dr. sc. Antonija Tomić

Viši znanstveni suradnik

E-mail

Antonija.Tomic@irb.hr

Telefon

+385 1 457 1251

Interni broj

1265

Zavod

Zavod za organsku kemiju i biokemiju

Laboratorij

Laboratorij za biokemiju proteina i molekulsko modeliranje

Adresa

Institut Ruđer Bošković
Bijenička cesta 54
10 000 Zagreb

Obrazovanje

2015. Zagreb, Prirodoslovno matematički fakultet Sveučilišta u Zagrebu, dr. sc.

2008. Zagreb, Prirodoslovno matematički fakultet Sveučilišta u Zagrebu, Dipl. Ing. kemije

Nagrade i priznanja

2007. Medalja Kemijskog odsjeka Prirodoslovno-matematičkog fakulteta u Zagrebu za izvrstan uspjeh u studiju kemije

Nastava

asistent na laboratorijskim vježbama iz fizikalne kemije na Prirodoslovno-matematičkom fakultetu, Sveučilište u Zagrebu, Hrvatska

Istaknute publikacije

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.

Publikacije - prilozi u časopisima

Izvorni znanstveni rad

Rinkovec, Tamara; Tarana, Siniša; Modrušan, Matija; Vidović, Nikolina; Tomić, Antonija; Cindro, Nikola; Speranza, Giovanna; Tomišić, Vladislav; Horvat, Gordan | Anion complexes of small Boc-protected lysine cyclopeptides in solution // Journal of molecular liquids, 433 (2025), 127837, 15. doi: 10.1016/j.molliq.2025.127837
doiwww.sciencedirect.com
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, 17. doi: 10.3390/app14020562
doifulir.irb.hrwww.mdpi.com
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
doiwww.mdpi.comfulir.irb.hr
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
doiwww.sciencedirect.comfulir.irb.hr
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
doiwww.mdpi.comdoi.orgfulir.irb.hr
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
doipubs.rsc.orgdoi.org
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
doipubs.acs.orgdoi.org
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
doifulir.irb.hrdoi.orgwww.tandfonline.com
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
doihrcak.srce.hrfulir.irb.hr
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
doipubs.rsc.orgpubs.rsc.orgfulir.irb.hr
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
doijournals.plos.orgdoi.orgfulir.irb.hrfulir.irb.hr
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
doihrcak.srce.hr
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
doipubs.rsc.org
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
doipubs.rsc.org
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
doipubs.rsc.org
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
doipubs.acs.org
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
doihrcak.srce.hr
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
doionlinelibrary.wiley.com
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
hrcak.srce.hr

Prikaz, osvrt, kritika

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

Pregledni rad (znanstveni)

Oskomić, Marina; Tomić, Antonija; Barbarić, Lea; Matić, Antonia; Kindl, Domagoj Christian; Matovina, Mihaela | KEAP1-NRF2 Interaction in Cancer: Competitive Interactors and Their Role in Carcinogenesis // Cancers, 17 (2025), 1-27. doi: 10.3390/cancers17030447
doiwww.mdpi.comfulir.irb.hr

Publikacije - prilozi sa skupa (u zborniku)

Sažetak izlaganja sa skupa

Tomić, Antonija | Position of the C-terminal α-helix could be important for understanding the molecular mechanism of cellular oxidative stress sensing by KEAP1 // 10th Regional Biophysics Conference & 15th International Summer School of Biophysics : Book of abstracts / Dolanski Babić, Sanja; Dutour Sikirić, Maja; Stepanić, Višnja et al. (ur.). | Split: Hrvatsko Biofizičko Društvo, 2024. str. 60-60
rbc2024.biofizika.hr
Tomić, Antonija | Molecular modeling study of the structure and dynamics of the KEAP1 dimer and its complex with the Neh2 domain of NRF2 // 8th BenBedPhar Scientific meeting : Abstract Book / Tenreiro, Sandra; Antunes, Fernando (ur.). | Lisabon: Cost, 2024. str. 43-43
benbedphar.org
Tomić, Antonija; Ozretić, Petar | Molecular Modeling Study of Sonic Hedgehog Protein Interaction with Sex Hormone Receptors // Computational Chemistry Day 2023 : Book of Abstracts / Hok, Lucija (ur.). | Zagreb: Prirodoslovno-matematički fakultet Sveučilišta u Zagrebu, 2023. str. 24-24
www.compchemday.org
Tomić, Antonija; Tomić, Sanja | Understanding Binding and Hydrolysis of Neuropeptides in the Active Site of Human Dipeptidyl Peptidase III // Computational Chemistry Day 2022 : book of abstracts. | Zagreb: Prirodoslovno-matematički fakultet Sveučilišta u Zagrebu, 2022. str. 19-19
drive.google.com
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. | Zagreb: Hrvatsko društvo za biokemiju i molekularnu biologiju (HDBMB), 2022. str. 105-105
congress2022.hdbmb.hr
Tomić, Sanja ; Karačić, Zrinka ; Tomić, Antonija ; Brkljačić, Lidija ; Šupljika, Filip | Neuropeptides - substrates of dipeptidyl peptidase III // From Science to Knowledge. | Zagreb: Hrvatsko Društvo za Biotehnologiju, 2022. str. 151-151
congress2022.hdbmb.hr
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
ccd19.pharma.hr
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). | 2022. str. 196-196
www.ceec-physchem.org
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. | Zagreb: Hrvatsko kemijsko društvo, 2022. str. 24-24
mcc.hkd.hr
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. | Zagreb: Hrvatsko kemijsko društvo, 2021. str. 42-42
mcc.hkd.hr
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. | Zagreb : Osijek: Hrvatsko društvo kemijskih inženjera i tehnologa (HDKI) ; Prehrambeno tehnološki fakultet Sveučilišta Josipa Jurja Strossmayera u Osijeku, 2020. str. 78-78
www.hdki.hr
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
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 ; 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. | Zagreb: Hrvatsko društvo kemijskih inženjera i tehnologa (HDKI), 2013. str. 177-177
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, 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 | 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. | Zagreb: Institut Ruđer Bošković i Hrvatsko biofizičko društvo, 2012. str. 104-104
www.irb.hr
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. | Zagreb: Hrvatsko društvo kemijskih inženjera i tehnologa (HDKI), 2012. str. 173-173
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 | Human dipeptidyl-peptidases (h.DPP III), sampling the substrate binding site - computational analysis // Book of Abstracts of the "Fourth Humboldt Conference on Computational Chemistry". | Sofija, 2010. str. 63.-63.
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". | Marburg: University of Marburg, 2010. str. 87-87
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 ; 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". | Zagreb: Centre for Computational Solutions in the Life Sciences, Ruđer Bošković Institute, 2009. str. 77-77
www.compsols.irb.hr
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.". | Zagreb: Hrvatsko geološko društvo, 2007. str. 15-16-x

Ostalo

Tomić, Sanja ; Abramić, Marija ; Brkić, Hrvoje ; Tomić, Antonija | Sprega kristalografije i modeliranja u proučavanju bioloških makromolekula // Kristalografija u Hrvatskoj. | 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. | Zagreb: Hrvatska akademija znanosti i umjetnosti (HAZU), 2013. str. 149-157

Publikacije - prilozi sa skupa (u časopisu)

Sažetak izlaganja sa skupa

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
Tomić, Sanja ; Tomić, Antonija | Ligand binding to the flexible metaloenzymes: protein dynamics and the active enzyme conformation // European biophysics journal, 44, Suppl. 1, 2015. str. 243-243. doi: 10.1007/s00249-015-1045-6
doilink.springer.com

Publikacije - prilozi sa skupa (neobjavljeni)

Neobjavljeni prilog sa skupa

Tomić, Antonija | Using high-performance computing to reveal mechanism of the KEAP1 protein conformational changes induced by oxidative stress // Srce Dani e-infrastrukture 2024. | Zagreb, Hrvatska, 16.04.2024-19.04.2024

Publikacije - ocjenski radovi

Doktorski rad

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

Članstva u profesionalnim udrugama / društvima

član Hrvatskog kemijskog društva

Član organizacijskog odbora znanstvenih susreta mladih istraživača (Znanstveni susreti 3. vrste) Instituta Ruđer Bošković 2011

Obrazovanje
Nagrade i priznanja
Nastava
Istaknute publikacije
Publikacije - prilozi u časopisima
Publikacije - prilozi sa skupa (u zborniku)
Publikacije - prilozi sa skupa (u časopisu)
Publikacije - prilozi sa skupa (neobjavljeni)
Publikacije - ocjenski radovi

Pretraži Institut Ruđer Bošković

dr. sc. Antonija Tomić

Obrazovanje

Nagrade i priznanja

Nastava

Istaknute publikacije

Publikacije - prilozi u časopisima

Izvorni znanstveni rad

Prikaz, osvrt, kritika

Pregledni rad (znanstveni)

Publikacije - prilozi sa skupa (u zborniku)

Sažetak izlaganja sa skupa

Ostalo

Izvorni znanstveni rad

Publikacije - prilozi sa skupa (u časopisu)

Sažetak izlaganja sa skupa

Publikacije - prilozi sa skupa (neobjavljeni)

Neobjavljeni prilog sa skupa

Publikacije - ocjenski radovi

Doktorski rad

Članstva u profesionalnim udrugama / društvima

Institut Ruđer Bošković

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