{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,6,29]],"date-time":"2025-06-29T05:10:01Z","timestamp":1751173801517,"version":"3.41.0"},"reference-count":15,"publisher":"Index Copernicus","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,12,20]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The mechanism of specific ligand binding by proteins is discussed using the PDZ domain complexing the pentapeptide. This process is critical for clustering the membrane ion channel. The traditional model based on the Beta-sheet extension by complexed pentapeptide is interpreted as a hydrophobic core extension supported by additional Beta-strand generated by complexed pentapeptide. The explanation is based on the fuzzy oil drop model applied to the crystal structure of PDZ-pentapeptide.<\/jats:p>","DOI":"10.1515\/bams-2017-0022","type":"journal-article","created":{"date-parts":[[2017,12,23]],"date-time":"2017-12-23T22:16:57Z","timestamp":1514067417000},"page":"175-178","source":"Crossref","is-referenced-by-count":0,"title":["Mechanism of ligand binding \u2013 PDZ domain taken as example"],"prefix":"10.5604","volume":"13","author":[{"given":"Dawid","family":"Du\u0142ak","sequence":"first","affiliation":[{"name":"Department of Bioinformatics and Telemedicine , Jagiellonian University \u2013 Medical College , Lazarza 16 , 31-530 Krakow , Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mateusz","family":"Banach","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Telemedicine , Jagiellonian University \u2013 Medical College , Lazarza 16 , 31-530 Krakow , Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zdzis\u0142aw","family":"Wi\u015bniowski","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Telemedicine , Jagiellonian University \u2013 Medical College , Lazarza 16 , 31-530 Krakow , Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Leszek","family":"Konieczny","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Telemedicine , Jagiellonian University \u2013 Medical College , Lazarza 16 , 31-530 Krakow , Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Irena","family":"Roterman","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Telemedicine , Jagiellonian University \u2013 Medical College , Lazarza 16 , 31-530 Krakow , Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"3689","published-online":{"date-parts":[[2017,12,23]]},"reference":[{"key":"2023010916555191014_j_bams-2017-0022_ref_001_w2aab3b7b2b1b6b1ab1b5b1Aa","doi-asserted-by":"crossref","unstructured":"Roche O, Kiyama R, Brooks CL 3rd. Ligand-protein database: linking protein-ligand complex structures to binding data. J Med Chem 2001;44:3592\u20138.1160612310.1021\/jm000467k","DOI":"10.1021\/jm000467k"},{"key":"2023010916555191014_j_bams-2017-0022_ref_002_w2aab3b7b2b1b6b1ab1b5b2Aa","doi-asserted-by":"crossref","unstructured":"Gao M, Skolnick J. The distribution of ligand-binding pockets around protein-protein interfaces suggests a general mechanism for pocket formation. Proc Natl Acad Sci U S A 2012;109:3784\u20139.2235514010.1073\/pnas.1117768109","DOI":"10.1073\/pnas.1117768109"},{"key":"2023010916555191014_j_bams-2017-0022_ref_003_w2aab3b7b2b1b6b1ab1b5b3Aa","doi-asserted-by":"crossref","unstructured":"Konieczny L, Brylinski M, Roterman I. Gauss-function-based model of hydrophobicity density in proteins. In Silico Biol 2006;6:15\u201322.16789910","DOI":"10.3233\/ISB-00217"},{"key":"2023010916555191014_j_bams-2017-0022_ref_004_w2aab3b7b2b1b6b1ab1b5b4Aa","doi-asserted-by":"crossref","unstructured":"Dygut J, Kalinowska B, Banach M, Piwowar M, Konieczny L, Roterman I. Structural interface forms and their involvement in stabilization of multidomain proteins or protein complexes. Int J Mol Sci 2016;17:1741.10.3390\/ijms17101741","DOI":"10.3390\/ijms17101741"},{"key":"2023010916555191014_j_bams-2017-0022_ref_005_w2aab3b7b2b1b6b1ab1b5b5Aa","doi-asserted-by":"crossref","unstructured":"Doyle DA, Lee A, Lewis J, Kim E, Sheng M, MacKinnon R. Crystal structures of a complexed and peptide-free membrane protein-binding domain: molecular basis of peptide recognition by PDZ. Cell 1996;85:1067\u201376.867411310.1016\/S0092-8674(00)81307-0","DOI":"10.1016\/S0092-8674(00)81307-0"},{"key":"2023010916555191014_j_bams-2017-0022_ref_006_w2aab3b7b2b1b6b1ab1b5b6Aa","doi-asserted-by":"crossref","unstructured":"Kalinowska B, Banach M, Konieczny L, Roterman I. Application of divergence entropy to characterize the structure of the hydrophobic core in DNA interacting proteins. Entropy 2015;17: 1477\u2013507.10.3390\/e17031477","DOI":"10.3390\/e17031477"},{"key":"2023010916555191014_j_bams-2017-0022_ref_007_w2aab3b7b2b1b6b1ab1b5b7Aa","doi-asserted-by":"crossref","unstructured":"Banach M, Kalinowska B, Konieczny L, Roterman I. Role of disulfide bonds in stabilizing the conformation of selected enzymes \u2013 an approach based on divergence entropy applied to the structure of hydrophobic core in proteins. Entropy 2016;18:67.10.3390\/e18030067","DOI":"10.3390\/e18030067"},{"key":"2023010916555191014_j_bams-2017-0022_ref_008_w2aab3b7b2b1b6b1ab1b5b8Aa","doi-asserted-by":"crossref","unstructured":"Banach M, Konieczny L, Roterman I. Ligand-binding site recognition. In: Roterman I, editor. Protein folding in silico \u2013 protein folding versus protein structure prediction. Cambridge, UK: Woodhead Publishing, 2012;79\u201394.","DOI":"10.1533\/9781908818256.79"},{"key":"2023010916555191014_j_bams-2017-0022_ref_009_w2aab3b7b2b1b6b1ab1b5b9Aa","doi-asserted-by":"crossref","unstructured":"Banach M, Konieczny L, Roterman I. Use of the \u201cfuzzy oil drop\u201d model to identify the complexation area in protein homodimers. In: Roterman I, editor. Protein folding in silico \u2013 protein folding versus protein structure prediction. Cambridge, UK: Woodhead Publishing, 2012:95\u2013122.","DOI":"10.1533\/9781908818256.95"},{"key":"2023010916555191014_j_bams-2017-0022_ref_010_w2aab3b7b2b1b6b1ab1b5c10Aa","doi-asserted-by":"crossref","unstructured":"Kullback S, Leibler RA. On information and sufficiency. Ann Math Stat 1951;22:79\u201386.10.1214\/aoms\/1177729694","DOI":"10.1214\/aoms\/1177729694"},{"key":"2023010916555191014_j_bams-2017-0022_ref_011_w2aab3b7b2b1b6b1ab1b5c11Aa","doi-asserted-by":"crossref","unstructured":"Konieczny L, Roterman I, Sp\u00f3lnik P. Systems biology. New York, Heidelberg, Dordrecht, London: Springer, 2014.","DOI":"10.1007\/978-3-319-01336-7"},{"key":"2023010916555191014_j_bams-2017-0022_ref_012_w2aab3b7b2b1b6b1ab1b5c12Aa","doi-asserted-by":"crossref","unstructured":"Biedermann F, Nau WM, Schneider H-J. The hydrophobic effect revisited \u2013 studies with supramolecular complexes imply high-energy water as a noncovaluent driving force. Angew Chem 2014;53:11158\u201371.10.1002\/anie.201310958","DOI":"10.1002\/anie.201310958"},{"key":"2023010916555191014_j_bams-2017-0022_ref_013_w2aab3b7b2b1b6b1ab1b5c13Aa","doi-asserted-by":"crossref","unstructured":"Ben-Naim A. Solvent-induced interactions: hydrophobic and hydrophilic phenomena. J Chem Phys 1989;90: 7412\u2013525.10.1063\/1.456221","DOI":"10.1063\/1.456221"},{"key":"2023010916555191014_j_bams-2017-0022_ref_014_w2aab3b7b2b1b6b1ab1b5c14Aa","doi-asserted-by":"crossref","unstructured":"Schutzius TM, Jung S, Maitra T, Graeber G, K\u00f6hme M, Poulikakos D. Spontaneous droplet trampolining on rigid superhydrophobic surfaces. Nature 2015;527:82\u20135.2653695910.1038\/nature15738","DOI":"10.1038\/nature15738"},{"key":"2023010916555191014_j_bams-2017-0022_ref_015_w2aab3b7b2b1b6b1ab1b5c15Aa","doi-asserted-by":"crossref","unstructured":"Banach M, Konieczny L, Roterman I. Why do antifreeze proteins require a solenoid? Biochimie 2018;144:74\u201384.2905480110.1016\/j.biochi.2017.10.011","DOI":"10.1016\/j.biochi.2017.10.011"}],"container-title":["Bio-Algorithms and Med-Systems"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.degruyter.com\/view\/j\/bams.2017.13.issue-4\/bams-2017-0022\/bams-2017-0022.xml","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/bams-2017-0022\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/bams-2017-0022\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,29]],"date-time":"2025-06-29T04:47:12Z","timestamp":1751172432000},"score":1,"resource":{"primary":{"URL":"https:\/\/bamsjournal.com\/resources\/html\/article\/details?id=617630"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,12,1]]},"references-count":15,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2017,11,15]]},"published-print":{"date-parts":[[2017,12,20]]}},"alternative-id":["10.1515\/bams-2017-0022"],"URL":"https:\/\/doi.org\/10.1515\/bams-2017-0022","relation":{},"ISSN":["1896-530X","1895-9091"],"issn-type":[{"type":"electronic","value":"1896-530X"},{"type":"print","value":"1895-9091"}],"subject":[],"published":{"date-parts":[[2017,12,1]]}}}