Dr. Antonija Tomić
Bijenička cesta 54
10 000 Zagreb
Education
2015 Dr., University of Zagreb, Faculty of Science, Department of Chemistry, Zagreb, Croatia
2008 B.Sc., University of Zagreb, Faculty of Science, Department of Chemistry, Zagreb, Croatia
Awards and Achievements
2007. award for excellent success during the study, Faculty of Science, Zagreb, Croatia
Classes
assistant in laboratory exercises in physical chemistry at Faculty of Science, University of Zagreb, Croatia
Featured Publications
1. Antonija Tomić; Hrvoje Brkić; Antonia Matić; Sanja Tomić. Unravelling the inhibitory zinc ion binding site and the metal exchange mechanism in human DPP III. Physical chemistry chemical physics 23 (2021), 13267-13275.
2. Antonija Tomić; Gordan Horvat; Michael Ramek; Dejan Agić; Hrvoje Brkić; Sanja Tomić. New zinc ion parameters suitable for classical MD simulations of zinc metallo-peptidases. Journal of chemical information and modeling 59 (2019), 8; 3437-3453.
3. Antonija Tomić; Borislav Kovačević; Sanja Tomić. Concerted nitrogen inversion and hydrogen bonding to Glu451 are responsible for protein-controlled suppression of the reverse reaction in the human DPP III. Physical Chemistry Chemical Physics 18 (2016), 39; 27245-27256.
4. Antonija Tomić; Sanja Tomić. Hunting the human DPP III active conformation: combined thermodynamic and QM/MM calculations. Dalton transactions 43 (2015) 15503-15514.
5. Antonija Tomić; Miguel Gonzalez; Sanja Tomić. The large scale conformational change of the human DPP III - substrate preferes the "closed" form. Journal of chemical information and modeling 52 (2012) 1583-1594.
6. Antonija Tomić; Marija Abramić; Jasminka Špoljarić; Dejan Agić; David M. Smith; Sanja Tomić. Human Dipeptidyl Peptidase III: Insights into Ligand Binding from a Combined Experimental and Computational Approach, Journal of Molecular Recognition, 24 (2011) 804-814.
Publications - journal articles
Izvorni znanstveni rad
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Tomić, Antonija ; Živković, Tomislav | On the vibrational interlacing rule in deuterated thiophenes : I. Out-of-plane vibrations // Croatica chemica acta, 82 (2009), 2; 561-566
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Tomić, Antonija ; Abramić, Marija ; Špoljarić, Jasminka ; Agić, Dejan ; Smith, David M. ; Tomić, Sanja | Human Dipeptidyl Peptidase III: Insights into Ligand Binding from a Combined Experimental and Computational Approach // Journal of molecular recognition, 24 (2011), 5; 804-814. doi: 10.1002/jmr.1115
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Špoljarić, Jasminka ; Tomić, Antonija ; Vukelić, Bojana ; Salopek-Sondi, Branka ; Agić, Dejan ; Tomić, Sanja ; Abramić, Marija | Human Dipeptidyl Peptidase III : the Role of Asn406 in Ligand Binding and Hydrolysis // Croatica chemica acta, 84 (2011), 2; 259-268. doi: 10.5562/cca1808
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Tomić, Antonija ; Gonzalez, Miguel ; Tomić, Sanja | The large scale conformational change of the human DPP III – substrate prefers the "closed" form // Journal of chemical information and modeling, 52 (2012), 6; 1583-1594. doi: 10.1021/ci300141k
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Tomić, Antonija ; Tomić, Sanja | Hunting the human DPP III active conformation : combined thermodynamic and QM/MM calculations // Dalton transactions, 43 (2014), 15503-15514. doi: 10.1039/C4DT02003K
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Tomić, Antonija ; Berynskyy, Mykhaylo ; Wade, Rebecca C. ; Tomić, Sanja | Molecular simulations reveal that the long range fluctuations of human DPP III change upon ligand binding // Molecular biosystems, 11 (2015), 3068-3080. doi: 10.1039/c5mb00465a
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Tomić, Antonija ; Kovačević, Borislav ; Tomić, Sanja | Concerted nitrogen inversion and hydrogen bonding to Glu451 are responsible for protein-controlled suppression of the reverse reaction in the human DPP III // PCCP. Physical chemistry chemical physics, 18 (2016), 39; 27245-27256. doi: 10.1039/C6CP04580D
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Gundić, Mario ; Tomić, Antonija ; Wade, Rebecca C. ; Matovina, Mihaela ; Karačić, Zrinka ; Kazazić, Saša ; Tomić, Sanja | Human DPP III – Keap1 Interactions : A Combined Experimental And Computational study // Croatica chemica acta, 89 (2016), 2; 217-228. doi: 10.5562/cca2916
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Sabljić, Igor ; Tomin, Marko ; Matovina, Mihaela ; Sučec, Iva ; Tomašić Paić, Ana ; Tomić, Antonija ; Abramić, Marija ; Tomić, Sanja | The first dipeptidyl peptidase III from a thermophile: Structural basis for thermal stability and reduced activity // PLoS One, 13 (2018), 2; e0192488, 25. doi: 10.1371/journal.pone.0192488
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Kazazić, Saša ; Karačić, Zrinka ; Sabljić, Igor ; Agić, Dejan ; Tomin, Marko ; Abramić, Marija ; Dadlez, Michal ; Tomić, Antonija ; Tomić, Sanja | Conservation of the conformational dynamics and ligand binding within M49 enzyme family // RSC Advances, 8 (2018), 24; 13310-13322. doi: 10.1039/c7ra13059g
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Tomin, Marko ; Tomić, Antonija ; Kovačević, Borislav ; Tomić, Sanja | The Mechanism of Peptide Hydrolysis Catalysed by Dipeptidyl Peptidase III from Bacteroides thetaiotaomicron // Croatica chemica acta, 91 (2018), 2; 187-193. doi: 10.5562/cca3343
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Agić, Dejan ; Brkić, Hrvoje ; Kazazić, Saša ; Tomić, Antonija ; Abramić, Marija | Aprotinin interacts with substrate-binding site of human dipeptidyl peptidase III // Journal of biomolecular structure & dynamics, 37 (2019), 14; 3596-3606. doi: 10.1080/07391102.2018.1521343
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Tomić, Antonija ; Horvat, Gordan ; Ramek, Michael ; Agić, Dejan ; Brkić, Hrvoje ; Tomić, Sanja | New zinc ion parameters suitable for classical MD simulations of zinc metallo-peptidases // Journal of chemical information and modeling, 59 (2019), 8; 3437-3453. doi: 10.1021/acs.jcim.9b00235
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Tomić, Antonija ; Brkić, Hrvoje ; Matić, Antonia ; Tomić, Sanja | Unravelling the inhibitory zinc ion binding site and the metal exchange mechanism in human DPP III // PCCP. Physical chemistry chemical physics, 23 (2021), 13267-13275. doi: 10.1039/D1CP01302E
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Tomić, Antonija ; Tomić, Sanja | Demystifying DPP III Catalyzed Peptide Hydrolysis— Computational Study of the Complete Catalytic Cycle of Human DPP III Catalyzed Tynorphin Hydrolysis // International journal of molecular sciences, 23 (2022), 3; 1858, 24. doi: 10.3390/ijms23031858
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Karačić, Zrinka ; Šupljika, Filip ; Tomić, Antonija ; Brkljačić, Lidija ; Tomašić Paić, Ana ; Ćehić, Mirsada ; Tomić, Sanja | Neuropeptides, substrates and inhibitors of human dipeptidyl peptidase III, experimental and computational study — A new substrate identified // International journal of biological macromolecules, 220 (2022), 1390-1401. doi: 10.1016/j.ijbiomac.2022.09.119
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Tomić, Antonija ; Karačić, Zrinka ; Tomić, Sanja | Influence of Mutations of Conserved Arginines on Neuropeptide Binding in the DPP III Active Site // Molecules, 28 (2023), 4; 1976, 17. doi: 10.3390/molecules28041976
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Tomić, Antonija; Čonkaš, Josipa; Ozretić, Petar | Let’s Talk about Sex Hormone Receptors and Their Physical Interaction with Sonic Hedgehog Protein: A Computational Study with Emphasis on Progesterone Receptor // Applied sciences (Basel), 14 (2024), 2; 562-x. doi: 10.3390/app14020562
doifulir.irb.hrwww.mdpi.com
Prikaz, osvrt, kritika
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Grabar Branilović, Marina ; Maršavelski, Aleksandra ; Tomić, Antonija ; Tomić, Sanja | Nobelova nagrada za kemiju za 2013. godinu // Kemija u industriji : časopis kemičara i tehnologa Hrvatske, 62 (2013), 11-12; 468-471
fulir.irb.hrhrcak.srce.hr
Publications - conference proceedings
Sažetak izlaganja sa skupa
Horvat, Gordan ; Magdić, Katja ; Tomić, Antonija ; Pitarević Svedružić, Lovorka ; Rončević, Sanda | Analiza sedimenta i vode Moslavačkog područja // Zbornik radova i sažetaka Znanstveno-edukativnog projekta Studentskog odsjeka HGD-a "Voda i mi. II." / Spevec, Siniša (ur.). Zagreb: Hrvatsko geološko društvo, 2007. str. 15-16-x
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Tomić, Antonija ; Abramić, Marija ; Smith, David ; Tomić, Sanja | Computational and experimental approach to the study of ligands binding into the active site of the human dipeptidyl-peptidases (DPPIII) // Book of Abstracts of the "The 3rd Adriatic Meeting On Computational Solutions in the Life Sciences" / Babić, Darko ; Došlić, Nađa ; Smith, David et al. (ur.). Zagreb: Centre for Computational Solutions in the Life Sciences, Ruđer Bošković Institute, 2009. str. 77-77
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Tomić, Antonija ; Abramić, Marija ; Smith, David ; Tomić, Sanja | Molecular dynamics simulations of ligands binding into the active site of human dipeptidyl-peptidases (DPPIII) // Book of Abstracts of the EMBO Young Scientists Forum. 2009. str. 53-53
bioinfo.hr Tomić, Antonija ; Špoljarić, Jasminka ; Abramić, Marija ; Tomić, Sanja | Ligand binding to human DPP III and its mutant H568N - computational analyses // Abstracts of the 6th International Workshop on New Approaches in Drug Design & Discovery "The Interactions :From Atom-Atom Contacts to Networks in System Biology" / Klebe, Gerhard ; Matter, Hans ; Sotriffer, Hans (ur.). Marburg: University of Marburg, 2010. str. 87-87
Tomić, Antonija ; Tomić, Sanja | Human dipeptidyl-peptidases (h.DPP III), sampling the substrate binding site - computational analysis // Book of Abstracts of the "Fourth Humboldt Conference on Computational Chemistry" / Petrova, P. Galina ; Vayssilov, N. Georgie (ur.). Sofija, 2010. str. 63.-63
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Tomić, Antonija ; Tomić, Sanja | MD simulations showed large conformational changes of the human free DPP III // Book of Abstracts - The Conference on Molecular Simulations in Biosystems and Material Science. Konstanz, 2011. str. 72-72
cms.uni-konstanz.de Tomić, Antonija ; Tomić, Sanja | QM/MM study of the zinc coordination in the active site of the human DPP III // Knjiga sažetaka - IX. Susret mladih kemijskih inženjera / Martinez, Sanja (ur.). Zagreb: Hrvatsko društvo kemijskih inženjera i tehnologa (HDKI), 2012. str. 173-173
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Tomić, Antonija ; Tomić, Sanja | Further study of the zinc coordination in the active site of the human DPP III - ONIOM calculations // Book of abstracts, 11th Greta Pifat-Mrzljak International School of Biophysics, Biomolecular complexes and assemblies / Hozić A., Vuletić T. (ur.). Zagreb: Institut Ruđer Bošković i Hrvatsko biofizičko društvo, 2012. str. 104-104
www.irb.hr Tomić, Sanja ; Tomić, Antonija ; Gonzalez, Miguel | Molecular dynamics based studies on human DPP III revealed determinants for its broad substrate selectivity. 2012
Tomić, Antonija ; Tomić, Sanja | Molecular Mechanics - Poisson Boltzmann Surface Area calculations using AMBER program package - application to the human dipeptidyl petidase III // Computational Electrostatics for Biological Applications - Book of Abstract. 2013. str. 39-39
Tomić, Antonija ; Tomić, Sanja | The recent findings on the zinc ion coordination and ligand binding in the human DPP III active site – implication on the chemical reaction mechanism // XXIII. hrvatski skup kemičara i kemijskih inženjera, knjiga sažetaka / Hadžiev, Andrea ; Blažeković, Zdenko (ur.). Zagreb: Hrvatsko društvo kemijskih inženjera i tehnologa (HDKI), 2013. str. 177-177
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Tomić, Sanja ; Tomić, Antonija ; Gundić, Mario | Influence of ligands and protein binding to structure and flexybility of human dipeptidyl peptidase III // Conference proceedings of ICBMB 2016, International Conference on Biochemistry and Molecular Biology. 2016. str. 9-9
biochem.conference-site.com Tomić, Antonija ; Ramek, Michael ; Tomić, Sanja | Development of new parameters for the Zn2+ ion for the specific environment of the DPP III enzyme catalytic site // Computational Chemistry Day Book of abstracts. Zagreb: Prirodoslovno-matematički fakultet Sveučilišta u Zagrebu, 2018. str. 15-15
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Matić, Antonia ; Karačić, Zrinka ; Tomić, Antonija ; Brkić, Hrvoje ; Tomić, Sanja | Ispitivanja inhibicije dipeptidil peptidaze III metalnim dikationima // Knjiga sažetaka - 18. Ružičkini dani: Danas znanost - Sutra industrija / Jukić, Ante (ur.). Zagreb : Osijek: Hrvatsko društvo kemijskih inženjera i tehnologa (HDKI) ; Prehrambeno tehnološki fakultet Sveučilišta Josipa Jurja Strossmayera u Osijeku, 2020. str. 78-78
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Tomić, Antonija ; Tomić, Sanja | Understanding the human DPP iii substrate specificity : QM/MM and MD calculations // Math/Chem/Comp 2021 : 32nd MC2 Conference : book of abstracts / Vančik, Hrvoj ; Cioslowski, Jerzy ; Namjesnik, Danijel (ur.). Zagreb: Hrvatsko kemijsko društvo, 2021. str. 42-42
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Tomić, Antonija ; Tomić, Sanja | Computational study of the human DPP III catalyzed peptide hydrolysis - difference between „good“ and „slow“ substrate // Math/Chem/Comp 2022 and 33rd MC2 Conference : Book of Abstracts / Vančik, Hrvoj ; Cioslowski, Jerzy ; Namjesnik, Danijel (ur.). Zagreb: Hrvatsko kemijsko društvo, 2022. str. 24-24
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Tomić, Antonija ; Karačić, Zrinka ; Šupljika, Filip ; Tomić, Sanja | Computational modelling an aid to understand binding and hydrolysis of neuropeptides in the active site of human DPP III // Book of abstracts of the 1st Central and Eastern European Conference on Physical Chemistry and Materials Science (CEEC-PCMS1) / Erceg, Matko ; Rotaru, Andrei ; Vrsalović, Ladislav (ur.). 2022. str. 196-196
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Tomić, Antonija ; Horvat, Gordan ; Ramek, Michael ; Agić, Dejan ; Brkić, Hrvoje ; Tomić, Sanja | Development of new zinc ion parameters suitable for classical MD simulations of zinc metallo-peptidases // Computational Chemistry Day 2019 :Book of abstracts. Zagreb: Prirodoslovno-matematički fakultet Sveučilišta u Zagrebu, 2019. str. 3-3
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Tomić, Sanja ; Karačić, Zrinka ; Tomić, Antonija ; Brkljačić, Lidija ; Šupljika, Filip | Neuropeptides - substrates of dipeptidyl peptidase III // From Science to Knowledge / Dulić, Morana ; Sinčić, Nino ; Vrhovac Madunić, Ivana (ur.). Zagreb: Hrvatsko Društvo za Biotehnologiju, 2022. str. 151-151
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Matić, Antonia ; Karačić, Zrinka ; Tomić, Antonija ; Brkić, Hrvoje ; Tomić Sanja | Dipeptidyl peptidase iii inhibition tests by metal dications // Book of Abstracts of the Congress of the Croatian Society of Biochemistry and Molecular Biology HDBMB22: From Science to Knowledge / Dulić, Morana ; Sinčić, Nino ; Vrhovac Madunić, Ivana (ur.). Zagreb: Hrvatsko društvo za biokemiju i molekularnu biologiju (HDBMB), 2022. str. 105-105
congress2022.hdbmb.hr Tomić, Antonija; Ozretić, Petar | Molecular Modeling Study of Sonic Hedgehog Protein Interaction with Sex Hormone Receptors // Computational Chemistry Day 2023 : Book of Abstracts. Zagreb: Prirodoslovno-matematički fakultet Sveučilišta u Zagrebu, 2023. str. 24-24
Ostalo
Tomić, Sanja ; Abramić, Marija ; Brkić, Hrvoje ; Tomić, Antonija | Sprega kristalografije i modeliranja u proučavanju bioloških makromolekula // Kristalografija u Hrvatskoj / Popović Stanko (ur.). Zagreb: Hrvatska akademija znanosti i umjetnosti (HAZU), 2013. str. 129-137
Izvorni znanstveni rad
Tomić, Sanja ; Brkić, Hrvoje ; Grabar Branilović, Marina ; Tomić, Antonija ; Branimir, Bertoša ; Mile, Šikić | Proteini i nukleinske kiseline u vremenu i prostoru // Bioinformatics and biological physics: proceedings of the scientific meeting / Paar, Vladimir (ur.). Zagreb: Hrvatska akademija znanosti i umjetnosti (HAZU), 2013. str. 149-157
Sažetak izlaganja sa skupa
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Tomić, Sanja ; Tomić, Antonija | Ligand binding to the flexible metaloenzymes: protein dynamics and the active enzyme conformation // European biophysics journal. 2015. str. 243-243 doi: 10.1007/s00249-015-1045-6
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Tomić, Sanja ; Kovačević, Borislav ; Tomić, Antonija ; Matovina, Mihaela ; Karačić, Zrinka ; Matić, Sara ; Abramić, Marija ; Agić, Dejan | Understanding h.DPP III mechanism – an aid in rationalization of the mutants (in)activity // European biophysics journal. 2017. str. S179-S179 doi: 10.1007/s00249-017-1222-x
doilink.springer.comlink.springer.com
Neobjavljeni prilog sa skupa
Tomić, Antonija; Tomić, Sanja | Understanding Binding and Hydrolysis of Neuropeptides in the Active Site of Human Dipeptidyl Peptidase III // Computational Chemistry Day 2022 | Zagreb, Hrvatska, 24.09.2022-24.09.2022
Doktorska disertacija
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Tomić, Antonija | Primjena računalnih pristupa različitih stupnjeva složenosti u svrhu razumijevanja strukture, dinamike i aktivnosti ljudske dipeptidil-peptidaze III / Tomić, Sanja (mentor); | Zagreb, Prirodoslovno-matematički fakultet, Zagreb, . 2015
repozitorij.pmf.unizg.hr
Membership in professional associations / societies
Member of the Croatian Chemical Society
Member of the organizing committee of the Rudjer Boskovic Institute young scientist festival, "Znanstveni susreti 3. vrste", 7-8 July 2011.