitih amina kao aktivatora polimerizacije na stepen kalemljenja polistirena na skrob, a ispitivanje ovog uticaj do sada nije zabeleţeno u literaturi. Promenom reakcione temperature, koncentracije monomera i inicijatora, pH vrednosti, vremena i količine aktivatora teţilo se dobijanju maksimalnih vrednosti stepena kalemljenja, a maksimalna dobijena vrednost iznosila je 32,55 %, što je za oko 8,5 % veće od najviše literaturne vrednosti.U drugom delu ovog rada sintetisani su kalemljeni kopolimeri poli(metakrilne kiseline) i skroba u vodi kao rastvaraču uz korišćenje različitih amina kao aktivatora polimerizacije (ovaj uticaj do sada nije ispitan u literaturi), sa ciljem dobijanja što većeg stepena kalemljenja. Da bi se dobile maksimalne vrednosti za stepen kalemljenja, praćen je uticaj promene reakcione temperature, reakcionog vremena, koncentracije monomera, količine inicijatora, količine aktivatora i pH vrednosti. Dobijene vrednosti za stepen kalemljenja kod kalemljenih kopolimera skroba i poli(metakrilne kiseline) su najveće do sada publikovane u literaturi. Maksimalna vrednost stepena kalemljenja iznosila je 40,92 %, što je za oko 10 % veće od najviše literaturne vrednosti.Dobijeni kopolimeri ispitivani su infracrvenom spektroskopijom sa Furijevom transformacijom i skenirajućom elektronskom mikroskopijom.U trećem delu doktorske teze praćeni su procesi degradacije dobijenih kopolimera u ţivotnoj sredini. Degradacija kopolimera u zemljištu, tj. u tri različita tipa zemljišta, trajala je 6 meseci, a za ovu namenu korišćeni su sledeći tipovi zemljišta: zemljište bogato humusom, zemljište za uzgajanje kaktusa i zemljište za uzgajanjeorhideja. TakoĎe, ispitivana je degradcija kalemljenih kopolimera u veštačkoj otpadnoj vodi, dobijenoj iz reke Save. Prilikom degradacije u vodi korišćen je kontinualni protočni sistem. Gubitak mase kopolimera tokom procesa degradacije korišćen je kod obe metode za odreĎivanje vrednosti stepena degradacije. Degradacija kalemljenih kopolimera skroba i poli(metakrilne kiseline) u zemljištu i degradacija obe vrste kopolimera u veštačkoj otpadnoj vodi do sada nije zabeleţena u literaturi.Ispitivanjem je utvrĎeno da je degradacija svih uzoraka kopolimera znatno brţa u veštačkoj otpadnoj vodi, gde ceo proces degradacije traje manje od mesec dana, nego u zemljištu. Rezultati degradacije u zemljištu pokazuju da je degradacija najbrţa u zemljištu za uzgajanje kaktusa (kod kalemljenih kopolimera polistirena i skroba), a kod kalemljenih kopolimera skroba i poli(metakrilne kiseline) u zemljištu za uzgajanje orhideja. Statističkom obradom podataka, utvrĎeno je postojanje značajne korelacije izmeĎu stepena degradacije i stepena kalemljenja kod kalemljenih kopolimera skroba i polistirena, kao i udeo skroba u kopolimerima koji je neophodan da bi došlo do biodegradacije, kao i udeo polistirena u kopolimerima koji bi doveo do sprečavanja biodegradacije., In the first part of this doctoral dissertation graft copolymers of polystyrene and starch were synthesized by emulsion polymerization in water with sodium dodecyl sulfate as an emulsifier. Influence of different amines, as activators of polymerization, on the percentage of grafting of polystyrene on starch was investigated and investigation of this influence has not been noted in the literature. Changes in reaction temperature, concentration of the monomer and initiator, pH value, time and amount of activator strive to obtain maximum value of percentage of grafting and maximal obtained value was 32.55 % which was about 8.5 % higher than maximal literature value.In the second part of this study, graft copolymers of poly(methacrylic acid) and starch were synthesized in aqueous media using different amines as activator of polymerization (there is no literature data about this influence) with the aim to obtaining a higher percentage of grafting. Influence of temperature, reaction time, monomer concentration, amount of initiator, amount of activator and pH value were monitored to obtain maximum values for percentage of grafting. Obtained values for percentage of grafting of starch and poly(methacrylic acid) grafted copolymers were the highest ever obtained in literature. The maximum value for percentage of grafting was 40.92 % which was about 10 % higher than maximal literatue value.The obtained copolymers were characterized by Fourier transformed infrared spectroscopy and by scanning electron microscopy.At the third part of this doctoral dissertation, the degradation processes of copolymers were monitored in environment. Degradation of copolymers in soil, i.e. inthree different type of soil, lasted for six months and for this study the following soil types were used: soil rich in humus, soil for cactus growing and soil for orchid growing. Also, degradation of graft copolymers in artificial wastewater obtaines from River Sava was monitored. During degradation in water, the continuous flow system was used. Mass loss of copolymers during degradation was used in both methods for obtaining values for measuring the degree of degradation. Degradation of poly(methacrylic acid) and starch grafted copolymers in soils and degradation of both types of copolymers in the artificial waste water have not been noted in the literature.Investigation has shown that the degradation of all samples of copolymers in artificial waste water was much faster, where all degradation processes lasted less than a month, than in soil. The results of degradation in soil show that degradation was fastest in soil for cactus growing (for grafted copolymers of polystyrene and starch) and for grafted copolymers of poly(methacrylic acid) and starch in soil for orchid growing. Statistical analysis of data show excellent correlation between degree of degradation and percentage of grafting for graft copolymers of polystyrene and starch and share of starch in copolymers which is necessary to biodegradation started and share of polystyrene in copolymers that prevented biodegradation.",
publisher = "Универзитет у Београду, Хемијски факултет",
journal = "Универзитет у Београду",
title = "Kopolimeri dobijeni kalemljenjem vinilnih monomera na skrob - uticaj amina na sintezu i procesi degradacije u životnoj sredini, Copolumers obtained by grafting of vinyl monomers on starch - influence of amines on synthesis and degradation processes in environment"
}

Assessment of arsenic and mercury contamination in the Tisa River sediments and industrial canal sediments (Danube alluvial formation), Serbia

Sakan, Sanja M.; Dordevic, Dragana S.; Lazic, Milojko M.; Tadić, Marin

(2012)

TY  - JOUR
AU  - Sakan, Sanja M.
AU  - Dordevic, Dragana S.
AU  - Lazic, Milojko M.
AU  - Tadić, Marin
PY  - 2012
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/4763
AB  - The purpose of this study was to examine the levels of As and Hg and mobility of these contaminants in the sediments of the River Tisa and canal sediments (alluvial formation of the Danube River, Serbia), in order to determine the degree to which the ecosystem is harmed by these pollutants. The sequential extraction procedure (modified Tessier method) was used to extract the metals from the sediments. Arsenic is extracted in the second, third and fifth fraction, with dominant extraction in the second fraction. This distribution indicates that As is significantly present in the form of carbonates, whereas the part of As is present in the form of oxides. The most important extraction of Hg is in the fifth stage (extraction with 6M HCl), with over 80 % of extracted element in both types of sediment, indicating a strong association between Hg and Fe crystalline oxides as well as presence of Hg in the form of sulfides. Based on arsenic and mercury content in sediments and results of sequential extraction it can be concluded that on the studied localities there is no significant As and Hg contamination.
T2  - Journal of Environmental Science and Health. Part A: Toxic Hazardous Substances and Environmental Engineering
T1  - Assessment of arsenic and mercury contamination in the Tisa River sediments and industrial canal sediments (Danube alluvial formation), Serbia
VL  - 47
IS  - 1
SP  - 109
EP  - 116
DO  - 10.1080/10934529.2012.630290
ER  - 
@article{
author = "Sakan, Sanja M. and Dordevic, Dragana S. and Lazic, Milojko M. and Tadić, Marin",
year = "2012",
url = "http://vinar.vin.bg.ac.rs/handle/123456789/4763",
abstract = "The purpose of this study was to examine the levels of As and Hg and mobility of these contaminants in the sediments of the River Tisa and canal sediments (alluvial formation of the Danube River, Serbia), in order to determine the degree to which the ecosystem is harmed by these pollutants. The sequential extraction procedure (modified Tessier method) was used to extract the metals from the sediments. Arsenic is extracted in the second, third and fifth fraction, with dominant extraction in the second fraction. This distribution indicates that As is significantly present in the form of carbonates, whereas the part of As is present in the form of oxides. The most important extraction of Hg is in the fifth stage (extraction with 6M HCl), with over 80 % of extracted element in both types of sediment, indicating a strong association between Hg and Fe crystalline oxides as well as presence of Hg in the form of sulfides. Based on arsenic and mercury content in sediments and results of sequential extraction it can be concluded that on the studied localities there is no significant As and Hg contamination.",
journal = "Journal of Environmental Science and Health. Part A: Toxic Hazardous Substances and Environmental Engineering",
title = "Assessment of arsenic and mercury contamination in the Tisa River sediments and industrial canal sediments (Danube alluvial formation), Serbia",
volume = "47",
number = "1",
pages = "109-116",
doi = "10.1080/10934529.2012.630290"
}
11
10
13

Non-canonical interactions of porphyrins in porphyrin-containing proteins

Stojanovic, Srdan D.; Isenović, Esma R.; Zarić, Božidarka

(2012)

TY  - JOUR
AU  - Stojanovic, Srdan D.
AU  - Isenović, Esma R.
AU  - Zarić, Božidarka
PY  - 2012
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/5045
AB  - In this study we have described the non-canonical interactions between the porphyrin ring and the protein part of porphyrin-containing proteins to better understand their stabilizing role. The analysis reported in this study shows that the predominant type of non-canonical interactions at porphyrins are CH center dot center dot center dot O and CH center dot center dot center dot N interactions, with a small percentage of CH center dot center dot center dot pi and non-canonical interactions involving sulfur atoms. The majority of non-canonical interactions are formed from side-chains of charged and polar amino acids, whereas backbone groups are not frequently involved. The main-chain non-canonical interactions might be slightly more linear than the side-chain interactions, and they have somewhat shorter median distances. The analysis, performed in this study, shows that about 44% of the total interactions in the dataset are involved in the formation of multiple (furcated) non-canonical interactions. The high number of porphyrin-water interactions show importance of the inclusion of solvent in protein-ligand interaction studies. Furthermore, in the present study we have observed that stabilization centers are composed predominantly from nonpolar amino acid residues. Amino acids deployed in the environment of porphyrin rings are deposited in helices and coils. The results from this study might be used for structure-based porphyrin protein prediction and as scaffolds for future porphyrin-containing protein design.
T2  - Amino Acids
T1  - Non-canonical interactions of porphyrins in porphyrin-containing proteins
VL  - 43
IS  - 4
SP  - 1535
EP  - 1546
DO  - 10.1007/s00726-012-1228-8
ER  - 
@article{
author = "Stojanovic, Srdan D. and Isenović, Esma R. and Zarić, Božidarka",
year = "2012",
url = "http://vinar.vin.bg.ac.rs/handle/123456789/5045",
abstract = "In this study we have described the non-canonical interactions between the porphyrin ring and the protein part of porphyrin-containing proteins to better understand their stabilizing role. The analysis reported in this study shows that the predominant type of non-canonical interactions at porphyrins are CH center dot center dot center dot O and CH center dot center dot center dot N interactions, with a small percentage of CH center dot center dot center dot pi and non-canonical interactions involving sulfur atoms. The majority of non-canonical interactions are formed from side-chains of charged and polar amino acids, whereas backbone groups are not frequently involved. The main-chain non-canonical interactions might be slightly more linear than the side-chain interactions, and they have somewhat shorter median distances. The analysis, performed in this study, shows that about 44% of the total interactions in the dataset are involved in the formation of multiple (furcated) non-canonical interactions. The high number of porphyrin-water interactions show importance of the inclusion of solvent in protein-ligand interaction studies. Furthermore, in the present study we have observed that stabilization centers are composed predominantly from nonpolar amino acid residues. Amino acids deployed in the environment of porphyrin rings are deposited in helices and coils. The results from this study might be used for structure-based porphyrin protein prediction and as scaffolds for future porphyrin-containing protein design.",
journal = "Amino Acids",
title = "Non-canonical interactions of porphyrins in porphyrin-containing proteins",
volume = "43",
number = "4",
pages = "1535-1546",
doi = "10.1007/s00726-012-1228-8"
}
12
12
12

Peroxisome Proliferator-Activated Receptors and Atherosclerosis

Soskić, Sanja S.; Dobutovic, Branislava D.; Sudar, Emina; Obradović, Milan M.; Nikolić, Dragana; Zarić, Božidarka; Stojanovic, Srdan D.; Stokić, Edita; Mikhailidis, Dimitri P.; Isenović, Esma R.

(2011)

TY  - JOUR
AU  - Soskić, Sanja S.
AU  - Dobutovic, Branislava D.
AU  - Sudar, Emina
AU  - Obradović, Milan M.
AU  - Nikolić, Dragana
AU  - Zarić, Božidarka
AU  - Stojanovic, Srdan D.
AU  - Stokić, Edita
AU  - Mikhailidis, Dimitri P.
AU  - Isenović, Esma R.
PY  - 2011
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/4519
AB  - The peroxisome proliferator-activated receptors (PPARs) represent the family of 3 nuclear receptor isoforms-PPAR alpha, -gamma, and -delta/beta, which are encoded by different genes. As lipid sensors, they are primarily involved in regulation of lipid metabolism and subsequently in inflammation and atherosclerosis. Atherosclerosis considers accumulation of the cells and extracellular matrix in the vessel wall leading to the formation of atherosclerotic plaque, atherothrombosis, and other vascular complications. Besides existence of natural ligands for PPARs, their more potent synthetic ligands are fibrates and thiazolidindiones. Future investigations should now focus on the mechanisms of PPARs activation, which might present new approaches involved in the antiatherosclerotic effects revealed in this review. In addition, in this review we are presenting latest data from recent performed clinical studies which have focus on novel approach to PPARs agonists as potential therapeutic agents in the treatment of complex disease such as atherosclerosis.
T2  - Angiology
T1  - Peroxisome Proliferator-Activated Receptors and Atherosclerosis
VL  - 62
IS  - 7
SP  - 523
EP  - 534
DO  - 10.1177/0003319711401012
ER  - 
@article{
author = "Soskić, Sanja S. and Dobutovic, Branislava D. and Sudar, Emina and Obradović, Milan M. and Nikolić, Dragana and Zarić, Božidarka and Stojanovic, Srdan D. and Stokić, Edita and Mikhailidis, Dimitri P. and Isenović, Esma R.",
year = "2011",
url = "http://vinar.vin.bg.ac.rs/handle/123456789/4519",
abstract = "The peroxisome proliferator-activated receptors (PPARs) represent the family of 3 nuclear receptor isoforms-PPAR alpha, -gamma, and -delta/beta, which are encoded by different genes. As lipid sensors, they are primarily involved in regulation of lipid metabolism and subsequently in inflammation and atherosclerosis. Atherosclerosis considers accumulation of the cells and extracellular matrix in the vessel wall leading to the formation of atherosclerotic plaque, atherothrombosis, and other vascular complications. Besides existence of natural ligands for PPARs, their more potent synthetic ligands are fibrates and thiazolidindiones. Future investigations should now focus on the mechanisms of PPARs activation, which might present new approaches involved in the antiatherosclerotic effects revealed in this review. In addition, in this review we are presenting latest data from recent performed clinical studies which have focus on novel approach to PPARs agonists as potential therapeutic agents in the treatment of complex disease such as atherosclerosis.",
journal = "Angiology",
title = "Peroxisome Proliferator-Activated Receptors and Atherosclerosis",
volume = "62",
number = "7",
pages = "523-534",
doi = "10.1177/0003319711401012"
}
17
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27

Contribution of Non-Canonical Interactions to the Stability of Sm/LSm Oligomeric Assemblies

Stojanovic, Srdan D.; Isenović, Esma R.; Zarić, Božidarka

(2011)

TY  - JOUR
AU  - Stojanovic, Srdan D.
AU  - Isenović, Esma R.
AU  - Zarić, Božidarka
PY  - 2011
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/4381
AB  - The distinguishing property of Sm/LSm protein assemblies is their high stability. In order to better understand the nature of Sm/LSm protein oligomers in this study we have analyzed the contribution of non-canonical interactions to the stability of assemblies. The predominant types of non-canonical interactions at Sm/LSm protein interfaces are CH center dot center dot center dot O, and CH center dot center dot center dot N interactions represented at interfaces. Our results show low percentages of XH-pi and non-canonical interactions involving sulfur atoms, while the backbone groups were less frequently involved. The data show a high percentage of non-canonical interactions in interfaces formed by charged residues with Lys and Arg, these being the major charged donors. The main chain non-canonical interactions might be slightly more linear than the side chain interactions, and they have somewhat shorter median distances. Comparing the stabilizing amino acid residues with amino acids which build non-canonical interactions at interfaces shows that certain amino acids like Phe, Pro, His and Tyr are involved with a high percentage. The high conservation score of amino acids that are involved in non-canonical interactions in protein interfaces is an additional strong argument for their importance in the stabilization of Sm/LSm protein assemblies.
T2  - Molecular Informatics
T1  - Contribution of Non-Canonical Interactions to the Stability of Sm/LSm Oligomeric Assemblies
VL  - 30
IS  - 5
SP  - 430
EP  - 442
DO  - 10.1002/minf.201000176
ER  - 
@article{
author = "Stojanovic, Srdan D. and Isenović, Esma R. and Zarić, Božidarka",
year = "2011",
url = "http://vinar.vin.bg.ac.rs/handle/123456789/4381",
abstract = "The distinguishing property of Sm/LSm protein assemblies is their high stability. In order to better understand the nature of Sm/LSm protein oligomers in this study we have analyzed the contribution of non-canonical interactions to the stability of assemblies. The predominant types of non-canonical interactions at Sm/LSm protein interfaces are CH center dot center dot center dot O, and CH center dot center dot center dot N interactions represented at interfaces. Our results show low percentages of XH-pi and non-canonical interactions involving sulfur atoms, while the backbone groups were less frequently involved. The data show a high percentage of non-canonical interactions in interfaces formed by charged residues with Lys and Arg, these being the major charged donors. The main chain non-canonical interactions might be slightly more linear than the side chain interactions, and they have somewhat shorter median distances. Comparing the stabilizing amino acid residues with amino acids which build non-canonical interactions at interfaces shows that certain amino acids like Phe, Pro, His and Tyr are involved with a high percentage. The high conservation score of amino acids that are involved in non-canonical interactions in protein interfaces is an additional strong argument for their importance in the stabilization of Sm/LSm protein assemblies.",
journal = "Molecular Informatics",
title = "Contribution of Non-Canonical Interactions to the Stability of Sm/LSm Oligomeric Assemblies",
volume = "30",
number = "5",
pages = "430-442",
doi = "10.1002/minf.201000176"
}
4
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5