Publications

Petrauskas, V.; Kazlauskas, E.; Gedgaudas, M.; Baranauskienė, L.; Zubrienė, A.; Matulis, D. Thermal Shift Assay for Protein–Ligand Dissociation Constant Determination. TrAC Trends in Analytical Chemistry 2024, 170, 117417. https://doi.org/10.1016/j.trac.2023.117417.

Paketurytė-Latvė, V.; Smirnov, A.; Manakova, E.; Baranauskiene, L.; Petrauskas, V.; Zubrienė, A.; Matulienė, J.; Dudutienė, V.; Čapkauskaitė, E.; Zakšauskas, A.; Leitans, J.; Gražulis, S.; Tars, K.; Matulis, D. From X-Ray Crystallographic Structure to Intrinsic Thermodynamics of Protein–Ligand Binding Using Carbonic Anhydrase Isozymes as a Model System. IUCrJ 2024, 11 (4). https://doi.org/10.1107/S2052252524004627.

Kairys, V.; Baranauskiene, L.; Kazlauskiene, M.; Zubrienė, A.; Petrauskas, V.; Matulis, D.; Kazlauskas, E. Recent Advances in Computational and Experimental Protein-Ligand Affinity Determination Techniques. Expert Opinion on Drug Discovery 2024, 19 (6), 649–670. https://doi.org/10.1080/17460441.2024.2349169.

Preikša, J.; Petrikaitė, V.; Petrauskas, V.; Matulis, D. Intrinsic Solubility of Ionizable Compounds from pKa Shift. ACS Omega 2023, 8 (47), 44571–44577. https://doi.org/10.1021/acsomega.3c04071.

Lingė, D.; Gedgaudas, M.; Merkys, A.; Petrauskas, V.; Vaitkus, A.; Grybauskas, A.; Paketurytė, V.; Zubrienė, A.; Zakšauskas, A.; Mickevičiūtė, A.; Smirnovienė, J.; Baranauskienė, L.; Čapkauskaitė, E.; Dudutienė, V.; Urniežius, E.; Konovalovas, A.; Kazlauskas, E.; Shubin, K.; Schiöth, H. B.; Chen, W.-Y.; Ladbury, J. E.; Gražulis, S.; Matulis, D. PLBD: Protein–Ligand Binding Database of Thermodynamic and Kinetic Intrinsic Parameters. Database 2023, 2023, baad040. https://doi.org/10.1093/database/baad040.

Toleikis, Z.; Bobrovs, R.; Janoniene, A.; Lends, A.; Ziaunys, M.; Baronaite, I.; Petrauskas, V.; Kitoka, K.; Smirnovas, V.; Jaudzems, K. Interactions between S100A9 and Alpha-Synuclein: Insight from NMR Spectroscopy. International Journal of Molecular Sciences 2022, 23 (12), 6781. https://doi.org/10.3390/ijms23126781.

Skvarnavičius, G.; Toleikis, Z.; Matulis, D.; Petrauskas, V. Denaturant- or Ligand-Induced Changes in Protein Volume by Pressure Shift Assay. Phys. Chem. Chem. Phys. 2022, 24 (28), 17279–17288. https://doi.org/10.1039/D2CP01046A.

Matulienė, J.; Žvinys, G.; Petrauskas, V.; Kvietkauskaitė, A.; Zakšauskas, A.; Shubin, K.; Zubrienė, A.; Baranauskienė, L.; Kačenauskaitė, L.; Kopanchuk, S.; Veiksina, S.; Paketurytė-Latvė, V.; Smirnovienė, J.; Juozapaitienė, V.; Mickevičiūtė, A.; Michailovienė, V.; Jachno, J.; Stravinskienė, D.; Sližienė, A.; Petrošiūtė, A.; Becker, H. M.; Kazokaitė-Adomaitienė, J.; Yaromina, A.; Čapkauskaitė, E.; Rinken, A.; Dudutienė, V.; Dubois, L. J.; Matulis, D. Picomolar Fluorescent Probes for Compound Affinity Determination to Carbonic Anhydrase IX Expressed in Live Cancer Cells. Sci Rep 2022, 12 (1), 17644. https://doi.org/10.1038/s41598-022-22436-1.

Grincevičienė, Š.; Vaitkienė, D.; Kanopienė, D.; Vansevičiūtė, R.; Tykvart, J.; Sukovas, A.; Celiešiūtė, J.; Ivanauskaitė Didžiokienė, E.; Čižauskas, A.; Laurinavičienė, A.; Král, V.; Hlavačková, A.; Zemanová, J.; Stravinskienė, D.; Sližienė, A.; Petrošiūtė, A.; Petrauskas, V.; Balsytė, R.; Grincevičius, J.; Navratil, V.; Jahn, U.; Konvalinka, J.; Žvirblienė, A.; Matulis, D.; Matulienė, J. Factors, Associated with Elevated Concentration of Soluble Carbonic Anhydrase IX in Plasma of Women with Cervical Dysplasia. Sci Rep 2022, 12 (1), 15397. https://doi.org/10.1038/s41598-022-19492-y.

Gedgaudas, M.; Baronas, D.; Kazlauskas, E.; Petrauskas, V.; Matulis, D. Thermott: A Comprehensive Online Tool for Protein–Ligand Binding Constant Determination. Drug Discovery Today 2022, 27 (8), 2076–2079. https://doi.org/10.1016/j.drudis.2022.05.008.

Toleikis, Z.; Ziaunys, M.; Baranauskiene, L.; Petrauskas, V.; Jaudzems, K.; Smirnovas, V. S100A9 Alters the Pathway of Alpha-Synuclein Amyloid Aggregation. International Journal of Molecular Sciences 2021, 22 (15), 7972. https://doi.org/10.3390/ijms22157972.

Smirnovienė, J.; Smirnov, A.; Zakšauskas, A.; Zubrienė, A.; Petrauskas, V.; Mickevičiūtė, A.; Michailovienė, V.; Čapkauskaitė, E.; Manakova, E.; Gražulis, S.; Baranauskienė, L.; Chen, W.-Y.; Ladbury, J. E.; Matulis, D. Switching the Inhibitor-Enzyme Recognition Profile via Chimeric Carbonic Anhydrase XII. ChemistryOpen 2021, 10 (5), 567–580. https://doi.org/10.1002/open.202100042.

Skvarnavičius, G.; Toleikis, Z.; Michailovienė, V.; Roumestand, C.; Matulis, D.; Petrauskas, V. Protein–Ligand Binding Volume Determined from a Single 2D NMR Spectrum with Increasing Pressure. J. Phys. Chem. B 2021, 125 (22), 5823–5831. https://doi.org/10.1021/acs.jpcb.1c02917.

Paketurytė, V.; Petrauskas, V.; Zubrienė, A.; Abian, O.; Bastos, M.; Chen, W.-Y.; Moreno, M. J.; Krainer, G.; Linkuvienė, V.; Sedivy, A.; Velazquez-Campoy, A.; Williams, M. A.; Matulis, D. Uncertainty in Protein–Ligand Binding Constants: Asymmetric Confidence Intervals versus Standard Errors. Eur. Biophys. J. 2021, 50, 661–670. https://doi.org/10.1007/s00249-021-01518-4.

Kazlauskas, E.; Petrauskas, V.; Paketurytė, V.; Matulis, D. Standard Operating Procedure for Fluorescent Thermal Shift Assay (FTSA) for Determination of Protein–Ligand Binding and Protein Stability. Eur. Biophys. J. 2021, 50, 373–379. https://doi.org/10.1007/s00249-021-01537-1.

Gulla, A.; Kazlauskas, E.; Liang, H.; Strupas, K.; Petrauskas, V.; Matulis, D.; Eshleman, J. R. Heat Shock Protein 90 Inhibitor Effects on Pancreatic Cancer Cell Cultures. Pancreas 2021, 50 (4), 625–632. https://doi.org/10.1097/mpa.0000000000001807.

DeLeeuw, L. W.; Monsen, R. C.; Petrauskas, V.; Gray, R. D.; Baranauskiene, L.; Matulis, D.; Trent, J. O.; Chaires, J. B. POT1 Stability and Binding Measured by Fluorescence Thermal Shift Assays. PLoS One 2021, 16 (3), e0245675. https://doi.org/10.1371/journal.pone.0245675.

Baranauskiene, L.; Škiudaitė, L.; Michailovienė, V.; Petrauskas, V.; Matulis, D. Thiazide and Other Cl-Benzenesulfonamide-Bearing Clinical Drug Affinities for Human Carbonic Anhydrases. PLOS ONE 2021, 16 (6), e0253608. https://doi.org/10.1371/journal.pone.0253608.

Skvarnavičius, G.; Matulis, D.; Petrauskas, V. Change in Volume Upon Inhibitor Binding to Carbonic Anhydrases by Fluorescent Pressure Shift Assay. In Carbonic Anhydrase as Drug Target: Thermodynamics and Structure of Inhibitor Binding; Matulis, D., Ed.; Springer International Publishing: Cham, 2019; pp 97–106. https://doi.org/10.1007/978-3-030-12780-0_7.

Skvarnavičius, G.; Dvareckas, D.; Matulis, D.; Petrauskas, V. Thermodynamics of Interactions Between Charged Surfactants and Ionic Poly(Amino Acids) by Isothermal Titration Calorimetry. ACS Omega 2019, 4 (17), 17527–17535. https://doi.org/10.1021/acsomega.9b02425.

Petrauskas, V.; Zubrienė, A.; Todd, M. J.; Matulis, D. Inhibitor Binding to Carbonic Anhydrases by Fluorescent Thermal Shift Assay. In Carbonic Anhydrase as Drug Target: Thermodynamics and Structure of Inhibitor Binding; Matulis, D., Ed.; Springer International Publishing: Cham, 2019; pp 63–78. https://doi.org/10.1007/978-3-030-12780-0_5.

Linkuvienė, V.; Zubrienė, A.; Manakova, E.; Petrauskas, V.; Baranauskienė, L.; Zakšauskas, A.; Smirnov, A.; Gražulis, S.; Ladbury, J. E.; Matulis, D. Thermodynamic, Kinetic, and Structural Parameterization of Human Carbonic Anhydrase Interactions toward Enhanced Inhibitor Design. Q. Rev. Biophys. 2018, 51, 1–48. https://doi.org/10.1017/S0033583518000082.

Skvarnavičius, G.; Toleikis, Z.; Grigaliūnas, M.; Smirnovienė, J.; Norvaišas, P.; Cimmperman, P.; Matulis, D.; Petrauskas, V. High Pressure Spectrofluorimetry – a Tool to Determine Protein-Ligand Binding Volume. J. Phys.: Conf. Ser. 2017, 950 (4), 042001. https://doi.org/10.1088/1742-6596/950/4/042001.

Toleikis, Z.; Sirotkin, V. A.; Skvarnavičius, G.; Smirnovienė, J.; Roumestand, C.; Matulis, D.; Petrauskas, V. Volume of Hsp90 Protein–Ligand Binding Determined by Fluorescent Pressure Shift Assay, Densitometry, and NMR. J. Phys. Chem. B 2016, 120 (37), 9903–9912. https://doi.org/10.1021/acs.jpcb.6b06863.

Petrauskas, V.; Baranauskienė, L.; Zubrienė, A.; Matulis, D. Isothermal Titration Calorimetry and Fluorescent Thermal and Pressure Shift Assays in Protein-Ligand Interactions. In Biocalorimetry; CRC Press, 2016; pp 261–280.

Redhead, M.; Satchell, R.; Morkūnaitė, V.; Swift, D.; Petrauskas, V.; Golding, E.; Onions, S.; Matulis, D.; Unitt, J. A Combinatorial Biophysical Approach; Ftsa and Spr for Identifying Small Molecule Ligands and Pains. Anal. Biochem. 2015, 479, 63–73. https://doi.org/10.1016/j.ab.2015.03.013.

Petrauskas, V.; Maximowitsch, E.; Matulis, D. Thermodynamics of Ion Pair Formations Between Charged Poly(Amino Acid)s. J. Phys. Chem. B 2015, 119 (37), 12164–12171. https://doi.org/10.1021/acs.jpcb.5b05767.

Dudutienė, V.; Matulienė, J.; Smirnov, A.; Timm, D. D.; Zubrienė, A.; Baranauskienė, L.; Morkūnaitė, V.; Smirnovienė, J.; Michailovienė, V.; Juozapaitienė, V.; Mickevičiūtė, A.; Kazokaitė, J.; Bakšytė, S.; Kasiliauskaitė, A.; Jachno, J.; Revuckienė, J.; Kišonaitė, M.; Pilipuitytė, V.; Ivanauskaitė, E.; Milinavičiūtė, G.; Smirnovas, V.; Petrikaitė, V.; Kairys, V.; Petrauskas, V.; Norvaišas, P.; Lingė, D.; Gibieža, P.; Čapkauskaitė, E.; Zakšauskas, A.; Kazlauskas, E.; Manakova, E.; Gražulis, S.; Ladbury, J. E.; Matulis, D. Discovery and Characterization of Novel Selective Inhibitors of Carbonic Anhydrase IX. J. Med. Chem. 2014, 57 (22), 9435–9446. https://doi.org/10.1021/jm501003k.

Petrauskas, V.; Gylytė, J.; Toleikis, Z.; Cimmperman, P.; Matulis, D. Volume of Hsp90 Ligand Binding and the Unfolding Phase Diagram as a Function of Pressure and Temperature. Eur. Biophys. J. 2013, 42 (5), 355–362. https://doi.org/10.1007/s00249-012-0884-7.

Toleikis, Z.; Cimmperman, P.; Petrauskas, V.; Matulis, D. Serum Albumin Ligand Binding Volumes Using High Pressure Denaturation. J. Chem. Thermodyn. 2012, 52, 24–29. https://doi.org/10.1016/j.jct.2011.12.026.

Norvaišas, P.; Petrauskas, V.; Matulis, D. Thermodynamics of Cationic and Anionic Surfactant Interaction. J. Phys. Chem. B 2012, 116 (7), 2138–2144. https://doi.org/10.1021/jp2095888.

Zubrienė, A.; Kazlauskas, E.; Baranauskienė, L.; Petrauskas, V.; Matulis, D. Isothermal Titration Calorimetry and Thermal Shift Assay in Drug Design. European Pharmaceutical Review 2011, 16, 56–59.

Toleikis, Z.; Cimmperman, P.; Petrauskas, V.; Matulis, D. Determination of the Volume Changes Induced by Ligand Binding to Heat Shock Protein 90 Using High-Pressure Denaturation. Anal. Biochem. 2011, 413 (2), 171–178. https://doi.org/10.1016/j.ab.2011.02.019.

Petrauskas, V.; Tornau, E. E. Formation of Stripe Structure Without Longer Range Interactions. Phys. Rev. B 2010, 82 (11), 115433. https://doi.org/10.1103/PhysRevB.82.115433.

Tornau, E. E.; Petrauskas, V.; Zvejnieks, G. Simulation of Oxidized Silicon Stripe Formation on Pd(111). Phys. Status Solidi C 2009, 6 (12), 2731–2733. https://doi.org/10.1002/pssc.200982523.

Tornau, E. E.; Petrauskas, V.; Joknys, A. Ising Model with Long Range Interactions: Phase Diagram and Transition Order of Stripe Structures. Ferroelectrics 2009, 379 (1), 128–135. https://doi.org/10.1080/00150190902851911.

Petrauskas, V.; Tornau, E. E. Simulation of Hydrogen-Induced Reconstruction of Oxygen on Pd(111). Acta Phys. Pol., A 2008, 113, 1075–1078. https://doi.org/10.12693/APhysPolA.113.1075.

Petrauskas, V.; Tornau, E. E. Modeling of Phase Transitions and Reaction Between Coadsorbed Oxygen and Hydrogen on Pd(111). J. Phys.: Conf. Ser. 2008, 100 (7), 072038. https://doi.org/10.1088/1742-6596/100/7/072038.

Petrauskas, V.; Tornau, E. E. Model for Hydrogen-Induced Sb Atoms Reconstruction <pre>$\sqrt 3 \times \sqrt 3 \rightarrow 2 \times 1$</Pre> on Si(111). J. Phys.: Conf. Ser. 2008, 100 (7), 072037. https://doi.org/10.1088/1742-6596/100/7/072037.

Petrauskas, V.; Tornau, E. E. Hydrogen-Induced Sb Atom Reconstruction <pre>$\sqrt 3 \times \sqrt 3 \rightarrow 2 \times 1$</Pre> on Si(111) as an Example of a Six-State Model. Phys. Rev. B 2007, 75 (11), 113308. https://doi.org/10.1103/PhysRevB.75.113308.

Zvejnieks, G.; Kuzovkov, V. N.; Petrauskas, V.; Tornau, E. E. Modelling of Phase Transitions and Reaction at CO Adsorption on Oxygen Precovered Pd(111). Appl. Surf. Sci. 2006, 252 (15), 5395–5398. https://doi.org/10.1016/j.apsusc.2005.12.048.

Tornau, E. E.; Petrauskas, V.; Zvejnieks, G. Surface Phase Transitions at O and CO Catalytic Reaction on Pd(111). Catal. Today 2006, 116 (1), 62–68. https://doi.org/10.1016/j.cattod.2006.02.081.

Petrauskas, V.; Tornau, E. E. Modelling of Grain Boundary Resistance in Thin Films of Lanthanum Manganites. Lith. J. Phys. 2006, 46, 191–198. https://doi.org/10.3952/lithjphys.46204.

Balevičius, S.; Cimmperman, P.; Petrauskas, V.; Stankevič, V.; Tornau, E. E.; Žurauskienė, N.; Abrutis, A.; Plaušinaitienė, V.; Sawicki, M.; Dietl, T.; Aleszkiewicz, M. Two-Phase Structure of Ultra-Thin La-Sr-MnO Films. Thin Solid Films 2006, 515 (2), 691–694. https://doi.org/10.1016/j.tsf.2005.12.240.

Tornau, E. E.; Petrauskas, V.; Crisan, O. Effect of Surface Anisotropy in Core-Shell Bimetallic Nanoparticles. Acta Phys. Pol., A 2005, 107 (2), 425–428. https://doi.org/10.12693/APhysPolA.107.425.

Petrauskas, V.; Tornau, E. E.; Lapinskas, S. Modelling of Subpc Self-Assembly on Ag(111). Acta Phys. Pol., A 2005, 107 (2), 388–391. https://doi.org/10.12693/APhysPolA.107.388.

Vengalis, B.; Lisauskas, V.; Šliužienė, K.; Petrauskas, V.; Dijken, S.; Bari, M.; Venkatesan, M.; Coey, J. M. D. Growth and Investigation of Oxide Heterostructures Containing Half-Metallic Fe<pre>$_3$</Pre>O<pre>$_4$</Pre>. Solid State Phenom. 2004, 99–100, 133–136. https://doi.org/10.4028/www.scientific.net/SSP.99-100.133.

Petrauskas, V.; Lapinskas, S.; Tornau, E. E. Phase Diagram of Subphtalocyanine Ordering on Ag(111). J. Chem. Phys. 2004, 120 (24), 11815. https://doi.org/10.1063/1.1755670.

Crisan, O.; Tornau, E. E.; Petrauskas, V.; Angelakeris, M. Monte Carlo Simulation Study of Magnetic Behaviour of Core-Shell Bimetallic Nanoparticles. Phys. Status Solidi C 2004, 1 (12), 3760–3763. https://doi.org/10.1002/pssc.200405549.

Petrauskas, V.; Tornau, E. E. Magnetization of Spin-Frustrated Ferromagnetic / Antiferromagnetic Superlattices. Lith. J. Phys. 2002, 42, 427–433.