Dataset Information

From the test tube to the cell: exploring the folding and aggregation of a beta-clam protein.

ABSTRACT: A crucial challenge in present biomedical research is the elucidation of how fundamental processes like protein folding and aggregation occur in the complex environment of the cell. Many new physico-chemical factors like crowding and confinement must be considered, and immense technical hurdles must be overcome in order to explore these processes in vivo. Understanding protein misfolding and aggregation diseases and developing therapeutic strategies to these diseases demand that we gain mechanistic insight into behaviors and misbehaviors of proteins as they fold in vivo. We have developed a fluorescence approach using FlAsH labeling to study the thermodynamics of folding of a model beta-rich protein, cellular retinoic acid binding protein (CRABP) in Escherichia coli cells. The labeling approach has also enabled us to follow aggregation of a modified version of CRABP and chimeras between CRABP and huntingtin exon 1 with its glutamine repeat tract. In this article, we review our recent results using FlAsH labeling to study in-vivo folding and present new observations that hint at fundamental differences between the thermodynamics and kinetics of protein folding in vivo and in vitro.

SUBMITTER: Ignatova Z

PROVIDER: S-EPMC2904568 | biostudies-literature | 2007

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

From the test tube to the cell: exploring the folding and aggregation of a beta-clam protein.

Ignatova Zoya Z Krishnan Beena B Bombardier Jeffrey P JP Marcelino Anna Marie C AM Hong Jiang J Gierasch Lila M LM

Biopolymers 20070101 2

A crucial challenge in present biomedical research is the elucidation of how fundamental processes like protein folding and aggregation occur in the complex environment of the cell. Many new physico-chemical factors like crowding and confinement must be considered, and immense technical hurdles must be overcome in order to explore these processes in vivo. Understanding protein misfolding and aggregation diseases and developing therapeutic strategies to these diseases demand that we gain mechanis ...[more]

PMID: 17206628

Similar Datasets

Project description:Aggregation of ?-Synuclein (?S) protein to amyloid fibrils is a neuropathological hallmark of Parkinson's disease (PD). Growing evidence suggests that extracellular ?S aggregation plays a pivotal role in neurodegeneration found in PD in addition to the intracellular ?S aggregates in Lewy bodies (LB). Here, we identified and compared a diverse set of molecules capable of mitigating protein aggregation and exogenous toxicity of ?SA53T, a more aggregation-prone ?S mutant found in familial PD. For the first time, we investigated the ?S anti-amyloid activity of semi-synthetic flavonoid 2', 3', 4' trihydroxyflavone or 2-D08, which was compared with natural flavones myricetin and transilitin, as well as such structurally diverse polyphenols as honokiol and punicalagin. Additionally, two novel synthetic compounds with a dibenzyl imidazolidine scaffold, Compound 1 and Compound 2, were also investigated as they exhibited favorable binding with ?SA53T. All seven compounds inhibited ?SA53T aggregation as demonstrated by Thioflavin T fluorescence assays, with modified fibril morphology observed by transmission electron microscopy. Ion mobility-mass spectrometry (IM-MS) was used to monitor the structural conversion of native ?SA53T into amyloidogenic conformations and all seven compounds preserved the native unfolded conformations of ?SA53T following 48 h incubation. The presence of each test compound in a 1:2 molar ratio was also shown to inhibit the neurotoxicity of preincubated ?SA53T using phaeochromocytoma (PC12) cell viability assays. Among the seven tested compounds 2-D08, honokiol, and the synthetic Compound 2 demonstrated the highest inhibition of aggregation, coupled with neuroprotection from preincubated ?SA53T in vitro. Molecular docking predicted that all compounds bound near the lysine-rich region of the N-terminus of ?SA53T, where the flavonoids and honokiol predominantly interacted with Lys 23. Overall, these findings highlight that (i) restricted vicinal trihydroxylation in the flavone B-ring is more effective in stabilizing the native ?S conformations, thus blocking amyloidogenic aggregation, than dihydroxylation aggregation in both A and B-ring, and (ii) honokiol, punicalagin, and the synthetic imidazolidine Compound 2 also inhibit ?S amyloidogenic aggregation by stabilizing its native conformations. This diverse set of molecules acting on a singular pathological target with predicted binding to ?SA53T in the folding-prone N-terminal region may contribute toward novel drug-design for PD.

Dataset Information

From the test tube to the cell: exploring the folding and aggregation of a beta-clam protein.

Publications

From the test tube to the cell: exploring the folding and aggregation of a beta-clam protein.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets