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2. Protein–Ligand Binding Database (PLBD) of crystal structures and intrinsic thermodynamic parameters

Author

Lingė, D., primary, Gedgaudas, M., additional, Merkys, A., additional, Petrauskas, V., additional, Vaitkus, A., additional, Grybauskas, A., additional, Paketurytė, V., additional, Zubrienė, A., additional, Zakšauskas, A., additional, Mickevičiūtė, A., additional, Smirnovienė, J., additional, Baranauskienė, L., additional, Čapkauskaitė, E., additional, Dudutienė, V., additional, Urniežius, E., additional, Konovalovas, A., additional, Kazlauskas, E., additional, Shubin, K., additional, Schiöth, H. B., additional, Chen, W.-Y., additional, Ladbury, J. E., additional, Gražulis, S., additional, and Matulis, D., additional

Published
2023
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4. Eine römische Villa im Barbaricum, 300 km vom Limes entfernt? Erste Forschungsergebnisse zur „Römischen Station" bei Buzovycja.

Author

Petrauskas V, Oleg, Bondar M, K., Didenko V, S., and Avramenko O, M.

Subjects
*GLASS beads, *CONCRETE floors, *ARCHAEOLOGICAL finds, *IRON, *FIELD research, *MORTAR, *ARCHAEOLOGICAL excavations, *DOMESTIC architecture, *AMPHORAS
Abstract

A Roman villa in the Barbaricum, 300 km from the Limes? First research results on the "Roman Station" at Buzovycja. In 2020–2021 a site of clear Roman origin was discovered near Buzovycja (Ukraine, Černivci region). First field research in 2020 already suggested the existence of buildings that were built according to Roman building traditions. Specific architectural remains have been identified in several places on the surface of the site. In addition to the usual finds of the Černjachiv culture, such accumulations also contained fragments of brick, mortar and stone. According to the results of a geomagnetic survey conducted in 2021, a promising anomaly in the central part of the settlement site was selected for test digging. The main task of the archaeological excavations that followed was to determine the architectural type of the object and to date it. The excavation revealed an area of buildings constructed of brick, stone and lime mortar. The width of the building was about 9.3 m, the possible length can be estimated at about 20 m. The exposed building floor was 1.4 m below today's surface level and was a „screed"of concrete mortar and limestone. In the central part of the building, three round bricks were discovered on the concrete floor, one of which was fixed in place. Complete blocks of bricks were found in places, with up to four layers and connected with lime mortar. A number of finds were recovered in the building. This included Černjachiv ceramics, Forlimpopoli amphorae, amphora stands, glass beads, an iron chain and other objects. The analysis of the finds and the remains of the building showed that the building dates back to the late Roman period (3rd – mid 5th century AD). The salvaged remains of the building ceramics and mortar indicate that it was built in the Roman architectural tradition. The presence of rectangular and round brick blocks in a layer of destruction suggests that the building had a hypocaust. Other archaeological finds from the Buzovycja-1 site belong mainly to the Černjachiv culture. According to the current state of investigation, the overall finding is interpreted as a local settlement with buildings erected in the Roman building tradition. [ABSTRACT FROM AUTHOR]

Published
2023
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6. Uncertainty of protein-ligand binding constants: asymmetric confidence intervals versus standard errors

Author

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, Mark A., and Matulis, D.

Subjects
bcs
Abstract

Equilibrium binding constants (Kb) between chemical compounds and target proteins or between interacting proteins provide a quantitative understanding of biological interaction mechanisms. Reporting uncertainties of measured experimental parameters are critical for decision making in many scientific areas, e.g., in lead compound discovery processes and in comparing computational predictions with experimental results. Uncertainties in measured Kb values are commonly represented by a symmetric normal distribution, often quoted in terms of the experimental value plus-minus the standard deviation. However, in general the distributions of measured Kb (and equivalent Kd) values and the corresponding free energy change DeltaGb are all asymmetric to varying degree. Here, using a simulation approach, we illustrate the effect of asymmetric Kb distributions within the realm of isothermal titration calorimetry (ITC) experiments. Further we illustrate the known, but perhaps not widely appreciated, fact that when distributions of any of Kb, Kd and DeltaGb are transformed into each other their degree of asymmetry is changed. Consequently, we recommend that a more accurate way of expressing the uncertainties of Kb, Kd, and DeltaGb values is to consistently report 95% confidence intervals, in line with other author’s suggestions. The ways to obtain such error ranges are discussed in detail and exemplified for a binding reaction obtained by ITC.

Published
2021

10. Phase diagram of subphtalocyanine ordering on Ag(111).

Author

Petrauskas, V., Lapinskas, S., and Tornau, E. E.

Subjects
*MOLECULES, *SILVER, *HONEYCOMB structures, *COAL gas, *MONTE Carlo method, *SIMULATION methods & models
Abstract

A model of subphtalocyanine molecules ordering on Ag(111) is proposed. We have demonstrated that the driving force of the ordering into honeycomb and hexagonal close packed patterns is a balance of intermolecular and subphtalocyanine–Ag interactions which can be generally expressed by a potential with infinite exclusion in a sufficiently large number of nearest coordination spheres of Ag(111) lattice and oscillatingly decaying behavior outside the sphere of exclusion. To cope with computational problems due to large size of the molecules compared to the substrate lattice period, we introduce the rescaling of Ag(111) lattice, and took into account an infinite exclusion of first, second, and third neighbors, attraction—of fourth and fifth, and repulsion—of sixth and seventh. The phase diagram is obtained by the lattice gas model using Monte Carlo simulations. Very strong first order phase transitions, causing the two-phase coexistence, were found between disordered and honeycomb as well as between disordered and hexagonal closed packed phases.© 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Published
2004
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11. Volume of Hsp90 Protein-Ligand Binding Determined by Fluorescent Pressure Shift Assay, Densitometry, and NMR

Author

Toleikis Z., Sirotkin V., Skvarnavičius G., Smirnoviene J., Roumestand C., Matulis D., and Petrauskas V.

Abstract

© 2016 American Chemical Society.Human heat shock protein 90 (Hsp90) is a key player in the homeostasis of the proteome and plays a role in numerous diseases, such as cancer. For the design of Hsp90 ATPase activity inhibitors, it is important to understand the relationship between an inhibitor structure and its inhibition potential. The volume of inhibitor binding is one of the most important such parameters that are rarely being studied. Here, the volumes of binding of several ligands to recombinant Hsp90 were obtained by three independent experimental techniques: fluorescent pressure shift assay, vibrating tube densitometry, and high-pressure NMR. Within the error range, all techniques provided similar volumetric parameters for the investigated protein-ligand systems. Protein-ligand binding volumes were negative, suggesting that the protein-ligand complex, together with its hydration shell, occupies less volume than the separate constituents with their hydration shells. Binding volumes of tightly binding, subnanomolar ligands were significantly more negative than those of weakly binding, millimolar ligands. The volumes of binding could be useful for designing inhibitors with desired recognition properties and further development as drugs.

Published
2016

16. Grand Rounds

Author

Fayolle, G., primary, Levick, W., additional, Lajiness-O'Neill, R., additional, Fastenau, P., additional, Briskin, S., additional, Bass, N., additional, Silva, M., additional, Critchfield, E., additional, Nakase-Richardson, R., additional, Hertza, J., additional, Loughan, A., additional, Perna, R., additional, Northington, S., additional, Boyd, S., additional, Anderson, A., additional, Peery, S., additional, Chafetz, M., additional, Maris, M., additional, Ramezani, A., additional, Sylvester, C., additional, Goldberg, K., additional, Constantinou, M., additional, Karekla, M., additional, Hall, J., additional, Edwards, M., additional, Balldin, V., additional, Strutt, A., additional, Pavlik, V., additional, Marquez de la Plata, C., additional, Cullum, M., additional, lacritz, l., additional, Reisch, J., additional, Massman, P., additional, Royall, D., additional, Barber, R., additional, Younes, S., additional, Wiechmann, A., additional, O'Bryant, S., additional, Patel, K., additional, Suhr, J., additional, Chari, S., additional, Yokoyama, J., additional, Bettcher, B., additional, Karydas, A., additional, Miller, B., additional, Kramer, J., additional, Zec, R., additional, Fritz, S., additional, Kohlrus, S., additional, Robbs, R., additional, Ala, T., additional, Gifford, K., additional, Cantwell, N., additional, Romano, R., additional, Jefferson, A., additional, Holland, A., additional, Newton, S., additional, Bunting, J., additional, Coe, M., additional, Carmona, J., additional, Harrison, D., additional, Puente, A., additional, Terry, D., additional, Faraco, C., additional, Brown, C., additional, Patel, A., additional, Watts, A., additional, Kent, A., additional, Siegel, J., additional, Miller, S., additional, Ernst, W., additional, Chelune, G., additional, Holdnack, J., additional, Sheehan, J., additional, Duff, K., additional, Pedraza, O., additional, Crawford, J., additional, Miller, L., additional, Hobson Balldin, V., additional, Benavides, H., additional, Johnson, L., additional, Tshuma, L., additional, Dezhkam, N., additional, Hayes, L., additional, Love, C., additional, Stephens, B., additional, Webbe, F., additional, Mulligan, K., additional, Dunham, K., additional, Shadi, S., additional, Sofko, C., additional, Denney, R., additional, Rolin, S., additional, Sibson, J., additional, Ogbeide, S., additional, Glover, M., additional, Warchol, A., additional, Hunter, B., additional, Nichols, C., additional, Riccio, C., additional, Cohen, M., additional, Dennison, A., additional, Wasserman, T., additional, Schleicher-Dilks, S., additional, Adler, M., additional, Golden, C., additional, Olivier, T., additional, LeMonda, B., additional, McGinley, J., additional, Pritchett, A., additional, Chang, L., additional, Cloak, C., additional, Cunningham, E., additional, Lohaugen, G., additional, Skranes, J., additional, Ernst, T., additional, Parke, E., additional, Thaler, N., additional, Etcoff, L., additional, Allen, D., additional, Andrews, P., additional, McGregor, S., additional, Daniels, R., additional, Hochsztein, N., additional, Miles-Mason, E., additional, Granader, Y., additional, Vasserman, M., additional, MacAllister, W., additional, Casto, B., additional, Patrick, K., additional, Hurewitz, F., additional, Chute, D., additional, Booth, A., additional, Koch, C., additional, Roid, G., additional, Balkema, N., additional, Kiefel, J., additional, Bell, L., additional, Maerlender, A., additional, Belkin, T., additional, Katzenstein, J., additional, Semerjian, C., additional, Culotta, V., additional, Band, E., additional, Yosick, R., additional, Burns, T., additional, Arenivas, A., additional, Bearden, D., additional, Olson, K., additional, Jacobson, K., additional, Ubogy, S., additional, Sterling, C., additional, Taub, E., additional, Griffin, A., additional, Rickards, T., additional, Uswatte, G., additional, Davis, D., additional, Sweeney, K., additional, Llorente, A., additional, Boettcher, A., additional, Hill, B., additional, Ploetz, D., additional, Kline, J., additional, Rohling, M., additional, O'Jile, J., additional, Holler, K., additional, Petrauskas, V., additional, Long, J., additional, Casey, J., additional, Duda, T., additional, Hodsman, S., additional, Stricker, S., additional, Martner, S., additional, Hansen, R., additional, Ferraro, F., additional, Tangen, R., additional, Hanratty, A., additional, Tanabe, M., additional, O'Callaghan, E., additional, Houskamp, B., additional, McDonald, L., additional, Pick, L., additional, Guardino, D., additional, Pietz, T., additional, Kayser, K., additional, Gray, R., additional, Letteri, A., additional, Crisologo, A., additional, Witkin, G., additional, Sanders, J., additional, Mrazik, M., additional, Harley, A., additional, Phoong, M., additional, Melville, T., additional, La, D., additional, Gomez, R., additional, Berthelson, L., additional, Robbins, J., additional, Lane, E., additional, Rahman, P., additional, Konopka, L., additional, Fasfous, A., additional, Zink, D., additional, Peralta-Ramirez, N., additional, Perez-Garcia, M., additional, Su, S., additional, Lin, G., additional, Kiely, T., additional, Schatzberg, A., additional, Keller, J., additional, Dykstra, J., additional, Feigon, M., additional, Renteria, L., additional, Fong, M., additional, Piper, L., additional, Lee, E., additional, Vordenberg, J., additional, Contardo, C., additional, Magnuson, S., additional, Doninger, N., additional, Luton, L., additional, Drane, D., additional, Phelan, A., additional, Stricker, W., additional, Poreh, A., additional, Wolkenberg, F., additional, Spira, J., additional, DeRight, J., additional, Jorgensen, R., additional, Fitzpatrick, L., additional, Crowe, S., additional, Woods, S., additional, Doyle, K., additional, Weber, E., additional, Cameron, M., additional, Cattie, J., additional, Cushman, C., additional, Grant, I., additional, Blackstone, K., additional, Moore, D., additional, Roberg, B., additional, Somogie, M., additional, Thelen, J., additional, Lovelace, C., additional, Bruce, J., additional, Gerstenecker, A., additional, Mast, B., additional, Litvan, I., additional, Hargrave, D., additional, Schroeder, R., additional, Buddin, W., additional, Baade, L., additional, Heinrichs, R., additional, Boseck, J., additional, Berry, K., additional, Koehn, E., additional, Davis, A., additional, Meyer, B., additional, Gelder, B., additional, Sussman, Z., additional, Espe-Pfeifer, P., additional, Musso, M., additional, Barker, A., additional, Jones, G., additional, Gouvier, W., additional, Johnson, V., additional, Zaytsev, L., additional, Freier-Randall, M., additional, Sutton, G., additional, Ringdahl, E., additional, Olsen, J., additional, Byrd, D., additional, Rivera-Mindt, M., additional, Fellows, R., additional, Morgello, S., additional, Wheaton, V., additional, Jaehnert, S., additional, Ellis, C., additional, Olavarria, H., additional, Loftis, J., additional, Huckans, M., additional, Pimental, P., additional, Frawley, J., additional, Welch, M., additional, Jennette, K., additional, Rinehardt, E., additional, Schoenberg, M., additional, Strober, L., additional, Genova, H., additional, Wylie, G., additional, DeLuca, J., additional, Chiaravalloti, N., additional, Ibrahim, E., additional, Seiam, A., additional, Bohlega, S., additional, Lloyd, H., additional, Goldberg, M., additional, Marceaux, J., additional, Fallows, R., additional, McCoy, K., additional, Yehyawi, N., additional, Luther, E., additional, Hilsabeck, R., additional, Fulton, R., additional, Stevens, P., additional, Erickson, S., additional, Dodzik, P., additional, Williams, R., additional, Dsurney, J., additional, Najafizadeh, L., additional, McGovern, J., additional, Chowdhry, F., additional, Acevedo, A., additional, Bakhtiar, A., additional, Karamzadeh, N., additional, Amyot, F., additional, Gandjbakhche, A., additional, Haddad, M., additional, Johnson, M., additional, Wade, J., additional, Harper, L., additional, Barghi, A., additional, Mark, V., additional, Christopher, G., additional, Marcus, D., additional, Spady, M., additional, Bloom, J., additional, Zimmer, A., additional, Miller, M., additional, Schuster, D., additional, Ebner, H., additional, Mortimer, B., additional, Palmer, G., additional, Happe, M., additional, Paxson, J., additional, Jurek, B., additional, Graca, J., additional, Meyers, J., additional, Lange, R., additional, Brickell, T., additional, French, L., additional, Iverson, G., additional, Shewchuk, J., additional, Madler, B., additional, Heran, M., additional, Brubacher, J., additional, Ivins, B., additional, Baldassarre, M., additional, Paper, T., additional, Herrold, A., additional, Chin, A., additional, Zgaljardic, D., additional, Oden, K., additional, Lambert, M., additional, Dickson, S., additional, Miller, R., additional, Plenger, P., additional, Sutherland, E., additional, Glatts, C., additional, Schatz, P., additional, Walker, K., additional, Philip, N., additional, McClaughlin, S., additional, Mooney, S., additional, Seats, E., additional, Carnell, V., additional, Raintree, J., additional, Brown, D., additional, Hodges, C., additional, Amerson, E., additional, Kennedy, C., additional, Moore, J., additional, Ferris, C., additional, Roebuck-Spencer, T., additional, Vincent, A., additional, Bryan, C., additional, Catalano, D., additional, Warren, A., additional, Monden, K., additional, Driver, S., additional, Chau, P., additional, Seegmiller, R., additional, Baker, M., additional, Malach, S., additional, Mintz, J., additional, Villarreal, R., additional, Peterson, A., additional, Leininger, S., additional, Strong, C., additional, Donders, J., additional, Merritt, V., additional, Vargas, G., additional, Rabinowitz, A., additional, Arnett, P., additional, Whipple, E., additional, Schultheis, M., additional, Robinson, K., additional, Iacovone, D., additional, Biester, R., additional, Alfano, D., additional, Nicholls, M., additional, Klas, P., additional, Jeffay, E., additional, Zakzanis, K., additional, Vandermeer, M., additional, Womble, M., additional, Corley, E., additional, Considine, C., additional, Fichtenberg, N., additional, Harrison, J., additional, Pollock, M., additional, Mouanoutoua, A., additional, Brimager, A., additional, Lebby, P., additional, Sullivan, K., additional, Edmed, S., additional, Kieffer, K., additional, McCarthy, M., additional, Wiegand, L., additional, Lindsey, H., additional, Hernandez, M., additional, Noniyeva, Y., additional, Lapis, Y., additional, Padua, M., additional, Poole, J., additional, Brooks, B., additional, McKay, C., additional, Meeuwisse, W., additional, Emery, C., additional, Mazur-Mosiewicz, A., additional, Sherman, E., additional, Kirkwood, M., additional, Gunner, J., additional, Miele, A., additional, Silk-Eglit, G., additional, Lynch, J., additional, McCaffrey, R., additional, Stewart, J., additional, Tsou, J., additional, Scarisbrick, D., additional, Chan, R., additional, Bure-Reyes, A., additional, Cortes, L., additional, Gindy, S., additional, Biddle, C., additional, Shah, D., additional, Jaberg, P., additional, Moss, R., additional, Horner, M., additional, VanKirk, K., additional, Dismuke, C., additional, Turner, T., additional, Muzzy, W., additional, Dunnam, M., additional, Warner, G., additional, Donnelly, K., additional, Donnelly, J., additional, Kittleson, J., additional, Bradshaw, C., additional, Alt, M., additional, Margolis, S., additional, Ostroy, E., additional, Higgins, K., additional, Eng, K., additional, Akeson, S., additional, Wall, J., additional, Davis, J., additional, Hansel, J., additional, Wang, B., additional, Gervais, R., additional, Greiffenstein, M., additional, Denning, J., additional, VonDran, E., additional, Campbell, E., additional, Brockman, C., additional, Teichner, G., additional, Waid, R., additional, Buican, B., additional, Armistead-Jehle, P., additional, Bailie, J., additional, Dilay, A., additional, Cottingham, M., additional, Boyd, C., additional, Asmussen, S., additional, Neff, J., additional, Schalk, S., additional, Jensen, L., additional, DenBoer, J., additional, Hall, S., additional, Holcomb, E., additional, Axelrod, B., additional, Demakis, G., additional, Rimland, C., additional, Ward, J., additional, Ross, M., additional, Bailey, M., additional, Stubblefield, A., additional, Smigielski, J., additional, Geske, J., additional, Karpyak, V., additional, Reese, C., additional, Larrabee, G., additional, Allen, L., additional, Celinski, M., additional, Gilman, J., additional, LaDuke, C., additional, DeMatteo, D., additional, Heilbrun, K., additional, Swirsky-Sacchetti, T., additional, Dedman, A., additional, Withers, K., additional, Deneen, T., additional, Fisher, J., additional, Spray, B., additional, Savage, R., additional, Wiener, H., additional, Tyer, J., additional, Ningaonkar, V., additional, Devlin, B., additional, Go, R., additional, Sharma, V., additional, Fontanetta, R., additional, Calderon, C., additional, Coad, S., additional, Fontaneta, R., additional, Vertinski, M., additional, Verbiest, R., additional, Snyder, J., additional, Kinney, J., additional, Rach, A., additional, Young, J., additional, Crouse, E., additional, Schretlen, D., additional, Weaver, J., additional, Buchholz, A., additional, Gordon, B., additional, Macciocchi, S., additional, Seel, R., additional, Godsall, R., additional, Brotsky, J., additional, DiRocco, A., additional, Houghton-Faryna, E., additional, Bolinger, E., additional, Hollenbeck, C., additional, Hart, J., additional, Lee, B., additional, Strauss, G., additional, Adams, J., additional, Martins, D., additional, Catalano, L., additional, Waltz, J., additional, Gold, J., additional, Haas, G., additional, Brown, L., additional, Luther, J., additional, Goldstein, G., additional, Kelley, E., additional, Raba, C., additional, Trettin, L., additional, Solvason, H., additional, Buchanan, R., additional, Baldock, D., additional, Etherton, J., additional, Phelps, T., additional, Richmond, S., additional, Tapscott, B., additional, Thomlinson, S., additional, Cordeiro, L., additional, Wilkening, G., additional, Parikh, M., additional, Graham, L., additional, Grosch, M., additional, Hynan, L., additional, Weiner, M., additional, Cullum, C., additional, Menon, C., additional, Lacritz, L., additional, Castro-Couch, M., additional, Irani, F., additional, Houshyarnejad, A., additional, Norman, M., additional, Fonseca, F., additional, Browne, B., additional, Alvarez, J., additional, Jiminez, Y., additional, Baez, V., additional, Resendiz, C., additional, Scott, B., additional, Farias, G., additional, York, M., additional, Lozano, V., additional, Mahoney, M., additional, Hernandez Mejia, M., additional, Pacheco, E., additional, Homs, A., additional, Ownby, R., additional, Nici, J., additional, Hom, J., additional, Lutz, J., additional, Dean, R., additional, Finch, H., additional, Pierce, S., additional, Moses, J., additional, Mann, S., additional, Feinberg, J., additional, Choi, A., additional, Kaminetskaya, M., additional, Pierce, C., additional, Zacharewicz, M., additional, Gavett, B., additional, Horwitz, J., additional, Ory, J., additional, Carbuccia, K., additional, Morra, L., additional, Garcon, S., additional, Lucas, M., additional, Donovick, P., additional, Whearty, K., additional, Campbell, K., additional, Camlic, S., additional, Brinckman, D., additional, Ehrhart, L., additional, Weisser, V., additional, Medaglia, J., additional, Merzagora, A., additional, Reckess, G., additional, Ho, T., additional, Testa, S., additional, Woolery, H., additional, Farcello, C., additional, Klimas, N., additional, Meyer, J., additional, Barwick, F., additional, Drayer, K., additional, Galusha, J., additional, Schmitt, A., additional, Livingston, R., additional, Stewart, R., additional, Quarles, L., additional, Pagitt, M., additional, Barke, C., additional, Baker, A., additional, Baker, N., additional, Cook, N., additional, Ahern, D., additional, Correia, S., additional, Resnik, L., additional, Barnabe, K., additional, Gnepp, D., additional, Benjamin, M., additional, Zlatar, Z., additional, Garcia, A., additional, Harnish, S., additional, Crosson, B., additional, Vaughan, L., additional, Fedio, A., additional, Sexton, J., additional, Cummings, S., additional, Logemann, A., additional, Lassiter, N., additional, Fedio, P., additional, Gremillion, A., additional, Nemeth, D., additional, Whittington, T., additional, Reckow, J., additional, Lewandowski, C., additional, Cole, J., additional, Lewandowski, A., additional, Spector, J., additional, Ford-Johnson, L., additional, Lengenfelder, J., additional, Sumowski, J., additional, Morse, C., additional, McKeever, J., additional, Zhao, L., additional, Leist, T., additional, Marcinak, J., additional, Piecora, K., additional, Al-Khalil, K., additional, Martin, P., additional, Thompson, L., additional, Kowalczyk, W., additional, Golub, S., additional, Lemann, E., additional, Piehl, J., additional, Rita, N., additional, Moss, L., additional, Nogin, R., additional, Drapeau, C., additional, Malm, S., additional, Armstrong, L., additional, Glidewell, R., additional, Orr, W., additional, Mears, G., additional, Allen, C., additional, Pierson, E., additional, Kavanaugh, B., additional, Tayim, F., additional, Llanes, S., additional, Poston, K., additional, Beathard, J., additional, Stolberg, P., additional, Jones, W., additional, Mayfield, J., additional, Weller, J., additional, Demireva, P., additional, McInerney, K., additional, Riddle, T., additional, Primus, M., additional, Highsmith, J., additional, Everhart, D., additional, Lehockey, K., additional, Sullivan, S., additional, Mandava, S., additional, Murphy, B., additional, Lalwani, L., additional, Rosselli, M., additional, Carrasco, R., additional, Zuckerman, S., additional, Brand, J., additional, Rivera Mindt, M., additional, Schaffer, S., additional, Alper, K., additional, Devinsky, O., additional, Barr, W., additional, Langer, K., additional, Fraiman, J., additional, Scagliola, J., additional, Roman, E., additional, Martinez, A., additional, Konopacki, K., additional, Juliano, A., additional, Whiteside, D., additional, Widmann, G., additional, Franzwa, M., additional, Sokal, B., additional, Morgan, E., additional, Bondi, M., additional, Delano-Wood, L., additional, Cormier, R., additional, Cumley, N., additional, Elek, M., additional, Green, M., additional, Kruger, A., additional, Pacheco, L., additional, Robinson, G., additional, Welch, H., additional, Parriott, D., additional, Loe, S., additional, Hughes, L., additional, Natta, L., additional, Quenicka, W., additional, McGoldirck, K., additional, Bennett, T., additional, Soper, H., additional, Collier, S., additional, Connolly, M., additional, Di Pinto, M., additional, Handel, E., additional, Davidson, K., additional, Livers, E., additional, Frantz, S., additional, Allen, J., additional, Jerard, T., additional, Sakhai, S., additional, Barney, S., additional, McGoldrick, K., additional, Sordahl, J., additional, Torrence, N., additional, and John, S., additional

Published
2012
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33. Investigation of spin-polarized carrier injection effect in|YBa2Cu3O7/SrTiO3/La0.67/Sr0.33MnO3and YBa2Cu3O7/La0.67Sr0.33MnO3heterostructures

Author

Vengalis, B., Plausinaitiene, V., Abrutis, A., Saltyte, Z., Butkute, R., Petrauskas, V., Maria, J., Bonfait, G., Vengalis, B., Plausinaitiene, V., Abrutis, A., Saltyte, Z., Butkute, R., Petrauskas, V., Maria, J., and Bonfait, G.

Abstract

We report preparation and electrical properties of the YBa2Cu3O7SrTiO3(d ≈ 5.0 nm)/La0.67Sr0.33MnO3(YBCO/STO/LSMO) and YBCO/LSMO multilayer structures grown heteroepitaxially on LaAlO3(100) substrates by single source pulsed injection MOCVD. The heterostructures were patterned in a cross-strip geometry to perform electrical measurements at T=78/300 K under magnetic field μ0H= 0/16 T using 4-probe dc method. Suppression of a supercurrent of the patterned YBCO stripes was indicated for the YBCO/LSMO heterostructure by injecting tunneling spin-polarized current fiom the underlying FM layer. The transport effects were modelled taking into account current redistribution in the adjacent conducting HTS and FM layers.

Published
2001
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37. Online Decision Support System for Dairy Farm.

Author

Elleithy, Khaled, Savilionis, A., Zajančkauskas, A., Petrauskas, V., and Juknevičius, S.

Abstract

online decision support system for dairy farm was created for helping Lithuanian dairy farmers, scientists, dairy technology producers, students and other peoples interesting in dairy business. It enable they use newest information and technology for planning own business [ABSTRACT FROM AUTHOR]

Published
2007
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40. Volume of Hsp90 Protein-Ligand Binding Determined by Fluorescent Pressure Shift Assay, Densitometry, and NMR

Author

Toleikis Z., Sirotkin V., Skvarnavičius G., Smirnoviene J., Roumestand C., Matulis D., Petrauskas V., Toleikis Z., Sirotkin V., Skvarnavičius G., Smirnoviene J., Roumestand C., Matulis D., and Petrauskas V.

Abstract

© 2016 American Chemical Society.Human heat shock protein 90 (Hsp90) is a key player in the homeostasis of the proteome and plays a role in numerous diseases, such as cancer. For the design of Hsp90 ATPase activity inhibitors, it is important to understand the relationship between an inhibitor structure and its inhibition potential. The volume of inhibitor binding is one of the most important such parameters that are rarely being studied. Here, the volumes of binding of several ligands to recombinant Hsp90 were obtained by three independent experimental techniques: fluorescent pressure shift assay, vibrating tube densitometry, and high-pressure NMR. Within the error range, all techniques provided similar volumetric parameters for the investigated protein-ligand systems. Protein-ligand binding volumes were negative, suggesting that the protein-ligand complex, together with its hydration shell, occupies less volume than the separate constituents with their hydration shells. Binding volumes of tightly binding, subnanomolar ligands were significantly more negative than those of weakly binding, millimolar ligands. The volumes of binding could be useful for designing inhibitors with desired recognition properties and further development as drugs.

41. Volume of Hsp90 Protein-Ligand Binding Determined by Fluorescent Pressure Shift Assay, Densitometry, and NMR

Author

Toleikis Z., Sirotkin V., Skvarnavičius G., Smirnoviene J., Roumestand C., Matulis D., Petrauskas V., Toleikis Z., Sirotkin V., Skvarnavičius G., Smirnoviene J., Roumestand C., Matulis D., and Petrauskas V.

Abstract

© 2016 American Chemical Society.Human heat shock protein 90 (Hsp90) is a key player in the homeostasis of the proteome and plays a role in numerous diseases, such as cancer. For the design of Hsp90 ATPase activity inhibitors, it is important to understand the relationship between an inhibitor structure and its inhibition potential. The volume of inhibitor binding is one of the most important such parameters that are rarely being studied. Here, the volumes of binding of several ligands to recombinant Hsp90 were obtained by three independent experimental techniques: fluorescent pressure shift assay, vibrating tube densitometry, and high-pressure NMR. Within the error range, all techniques provided similar volumetric parameters for the investigated protein-ligand systems. Protein-ligand binding volumes were negative, suggesting that the protein-ligand complex, together with its hydration shell, occupies less volume than the separate constituents with their hydration shells. Binding volumes of tightly binding, subnanomolar ligands were significantly more negative than those of weakly binding, millimolar ligands. The volumes of binding could be useful for designing inhibitors with desired recognition properties and further development as drugs.

44. 479. Application of the planar histogram and a set of two single-dimension histograms for human posture disorder classification problem.

Author

Jasinevicius, R., Krusinskiene, R., Satkunskiene, D., and Petrauskas, V.

Subjects
*VIBRATION (Mechanics), *PRESSURE, *OSCILLATIONS, *POSTURE, *STANDING position, *MULTIPLE sclerosis, *LINEAR programming
Abstract

The time law of small vibrations of the center of pressure (COP) of humans in standing position (human posture) may provide useful information about health condition of an individual. Very popular method to analyze the posture stability is to draw planar or two single-dimension histograms of COP. In this paper both types of histograms are used as a discriminative tool to distinguish two classes of subjects - healthy ones and those who suffer from multiple sclerosis disability. The pattern recognition method based on solving linear programming problem is presented in this paper. The method was applied for classification of histograms. Numerical experiments demonstrate that planar histograms may be used as a discriminative tool to classify subjects into two classes - healthy and suffering from multiple sclerosis disability. A set of two single-dimension histograms failed to indicate that ability. [ABSTRACT FROM AUTHOR]

Published
2009

45. From X-ray crystallographic structure to intrinsic thermodynamics of protein-ligand binding using carbonic anhydrase isozymes as a model system.

Author

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, and Matulis D

Subjects
Humans, Crystallography, X-Ray, Ligands, Carbonic Anhydrase Inhibitors chemistry, Carbonic Anhydrase Inhibitors pharmacology, Carbonic Anhydrase IX metabolism, Carbonic Anhydrase IX chemistry, Models, Molecular, Thermodynamics, Carbonic Anhydrases metabolism, Carbonic Anhydrases chemistry, Isoenzymes metabolism, Isoenzymes chemistry, Sulfonamides chemistry, Sulfonamides pharmacology, Protein Binding
Abstract

Carbonic anhydrase (CA) was among the first proteins whose X-ray crystal structure was solved to atomic resolution. CA proteins have essentially the same fold and similar active centers that differ in only several amino acids. Primary sulfonamides are well defined, strong and specific binders of CA. However, minor variations in chemical structure can significantly alter their binding properties. Over 1000 sulfonamides have been designed, synthesized and evaluated to understand the correlations between the structure and thermodynamics of their binding to the human CA isozyme family. Compound binding was determined by several binding assays: fluorescence-based thermal shift assay, stopped-flow enzyme activity inhibition assay, isothermal titration calorimetry and competition assay for enzyme expressed on cancer cell surfaces. All assays have advantages and limitations but are necessary for deeper characterization of these protein-ligand interactions. Here, the concept and importance of intrinsic binding thermodynamics is emphasized and the role of structure-thermodynamics correlations for the novel inhibitors of CA IX is discussed - an isozyme that is overexpressed in solid hypoxic tumors, and thus these inhibitors may serve as anticancer drugs. The abundant structural and thermodynamic data are assembled into the Protein-Ligand Binding Database to understand general protein-ligand recognition principles that could be used in drug discovery., (open access.)

Published
2024
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46. Recent advances in computational and experimental protein-ligand affinity determination techniques.

Author

Kairys V, Baranauskiene L, Kazlauskiene M, Zubrienė A, Petrauskas V, Matulis D, and Kazlauskas E

Subjects
Ligands, Humans, Protein Binding, High-Throughput Screening Assays methods, Proteins metabolism, Drug Discovery methods, Drug Design methods
Abstract

Introduction: Modern drug discovery revolves around designing ligands that target the chosen biomolecule, typically proteins. For this, the evaluation of affinities of putative ligands is crucial. This has given rise to a multitude of dedicated computational and experimental methods that are constantly being developed and improved., Areas Covered: In this review, the authors reassess both the industry mainstays and the newest trends among the methods for protein - small-molecule affinity determination. They discuss both computational affinity predictions and experimental techniques, describing their basic principles, main limitations, and advantages. Together, this serves as initial guide to the currently most popular and cutting-edge ligand-binding assays employed in rational drug design., Expert Opinion: The affinity determination methods continue to develop toward miniaturization, high-throughput, and in-cell application. Moreover, the availability of data analysis tools has been constantly increasing. Nevertheless, cross-verification of data using at least two different techniques and careful result interpretation remain of utmost importance.

Published
2024
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47. Intrinsic Solubility of Ionizable Compounds from p K a Shift.

Author

Preikša JB, Petrikaitė V, Petrauskas V, and Matulis D

Abstract

Aqueous solubility of pharmaceutical substances plays an important role in small molecule drug discovery and development, with ionizable groups often employed to enhance solubility. Drug candidate compounds often contain ionizable groups to increase their solubility. Recognizing that the electrostatically charged form of the compound is much more soluble than the uncharged form, this work proposes a model to explore the relationship between the p K a shift of the ionizable group and dissolution equilibria. The model considers three forms of a compound: dissolved-charged, dissolved-uncharged, and aggregated-uncharged. It analyzes two linked equilibria: the protonation of the ionizable group and the dissolution-aggregation of the uncharged form, with the observed p K a shift depending on the total concentration of the compound. The active concentration of the aggregates determines this shift. The model was explored through the determination of the p K a shift and intrinsic solubility of specific compounds, such as ICPD47, a high-affinity inhibitor of the Hsp90 chaperone protein and anticancer target, as well as benzoic acid and benzydamine. The model holds the potential for a more nuanced understanding of intrinsic solubility and may lead to advancements in drug discovery and development., Competing Interests: The authors declare no competing financial interest., (© 2023 The Authors. Published by American Chemical Society.)

Published
2023
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48. PLBD: protein-ligand binding database of thermodynamic and kinetic intrinsic parameters.

Author

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 HB, Chen WY, Ladbury JE, Gražulis S, and Matulis D

Subjects
Humans, Ligands, Thermodynamics, Protein Binding, Carbonic Anhydrase Inhibitors pharmacology, Carbonic Anhydrase Inhibitors chemistry, Carbonic Anhydrase Inhibitors metabolism, Carbonic Anhydrases chemistry, Carbonic Anhydrases metabolism
Abstract

We introduce a protein-ligand binding database (PLBD) that presents thermodynamic and kinetic data of reversible protein interactions with small molecule compounds. The manually curated binding data are linked to protein-ligand crystal structures, enabling structure-thermodynamics correlations to be determined. The database contains over 5500 binding datasets of 556 sulfonamide compound interactions with the 12 catalytically active human carbonic anhydrase isozymes defined by fluorescent thermal shift assay, isothermal titration calorimetry, inhibition of enzymatic activity and surface plasmon resonance. In the PLBD, the intrinsic thermodynamic parameters of interactions are provided, which account for the binding-linked protonation reactions. In addition to the protein-ligand binding affinities, the database provides calorimetrically measured binding enthalpies, providing additional mechanistic understanding. The PLBD can be applied to investigations of protein-ligand recognition and could be integrated into small molecule drug design. Database URL https://plbd.org/., (© The Author(s) 2023. Published by Oxford University Press.)

Published
2023
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49. Aberrant pancreas adenocarcinoma in the stomach: A case report and literature review.

Author

Petrauskas V, Stulpinas R, Mickys U, Luksaite-Lukste R, Strupas K, and Poskus E

Subjects
Male, Humans, Adult, Neoplasm Recurrence, Local, Pancreas diagnostic imaging, Pancreas pathology, Pylorus pathology, Endoscopy, Gastrointestinal, Pancreatic Neoplasms, Stomach Diseases surgery, Adenocarcinoma diagnosis, Adenocarcinoma surgery, Adenocarcinoma pathology, Pyloric Stenosis, Stomach Neoplasms diagnosis, Stomach Neoplasms surgery, Stomach Neoplasms pathology
Abstract

Rationale: Aberrant pancreatic tissue in the gastrointestinal tract is a relatively common finding. However, malignant transformation is extremely rare. Herein, we report a case of ectopic pancreatic ductal adenocarcinoma in the stomach wall., Patient Concerns: A 38 year old male presented with nausea, bloating, abdominal distention and weight loss for 4 months., Diagnoses: Endoscopy of upper gastrointestinal tract was performed twice with 2 months interval and a stenotic pyloric part was observed with a suspected submucosal lesion. It was sampled both times, however the pathology findings of the mucosal biopsies were unremarkable with no identifiable neoplastic structures. CT scan and MRI was performed and showed a thickened pyloric wall with a submucosal lesion 15 × 15 mm in diameter. Blood levels of tumor markers carcinoembrionic antigen and carbohydrate antigen 19-9 were within a normal range., Interventions: Pyloric stenosis progressed and the patient underwent a Billroth type I distal gastric resection with D2 lymphadenectomy. Pathologic examination revealed a well differentiated ductal adenocarcinoma arising in the heterotopic pancreatic tissue (Heinrich type III). The resection margins and lymph nodes were free of tumor. The patient received adjuvant chemotherapy with 6 courses of XELOX., Outcomes: No disease recurrence is reported in 12 months follow-up., Lessons: Aberrant pancreatic ductal adenocarcinoma in the stomach is a rare finding, however this pathology should be included in the differential diagnosis of gastric submucosal lesion causing pyloric stenosis., Competing Interests: The authors have no conflicts of interest to disclose., (Copyright © 2023 the Author(s). Published by Wolters Kluwer Health, Inc.)

Published
2023
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50. Picomolar fluorescent probes for compound affinity determination to carbonic anhydrase IX expressed in live cancer cells.

Author

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 HM, Kazokaitė-Adomaitienė J, Yaromina A, Čapkauskaitė E, Rinken A, Dudutienė V, Dubois LJ, and Matulis D

Subjects
Humans, Carbonic Anhydrase IX genetics, Carbonic Anhydrase IX metabolism, Fluorescent Dyes, Cell Line, Tumor, Antigens, Neoplasm metabolism, Sulfonamides pharmacology, Fluoresceins, Carbonic Anhydrases metabolism, Neoplasms
Abstract

Numerous human cancers, especially hypoxic solid tumors, express carbonic anhydrase IX (CAIX), a transmembrane protein with its catalytic domain located in the extracellular space. CAIX acidifies the tumor microenvironment, promotes metastases and invasiveness, and is therefore considered a promising anticancer target. We have designed a series of high affinity and high selectivity fluorescein-labeled compounds targeting CAIX to visualize and quantify CAIX expression in cancer cells. The competitive binding model enabled the determination of common CA inhibitors' dissociation constants for CAIX expressed in exponentially growing cancer cells. All tested sulfonamide compounds bound the proliferating cells with similar affinity as to recombinantly purified CAIX. The probes are applicable for the design of selective drug-like compounds for CAIX and the competition strategy could be applied to other drug targets., (© 2022. The Author(s).)

Published
2022
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