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For: Estácio SG, Shakhnovich EI, Faísca PF. Assessing the effect of loop mutations in the folding space of β2-microglobulin with molecular dynamics simulations. Int J Mol Sci 2013;14:17256-78. [PMID: 23975166 DOI: 10.3390/ijms140917256] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 07/27/2013] [Accepted: 07/30/2013] [Indexed: 12/15/2022]  Open
Number Cited by Other Article(s)
1
Oliveira NFB, Rodrigues FEP, Vitorino JNM, Loureiro RJS, Faísca PFN, Machuqueiro M. Predicting stable binding modes from simulated dimers of the D76N mutant of β 2-microglobulin. Comput Struct Biotechnol J 2021;19:5160-5169. [PMID: 34630936 PMCID: PMC8473664 DOI: 10.1016/j.csbj.2021.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/02/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022]  Open
2
Morand J, Nunes A, Faísca PFN. The folding space of proteinβ2-microglobulin is modulated by a single disulfide bridge. Phys Biol 2021;18. [PMID: 34098544 DOI: 10.1088/1478-3975/ac08ec] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/07/2021] [Indexed: 11/11/2022]
3
Loureiro RJS, Faísca PFN. The Early Phase of β2-Microglobulin Aggregation: Perspectives From Molecular Simulations. Front Mol Biosci 2020;7:578433. [PMID: 33134317 PMCID: PMC7550760 DOI: 10.3389/fmolb.2020.578433] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/08/2020] [Indexed: 11/24/2022]  Open
4
J S Loureiro R, Vila-Viçosa D, Machuqueiro M, Shakhnovich EI, F N Faísca P. The Early Phase of β2m Aggregation: An Integrative Computational Study Framed on the D76N Mutant and the ΔN6 Variant. Biomolecules 2019;9:biom9080366. [PMID: 31416179 PMCID: PMC6722664 DOI: 10.3390/biom9080366] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 08/08/2019] [Accepted: 08/13/2019] [Indexed: 12/12/2022]  Open
5
Palese LL. A random version of principal component analysis in data clustering. Comput Biol Chem 2018;73:57-64. [PMID: 29428276 DOI: 10.1016/j.compbiolchem.2018.01.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 10/05/2017] [Accepted: 01/23/2018] [Indexed: 01/01/2023]
6
Peng Y, Myers R, Zhang W, Alexov E. Computational Investigation of the Missense Mutations in DHCR7 Gene Associated with Smith-Lemli-Opitz Syndrome. Int J Mol Sci 2018;19:E141. [PMID: 29300326 PMCID: PMC5796090 DOI: 10.3390/ijms19010141] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/29/2017] [Accepted: 12/30/2017] [Indexed: 12/25/2022]  Open
7
Loureiro RJS, Vila-Viçosa D, Machuqueiro M, Shakhnovich EI, Faísca PFN. A tale of two tails: The importance of unstructured termini in the aggregation pathway of β2-microglobulin. Proteins 2017;85:2045-2057. [DOI: 10.1002/prot.25358] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 07/13/2017] [Accepted: 07/22/2017] [Indexed: 12/14/2022]
8
Narang SS, Shuaib S, Goyal D, Goyal B. Assessing the effect of D59P mutation in the DE loop region in amyloid aggregation propensity of β2‐microglobulin: A molecular dynamics simulation study. J Cell Biochem 2017;119:782-792. [DOI: 10.1002/jcb.26241] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 06/27/2017] [Indexed: 02/06/2023]
9
Carrillo-Parramon O, Brancolini G, Corni S. A dynamical coarse-grained model to disclose allosteric control of misfolding β2-microglobulin. RSC Adv 2016. [DOI: 10.1039/c6ra15491c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]  Open
10
Estácio SG, Martiniano HFMC, Faísca PFN. Thermal unfolding simulations of NBD1 domain variants reveal structural motifs associated with the impaired folding of F508del-CFTR. MOLECULAR BIOSYSTEMS 2016;12:2834-48. [DOI: 10.1039/c6mb00193a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
11
Faísca PF. Knotted proteins: A tangled tale of Structural Biology. Comput Struct Biotechnol J 2015;13:459-68. [PMID: 26380658 PMCID: PMC4556803 DOI: 10.1016/j.csbj.2015.08.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 07/31/2015] [Accepted: 08/07/2015] [Indexed: 01/19/2023]  Open
12
Estácio SG, Leal SS, Cristóvão JS, Faísca PFN, Gomes CM. Calcium binding to gatekeeper residues flanking aggregation-prone segments underlies non-fibrillar amyloid traits in superoxide dismutase 1 (SOD1). BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014;1854:118-26. [PMID: 25463043 DOI: 10.1016/j.bbapap.2014.11.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 11/14/2014] [Accepted: 11/18/2014] [Indexed: 12/26/2022]
13
Estácio SG, Krobath H, Vila-Viçosa D, Machuqueiro M, Shakhnovich EI, Faísca PFN. A simulated intermediate state for folding and aggregation provides insights into ΔN6 β2-microglobulin amyloidogenic behavior. PLoS Comput Biol 2014;10:e1003606. [PMID: 24809460 PMCID: PMC4014404 DOI: 10.1371/journal.pcbi.1003606] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 03/16/2014] [Indexed: 01/26/2023]  Open
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