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For: Carter L, Kim SJ, Schneidman-Duhovny D, Stöhr J, Poncet-Montange G, Weiss TM, Tsuruta H, Prusiner SB, Sali A. Prion Protein-Antibody Complexes Characterized by Chromatography-Coupled Small-Angle X-Ray Scattering. Biophys J 2016;109:793-805. [PMID: 26287631 DOI: 10.1016/j.bpj.2015.06.065] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 06/22/2015] [Accepted: 06/30/2015] [Indexed: 10/23/2022]  Open
Number Cited by Other Article(s)
1
Durer ZA, İnce Hİ, Düvenci ZŞ, Timuçin E, Gräwert T, Orun O, Kan B, Sayers Z. Insights into the solution structure of the actin-binding tail domain of metavinculin by small angle X-ray scattering and molecular dynamics simulations. Int J Biol Macromol 2025:144376. [PMID: 40409637 DOI: 10.1016/j.ijbiomac.2025.144376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2025] [Revised: 05/07/2025] [Accepted: 05/17/2025] [Indexed: 05/25/2025]
2
Fiorucci L, Schiavina M, Felli IC, Pierattelli R, Ravera E. Are Protein Conformational Ensembles in Agreement with Experimental Data? A Geometrical Interpretation of the Problem. J Chem Inf Model 2024;64:5392-5401. [PMID: 38959217 DOI: 10.1021/acs.jcim.4c00582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
3
Cohen T, Halfon M, Carter L, Sharkey B, Jain T, Sivasubramanian A, Schneidman-Duhovny D. Multi-state modeling of antibody-antigen complexes with SAXS profiles and deep-learning models. Methods Enzymol 2022;678:237-262. [PMID: 36641210 DOI: 10.1016/bs.mie.2022.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
4
Linsenmeier L, Mohammadi B, Shafiq M, Frontzek K, Bär J, Shrivastava AN, Damme M, Song F, Schwarz A, Da Vela S, Massignan T, Jung S, Correia A, Schmitz M, Puig B, Hornemann S, Zerr I, Tatzelt J, Biasini E, Saftig P, Schweizer M, Svergun D, Amin L, Mazzola F, Varani L, Thapa S, Gilch S, Schätzl H, Harris DA, Triller A, Mikhaylova M, Aguzzi A, Altmeppen HC, Glatzel M. Ligands binding to the prion protein induce its proteolytic release with therapeutic potential in neurodegenerative proteinopathies. SCIENCE ADVANCES 2021;7:eabj1826. [PMID: 34818048 PMCID: PMC8612689 DOI: 10.1126/sciadv.abj1826] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/20/2021] [Indexed: 05/07/2023]
5
Chen EHL, Lin KM, Sang JC, Ho MR, Lee CH, Shih O, Su CJ, Yeh YQ, Jeng US, Chen RPY. Condition-dependent structural collapse in the intrinsically disordered N-terminal domain of prion protein. IUBMB Life 2021;74:780-793. [PMID: 34288372 DOI: 10.1002/iub.2528] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/25/2021] [Accepted: 06/27/2021] [Indexed: 11/06/2022]
6
Ding C, Wang S, Zhang Z. Integrating an Enhanced Sampling Method and Small-Angle X-Ray Scattering to Study Intrinsically Disordered Proteins. Front Mol Biosci 2021;8:621128. [PMID: 34150843 PMCID: PMC8213455 DOI: 10.3389/fmolb.2021.621128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 02/08/2021] [Indexed: 11/23/2022]  Open
7
Sali A. From integrative structural biology to cell biology. J Biol Chem 2021;296:100743. [PMID: 33957123 PMCID: PMC8203844 DOI: 10.1016/j.jbc.2021.100743] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/09/2021] [Accepted: 04/30/2021] [Indexed: 12/16/2022]  Open
8
Antibody Fragments as Tools for Elucidating Structure-Toxicity Relationships and for Diagnostic/Therapeutic Targeting of Neurotoxic Amyloid Oligomers. Int J Mol Sci 2020;21:ijms21238920. [PMID: 33255488 PMCID: PMC7727795 DOI: 10.3390/ijms21238920] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/01/2020] [Accepted: 10/01/2020] [Indexed: 02/06/2023]  Open
9
Lansky S, Salama R, Shulami S, Lavid N, Sen S, Schapiro I, Shoham Y, Shoham G. Carbohydrate-Binding Capability and Functional Conformational Changes of AbnE, an Arabino-oligosaccharide Binding Protein. J Mol Biol 2020;432:2099-2120. [PMID: 32067952 DOI: 10.1016/j.jmb.2020.01.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/19/2020] [Accepted: 01/30/2020] [Indexed: 11/27/2022]
10
Rout MP, Sali A. Principles for Integrative Structural Biology Studies. Cell 2020;177:1384-1403. [PMID: 31150619 DOI: 10.1016/j.cell.2019.05.016] [Citation(s) in RCA: 185] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/24/2019] [Accepted: 05/06/2019] [Indexed: 12/22/2022]
11
Salzano G, Brennich M, Mancini G, Tran TH, Legname G, D'Angelo P, Giachin G. Deciphering Copper Coordination in the Mammalian Prion Protein Amyloidogenic Domain. Biophys J 2020;118:676-687. [PMID: 31952810 DOI: 10.1016/j.bpj.2019.12.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 12/17/2022]  Open
12
Structural Organization and Dynamics of Homodimeric Cytohesin Family Arf GTPase Exchange Factors in Solution and on Membranes. Structure 2019;27:1782-1797.e7. [PMID: 31601460 PMCID: PMC6948192 DOI: 10.1016/j.str.2019.09.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/03/2019] [Accepted: 09/16/2019] [Indexed: 12/30/2022]
13
Wu H, Saltzberg DJ, Kratochvil HT, Jo H, Sali A, DeGrado WF. Glutamine Side Chain 13C═18O as a Nonperturbative IR Probe of Amyloid Fibril Hydration and Assembly. J Am Chem Soc 2019;141:7320-7326. [PMID: 30998340 DOI: 10.1021/jacs.9b00577] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
14
Braitbard M, Schneidman-Duhovny D, Kalisman N. Integrative Structure Modeling: Overview and Assessment. Annu Rev Biochem 2019;88:113-135. [PMID: 30830798 DOI: 10.1146/annurev-biochem-013118-111429] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
15
Saltzberg D, Greenberg CH, Viswanath S, Chemmama I, Webb B, Pellarin R, Echeverria I, Sali A. Modeling Biological Complexes Using Integrative Modeling Platform. Methods Mol Biol 2019;2022:353-377. [PMID: 31396911 DOI: 10.1007/978-1-4939-9608-7_15] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
16
Piiadov V, Ares de Araújo E, Oliveira Neto M, Craievich AF, Polikarpov I. SAXSMoW 2.0: Online calculator of the molecular weight of proteins in dilute solution from experimental SAXS data measured on a relative scale. Protein Sci 2018;28:454-463. [PMID: 30371978 DOI: 10.1002/pro.3528] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/05/2018] [Accepted: 10/08/2018] [Indexed: 11/07/2022]
17
Hardouin P, Velours C, Bou-Nader C, Assrir N, Laalami S, Putzer H, Durand D, Golinelli-Pimpaneau B. Dissociation of the Dimer of the Intrinsically Disordered Domain of RNase Y upon Antibody Binding. Biophys J 2018;115:2102-2113. [PMID: 30447990 DOI: 10.1016/j.bpj.2018.10.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 09/17/2018] [Accepted: 10/17/2018] [Indexed: 12/12/2022]  Open
18
Bhattacharya S, Xu L, Thompson D. Revisiting the earliest signatures of amyloidogenesis: Roadmaps emerging from computational modeling and experiment. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1359] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
19
Schneidman-Duhovny D, Hammel M. Modeling Structure and Dynamics of Protein Complexes with SAXS Profiles. Methods Mol Biol 2018;1764:449-473. [PMID: 29605933 PMCID: PMC6022765 DOI: 10.1007/978-1-4939-7759-8_29] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
20
Kadowaki MAS, Higasi P, de Godoy MO, Prade RA, Polikarpov I. Biochemical and structural insights into a thermostable cellobiohydrolase from Myceliophthora thermophila. FEBS J 2018;285:559-579. [PMID: 29222836 DOI: 10.1111/febs.14356] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 10/20/2017] [Accepted: 12/05/2017] [Indexed: 12/27/2022]
21
Malaby AW, Das S, Chakravarthy S, Irving TC, Bilsel O, Lambright DG. Structural Dynamics Control Allosteric Activation of Cytohesin Family Arf GTPase Exchange Factors. Structure 2017;26:106-117.e6. [PMID: 29276036 PMCID: PMC5752578 DOI: 10.1016/j.str.2017.11.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 10/22/2017] [Accepted: 11/27/2017] [Indexed: 11/16/2022]
22
Trewhella J, Duff AP, Durand D, Gabel F, Guss JM, Hendrickson WA, Hura GL, Jacques DA, Kirby NM, Kwan AH, Pérez J, Pollack L, Ryan TM, Sali A, Schneidman-Duhovny D, Schwede T, Svergun DI, Sugiyama M, Tainer JA, Vachette P, Westbrook J, Whitten AE. 2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update. Acta Crystallogr D Struct Biol 2017;73:710-728. [PMID: 28876235 PMCID: PMC5586245 DOI: 10.1107/s2059798317011597] [Citation(s) in RCA: 196] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/07/2017] [Indexed: 12/02/2022]  Open
23
Orchestrated Domain Movement in Catalysis by Cytochrome P450 Reductase. Sci Rep 2017;7:9741. [PMID: 28852004 PMCID: PMC5575293 DOI: 10.1038/s41598-017-09840-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/31/2017] [Indexed: 12/16/2022]  Open
24
Patel S, Sasidhar YU, Chary KVR. Mechanism of Initiation, Association, and Formation of Amyloid Fibrils Modeled with the N-Terminal Peptide Fragment, IKYLEFIS, of Myoglobin G-Helix. J Phys Chem B 2017;121:7536-7549. [PMID: 28707888 DOI: 10.1021/acs.jpcb.7b02205] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
25
Stamogiannos A, Maben Z, Papakyriakou A, Mpakali A, Kokkala P, Georgiadis D, Stern LJ, Stratikos E. Critical Role of Interdomain Interactions in the Conformational Change and Catalytic Mechanism of Endoplasmic Reticulum Aminopeptidase 1. Biochemistry 2017;56:1546-1558. [PMID: 28218509 DOI: 10.1021/acs.biochem.6b01170] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
26
Raghuwanshi B, Pehlajani NK, Sinha MK, Tripathy S. A retrospective study of transfusion practices in a Tertiary Care Institute. Indian J Anaesth 2017;61:24-28. [PMID: 28216700 PMCID: PMC5296802 DOI: 10.4103/0019-5049.198395] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]  Open
27
Brookes E, Vachette P, Rocco M, Pérez J. US-SOMO HPLC-SAXS module: dealing with capillary fouling and extraction of pure component patterns from poorly resolved SEC-SAXS data. J Appl Crystallogr 2016;49:1827-1841. [PMID: 27738419 PMCID: PMC5045733 DOI: 10.1107/s1600576716011201] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 07/10/2016] [Indexed: 11/23/2022]  Open
28
Petrvalska O, Kosek D, Kukacka Z, Tosner Z, Man P, Vecer J, Herman P, Obsilova V, Obsil T. Structural Insight into the 14-3-3 Protein-dependent Inhibition of Protein Kinase ASK1 (Apoptosis Signal-regulating kinase 1). J Biol Chem 2016;291:20753-65. [PMID: 27514745 DOI: 10.1074/jbc.m116.724310] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Indexed: 11/06/2022]  Open
29
Vestergaard B. Analysis of biostructural changes, dynamics, and interactions – Small-angle X-ray scattering to the rescue. Arch Biochem Biophys 2016;602:69-79. [DOI: 10.1016/j.abb.2016.02.029] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 02/17/2016] [Accepted: 02/26/2016] [Indexed: 12/27/2022]
30
LoPiccolo J, Kim SJ, Shi Y, Wu B, Wu H, Chait BT, Singer RH, Sali A, Brenowitz M, Bresnick AR, Backer JM. Assembly and Molecular Architecture of the Phosphoinositide 3-Kinase p85α Homodimer. J Biol Chem 2015;290:30390-405. [PMID: 26475863 DOI: 10.1074/jbc.m115.689604] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Indexed: 11/06/2022]  Open
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