Literature DB >> 22509003

Intrinsic disorder modulates protein self-assembly and aggregation.

Alfonso De Simone1, Craig Kitchen, Ann H Kwan, Margaret Sunde, Christopher M Dobson, Daan Frenkel.   

Abstract

Protein molecules have evolved to adopt distinctive and well-defined functional and soluble states under physiological conditions. In some circumstances, however, proteins can self-assemble into fibrillar aggregates designated as amyloid fibrils. In vivo these processes are normally associated with severe pathological conditions but can sometimes have functional relevance. One such example is the hydrophobins, whose aggregation at air-water interfaces serves to create robust protein coats that help fungal spores to resist wetting and thus facilitate their dispersal in the air. We have performed multiscale simulations to address the molecular determinants governing the formation of functional amyloids by the class I fungal hydrophobin EAS. Extensive samplings of full-atom replica-exchange molecular dynamics and coarse-grained simulations have allowed us to identify factors that distinguish aggregation-prone from highly soluble states of EAS. As a result of unfavourable entropic terms, highly dynamical regions are shown to exert a crucial influence on the propensity of the protein to aggregate under different conditions. More generally, our findings suggest a key role that specific flexible structural elements can play to ensure the existence of soluble and functional states of proteins under physiological conditions.

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Year:  2012        PMID: 22509003      PMCID: PMC3344965          DOI: 10.1073/pnas.1118048109

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  40 in total

1.  Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation.

Authors:  Jane S Richardson; David C Richardson
Journal:  Proc Natl Acad Sci U S A       Date:  2002-03-05       Impact factor: 11.205

Review 2.  Emerging ideas on the molecular basis of protein and peptide aggregation.

Authors:  D Thirumalai; D K Klimov; R I Dima
Journal:  Curr Opin Struct Biol       Date:  2003-04       Impact factor: 6.809

Review 3.  Protein folding and misfolding.

Authors:  Christopher M Dobson
Journal:  Nature       Date:  2003-12-18       Impact factor: 49.962

4.  Rationalization of the effects of mutations on peptide and protein aggregation rates.

Authors:  Fabrizio Chiti; Massimo Stefani; Niccolò Taddei; Giampietro Ramponi; Christopher M Dobson
Journal:  Nature       Date:  2003-08-14       Impact factor: 49.962

5.  A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.

Authors:  Yong Duan; Chun Wu; Shibasish Chowdhury; Mathew C Lee; Guoming Xiong; Wei Zhang; Rong Yang; Piotr Cieplak; Ray Luo; Taisung Lee; James Caldwell; Junmei Wang; Peter Kollman
Journal:  J Comput Chem       Date:  2003-12       Impact factor: 3.376

Review 6.  Protein misfolding, functional amyloid, and human disease.

Authors:  Fabrizio Chiti; Christopher M Dobson
Journal:  Annu Rev Biochem       Date:  2006       Impact factor: 23.643

7.  Life on the edge: a link between gene expression levels and aggregation rates of human proteins.

Authors:  Gian Gaetano Tartaglia; Sebastian Pechmann; Christopher M Dobson; Michele Vendruscolo
Journal:  Trends Biochem Sci       Date:  2007-04-06       Impact factor: 13.807

8.  The hydrophobin EAS is largely unstructured in solution and functions by forming amyloid-like structures.

Authors:  J P Mackay; J M Matthews; R D Winefield; L G Mackay; R G Haverkamp; M D Templeton
Journal:  Structure       Date:  2001-02-07       Impact factor: 5.006

9.  Designed protein tetramer zipped together with a hydrophobic Alzheimer homology: a structural clue to amyloid assembly.

Authors:  D E Otzen; O Kristensen; M Oliveberg
Journal:  Proc Natl Acad Sci U S A       Date:  2000-08-29       Impact factor: 11.205

10.  Intrinsic protein disorder in complete genomes.

Authors:  A K Dunker; Z Obradovic; P Romero; E C Garner; C J Brown
Journal:  Genome Inform Ser Workshop Genome Inform       Date:  2000
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  35 in total

1.  Protective spin-labeled fluorenes maintain amyloid beta peptide in small oligomers and limit transitions in secondary structure.

Authors:  Robin Altman; Sonny Ly; Silvia Hilt; Jitka Petrlova; Izumi Maezawa; Tamás Kálai; Kálmán Hideg; Lee-Way Jin; Ted A Laurence; John C Voss
Journal:  Biochim Biophys Acta       Date:  2015-09-14

2.  Oligomerization Alters Binding Affinity Between Amyloid Beta and a Modulator of Peptide Aggregation.

Authors:  Silvia Hilt; Tatu Rojalin; Tapani Viitala; Artturi Koivuniemi; Alex Bunker; Sebastian Wachsmann Hogiu; Tamás Kálai; Kálmán Hideg; Marjo Yliperttula; John C Voss
Journal:  J Phys Chem C Nanomater Interfaces       Date:  2017-10-10       Impact factor: 4.126

Review 3.  Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies.

Authors:  Jessica Nasica-Labouze; Phuong H Nguyen; Fabio Sterpone; Olivia Berthoumieu; Nicolae-Viorel Buchete; Sébastien Coté; Alfonso De Simone; Andrew J Doig; Peter Faller; Angel Garcia; Alessandro Laio; Mai Suan Li; Simone Melchionna; Normand Mousseau; Yuguang Mu; Anant Paravastu; Samuela Pasquali; David J Rosenman; Birgit Strodel; Bogdan Tarus; John H Viles; Tong Zhang; Chunyu Wang; Philippe Derreumaux
Journal:  Chem Rev       Date:  2015-03-19       Impact factor: 60.622

4.  SODA: prediction of protein solubility from disorder and aggregation propensity.

Authors:  Lisanna Paladin; Damiano Piovesan; Silvio C E Tosatto
Journal:  Nucleic Acids Res       Date:  2017-07-03       Impact factor: 16.971

5.  Chaperone activation by unfolding.

Authors:  Linda Foit; Jenny S George; Bin W Zhang; Charles L Brooks; James C A Bardwell
Journal:  Proc Natl Acad Sci U S A       Date:  2013-03-04       Impact factor: 11.205

6.  Propensity to form amyloid fibrils is encoded as excitations in the free energy landscape of monomeric proteins.

Authors:  Pavel I Zhuravlev; Govardhan Reddy; John E Straub; D Thirumalai
Journal:  J Mol Biol       Date:  2014-05-17       Impact factor: 5.469

7.  Structural dynamics and conformational equilibria of SERCA regulatory proteins in membranes by solid-state NMR restrained simulations.

Authors:  Alfonso De Simone; Kaustubh R Mote; Gianluigi Veglia
Journal:  Biophys J       Date:  2014-06-17       Impact factor: 4.033

8.  Botcinic acid biosynthesis in Botrytis cinerea relies on a subtelomeric gene cluster surrounded by relics of transposons and is regulated by the Zn2Cys6 transcription factor BcBoa13.

Authors:  Antoine Porquier; Javier Moraga; Guillaume Morgant; Bérengère Dalmais; Adeline Simon; Hind Sghyer; Isidro G Collado; Muriel Viaud
Journal:  Curr Genet       Date:  2019-03-08       Impact factor: 3.886

9.  The first year.

Authors:  Johannes Attems
Journal:  Acta Neuropathol       Date:  2019-12-12       Impact factor: 17.088

10.  Structure insight of GSDMD reveals the basis of GSDMD autoinhibition in cell pyroptosis.

Authors:  Siyun Kuang; Jun Zheng; Hui Yang; Suhua Li; Shuyan Duan; Yanfang Shen; Chaoneng Ji; Jianhua Gan; Xue-Wei Xu; Jixi Li
Journal:  Proc Natl Acad Sci U S A       Date:  2017-09-19       Impact factor: 11.205

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