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For: Likić VA, Juranić N, Macura S, Prendergast FG. A "structural" water molecule in the family of fatty acid binding proteins. Protein Sci 2000;9:497-504. [PMID: 10752611 PMCID: PMC2144571 DOI: 10.1110/ps.9.3.497] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Number Cited by Other Article(s)
1
Predicting Conserved Water Molecules in Binding Sites of Proteins Using Machine Learning Methods and Combining Features. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022;2022:5104464. [PMID: 36226242 PMCID: PMC9550495 DOI: 10.1155/2022/5104464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/15/2022] [Indexed: 11/17/2022]
2
Meloche R, Vučković I, Mishra PK, Macura S. Transverse relaxation in fixed tissue: Influence of temperature and resolution on image contrast in magnetic resonance microscopy. NMR IN BIOMEDICINE 2022;35:e4747. [PMID: 35467776 DOI: 10.1002/nbm.4747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 06/14/2023]
3
Kumar SU, Priya Doss CG. Residue interaction networks of K-Ras protein with water molecules identifies the potential role of switch II and P-loop. Comput Biol Med 2021;135:104597. [PMID: 34237589 DOI: 10.1016/j.compbiomed.2021.104597] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/01/2021] [Accepted: 06/17/2021] [Indexed: 02/07/2023]
4
Blaber M. Conserved buried water molecules enable the β-trefoil architecture. Protein Sci 2020;29:1794-1802. [PMID: 32542709 DOI: 10.1002/pro.3899] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/12/2020] [Accepted: 06/12/2020] [Indexed: 12/24/2022]
5
Lei C, Li M, Zhang M, Wang S, Tian J, Wen J, Li Y. Cloning, molecular characterization, and nutritional regulation of fatty acid-binding protein family genes in gold pompanos (Trachinotus ovatus). Comp Biochem Physiol B Biochem Mol Biol 2020;246-247:110463. [PMID: 32526355 DOI: 10.1016/j.cbpb.2020.110463] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 04/05/2020] [Accepted: 05/11/2020] [Indexed: 11/26/2022]
6
Ruskamo S, Nieminen T, Kristiansen CK, Vatne GH, Baumann A, Hallin EI, Raasakka A, Joensuu P, Bergmann U, Vattulainen I, Kursula P. Molecular mechanisms of Charcot-Marie-Tooth neuropathy linked to mutations in human myelin protein P2. Sci Rep 2017;7:6510. [PMID: 28747762 PMCID: PMC5529448 DOI: 10.1038/s41598-017-06781-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 06/16/2017] [Indexed: 02/06/2023]  Open
7
Hunter NH, Bakula BC, Bruce CD. Molecular dynamics simulations of apo and holo forms of fatty acid binding protein 5 and cellular retinoic acid binding protein II reveal highly mobile protein, retinoic acid ligand, and water molecules. J Biomol Struct Dyn 2017;36:1893-1907. [PMID: 28566049 DOI: 10.1080/07391102.2017.1337591] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
8
Howard EI, Guillot B, Blakeley MP, Haertlein M, Moulin M, Mitschler A, Cousido-Siah A, Fadel F, Valsecchi WM, Tomizaki T, Petrova T, Claudot J, Podjarny A. High-resolution neutron and X-ray diffraction room-temperature studies of an H-FABP-oleic acid complex: study of the internal water cluster and ligand binding by a transferred multipolar electron-density distribution. IUCRJ 2016;3:115-26. [PMID: 27006775 PMCID: PMC4775160 DOI: 10.1107/s2052252515024161] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/16/2015] [Indexed: 05/24/2023]
9
Statistical survey of the buried waters in the Protein Data Bank. Amino Acids 2015;48:193-202. [PMID: 26315961 DOI: 10.1007/s00726-015-2064-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 07/29/2015] [Indexed: 12/18/2022]
10
Kaieda S, Halle B. Time Scales of Conformational Gating in a Lipid-Binding Protein. J Phys Chem B 2015;119:7957-67. [DOI: 10.1021/acs.jpcb.5b03214] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
11
Ruskamo S, Yadav RP, Sharma S, Lehtimäki M, Laulumaa S, Aggarwal S, Simons M, Bürck J, Ulrich AS, Juffer AH, Kursula I, Kursula P. Atomic resolution view into the structure-function relationships of the human myelin peripheral membrane protein P2. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014;70:165-76. [PMID: 24419389 PMCID: PMC3919267 DOI: 10.1107/s1399004713027910] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 10/11/2013] [Indexed: 01/03/2023]
12
Insight of Endo-1,4-Xylanase II from Trichoderma reesei: Conserved Water-Mediated H-Bond and Ion Pairs Interactions. Protein J 2013;32:649-56. [DOI: 10.1007/s10930-013-9528-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
13
Prakash P, Sayyed-Ahmad A, Gorfe AA. The role of conserved waters in conformational transitions of Q61H K-ras. PLoS Comput Biol 2012;8:e1002394. [PMID: 22359497 PMCID: PMC3280954 DOI: 10.1371/journal.pcbi.1002394] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 01/04/2012] [Indexed: 12/30/2022]  Open
14
Dileep KV, Tintu I, Vinod NV, Saliha PP, Sadasivan C. Role of invariant water molecules in retaining the active site geometry of β-lactamase: a molecular dynamics simulation study. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2011.590984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
15
Majava V, Polverini E, Mazzini A, Nanekar R, Knoll W, Peters J, Natali F, Baumgärtel P, Kursula I, Kursula P. Structural and functional characterization of human peripheral nervous system myelin protein P2. PLoS One 2010;5:e10300. [PMID: 20421974 PMCID: PMC2858655 DOI: 10.1371/journal.pone.0010300] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Accepted: 03/24/2010] [Indexed: 11/19/2022]  Open
16
Franzoni L, Cavazzini D, Rossi GL, Lücke C. New insights on the protein-ligand interaction differences between the two primary cellular retinol carriers. J Lipid Res 2009;51:1332-43. [PMID: 19965581 DOI: 10.1194/jlr.m002006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
17
Insight into the interaction sites between fatty acid binding proteins and their ligands. J Mol Model 2009;16:929-38. [DOI: 10.1007/s00894-009-0599-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Accepted: 09/20/2009] [Indexed: 10/20/2022]
18
Hajjar E, Dejaegere A, Reuter N. Challenges in pKa Predictions for Proteins: The case of Asp213 in Human Proteinase 3. J Phys Chem A 2009;113:11783-92. [DOI: 10.1021/jp902930u] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
19
Grishin AV, Alexeevsky AV, Spirin SA, Karyagina AS. Conserved structural features of ETS domain-DNA complexes. Mol Biol 2009. [DOI: 10.1134/s002689330904013x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
20
Szep S, Park S, Boder ET, Van Duyne GD, Saven JG. Structural coupling between FKBP12 and buried water. Proteins 2009;74:603-11. [PMID: 18704951 PMCID: PMC2629809 DOI: 10.1002/prot.22176] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
21
Levin LBA, Nachliel E, Gutman M, Tsfadia Y. Molecular dynamics study of the interaction between fatty acid binding proteins with palmitate mini-micelles. Mol Cell Biochem 2009;326:29-33. [DOI: 10.1007/s11010-008-0010-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2007] [Accepted: 06/10/2008] [Indexed: 11/29/2022]
22
Ricchiuto P, Rocco AG, Gianazza E, Corrada D, Beringhelli T, Eberini I. Structural and dynamic roles of permanent water molecules in ligand molecular recognition by chicken liver bile acid binding protein. J Mol Recognit 2008;21:348-54. [DOI: 10.1002/jmr.908] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
23
Damjanović A, Schlessman JL, Fitch CA, García AE, García-Moreno E B. Role of flexibility and polarity as determinants of the hydration of internal cavities and pockets in proteins. Biophys J 2007;93:2791-804. [PMID: 17604315 PMCID: PMC1989710 DOI: 10.1529/biophysj.107.104182] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
24
Damjanović A, García-Moreno B, Lattman EE, García AE. Molecular dynamics study of water penetration in staphylococcal nuclease. Proteins 2006;60:433-49. [PMID: 15971206 DOI: 10.1002/prot.20486] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
25
Park S, Saven JG. Statistical and molecular dynamics studies of buried waters in globular proteins. Proteins 2006;60:450-63. [PMID: 15937899 DOI: 10.1002/prot.20511] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
26
Bottoms CA, White TA, Tanner JJ. Exploring structurally conserved solvent sites in protein families. Proteins 2006;64:404-21. [PMID: 16700049 DOI: 10.1002/prot.21014] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
27
Friedman R, Nachliel E, Gutman M. Fatty acid binding proteins: same structure but different binding mechanisms? Molecular dynamics simulations of intestinal fatty acid binding protein. Biophys J 2005;90:1535-45. [PMID: 16361342 PMCID: PMC1367305 DOI: 10.1529/biophysj.105.071571] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
28
Prévost M. Dynamics of water molecules buried in cavities of apolipoprotein E studied by molecular dynamics simulations and continuum electrostatic calculations. Biopolymers 2004;75:196-207. [PMID: 15356873 DOI: 10.1002/bip.20116] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
29
Modig K, Kurian E, Prendergast FG, Halle B. Water and urea interactions with the native and unfolded forms of a beta-barrel protein. Protein Sci 2004;12:2768-81. [PMID: 14627737 PMCID: PMC2366985 DOI: 10.1110/ps.03262603] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
30
Modig K, Rademacher M, Lücke C, Halle B. Water dynamics in the large cavity of three lipid-binding proteins monitored by (17)O magnetic relaxation dispersion. J Mol Biol 2003;332:965-77. [PMID: 12972265 DOI: 10.1016/s0022-2836(03)00968-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
31
Jakobsson E, Alvite G, Bergfors T, Esteves A, Kleywegt GJ. The crystal structure of Echinococcus granulosus fatty-acid-binding protein 1. BIOCHIMICA ET BIOPHYSICA ACTA 2003;1649:40-50. [PMID: 12818189 DOI: 10.1016/s1570-9639(03)00151-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
32
Falconi M, Brunelli M, Pesce A, Ferrario M, Bolognesi M, Desideri A. Static and dynamic water molecules in Cu,Zn superoxide dismutase. Proteins 2003;51:607-15. [PMID: 12784219 DOI: 10.1002/prot.10377] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
33
Rigden DJ, Lamani E, Mello LV, Littlejohn JE, Jedrzejas MJ. Insights into the catalytic mechanism of cofactor-independent phosphoglycerate mutase from X-ray crystallography, simulated dynamics and molecular modeling. J Mol Biol 2003;328:909-20. [PMID: 12729763 DOI: 10.1016/s0022-2836(03)00350-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
34
Lücke C, Huang S, Rademacher M, Rüterjans H. New insights into intracellular lipid binding proteins: The role of buried water. Protein Sci 2002;11:2382-92. [PMID: 12237460 PMCID: PMC2373707 DOI: 10.1110/ps.0212902] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
35
Bottoms CA, Smith PE, Tanner JJ. A structurally conserved water molecule in Rossmann dinucleotide-binding domains. Protein Sci 2002;11:2125-37. [PMID: 12192068 PMCID: PMC2373605 DOI: 10.1110/ps.0213502] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
36
Bakowies D, van Gunsteren WF. Simulations of apo and holo-fatty acid binding protein: structure and dynamics of protein, ligand and internal water. J Mol Biol 2002;315:713-36. [PMID: 11812142 DOI: 10.1006/jmbi.2001.5202] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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