{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,25]],"date-time":"2025-07-25T10:17:40Z","timestamp":1753438660257},"publisher-location":"Berlin, Heidelberg","reference-count":29,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783540855569"},{"type":"electronic","value":"9783540855576"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"DOI":"10.1007\/978-3-540-85557-6_7","type":"book-chapter","created":{"date-parts":[[2008,8,27]],"date-time":"2008-08-27T14:23:10Z","timestamp":1219846990000},"page":"68-78","source":"Crossref","is-referenced-by-count":1,"title":["Molecular Models to Emulate Confinement Effects on the Internal Dynamics of Organophosphorous Hydrolase"],"prefix":"10.1007","author":[{"given":"Diego E. B.","family":"Gomes","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Roberto D.","family":"Lins","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pedro G.","family":"Pascutti","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tjerk P.","family":"Straatsma","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thereza A.","family":"Soares","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"key":"7_CR1","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1016\/j.cbpa.2005.02.014","volume":"9","author":"L. Cao","year":"2005","unstructured":"Cao, L.: Immobilized Enzymes: science or art. Current Opinion in Chemical Biology\u00a09, 217\u2013226 (2005)","journal-title":"Current Opinion in Chemical Biology"},{"key":"7_CR2","doi-asserted-by":"publisher","first-page":"11242","DOI":"10.1021\/ja026855o","volume":"124","author":"C. Lei","year":"2002","unstructured":"Lei, C., Shin, Y., Liu, J., Ackerman, E.J.: Entrapping enzyme in a functionalized nanoporous support. Journal of the American Chemical Society\u00a0124, 11242\u201311243 (2002)","journal-title":"Journal of the American Chemical Society"},{"key":"7_CR3","doi-asserted-by":"crossref","first-page":"13278","DOI":"10.1016\/S0021-9258(18)42207-7","volume":"267","author":"G.A. Omburo","year":"1992","unstructured":"Omburo, G.A., Kuo, J.M., Mullins, L.S., Raushel, F.M.: Characterization of the zinc binding site of bacterial phosphotriesterase. Journal of Biological Chemistry\u00a0267, 13278\u201313283 (1992)","journal-title":"Journal of Biological Chemistry"},{"key":"7_CR4","doi-asserted-by":"publisher","first-page":"627","DOI":"10.1042\/BJ20031861","volume":"380","author":"D. Rochu","year":"2004","unstructured":"Rochu, D., Renault, F., Viguille, N., Crouzier, D., Froment, M.T., Masson, P.: Contribution of the active-site metal cation to the catalytic activity and to the conformational stability of phosphotriesterase: temperature- and pH-dependence. Biochemical Journal\u00a0380, 627\u2013633 (2004)","journal-title":"Biochemical Journal"},{"key":"7_CR5","doi-asserted-by":"publisher","first-page":"288","DOI":"10.1016\/S1369-5274(02)00314-4","volume":"5","author":"F.M. Raushel","year":"2002","unstructured":"Raushel, F.M.: Bacterial detoxification of organophosphate nerve agents. Current Opinion in Microbiology\u00a05, 288\u2013295 (2002)","journal-title":"Current Opinion in Microbiology"},{"key":"7_CR6","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1002\/bip.10058","volume":"67","author":"E. Bismuto","year":"2002","unstructured":"Bismuto, E., Martelli, P.L., Maio, A.D., Mita, D.G., Irace, G., Casadio, R.: Effect of molecular confinement on internal enzyme dynamics: Frequency domain fluorometry and molecular dynamics simulation studies. Biopolymers\u00a067, 85\u201395 (2002)","journal-title":"Biopolymers"},{"key":"7_CR7","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1016\/j.jmb.2003.11.056","volume":"336","author":"D. Bolis","year":"2004","unstructured":"Bolis, D., Politou, A.S., Kelly, G., Pastore, A., Temussi, P.A.: Protein stability in nanocages: a novel approach for influencing protein stability by molecular confinement. Journal of Molecular Biology\u00a0336, 203\u2013212 (2004)","journal-title":"Journal of Molecular Biology"},{"key":"7_CR8","doi-asserted-by":"publisher","first-page":"250","DOI":"10.1110\/ps.36201","volume":"10","author":"D.K. Eggers","year":"2001","unstructured":"Eggers, D.K., Valentine, J.S.: Molecular confinement influences protein structure and enhances thermal stability. Protein Science\u00a010, 250\u2013261 (2001)","journal-title":"Protein Science"},{"key":"7_CR9","doi-asserted-by":"publisher","first-page":"1050","DOI":"10.1021\/nl070255b","volume":"7","author":"C. Lei","year":"2007","unstructured":"Lei, C., Shin, Y., Liu, J., Ackerman, E.J.: Synergetic effects of nanoporous support and urea on enzyme activity. Nano Letters\u00a07, 1050\u20131053 (2007)","journal-title":"Nano Letters"},{"key":"7_CR10","doi-asserted-by":"crossref","unstructured":"Lei, C., Soares, T.A., Shin, Y., Liu, J., Ackerman, E.J.: Enzyme specific activity in functionalized nanoporous supports Nanotechnology, vol.\u00a019, pp. 125102\u2013125111 (2008)","DOI":"10.1088\/0957-4484\/19\/12\/125102"},{"key":"7_CR11","doi-asserted-by":"publisher","first-page":"10430","DOI":"10.1073\/pnas.0608256104","volume":"104","author":"D. Lucent","year":"2007","unstructured":"Lucent, D., Vishal, V., Pande, V.S.: Protein folding under confinement: A role for solvent. Proceedings of the National Academy of Sciences USA\u00a0104, 10430\u201310434 (2007)","journal-title":"Proceedings of the National Academy of Sciences USA"},{"key":"7_CR12","first-page":"10577","volume":"276","author":"A.P. Minton","year":"2001","unstructured":"Minton, A.P.: The influence of macromolecular crowding on HIV-1 protease internal dynamics. Proceedings of the National Academy of Sciences USA\u00a0276, 10577\u201310580 (2001)","journal-title":"Proceedings of the National Academy of Sciences USA"},{"key":"7_CR13","doi-asserted-by":"publisher","first-page":"11195","DOI":"10.1073\/pnas.2035072100","volume":"100","author":"D. Thurmalai","year":"2003","unstructured":"Thurmalai, D., Klimov, D.K., Lorimer, G.H.: Caging helps proteins fold. Proceedings of the National Academy of Sciences USA\u00a0100, 11195\u201311197 (2003)","journal-title":"Proceedings of the National Academy of Sciences USA"},{"key":"7_CR14","doi-asserted-by":"publisher","first-page":"11289","DOI":"10.1021\/bi0155504","volume":"40","author":"H.X. Zhou","year":"2001","unstructured":"Zhou, H.X., Dill, K.A.: Stabilization of proteins in confined spaces. Biochemistry\u00a040, 11289\u201311293 (2001)","journal-title":"Biochemistry"},{"key":"7_CR15","doi-asserted-by":"publisher","first-page":"8019","DOI":"10.1073\/pnas.072220699","volume":"99","author":"D.K. Klimov","year":"2002","unstructured":"Klimov, D.K., Newfield, D., Thirumalai, D.: Simulations of beta-hairpin folding spherical pores using distributed computing. Proceedings of the National Academy of Sciences USA\u00a099, 8019\u20138024 (2002)","journal-title":"Proceedings of the National Academy of Sciences USA"},{"key":"7_CR16","doi-asserted-by":"publisher","first-page":"11367","DOI":"10.1073\/pnas.1831920100","volume":"100","author":"F. Takagi","year":"2003","unstructured":"Takagi, F., Koga, N., Takada, S.: How protein thermodynamics and folding mechanisms are altered by the chaperonin cage: Molecular simulations. Proceedings of the National Academy of Sciences USA\u00a0100, 11367\u201311372 (2003)","journal-title":"Proceedings of the National Academy of Sciences USA"},{"key":"7_CR17","doi-asserted-by":"publisher","first-page":"3224","DOI":"10.1529\/biophysj.105.071761","volume":"90","author":"D. Lu","year":"2006","unstructured":"Lu, D., Liu, Z., Wu, J.: Structural transitions of confined model proteins: molecular dynamics simulation and experimental validation. Biophysical Journal\u00a090, 3224\u20133238 (2006)","journal-title":"Biophysical Journal"},{"key":"7_CR18","doi-asserted-by":"publisher","first-page":"1767","DOI":"10.1529\/biophysj.105.071076","volume":"90","author":"N. Rathore","year":"2006","unstructured":"Rathore, N., Knotts-IV, T.A., de Pablo, J.J.: Confinement effects on the thermodynamics of protein folding: Monte Carlo simulations. Biophysical Journal\u00a090, 1767\u20131773 (2006)","journal-title":"Biophysical Journal"},{"key":"7_CR19","doi-asserted-by":"publisher","first-page":"1569","DOI":"10.1021\/ct700024h","volume":"3","author":"T.A. Soares","year":"2007","unstructured":"Soares, T.A., Osman, M., Straatsma, T.P.: Molecular dynamics of organophosphorous hydrolases bound to the nerve agent soman. Journal of Chemical Theory and Computation\u00a03, 1569\u20131579 (2007)","journal-title":"Journal of Chemical Theory and Computation"},{"key":"7_CR20","doi-asserted-by":"publisher","first-page":"30556","DOI":"10.1074\/jbc.M003852200","volume":"275","author":"M.M. Benning","year":"2000","unstructured":"Benning, M.M., Hong, S.B., Raushel, F.M., Holden, H.M.: The binding of substrate analogs to phosphotriesterase. Journal of Biological Chemistry\u00a0275, 30556\u201330560 (2000)","journal-title":"Journal of Biological Chemistry"},{"key":"7_CR21","doi-asserted-by":"publisher","first-page":"5179","DOI":"10.1021\/ja00124a002","volume":"117","author":"W.D. Cornell","year":"1995","unstructured":"Cornell, W.D., Cieplak, P., Bayly, C.I., Gould, I.R., Merz, K.M., Ferguson, D.M., Spellmeyer, D.C., Fox, T., Caldwell, W., Kollman, P.A.: A second generation force field for the simulation of proteins and nucleic acids. Journal of the American Chemical Society\u00a0117, 5179\u20135197 (1995)","journal-title":"Journal of the American Chemical Society"},{"key":"7_CR22","doi-asserted-by":"publisher","first-page":"10037","DOI":"10.1073\/pnas.181342398","volume":"98","author":"N.A. Baker","year":"2001","unstructured":"Baker, N.A., Sept, D., Joseph, S., Holst, M.J., McCammon, J.A.: Electrostatics of nanosystems: application to microtubules and the ribosome. Proceedings of the National Academy of Sciences USA\u00a098, 10037\u201310041 (2001)","journal-title":"Proceedings of the National Academy of Sciences USA"},{"key":"7_CR23","doi-asserted-by":"publisher","first-page":"186","DOI":"10.1002\/bip.10425","volume":"70","author":"G.I. Mustata","year":"2003","unstructured":"Mustata, G.I., Soares, T.A., Briggs, J.M.: Molecular dynamics studies of alanine racemase: A structural model for drug design. Biopolymers\u00a070, 186\u2013200 (2003)","journal-title":"Biopolymers"},{"key":"7_CR24","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1002\/bip.10252","volume":"65","author":"T.A. Soares","year":"2002","unstructured":"Soares, T.A., Lins, R.D., Straatsma, T.P., Briggs, J.M.: Internal dynamics and ionization states of the macrophage migration inhibitory factor: Comparison between wild-type and mutant forms. Biopolymers\u00a065, 313\u2013323 (2002)","journal-title":"Biopolymers"},{"key":"7_CR25","unstructured":"Bylaska, E.J., Jong, W.A.d., Kowalski, K., Straatsma, T.P., Valiev, M., Wang, D., Apr\u00e0, E., Windus, T.L., Hirata, S., Hackler, M.T., Zhao, Y., Fan, P.-D., Harrison, R.J., Dupuis, M., Smith, D.M.A., Nieplocha, J., Tipparaju, V., Krishnan, M., Auer, A.A., Nooijen, M., Brown, E., Cisneros, G., Fann, G.I., Fr\u00fccht, H., Garza, J., Hirao, K., Kendall, R., Nichols, J.A., Tsemekhman, K., Wolinsk, K., Anchell, J., Bernholdt, D., Borowski, P., Clark, T., Clerc, D., Dachsel, H., Deegan, M., Dyall, K., Elwood, D., Glendening, E., Gutowski, M., Hess, A., Jaffe, J., Johnson, B., Ju, J., Kobayashi, R., Kutteh, R., Lin, Z., Littlefield, R., Long, X., Meng, B., Nakajima, T., Niu, S., Pollack, L., Rosing, M., Sandrone, G., Stave, M., Taylor, H., Thomas, G., Lenthe, J.v., Wong, A., Zhang, Z.: NWChem, A Computational Chemistry Package for Parallel Computers, Version 5.0. Pacific Northwest National Laboratory, Richland, Washington 99352-0999, USA (A modified version) (2006)"},{"key":"7_CR26","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1007\/s008940100045","volume":"7","author":"E. Lindahl","year":"2001","unstructured":"Lindahl, E., Hess, B., Spoel, D.v.d.: GROMACS 3.0: A package for molecular simulation and trajectory analysis. Journal of Molecular Modeling\u00a07, 306\u2013317 (2001)","journal-title":"Journal of Molecular Modeling"},{"key":"7_CR27","doi-asserted-by":"publisher","first-page":"2696","DOI":"10.1103\/PhysRevLett.68.2696","volume":"68","author":"A.E. Garc\u00eda","year":"1992","unstructured":"Garc\u00eda, A.E.: Large-amplitude nonlinear motions in proteins. Physical Review Letters\u00a068, 2696\u20132699 (1992)","journal-title":"Physical Review Letters"},{"key":"7_CR28","doi-asserted-by":"publisher","first-page":"3055","DOI":"10.1021\/cr050312q","volume":"106","author":"D.D. Boehr","year":"2006","unstructured":"Boehr, D.D., Dyson, H.J., Wright, P.E.: An NMR Perspective on Enzyme Dynamics. Chemical Reviews\u00a0106, 3055\u20133079 (2006)","journal-title":"Chemical Reviews"},{"key":"7_CR29","doi-asserted-by":"publisher","first-page":"4282","DOI":"10.1073\/pnas.0407499102","volume":"102","author":"S.T. Whitten","year":"2005","unstructured":"Whitten, S.T., Garcia-Moreno, E.B., Hilser, V.J.: Local conformational fluctuations can modulate the coupling between proton binding and global structural transitions in proteins. Proceedings of the National Academy of Sciences USA\u00a0102, 4282\u20134287 (2005)","journal-title":"Proceedings of the National Academy of Sciences USA"}],"container-title":["Lecture Notes in Computer Science","Advances in Bioinformatics and Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-540-85557-6_7.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,15]],"date-time":"2021-09-15T15:27:11Z","timestamp":1631719631000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-540-85557-6_7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[null]]},"ISBN":["9783540855569","9783540855576"],"references-count":29,"URL":"https:\/\/doi.org\/10.1007\/978-3-540-85557-6_7","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[]}}