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For: Brylinski M, Konieczny L, Roterman I. Hydrophobic collapse in (in silico) protein folding. Comput Biol Chem 2006;30:255-67. [PMID: 16798094 DOI: 10.1016/j.compbiolchem.2006.04.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2005] [Revised: 04/06/2006] [Accepted: 04/06/2006] [Indexed: 11/28/2022]
Number Cited by Other Article(s)
1
Zheng X, Zou B, Cai W, Xu X, Du M, Na X, Zhu B, Wu C. Heat-induced agglomeration of water-soluble cod proteins toward gelled structures. Int J Biol Macromol 2024;260:129418. [PMID: 38232880 DOI: 10.1016/j.ijbiomac.2024.129418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/19/2023] [Accepted: 01/09/2024] [Indexed: 01/19/2024]
2
Colberg M, Schofield J. Diffusive dynamics of a model protein chain in solution. J Chem Phys 2024;160:075101. [PMID: 38375905 DOI: 10.1063/5.0182607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/24/2024] [Indexed: 02/21/2024]  Open
3
Zou B, Zheng X, Na X, Cheng S, Qie Z, Xu X, Du M, Wu C. Constructing a strongly interacting Pea-Cod binary protein system by introducing metal cations toward enhanced gelling properties. Food Res Int 2024;178:113955. [PMID: 38309874 DOI: 10.1016/j.foodres.2024.113955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/27/2023] [Accepted: 01/02/2024] [Indexed: 02/05/2024]
4
Zhang J, Zou Y, Yan B, Zhang N, Zhao J, Zhang H, Chen W, Fan D. Microwave treatment on structure and digestibility characteristics of Spirulina platensis protein. Curr Res Food Sci 2023;7:100581. [PMID: 37691697 PMCID: PMC10484979 DOI: 10.1016/j.crfs.2023.100581] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/14/2023] [Accepted: 08/28/2023] [Indexed: 09/12/2023]  Open
5
Zheng X, Zou B, Ren C, Xu X, Du M, Wu C. Mechanisms of heat-mediated aggregation behavior of water-soluble cod protein. Food Chem 2023;419:135973. [PMID: 37011572 DOI: 10.1016/j.foodchem.2023.135973] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/20/2023] [Accepted: 03/15/2023] [Indexed: 04/05/2023]
6
Huang K, Shi J, Li M, Sun R, Guan W, Cao H, Guan X, Zhang Y. Intervention of microwave irradiation on structure and quality characteristics of quinoa protein aggregates. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.107677] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
7
Sakaguchi M, Mukaeda H, Kume A, Toyoda Y, Sakoh T, Kawakita M. Evaluation of the roles of hydrophobic residues in the N-terminal region of archaeal trehalase in its folding. Appl Microbiol Biotechnol 2021;105:3181-3194. [PMID: 33791835 DOI: 10.1007/s00253-021-11237-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/01/2021] [Accepted: 03/14/2021] [Indexed: 11/30/2022]
8
Hattori LT, Gutoski M, Vargas Benítez CM, Nunes LF, Lopes HS. A benchmark of optimally folded protein structures using integer programming and the 3D-HP-SC model. Comput Biol Chem 2020;84:107192. [PMID: 31918170 DOI: 10.1016/j.compbiolchem.2019.107192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 01/04/2023]
9
Brylinski M. eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models. PLoS Comput Biol 2014;10:e1003829. [PMID: 25232727 PMCID: PMC4168975 DOI: 10.1371/journal.pcbi.1003829] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 07/24/2014] [Indexed: 01/26/2023]  Open
10
Melnik TN, Majorina MA, Larina DS, Kashparov IA, Samatova EN, Glukhov AS, Melnik BS. Independent of their localization in protein the hydrophobic amino acid residues have no effect on the molten globule state of apomyoglobin and the disulfide bond on the surface of apomyoglobin stabilizes this intermediate state. PLoS One 2014;9:e98645. [PMID: 24892675 PMCID: PMC4043776 DOI: 10.1371/journal.pone.0098645] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Accepted: 05/06/2014] [Indexed: 01/07/2023]  Open
11
Piwowar M, Banach M, Konieczny L, Chomilier J, Roterman I. Structural role of exons in hemoglobin. BIO-ALGORITHMS AND MED-SYSTEMS 2013. [DOI: 10.1515/bams-2013-0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
12
Wu X, Yang G, Zu Y, Fu Y, Zhou L, Yuan X. The Trp-cage miniprotein with single-site mutations: Studies of stability and dynamics using molecular dynamics. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.06.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
13
Signature of hydrophobic hydration in a single polymer. Proc Natl Acad Sci U S A 2011;108:16527-32. [PMID: 21911397 DOI: 10.1073/pnas.1105450108] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
14
Jani V, Sonavane UB, Joshi R. Microsecond scale replica exchange molecular dynamic simulation of villin headpiece: an insight into the folding landscape. J Biomol Struct Dyn 2011;28:845-60. [PMID: 21469746 DOI: 10.1080/07391102.2011.10508612] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
15
Roterman I, Konieczny L, Banach M, Jurkowski W. Intermediates in the protein folding process: a computational model. Int J Mol Sci 2011;12:4850-60. [PMID: 21954329 PMCID: PMC3179136 DOI: 10.3390/ijms11084850] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 06/07/2011] [Accepted: 07/25/2011] [Indexed: 11/25/2022]  Open
16
Hamacher K. Free energy of contact formation in proteins: efficient computation in the elastic network approximation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011;84:016703. [PMID: 21867339 DOI: 10.1103/physreve.84.016703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Indexed: 05/31/2023]
17
Roterman I, Konieczny L, Jurkowski W, Prymula K, Banach M. Two-intermediate model to characterize the structure of fast-folding proteins. J Theor Biol 2011;283:60-70. [PMID: 21635900 DOI: 10.1016/j.jtbi.2011.05.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2010] [Revised: 05/17/2011] [Accepted: 05/18/2011] [Indexed: 01/15/2023]
18
Ji XL, Liu SQ. Is stoichiometry-driven protein folding getting out of thermodynamic control? J Biomol Struct Dyn 2011;28:621-3; discussion 669-674. [PMID: 21142237 DOI: 10.1080/07391102.2011.10508598] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
19
Li ITS, Walker GC. Interfacial Free Energy Governs Single Polystyrene Chain Collapse in Water and Aqueous Solutions. J Am Chem Soc 2010;132:6530-40. [DOI: 10.1021/ja101155h] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
20
Prymula K, Sałapa K, Roterman I. "Fuzzy oil drop" model applied to individual small proteins built of 70 amino acids. J Mol Model 2010;16:1269-82. [PMID: 20084418 DOI: 10.1007/s00894-009-0639-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2009] [Accepted: 12/07/2009] [Indexed: 12/25/2022]
21
Prymula K, Piwowar M, Kochanczyk M, Flis L, Malawski M, Szepieniec T, Evangelista G, Minervini G, Polticelli F, Wiśniowski Z, Sałapa K, Matczyńska E, Roterman I. In silico Structural Study of Random Amino Acid Sequence Proteins Not Present in Nature. Chem Biodivers 2009;6:2311-36. [DOI: 10.1002/cbdv.200800338] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
22
Zobnina V, Roterman I. Application of the fuzzy-oil-drop model to membrane protein simulation. Proteins 2009;77:378-94. [PMID: 19455711 DOI: 10.1002/prot.22443] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
23
Galat A. On transversal hydrophobicity of some proteins and their modules. J Chem Inf Model 2009;49:1821-30. [PMID: 19569645 DOI: 10.1021/ci9001316] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
24
Banach M, Stąpor K, Roterman I. Chaperonin structure: the large multi-subunit protein complex. Int J Mol Sci 2009;10:844-861. [PMID: 19399224 PMCID: PMC2672005 DOI: 10.3390/ijms10030844] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Revised: 02/23/2009] [Accepted: 02/26/2009] [Indexed: 11/16/2022]  Open
25
Minervini G, Evangelista G, Polticelli F, Piwowar M, Kochanczyk M, Flis L, Malawski M, Szepieniec T, Wiśniowski Z, Matczyńska E, Prymula K, Roterman I. Never born proteins as a test case for ab initio protein structures prediction. Bioinformation 2009;3:177-9. [PMID: 19238243 PMCID: PMC2637968 DOI: 10.6026/97320630003177] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2008] [Accepted: 11/23/2008] [Indexed: 12/03/2022]  Open
26
Stochastic protein folding simulation in the three-dimensional HP-model. Comput Biol Chem 2008;32:248-55. [PMID: 18485827 DOI: 10.1016/j.compbiolchem.2008.03.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2007] [Accepted: 03/17/2008] [Indexed: 11/23/2022]
27
Galat A, Gross G, Drevet P, Sato A, Ménez A. Conserved structural determinants in three-fingered protein domains. FEBS J 2008;275:3207-25. [DOI: 10.1111/j.1742-4658.2008.06473.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
28
Davis JE, Warren GL, Patel S. Revised charge equilibration potential for liquid alkanes. J Phys Chem B 2008;112:8298-310. [PMID: 18570394 DOI: 10.1021/jp8003129] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
29
Bryliński M, Prymula K, Jurkowski W, Kochańczyk M, Stawowczyk E, Konieczny L, Roterman I. Prediction of functional sites based on the fuzzy oil drop model. PLoS Comput Biol 2007;3:e94. [PMID: 17530916 PMCID: PMC1876487 DOI: 10.1371/journal.pcbi.0030094] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2006] [Accepted: 04/11/2007] [Indexed: 11/19/2022]  Open
30
Brylinski M, Kochanczyk M, Broniatowska E, Roterman I. Localization of ligand binding site in proteins identified in silico. J Mol Model 2007;13:665-75. [PMID: 17394030 DOI: 10.1007/s00894-007-0191-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Accepted: 02/26/2007] [Indexed: 01/21/2023]
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