WorldCat Identities

Plevin, Michael

Overview
Works: 6 works in 6 publications in 2 languages and 10 library holdings
Genres: Academic theses 
Roles: Other, Thesis advisor, Opponent
Publication Timeline
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Most widely held works by Michael Plevin
Etude structurale et fonctionnelle par RMN d'une chaperonine de 1 MDa en action by Guillaume Mas( )

1 edition published in 2015 in French and held by 2 WorldCat member libraries worldwide

Chaperonins are essential molecular chaperons for the refolding of proteins in the cells. Size and complexity of these biological machineries make complex the study of their structural and functional properties. NMR spectroscopy offers an unique ability to monitor structural and dynamic changes in real-time and at atomic resolution. However, the NMR studies of large proteins and complexes has been a real challenge for a long time. In the first part of this thesis, it has been shown that the combination of methyl specific labeling, optimized NMR spectroscopy for large assemblies and electron microscopy can be used to monitor the different states of the functional cycle of a 1 MDa chaperonin. To study this mechanism, the native chaperonin was reconstituted with a labeling of the methionines and valines methyl groups. Methionines residues have been used as probes to identify the NMR spectra corresponding to intermediates states and active species of the functional cycle. Thanks to theses probes, it has been possible to follow in real time the structural rearrangements corresponding to the different conformations of the chaperonin during its functional cycle. The second part deals with the characterization of the interaction between the chaperonin and an unfolded protein. Observation of the stabilization of the unfolded protein by the chaperonin allowed to identify the holdase activity of the chaperonin. Using a clever combination of a differential methyl labeling and optimized NMR spectroscopy for large assemblies, it has been possible to follow the refolding of the unfolded protein by the chaperonin and the effects of the unfolded protein on the functional cycle of the chaperonin in action
Dissection de TFIID, un facteur de transcription général humain : Études structurales etfonctionnelles des sous-ensembles du TFIID human by K. M Gupta( )

1 edition published in 2015 in French and held by 2 WorldCat member libraries worldwide

Eukaryotic genomes are highly complex and can be very large. For example, the human genome contains approximately 20,000-25,000 protein coding genes. Expression of these genes needs to be tightly regulated at many levels, including chromatin organization, gene transcription, mRNA processing and export and translation, for proper functioning of cellular machinery. Many proteins and protein complexes are involved in these essential regulatory processes, examples include chromatin remodelers, transcriptional activators and coactivators, transcriptional repressors and notably the general transcription machinery. Transcription of protein coding genes in eukaryotes is called Class II gene transcription, and is catalyzed by RNA polymerase II (Pol II). Gene transcription by Pol II requires the cooperative interaction of multiple proteins and protein complexes to facilitate the assembly of a preinitiation complex (PIC) at the core promoter. The PIC comprises Pol II and the General Transcription Factors (GTFs)- TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH, together with the Mediator complex and a large variety of transcriptional coactivators.A fundamental step in PIC assembly is recognition of the core promoter by GTF TFIID, a magdalton sized multiprotein complex. In humans, TFIID comprises about twenty subunits made up of 14 different proteins - the TATA box binding protein (TBP) and its associated factors (TAFs, numbered 1 to 13). A range of studies on human TFIID and its subassemblies have been carried out since its discovery more than two decades ago, to understand the structure and mechanism of this essential GTF, but the architecture of TFIID, its activities, its functions, its inner workings and the mechanisms of its cellular assembly have eluded detailed understanding to date.This thesis describes biochemical, biophysical, structural and functional studies carried out on three distinct human TFIID subassemblies. We used a number of structural biology techniques, including crystallization, nuclear magnetic resonance (NMR) spectroscopy and small angle X-ray scattering (SAXS) to analyse a complex formed by the human TBP associated factors TAF1 and TAF7. These structural studies provide detailed insights into the intricate interaction interface formed by TAF1 and TAF7, and, together with other data available from the literature, highlight the dynamic nature of the TAF1/TAF7 interaction in the human TFIID complex.In a second study, we analyzed a novel complex formed by TAF11, TAF13 and TBP using a range of biophysical and biochemical methods including electrophoretic mobility shift assay (EMSA), analytical ultracentrifugation (AUC), size exclusion chromatography (SEC) analysis, pull-down assay, native mass-spectroscopy and chemical cross-linking mass spectroscopy (CLMS). This complex is reminiscent of a so-called TATA-box mimicry discovered previously in a TAF1/TBP complex.As part of the ongoing efforts in the Berger laboratory to determine the structure of human holo-TFIID, we furthermore produced and purified a large (~900 kDa) TFIID subassembly called 9TAF, which is composed of nine different TBP associated factors. We carried out negative stain EM studies and random conical tilt (RCT) analysis on 9TAF to obtain low resolution structural information. These studies set the stage for future cryo-EM studies of this 9TAF complex to obtain a high(er) resolution model to decipher the inner workings of human TFIID
Etudes biophysiques de l'interaction entre la protéine humaine TRBP et un précurseur de microARN oncogène by Matthieu Benoit( )

1 edition published in 2013 in French and held by 2 WorldCat member libraries worldwide

MicroRNAs (miRNA) are a class of small non-coding RNAs that regulate gene expression through RNA interference (RNAi). Human miRNAs are generated via a series of enzymatic processing steps. In particular, in the cytoplasm, the precursor miRNA (pre-miRNA) is recognized and cleaved by a complex containing the RNase III enzyme Dicer and several non-catalytic accessory proteins. HIV TAR element-binding protein (TRBP) is a constituent of the Dicer complex, which augments complex stability, has effect on the cleavage kinetics and on the cleavage site and potentially functions in substrate recognition and product transfer to the RNA-induced silencing complex (RISC). TRBP is composed of three double stranded RNA binding domains (dsRBDs). The RNA binding region of TRBP is composed of the first two dsRBDs and an uncharacterized interdomain region. The present study reports the in vitro biophysical characterization of the RNA binding region of TRBP in the apo state and in the RNA bound state with the two successive cytoplasmic precursors of the oncogenic human microRNA miR-155, the hairpin pre-miR-155 and the related Dicer product miR-155/miR-155* duplex. The study shows that the RNA binding region of TRBP is monomeric and comprises two independent double-stranded RNA-binding domains connected by a 60 residues flexible linker. The first dsRBD, uncharacterized previously in solution, undergoes a full folding/unfolding equilibrium in a wide range of physico-chemical conditions. The two first dsRBDs of TRBP can interact with one microRNA precursor and two RNA binding regions can interact with one precursor molecule. The RNA-binding region of TRBP interacts with both pre-miR-155 and miR-155/miR-155* duplex with similar affinities. In the complex with one RNA binding region of TRBP bound to either pre-miR-155 or miR-155/miR-155* duplex, no evidence of contact between the two dsRBDs were observed and the protein interacts with both precursors via the same protein binding surface. The data presented here suggest that the RNA binding region of TRBP can play a role before and after processing of pre-miRNAs by Dicer, including in the RISC loading complex
Etudes de structure, interactions et dynamique dans des complexes de protéines "chaperone" à l'échelle atomique par spectroscopie RMN by Katharina Weinhaeupl( )

1 edition published in 2018 in English and held by 2 WorldCat member libraries worldwide

The diverse group of molecular chaperones is dedicated to accompany, fold and protect other proteins until they reach their final conformation and loca- tion inside the cell. To this end, molecular chaperones need to be specialized in performing specific tasks, like folding, transport or disaggregation, and versatile in their recognition pattern to engage many di erent client pro- teins. Moreover, molecular chaperones need to be able to interact with each other and with other components of the protein quality control system in a complex network. Interactions between the di erent partners in this network and between the substrate and the chaperone are often dynamic processes, which are especially di cult to study using standard structural biology tech- niques. Consequently, structural data on chaperone/substrate complexes are sparse, and the mechanisms of chaperone action are poorly understood. In this thesis I present investigations of the structure, dynamics and substrate- interactions of two molecular chaperones, using various biophysical and in vivo methods.In the first part I show that the mitochondrial membrane protein chap- erone TIM910 binds its substrates in a highly dynamic manner. Not only is the TIM910 complex in constant exchange between monomeric and hex- americ species, but also the bound substrate samples multiple conformations on a millisecond timescale. Based on nuclear magnetic resonance (NMR), small-angle X-ray scattering (SAXS), analytical ultracentrifugation (AUC) and in vivo mutational experiments I propose a structural model of the chap- erone/membrane protein interaction. TIM910 binds its substrates in a hy- drophobic pocket on the exterior of the chaperone in a modular fashion, where the number of TIM910 complexes bound depends on the length of the substrate.In the second part I studied the behavior of the N-terminal receptor do- main of the ClpC1 unfoldase from M.tuberculosis in the presence of di erent antibiotics and ligands. The N-terminal domain of ClpC1 is the binding site for various new antibiotics against M.tuberculosis. The antibiotic cyclomarin completely abolishes dynamics induced by the ligand arginine-phosphate. We propose that this suppression of dynamics is the underlying principle for the mechanism of action of this antibiotic.In both cases X-ray structures of the apo or antibiotic bound form were available, but not su cient to explain the mechanism of action. The X- ray structure of TIM910 provided no evidence on where or how substrates are bound. Likewise, X-ray structures of the apo and cyclomarin-bound N-terminal domain of ClpC1 show only minor di erences in structure.Both examples show that static structural data is often not enough to explain how a molecular system works, and only the combination of di er- ent techniques, including newly developed methods enable the atomic-level understanding of chaperone/substrate complexes
Molecular mechanisms and dynamics of the segregation of plasmid pB171 from an enteropathogenic strain of Escherichia coli by Iman Hussein Fadhiladeen Alnaqshabandy( )

1 edition published in 2020 in English and held by 1 WorldCat member library worldwide

Recognition of precursor microRNAs by the Dicer cofactor TRBP by Banushan Balansethupathy( )

1 edition published in 2018 in English and held by 1 WorldCat member library worldwide

 
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Audience Level
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Audience level: 0.94 (from 0.85 for Molecular ... to 0.96 for Etude stru ...)

Alternative Names
Michael J Plevin wetenschapper

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