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Characterizing Individual Protein Aggregates by Infrared Nanospectroscopy and Atomic Force Microscopy.

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

J Vis Exp. 2019 Sep 12;(151). doi: 10.3791/60108.


RNA Granules Hitchhike on Lysosomes for Long-Distance Transport, Using Annexin A11 as a Molecular Tether.

Liao YC, Fernandopulle MS, Wang G, Choi H, Hao L, Drerup CM, Patel R, Qamar S, Nixon-Abell J, Shen Y, Meadows W, Vendruscolo M, Knowles TPJ, Nelson M, Czekalska MA, Musteikyte G, Gachechiladze MA, Stephens CA, Pasolli HA, Forrest LR, St George-Hyslop P, Lippincott-Schwartz J, Ward ME.

Cell. 2019 Sep 19;179(1):147-164.e20. doi: 10.1016/j.cell.2019.08.050.


Probing the dynamic stalk region of the ribosome using solution NMR.

Wang X, Kirkpatrick JP, Launay HMM, de Simone A, Häussinger D, Dobson CM, Vendruscolo M, Cabrita LD, Waudby CA, Christodoulou J.

Sci Rep. 2019 Sep 19;9(1):13528. doi: 10.1038/s41598-019-49190-1.


Enhancement of the Anti-Aggregation Activity of a Molecular Chaperone Using a Rationally Designed Post-Translational Modification.

Lindstedt PR, Aprile FA, Matos MJ, Perni M, Bertoldo JB, Bernardim B, Peter Q, Jiménez-Osés G, Knowles TPJ, Dobson CM, Corzana F, Vendruscolo M, Bernardes GJL.

ACS Cent Sci. 2019 Aug 28;5(8):1417-1424. doi: 10.1021/acscentsci.9b00467. Epub 2019 Jul 19.


A Practical Guide to the Simultaneous Determination of Protein Structure and Dynamics Using Metainference.

Löhr T, Camilloni C, Bonomi M, Vendruscolo M.

Methods Mol Biol. 2019;2022:313-340. doi: 10.1007/978-1-4939-9608-7_13.


The Hsp70 Chaperone System Stabilizes a Thermo-sensitive Subproteome in E. coli.

Zhao L, Vecchi G, Vendruscolo M, Körner R, Hayer-Hartl M, Hartl FU.

Cell Rep. 2019 Jul 30;28(5):1335-1345.e6. doi: 10.1016/j.celrep.2019.06.081.


Soluble aggregates present in cerebrospinal fluid change in size and mechanism of toxicity during Alzheimer's disease progression.

De S, Whiten DR, Ruggeri FS, Hughes C, Rodrigues M, Sideris DI, Taylor CG, Aprile FA, Muyldermans S, Knowles TPJ, Vendruscolo M, Bryant C, Blennow K, Skoog I, Kern S, Zetterberg H, Klenerman D.

Acta Neuropathol Commun. 2019 Jul 26;7(1):120. doi: 10.1186/s40478-019-0777-4.


Differential Interactome and Innate Immune Response Activation of Two Structurally Distinct Misfolded Protein Oligomers.

Mannini B, Vecchi G, Labrador-Garrido A, Fabre B, Fani G, Franco JM, Lilley K, Pozo D, Vendruscolo M, Chiti F, Dobson CM, Roodveldt C.

ACS Chem Neurosci. 2019 Aug 21;10(8):3464-3478. doi: 10.1021/acschemneuro.9b00088. Epub 2019 Aug 2.


Fast Fluorescence Lifetime Imaging Reveals the Aggregation Processes of α-Synuclein and Polyglutamine in Aging Caenorhabditis elegans.

Laine RF, Sinnige T, Ma KY, Haack AJ, Poudel C, Gaida P, Curry N, Perni M, Nollen EAA, Dobson CM, Vendruscolo M, Kaminski Schierle GS, Kaminski CF.

ACS Chem Biol. 2019 Jul 19;14(7):1628-1636. doi: 10.1021/acschembio.9b00354. Epub 2019 Jun 27.


Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates the associated behavioural response.

Sinnige T, Ciryam P, Casford S, Dobson CM, de Bono M, Vendruscolo M.

PLoS One. 2019 May 31;14(5):e0217746. doi: 10.1371/journal.pone.0217746. eCollection 2019.


Common Regulatory Pathways Mediate Activity of MicroRNAs Inducing Cardiomyocyte Proliferation.

Torrini C, Cubero RJ, Dirkx E, Braga L, Ali H, Prosdocimo G, Gutierrez MI, Collesi C, Licastro D, Zentilin L, Mano M, Zacchigna S, Vendruscolo M, Marsili M, Samal A, Giacca M.

Cell Rep. 2019 May 28;27(9):2759-2771.e5. doi: 10.1016/j.celrep.2019.05.005.


Effects of α-tubulin acetylation on microtubule structure and stability.

Eshun-Wilson L, Zhang R, Portran D, Nachury MV, Toso DB, Löhr T, Vendruscolo M, Bonomi M, Fraser JS, Nogales E.

Proc Natl Acad Sci U S A. 2019 May 21;116(21):10366-10371. doi: 10.1073/pnas.1900441116. Epub 2019 May 9.


Probing the Origin of the Toxicity of Oligomeric Aggregates of α-Synuclein with Antibodies.

Cascella R, Perni M, Chen SW, Fusco G, Cecchi C, Vendruscolo M, Chiti F, Dobson CM, De Simone A.

ACS Chem Biol. 2019 Jun 21;14(6):1352-1362. doi: 10.1021/acschembio.9b00312. Epub 2019 May 14.


Intrinsically aggregation-prone proteins form amyloid-like aggregates and contribute to tissue aging in Caenorhabditis elegans.

Huang C, Wagner-Valladolid S, Stephens AD, Jung R, Poudel C, Sinnige T, Lechler MC, Schlörit N, Lu M, Laine RF, Michel CH, Vendruscolo M, Kaminski CF, Kaminski Schierle GS, David DC.

Elife. 2019 May 3;8. pii: e43059. doi: 10.7554/eLife.43059.


Secondary nucleation and elongation occur at different sites on Alzheimer's amyloid-β aggregates.

Scheidt T, Łapińska U, Kumita JR, Whiten DR, Klenerman D, Wilson MR, Cohen SIA, Linse S, Vendruscolo M, Dobson CM, Knowles TPJ, Arosio P.

Sci Adv. 2019 Apr 17;5(4):eaau3112. doi: 10.1126/sciadv.aau3112. eCollection 2019 Apr.


Identifying A- and P-site locations on ribosome-protected mRNA fragments using Integer Programming.

Ahmed N, Sormanni P, Ciryam P, Vendruscolo M, Dobson CM, O'Brien EP.

Sci Rep. 2019 Apr 18;9(1):6256. doi: 10.1038/s41598-019-42348-x.


The free energy landscape of the oncogene protein E7 of human papillomavirus type 16 reveals a complex interplay between ordered and disordered regions.

Kukic P, Lo Piccolo GM, Nogueira MO, Svergun DI, Vendruscolo M, Felli IC, Pierattelli R.

Sci Rep. 2019 Apr 9;9(1):5822. doi: 10.1038/s41598-019-41925-4.


The metastability of the proteome of spinal motor neurons underlies their selective vulnerability in ALS.

Yerbury JJ, Ooi L, Blair IP, Ciryam P, Dobson CM, Vendruscolo M.

Neurosci Lett. 2019 Jun 21;704:89-94. doi: 10.1016/j.neulet.2019.04.001. Epub 2019 Apr 3.


Different soluble aggregates of Aβ42 can give rise to cellular toxicity through different mechanisms.

De S, Wirthensohn DC, Flagmeier P, Hughes C, Aprile FA, Ruggeri FS, Whiten DR, Emin D, Xia Z, Varela JA, Sormanni P, Kundel F, Knowles TPJ, Dobson CM, Bryant C, Vendruscolo M, Klenerman D.

Nat Commun. 2019 Apr 4;10(1):1541. doi: 10.1038/s41467-019-09477-3.


The Amyloid Phenomenon and Its Significance in Biology and Medicine.

Dobson CM, Knowles TPJ, Vendruscolo M.

Cold Spring Harb Perspect Biol. 2019 Apr 1. pii: a033878. doi: 10.1101/cshperspect.a033878. [Epub ahead of print]


A method of predicting the in vitro fibril formation propensity of Aβ40 mutants based on their inclusion body levels in E. coli.

Sanagavarapu K, Nüske E, Nasir I, Meisl G, Immink JN, Sormanni P, Vendruscolo M, Knowles TPJ, Malmendal A, Cabaleiro-Lago C, Linse S.

Sci Rep. 2019 Mar 6;9(1):3680. doi: 10.1038/s41598-019-39216-z.


Protein Solubility Predictions Using the CamSol Method in the Study of Protein Homeostasis.

Sormanni P, Vendruscolo M.

Cold Spring Harb Perspect Biol. 2019 Mar 4. pii: a033845. doi: 10.1101/cshperspect.a033845. [Epub ahead of print]


Atomic force microscopy for single molecule characterisation of protein aggregation.

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

Arch Biochem Biophys. 2019 Mar 30;664:134-148. doi: 10.1016/ Epub 2019 Feb 8. 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. 2019 Apr;87(4):302-312. doi: 10.1002/prot.25652. Epub 2019 Feb 5.


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, Hernandez Villegas NC, 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. 2019 Jun;56:37-45. doi: 10.1016/ Epub 2018 Nov 28. 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 Dec 11;14(12):6632-6641. doi: 10.1021/acs.jctc.8b00738. Epub 2018 Nov 28.


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 Dec 19;9(12):2959-2971. doi: 10.1021/acschemneuro.8b00141. Epub 2018 Aug 10.


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.

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