{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T12:53:46Z","timestamp":1791377626104,"version":"4.3.2"},"reference-count":46,"publisher":"Springer Science and Business Media LLC","issue":"11","license":[{"start":{"date-parts":[[2012,7,4]],"date-time":"2012-07-04T00:00:00Z","timestamp":1341360000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J Mol Model"],"published-print":{"date-parts":[[2013,11]]},"DOI":"10.1007\/s00894-012-1507-z","type":"journal-article","created":{"date-parts":[[2012,7,3]],"date-time":"2012-07-03T02:46:00Z","timestamp":1341283560000},"page":"4701-4711","source":"Crossref","is-referenced-by-count":44,"title":["Interaction of organic solvents with protein structures at protein-solvent interface"],"prefix":"10.1007","volume":"19","author":[{"given":"Morteza","family":"Khabiri","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Babak","family":"Minofar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan","family":"Brezovsk\u00fd","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ji\u0159\u00ed","family":"Damborsk\u00fd","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rudiger","family":"Ettrich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2012,7,4]]},"reference":[{"key":"1507_CR1","first-page":"641","volume":"58","author":"S Fetzner","year":"1994","unstructured":"Fetzner S, Lingens F (1994) Bacterial dehalogenases: biochemistry, genetics, and biotechnological applications. Microbiol Mol Biol Rev 58:641\u2013685","journal-title":"Microbiol Mol Biol Rev"},{"key":"1507_CR2","doi-asserted-by":"crossref","first-page":"2681","DOI":"10.1002\/etc.5620201205","volume":"20","author":"J Damborsk\u00fd","year":"2001","unstructured":"Damborsk\u00fd J, Rorije E, Jesensk\u00e1 A, Nagata Y, Klopman G, Peijnenburg WJ (2001) Structure-specificity relationships for haloalkane dehalogenases. Environ Toxicol Chem 20:2681\u20132689","journal-title":"Environ Toxicol Chem"},{"key":"1507_CR3","doi-asserted-by":"crossref","first-page":"2339","DOI":"10.1021\/es00009a028","volume":"29","author":"G Stucki","year":"1995","unstructured":"Stucki G, Thueer M (1995) Experiences of a large-scale application of 1,2-dichloroethane degradation microorganisms for groundwater treatment. Environ Sci Technol 29:2339\u20132345","journal-title":"Environ Sci Technol"},{"key":"1507_CR4","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1093\/protein\/5.3.197","volume":"5","author":"DL Ollis","year":"1992","unstructured":"Ollis DL, Cheah E, Cygler M, Dijkstra B, Frolow F, Franken SM, Harel M, Remington SJ, Silman I, Schrag J (1992) The alpha\/beta hydrolase fold. Protein Eng 5:197\u2013211","journal-title":"Protein Eng"},{"key":"1507_CR5","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1016\/j.cbpa.2004.02.012","volume":"8","author":"DB Janssen","year":"2004","unstructured":"Janssen DB (2004) Evolving haloalkane dehalogenases. Curr Opin Chem Biol 8:150\u2013159","journal-title":"Curr Opin Chem Biol"},{"key":"1507_CR6","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1002\/prot.21313","volume":"67","author":"E Chovancova","year":"2007","unstructured":"Chovancova E, Kosinski J, Bujnicki JM, Damborsky J (2007) Phylogenetic analysis of haloalkane dehalogenases. Proteins 67:305\u2013316","journal-title":"Proteins"},{"key":"1507_CR7","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1080\/07388550600851423","volume":"26","author":"J Kaur","year":"2006","unstructured":"Kaur J, Sharma R (2006) Directed evolution: an approach to engineer enzymes. Crit Rev Biotechnol 26:165\u2013199","journal-title":"Crit Rev Biotechnol"},{"key":"1507_CR8","doi-asserted-by":"crossref","unstructured":"Prokop Z, Sato Y, Brezovsky J, Mozga T, Chaloupkova R, Koudelakova T, Jerabek P, Stepankova V, Natsume R, van Leeuwen JG, Janssen DB, Florian J, Nagata Y, Senda T, Damborsky J (2010) Enantioselectivity of haloalkane dehalogenases and its modulation by surface loop engineering. Angew Chem Int Ed Engl 49:6111\u20136115","DOI":"10.1002\/anie.201001753"},{"key":"1507_CR9","doi-asserted-by":"crossref","first-page":"16105","DOI":"10.1021\/bi9913855","volume":"38","author":"J Newman","year":"1999","unstructured":"Newman J, Peat TS, Richard R, Kan L, Swanson PE, Affholter JA, Holmes IH, Schindler JF, Unkefer CJ, Terwilliger TC (1999) Haloalkane dehalogenases: structure of a Rhodococcus enzyme. Biochemistry 38:16105\u201316114","journal-title":"Biochemistry"},{"key":"1507_CR10","doi-asserted-by":"crossref","first-page":"14082","DOI":"10.1021\/bi001539c","volume":"39","author":"J Marek","year":"2000","unstructured":"Marek J, V\u00e9vodov\u00e1 J, Smatanov\u00e1 IK, Nagata Y, Svensson LA, Newman J, Takagi M, Damborsk\u00fd J (2000) Crystal structure of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26. Biochemistry 39:14082\u201314086","journal-title":"Biochemistry"},{"key":"1507_CR11","doi-asserted-by":"crossref","unstructured":"Chaloupkova R, Sykorova J, Prokop Z, Jesenska A, Monincova M, Pavlova M, Tsuda M, Nagata Y, Damborsky J (2003) Modification of activity and specificity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26 by engineering of its entrance tunnel. J Biol Chem 278:52622\u201352628","DOI":"10.1074\/jbc.M306762200"},{"key":"1507_CR12","doi-asserted-by":"crossref","unstructured":"\u0160t\u011bp\u00e1nkov\u00e1 V, Khabiri M, Brezovsk\u00fd J, Pavelka A, S\u00fdkora J, Amaro M, Minofar B, Prokop Z, Hof M, Ettrich R, Damborsk\u00fd J, Chaloupkov\u00e1 R (2012) Expansion of tunnels and active-site cavities influence catalytic activity of haloalkane dehalogenases in organic co-solvents. submitted","DOI":"10.1002\/cbic.201200733"},{"key":"1507_CR13","doi-asserted-by":"crossref","first-page":"1287","DOI":"10.1098\/rstb.2004.1505","volume":"359","author":"PJ Halling","year":"2004","unstructured":"Halling PJ (2004) What can we learn by studying enzymes in non-aqueous media? Philos Trans R Soc Lond B Biol Sci 359:1287\u20131296","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"key":"1507_CR14","first-page":"220","volume-title":"The hydrophobic effect: formation of micelles and biological membranes","author":"T Charles","year":"1973","unstructured":"Charles T (1973) The hydrophobic effect: formation of micelles and biological membranes. John Wiley & Sons, New York, p 220"},{"key":"1507_CR15","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1038\/35051719","volume":"409","author":"AM Klibanov","year":"2001","unstructured":"Klibanov AM (2001) Improving enzymes by using them in organic solvents. Nature 409:241\u2013246","journal-title":"Nature"},{"key":"1507_CR16","first-page":"271","volume":"42","author":"S Torres","year":"2004","unstructured":"Torres S, Castro G (2004) Non-aqueous biocatalysis in homogeneous solvent systems. Food Technol Biotechnol 42:271\u2013277","journal-title":"Food Technol Biotechnol"},{"key":"1507_CR17","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1016\/0005-2744(78)90226-7","volume":"525","author":"P Maurel","year":"1978","unstructured":"Maurel P, Douzou P, Waldmann J, Yonetani T (1978) Enzyme behaviour and molecular environment. The effects of ionic strength, detergents, linear polyanions and phospholipids on the pH profile of soluble cytochrome oxidase. Biochim Biophys Acta 525:314\u2013324","journal-title":"Biochim Biophys Acta"},{"key":"1507_CR18","doi-asserted-by":"crossref","first-page":"812","DOI":"10.1529\/biophysj.104.041269","volume":"87","author":"L Yang","year":"2004","unstructured":"Yang L, Dordick JS, Garde S (2004) Hydration of enzyme in nonaqueous media is consistent with solvent dependence of its activity. Biophys J 87:812\u2013821","journal-title":"Biophys J"},{"key":"1507_CR19","doi-asserted-by":"crossref","first-page":"1628","DOI":"10.1016\/S0006-3495(03)74972-8","volume":"84","author":"CM Soares","year":"2003","unstructured":"Soares CM, Teixeira VH, Baptista AM (2003) Protein structure and dynamics in nonaqueous solvents: insights from molecular dynamics simulation studies. Biophys J 84:1628\u20131641","journal-title":"Biophys J"},{"key":"1507_CR20","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1016\/j.copbio.2005.10.004","volume":"16","author":"EP Hudson","year":"2005","unstructured":"Hudson EP, Eppler RK, Clark DS (2005) Biocatalysis in semi-aqueous and nearly anhydrous conditions. Curr Opin Biotechnol 16:637\u2013643","journal-title":"Curr Opin Biotechnol"},{"key":"1507_CR21","doi-asserted-by":"crossref","first-page":"2424","DOI":"10.1111\/j.1742-4658.2007.05781.x","volume":"274","author":"NM Mica\u00ealo","year":"2007","unstructured":"Mica\u00ealo NM, Soares CM (2007) Modeling hydration mechanisms of enzymes in nonpolar and polar organic solvents. FEBS J 274:2424\u20132436","journal-title":"FEBS J"},{"key":"1507_CR22","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1016\/j.tibtech.2007.10.007","volume":"26","author":"AL Serdakowski","year":"2008","unstructured":"Serdakowski AL, Dordick JS (2008) Enzyme activation for organic solvents made easy. Trends Biotechnol 26:48\u201354","journal-title":"Trends Biotechnol"},{"key":"1507_CR23","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1016\/j.sbi.2007.03.006","volume":"17","author":"FE Boas","year":"2007","unstructured":"Boas FE, Harbury PB (2007) Potential energy functions for protein design. Curr Opin Struct Biol 17:199\u2013204","journal-title":"Curr Opin Struct Biol"},{"key":"1507_CR24","doi-asserted-by":"crossref","first-page":"235103","DOI":"10.1063\/1.3430628","volume":"132","author":"GN Patargias","year":"2010","unstructured":"Patargias GN, Harris SA, Harding JH (2010) A demonstration of the inhomogeneity of the local dielectric response of proteins by molecular dynamics simulations. J Chem Phys 132:235103\u2013235111","journal-title":"J Chem Phys"},{"key":"1507_CR25","volume-title":"Gaussian 03","author":"MJ Frisch","year":"2004","unstructured":"Frisch MJ et al. (2004) Gaussian 03. Gaussian Inc, Wallingford"},{"key":"1507_CR26","doi-asserted-by":"crossref","first-page":"1433","DOI":"10.1590\/S0103-50532008000700031","volume":"19","author":"BAC Horta","year":"2008","unstructured":"Horta BAC, Alencastro RBD, Ribeiro AAST (2008) MKTOP: a program for automatic construction of molecular topologies. J Braz Chem Soc 19:1433\u20131435","journal-title":"J Braz Chem Soc"},{"key":"1507_CR27","doi-asserted-by":"crossref","first-page":"977","DOI":"10.1002\/jcc.10051","volume":"23","author":"TC Bruice","year":"2002","unstructured":"Bruice TC, Kahn K (2002) Parameterization of OPLS-AA force field for the conformational analysis of macrocyclic polyketides. J Comput Chem 23:977\u2013996","journal-title":"J Comput Chem"},{"key":"1507_CR28","doi-asserted-by":"crossref","first-page":"11225","DOI":"10.1021\/ja9621760","volume":"118","author":"WL Jorgensen","year":"1996","unstructured":"Jorgensen WL, Maxwell DS, Tirado-Rives J (1996) Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 118:11225\u201311236","journal-title":"J Am Chem Soc"},{"key":"1507_CR29","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1016\/0301-0104(94)00320-A","volume":"190","author":"YP Puhovski","year":"1995","unstructured":"Puhovski YP, Rode BM (1995) Structure and dynamics of liquid formamide. Chem Phys 190:61\u201382","journal-title":"Chem Phys"},{"key":"1507_CR30","doi-asserted-by":"crossref","unstructured":"Kulakova AN, Larkin MJ, Kulakov LA (1997) The plasmid-located haloalkane dehalogenase gene from Rhodococcus rhodochrous NCIMB 13064. Microbiology 143:109\u2013115","DOI":"10.1099\/00221287-143-1-109"},{"key":"1507_CR31","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1002\/prot.10104","volume":"47","author":"E Krieger","year":"2002","unstructured":"Krieger E, Koraimann G, Vriend G (2002) Increasing the precision of comparative models with YASARA NOVA\u2013a self-parameterizing force field. Proteins 47:393\u2013402","journal-title":"Proteins"},{"key":"1507_CR32","doi-asserted-by":"crossref","first-page":"6269","DOI":"10.1021\/j100308a038","volume":"91","author":"HJC Berendsen","year":"1987","unstructured":"Berendsen HJC, Grigera JR, Straatsma TP (1987) The missing term in effective pair potential. J Phys Chem 91:6269\u20136271","journal-title":"J Phys Chem"},{"key":"1507_CR33","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/0010-4655(95)00042-E","volume":"91","author":"HJC Berendsen","year":"1995","unstructured":"Berendsen HJC, van der Spoel D, van Drunen R (1995) GROMACS: a message-passing parallel molecular dynamics implementation. Comput Phys Commun 91:43\u201356","journal-title":"Comput Phys Commun"},{"key":"1507_CR34","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1007\/s008940100045","volume":"7","author":"E Lindahl","year":"2001","unstructured":"Lindahl E, Hess B, van der Spoel D (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 7:306\u2013317","journal-title":"J Mol Model"},{"key":"1507_CR35","doi-asserted-by":"crossref","first-page":"3684","DOI":"10.1063\/1.448118","volume":"81","author":"HJC Berendsen","year":"1984","unstructured":"Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684\u20133690","journal-title":"J Chem Phys"},{"key":"1507_CR36","doi-asserted-by":"crossref","first-page":"8577","DOI":"10.1063\/1.470117","volume":"103","author":"U Essmann","year":"1995","unstructured":"Essmann U, Perera L, Berkowitz M (1995) A smooth particle mesh Ewald method. J Chem Phys 103:8577\u20138592","journal-title":"J Chem Phys"},{"key":"1507_CR37","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1002\/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H","volume":"18","author":"B Hess","year":"1997","unstructured":"Hess B, Bekker H, Berendsen HJC, Fraaije JG (1997) LINCS: a linear constraint solver for molecular simulations. J Comput Chem 18:1463\u20131742","journal-title":"J Comput Chem"},{"key":"1507_CR38","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","volume":"14","author":"W Humphrey","year":"1996","unstructured":"Humphrey W, Dalke A, Schulten K (1996) VMD-visual molecular dynamics. J Mol Graph 14:33\u201338","journal-title":"J Mol Graph"},{"key":"1507_CR39","volume-title":"The PyMOL molecular graphics system","author":"WL DeLano","year":"2002","unstructured":"DeLano WL (2002) The PyMOL molecular graphics system. DeLano Scientific, San Carlos"},{"issue":"3","key":"1507_CR40","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1002\/(SICI)1097-0134(199703)27:3<395::AID-PROT7>3.0.CO;2-C","volume":"27","author":"H Kovacs","year":"1997","unstructured":"Kovacs H, Mark AE, van Gunsteren WF (1997) Solvent structure at a hydrophobic protein surface. Proteins 27:395\u2013404","journal-title":"Proteins"},{"key":"1507_CR41","doi-asserted-by":"crossref","first-page":"1123","DOI":"10.1002\/(SICI)1097-461X(1997)63:6<1123::AID-QUA5>3.0.CO;2-Z","volume":"63","author":"J Oberbrodhage","year":"1997","unstructured":"Oberbrodhage J, Morgner H, Tapia O, Siegbahn HOG (1997) Molecular dynamics simulation of the free surface of liquid formamide. Int J Quantum Chem 63:1123\u20131131","journal-title":"Int J Quantum Chem"},{"key":"1507_CR42","doi-asserted-by":"crossref","first-page":"2942","DOI":"10.1039\/b504133c","volume":"7","author":"G Andersson","year":"2007","unstructured":"Andersson G (2007) Angle resolved ion scattering spectroscopy at surfaces of pure liquids: topography and orientation of molecules. Phys Chem Chem Phys 7:2942\u20132947","journal-title":"Phys Chem Chem Phys"},{"key":"1507_CR43","doi-asserted-by":"crossref","first-page":"8053","DOI":"10.1021\/jp050188e","volume":"109","author":"H Chen","year":"2005","unstructured":"Chen H, Gan W, Wu BH, Wu D, Guo Y, Wang HF (2005) Determination of structure and energetics for Gibbs surface adsorption layers of binary liquid mixture 1. Acetone\u2009+\u2009water. J Phys Chem B 109:8053\u20138063","journal-title":"J Phys Chem B"},{"key":"1507_CR44","doi-asserted-by":"crossref","first-page":"8452","DOI":"10.1021\/ja960884f","volume":"118","author":"T Simonson","year":"1996","unstructured":"Simonson T, Brooks LC (1996) Charge screening and the dielectric constant of proteins: Insights from molecular dynamics. J Am Chem Soc 118:8452\u20138458","journal-title":"J Am Chem Soc"},{"key":"1507_CR45","doi-asserted-by":"crossref","first-page":"5516","DOI":"10.1021\/ja060156k","volume":"128","author":"S Kataoka","year":"2006","unstructured":"Kataoka S (2006) Cremer PS Probing molecular structure at interfaces for comparison with bulk solution behavior: water\/2-propanol mixtures monitored by vibrational sum frequency spectroscopy. J Am Chem Soc 128:5516\u20135522","journal-title":"J Am Chem Soc"},{"key":"1507_CR46","doi-asserted-by":"crossref","unstructured":"Chovancov\u00e1 E, Pavelka A, Bene\u0161 P, Strnad O, Brezovsk\u00fd J, Kozl\u00edkov\u00e1 B, Gora A, \u0160ustr V, Klva\u0148a M, Medek P, Biedermannov\u00e1 L, Sochor J, Damborsk\u00fd J (2012) CAVER 3.0: a tool for analysis of transport pathways in dynamic protein structures. PLOS Computational Biology, under review","DOI":"10.1371\/journal.pcbi.1002708"}],"container-title":["Journal of Molecular Modeling"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s00894-012-1507-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s00894-012-1507-z\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s00894-012-1507-z","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,4,26]],"date-time":"2024-04-26T09:40:31Z","timestamp":1714124431000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s00894-012-1507-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,7,4]]},"references-count":46,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2013,11]]}},"alternative-id":["1507"],"URL":"https:\/\/doi.org\/10.1007\/s00894-012-1507-z","relation":{},"ISSN":["1610-2940","0948-5023"],"issn-type":[{"value":"1610-2940","type":"print"},{"value":"0948-5023","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,7,4]]}}}