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Atomic force microscopy for single molecule characterisation of protein aggregation.

Ruggeri FS, Šneideris T, Vendruscolo M, Knowles TPJ.

Arch Biochem Biophys. 2019 Feb 8. pii: S0003-9861(18)30933-0. doi: 10.1016/ [Epub ahead of print] Review.


Trodusquemine enhances Aβ42 aggregation but suppresses its toxicity by displacing oligomers from cell membranes.

Limbocker R, Chia S, Ruggeri FS, Perni M, Cascella R, Heller GT, Meisl G, Mannini B, Habchi J, Michaels TCT, Challa PK, Ahn M, Casford ST, Fernando N, Xu CK, Kloss ND, Cohen SIA, Kumita JR, Cecchi C, Zasloff M, Linse S, Knowles TPJ, Chiti F, Vendruscolo M, Dobson CM.

Nat Commun. 2019 Jan 15;10(1):225. doi: 10.1038/s41467-018-07699-5.


Chemical and mechanistic analysis of photodynamic inhibition of Alzheimer's β-amyloid aggregation.

Ahn M, Lee BI, Chia S, Habchi J, Kumita JR, Vendruscolo M, Dobson CM, Park CB.

Chem Commun (Camb). 2019 Jan 25;55(8):1152-1155. doi: 10.1039/c8cc09288e. Epub 2019 Jan 11.


Automated Behavioral Analysis of Large C. elegans Populations Using a Wide Field-of-view Tracking Platform.

Perni M, Casford S, Aprile FA, Nollen EA, Knowles TPJ, Vendruscolo M, Dobson CM.

J Vis Exp. 2018 Nov 28;(141). doi: 10.3791/58643.


A superposition free method for protein conformational ensemble analyses and local clustering based on a differential geometry representation of backbone.

da Silva Neto AM, Silva SR, Vendruscolo M, Camilloni C, Montalvão RW.

Proteins. 2018 Dec 23. doi: 10.1002/prot.25652. [Epub ahead of print]


A tau homeostasis signature is linked with the cellular and regional vulnerability of excitatory neurons to tau pathology.

Fu H, Possenti A, Freer R, Nakano Y, Villegas NCH, Tang M, Cauhy PVM, Lassus BA, Chen S, Fowler SL, Figueroa HY, Huey ED, Johnson GVW, Vendruscolo M, Duff KE.

Nat Neurosci. 2019 Jan;22(1):47-56. doi: 10.1038/s41593-018-0298-7. Epub 2018 Dec 17.


In vitro and in silico assessment of the developability of a designed monoclonal antibody library.

Wolf Pérez AM, Sormanni P, Andersen JS, Sakhnini LI, Rodriguez-Leon I, Bjelke JR, Gajhede AJ, De Maria L, Otzen DE, Vendruscolo M, Lorenzen N.

MAbs. 2019 Feb/Mar;11(2):388-400. doi: 10.1080/19420862.2018.1556082. Epub 2019 Jan 18.


Determination of protein structural ensembles using cryo-electron microscopy.

Bonomi M, Vendruscolo M.

Curr Opin Struct Biol. 2018 Nov 28;56:37-45. doi: 10.1016/ [Epub ahead of print] Review.


Determination of Structural Ensembles of Proteins: Restraining vs Reweighting.

Rangan R, Bonomi M, Heller GT, Cesari A, Bussi G, Vendruscolo M.

J Chem Theory Comput. 2018 Nov 28. doi: 10.1021/acs.jctc.8b00738. [Epub ahead of print]


Bayesian Weighing of Electron Cryo-Microscopy Data for Integrative Structural Modeling.

Bonomi M, Hanot S, Greenberg CH, Sali A, Nilges M, Vendruscolo M, Pellarin R.

Structure. 2019 Jan 2;27(1):175-188.e6. doi: 10.1016/j.str.2018.09.011. Epub 2018 Nov 1.


Third generation antibody discovery methods: in silico rational design.

Sormanni P, Aprile FA, Vendruscolo M.

Chem Soc Rev. 2018 Dec 10;47(24):9137-9157. doi: 10.1039/c8cs00523k. Review.


SAR by kinetics for drug discovery in protein misfolding diseases.

Chia S, Habchi J, Michaels TCT, Cohen SIA, Linse S, Dobson CM, Knowles TPJ, Vendruscolo M.

Proc Natl Acad Sci U S A. 2018 Oct 9;115(41):10245-10250. doi: 10.1073/pnas.1807884115. Epub 2018 Sep 26.


Microfluidic deposition for resolving single-molecule protein architecture and heterogeneity.

Ruggeri FS, Charmet J, Kartanas T, Peter Q, Chia S, Habchi J, Dobson CM, Vendruscolo M, Knowles TPJ.

Nat Commun. 2018 Sep 24;9(1):3890. doi: 10.1038/s41467-018-06345-4.


Systematic mapping of free energy landscapes of a growing filamin domain during biosynthesis.

Waudby CA, Wlodarski T, Karyadi ME, Cassaignau AME, Chan SHS, Wentink AS, Schmidt-Engler JM, Camilloni C, Vendruscolo M, Cabrita LD, Christodoulou J.

Proc Natl Acad Sci U S A. 2018 Sep 25;115(39):9744-9749. doi: 10.1073/pnas.1716252115. Epub 2018 Sep 10.


Author Correction: The molecular chaperones DNAJB6 and Hsp70 cooperate to suppress α-synuclein aggregation.

Aprile FA, Källstig E, Limorenko G, Vendruscolo M, Ron D, Hansen C.

Sci Rep. 2018 Aug 2;8(1):11848. doi: 10.1038/s41598-018-29893-7.


Determination of the conformational states of strychnine in solution using NMR residual dipolar couplings in a tensor-free approach.

Tomba G, Camilloni C, Vendruscolo M.

Methods. 2018 Sep 15;148:4-8. doi: 10.1016/j.ymeth.2018.07.005. Epub 2018 Jul 21.


Structural differences between toxic and nontoxic HypF-N oligomers.

Capitini C, Patel JR, Natalello A, D'Andrea C, Relini A, Jarvis JA, Birolo L, Peduzzo A, Vendruscolo M, Matteini P, Dobson CM, De Simone A, Chiti F.

Chem Commun (Camb). 2018 Aug 11;54(62):8637-8640. doi: 10.1039/c8cc03446j. Epub 2018 Jul 18.


Molecular dynamics ensemble refinement of the heterogeneous native state of NCBD using chemical shifts and NOEs.

Papaleo E, Camilloni C, Teilum K, Vendruscolo M, Lindorff-Larsen K.

PeerJ. 2018 Jul 4;6:e5125. doi: 10.7717/peerj.5125. eCollection 2018.


Stabilization and Characterization of Cytotoxic Aβ40 Oligomers Isolated from an Aggregation Reaction in the Presence of Zinc Ions.

Mannini B, Habchi J, Chia S, Ruggeri FS, Perni M, Knowles TPJ, Dobson CM, Vendruscolo M.

ACS Chem Neurosci. 2018 Aug 10. doi: 10.1021/acschemneuro.8b00141. [Epub ahead of print]


Multistep Inhibition of α-Synuclein Aggregation and Toxicity in Vitro and in Vivo by Trodusquemine.

Perni M, Flagmeier P, Limbocker R, Cascella R, Aprile FA, Galvagnion C, Heller GT, Meisl G, Chen SW, Kumita JR, Challa PK, Kirkegaard JB, Cohen SIA, Mannini B, Barbut D, Nollen EAA, Cecchi C, Cremades N, Knowles TPJ, Chiti F, Zasloff M, Vendruscolo M, Dobson CM.

ACS Chem Biol. 2018 Aug 17;13(8):2308-2319. doi: 10.1021/acschembio.8b00466. Epub 2018 Jun 28.


Reversible inhibition of the ClpP protease via an N-terminal conformational switch.

Vahidi S, Ripstein ZA, Bonomi M, Yuwen T, Mabanglo MF, Juravsky JB, Rizzolo K, Velyvis A, Houry WA, Vendruscolo M, Rubinstein JL, Kay LE.

Proc Natl Acad Sci U S A. 2018 Jul 10;115(28):E6447-E6456. doi: 10.1073/pnas.1805125115. Epub 2018 Jun 25.


A method for partitioning the information contained in a protein sequence between its structure and function.

Possenti A, Vendruscolo M, Camilloni C, Tiana G.

Proteins. 2018 Sep;86(9):956-964. doi: 10.1002/prot.25527.


Cooperative Assembly of Hsp70 Subdomain Clusters.

Wright MA, Aprile FA, Bellaiche MMJ, Michaels TCT, Müller T, Arosio P, Vendruscolo M, Dobson CM, Knowles TPJ.

Biochemistry. 2018 Jul 3;57(26):3641-3649. doi: 10.1021/acs.biochem.8b00151. Epub 2018 May 29.


A Rationally Designed Hsp70 Variant Rescues the Aggregation-Associated Toxicity of Human IAPP in Cultured Pancreatic Islet β-Cells.

Bongiovanni MN, Aprile FA, Sormanni P, Vendruscolo M.

Int J Mol Sci. 2018 May 12;19(5). pii: E1443. doi: 10.3390/ijms19051443.


Cholesterol catalyses Aβ42 aggregation through a heterogeneous nucleation pathway in the presence of lipid membranes.

Habchi J, Chia S, Galvagnion C, Michaels TCT, Bellaiche MMJ, Ruggeri FS, Sanguanini M, Idini I, Kumita JR, Sparr E, Linse S, Dobson CM, Knowles TPJ, Vendruscolo M.

Nat Chem. 2018 Jun;10(6):673-683. doi: 10.1038/s41557-018-0031-x. Epub 2018 May 7.


FUS Phase Separation Is Modulated by a Molecular Chaperone and Methylation of Arginine Cation-π Interactions.

Qamar S, Wang G, Randle SJ, Ruggeri FS, Varela JA, Lin JQ, Phillips EC, Miyashita A, Williams D, Ströhl F, Meadows W, Ferry R, Dardov VJ, Tartaglia GG, Farrer LA, Kaminski Schierle GS, Kaminski CF, Holt CE, Fraser PE, Schmitt-Ulms G, Klenerman D, Knowles T, Vendruscolo M, St George-Hyslop P.

Cell. 2018 Apr 19;173(3):720-734.e15. doi: 10.1016/j.cell.2018.03.056.


Parapred: antibody paratope prediction using convolutional and recurrent neural networks.

Liberis E, Velickovic P, Sormanni P, Vendruscolo M, Liò P.

Bioinformatics. 2018 Sep 1;34(17):2944-2950. doi: 10.1093/bioinformatics/bty305.


Simultaneous Determination of Protein Structure and Dynamics Using Cryo-Electron Microscopy.

Bonomi M, Pellarin R, Vendruscolo M.

Biophys J. 2018 Apr 10;114(7):1604-1613. doi: 10.1016/j.bpj.2018.02.028.


Exploring the role of post-translational modifications in regulating α-synuclein interactions by studying the effects of phosphorylation on nanobody binding.

El Turk F, De Genst E, Guilliams T, Fauvet B, Hejjaoui M, Di Trani J, Chiki A, Mittermaier A, Vendruscolo M, Lashuel HA, Dobson CM.

Protein Sci. 2018 Jul;27(7):1262-1274. doi: 10.1002/pro.3412.


Molecular determinants of the interaction of EGCG with ordered and disordered proteins.

Fusco G, Sanz-Hernandez M, Ruggeri FS, Vendruscolo M, Dobson CM, De Simone A.

Biopolymers. 2018 Aug;109(10):e23117. doi: 10.1002/bip.23117. Epub 2018 Mar 30.


Structural Ensemble Modulation upon Small-Molecule Binding to Disordered Proteins.

Heller GT, Bonomi M, Vendruscolo M.

J Mol Biol. 2018 Aug 3;430(16):2288-2292. doi: 10.1016/j.jmb.2018.03.015. Epub 2018 Mar 26. Review.


Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide.

Cohen SIA, Cukalevski R, Michaels TCT, Šarić A, Törnquist M, Vendruscolo M, Dobson CM, Buell AK, Knowles TPJ, Linse S.

Nat Chem. 2018 May;10(5):523-531. doi: 10.1038/s41557-018-0023-x. Epub 2018 Mar 26.


Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation.

Michaels TCT, Šarić A, Habchi J, Chia S, Meisl G, Vendruscolo M, Dobson CM, Knowles TPJ.

Annu Rev Phys Chem. 2018 Apr 20;69:273-298. doi: 10.1146/annurev-physchem-050317-021322. Epub 2018 Feb 28. Review.


Massively parallel C. elegans tracking provides multi-dimensional fingerprints for phenotypic discovery.

Perni M, Challa PK, Kirkegaard JB, Limbocker R, Koopman M, Hardenberg MC, Sormanni P, Müller T, Saar KL, Roode LWY, Habchi J, Vecchi G, Fernando N, Casford S, Nollen EAA, Vendruscolo M, Dobson CM, Knowles TPJ.

J Neurosci Methods. 2018 Aug 1;306:57-67. doi: 10.1016/j.jneumeth.2018.02.005. Epub 2018 Feb 13.


Structural basis of membrane disruption and cellular toxicity by α-synuclein oligomers.

Fusco G, Chen SW, Williamson PTF, Cascella R, Perni M, Jarvis JA, Cecchi C, Vendruscolo M, Chiti F, Cremades N, Ying L, Dobson CM, De Simone A.

Science. 2017 Dec 15;358(6369):1440-1443. doi: 10.1126/science.aan6160.


Scaling behaviour and rate-determining steps in filamentous self-assembly.

Meisl G, Rajah L, Cohen SAI, Pfammatter M, Šarić A, Hellstrand E, Buell AK, Aguzzi A, Linse S, Vendruscolo M, Dobson CM, Knowles TPJ.

Chem Sci. 2017 Oct 1;8(10):7087-7097. doi: 10.1039/c7sc01965c. Epub 2017 Aug 31.


MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins.

Piovesan D, Tabaro F, Paladin L, Necci M, Micetic I, Camilloni C, Davey N, Dosztányi Z, Mészáros B, Monzon AM, Parisi G, Schad E, Sormanni P, Tompa P, Vendruscolo M, Vranken WF, Tosatto SCE.

Nucleic Acids Res. 2018 Jan 4;46(D1):D471-D476. doi: 10.1093/nar/gkx1071.


Delivery of Native Proteins into C. elegans Using a Transduction Protocol Based on Lipid Vesicles.

Perni M, Aprile FA, Casford S, Mannini B, Sormanni P, Dobson CM, Vendruscolo M.

Sci Rep. 2017 Nov 8;7(1):15045. doi: 10.1038/s41598-017-13755-9.


Influence of Harvest Season and Cultivar on the Variation of Phenolic Compounds Composition and Antioxidant Properties in Vaccinium ashei Leaves.

Cezarotto VS, Giacomelli SR, Vendruscolo MH, Vestena AS, Cezarotto CS, da Cruz RC, Maurer LH, Ferreira LM, Emanuelli T, Cruz L.

Molecules. 2017 Sep 30;22(10). pii: E1603. doi: 10.3390/molecules22101603.


In vitro and in silico activity of iridoids against Leishmania amazonensis.

von Poser GL, Vendruscolo MH, Neves GM, Kagami LP, Rodrigues LC, Diehl ML, Gnoatto SCB, de Loreto Bordignon SA, Romão PRT, Lima VLE.

Curr Drug Discov Technol. 2017 Oct 2. doi: 10.2174/1570163814666171002102058. [Epub ahead of print]


Oxetane Grafts Installed Site-Selectively on Native Disulfides to Enhance Protein Stability and Activity In Vivo.

Martínez-Sáez N, Sun S, Oldrini D, Sormanni P, Boutureira O, Carboni F, Compañón I, Deery MJ, Vendruscolo M, Corzana F, Adamo R, Bernardes GJL.

Angew Chem Int Ed Engl. 2017 Nov 20;56(47):14963-14967. doi: 10.1002/anie.201708847. Epub 2017 Oct 20.


The molecular chaperones DNAJB6 and Hsp70 cooperate to suppress α-synuclein aggregation.

Aprile FA, Källstig E, Limorenko G, Vendruscolo M, Ron D, Hansen C.

Sci Rep. 2017 Aug 22;7(1):9039. doi: 10.1038/s41598-017-08324-z. Erratum in: Sci Rep. 2018 Aug 2;8(1):11848.


Rapid and accurate in silico solubility screening of a monoclonal antibody library.

Sormanni P, Amery L, Ekizoglou S, Vendruscolo M, Popovic B.

Sci Rep. 2017 Aug 15;7(1):8200. doi: 10.1038/s41598-017-07800-w.


Sequence Specificity in the Entropy-Driven Binding of a Small Molecule and a Disordered Peptide.

Heller GT, Aprile FA, Bonomi M, Camilloni C, De Simone A, Vendruscolo M.

J Mol Biol. 2017 Sep 1;429(18):2772-2779. doi: 10.1016/j.jmb.2017.07.016. Epub 2017 Jul 22.


Monomeric and fibrillar α-synuclein exert opposite effects on the catalytic cycle that promotes the proliferation of Aβ42 aggregates.

Chia S, Flagmeier P, Habchi J, Lattanzi V, Linse S, Dobson CM, Knowles TPJ, Vendruscolo M.

Proc Natl Acad Sci U S A. 2017 Jul 25;114(30):8005-8010. doi: 10.1073/pnas.1700239114. Epub 2017 Jul 11.


Selective targeting of primary and secondary nucleation pathways in Aβ42 aggregation using a rational antibody scanning method.

Aprile FA, Sormanni P, Perni M, Arosio P, Linse S, Knowles TPJ, Dobson CM, Vendruscolo M.

Sci Adv. 2017 Jun 21;3(6):e1700488. doi: 10.1126/sciadv.1700488. eCollection 2017 Jun.


Nanobodies raised against monomeric ɑ-synuclein inhibit fibril formation and destabilize toxic oligomeric species.

Iljina M, Hong L, Horrocks MH, Ludtmann MH, Choi ML, Hughes CD, Ruggeri FS, Guilliams T, Buell AK, Lee JE, Gandhi S, Lee SF, Bryant CE, Vendruscolo M, Knowles TPJ, Dobson CM, De Genst E, Klenerman D.

BMC Biol. 2017 Jul 3;15(1):57. doi: 10.1186/s12915-017-0390-6.


Protein homeostasis of a metastable subproteome associated with Alzheimer's disease.

Kundra R, Ciryam P, Morimoto RI, Dobson CM, Vendruscolo M.

Proc Natl Acad Sci U S A. 2017 Jul 11;114(28):E5703-E5711. doi: 10.1073/pnas.1618417114. Epub 2017 Jun 26.


Methods of probing the interactions between small molecules and disordered proteins.

Heller GT, Aprile FA, Vendruscolo M.

Cell Mol Life Sci. 2017 Sep;74(17):3225-3243. doi: 10.1007/s00018-017-2563-4. Epub 2017 Jun 19. Review.


Phage display and kinetic selection of antibodies that specifically inhibit amyloid self-replication.

Munke A, Persson J, Weiffert T, De Genst E, Meisl G, Arosio P, Carnerup A, Dobson CM, Vendruscolo M, Knowles TPJ, Linse S.

Proc Natl Acad Sci U S A. 2017 Jun 20;114(25):6444-6449. doi: 10.1073/pnas.1700407114. Epub 2017 Jun 5.

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