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Showing 1 to 20 of 31 for “"protein unfolding"”.
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Multi-domain Protein Unfolding Pathway Studies by Single Molecule Techniques
<p>Large multi-domain proteins, which are ubiquitous in the proteomes in eukaryotic and prokaryotic organisms, still lack intensive studies on their folding mechanisms due to their complicated interactions between and inside of their domains. My work is broadly aimed at characterize folding …
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Probing static disorder in protein unfolding and chemical reactions by single-molecule force spectroscopy
… reactions under mechanical force, including protein unfolding and disulfide-bond reduction, probed at the single-molecule level. The advent of single-molecule force spectroscopy has allowed the direct measure of force-dependent reaction rates, providing a powerful approach to extract the …
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The mechanics of mussel byssal threads : a study in protein unfolding and graded structures
… with loading (an evolution that is dominated by protein unfolding). These material models will then be incorporated into three dimensional finite element model of the thread, in order to gain insight into the design of graded structures.
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Proteins on the edge : transitions of structure ensembles in protein unfolding and protein-protein binding
Proteins move. Their incessant fluctuations are governed by a complex interplay between thousands of atoms. Experimental structures, providing exact coordinates for every atom, hence only represent the average of a diverse ensemble of interchanging conformations. Molecular motion is often the …
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Mechanical unfolding of membrane proteins captured with single-molecule AFM techniques
… which serves as a model system for this class of proteins. Mechanical pulling of BetP molecules embedded into the lipid membranes resulted in a step-wise unfolding of the protein and revealed insights into its structural stability. Effect of the lipid environment, N- and C-terminal extensions on …
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Green fluorescent protein as a mechanical sensor
… dynamics. To this end, the green fluorescent protein (GFP) is considered as a mechanical sensor candidate with many desirable characteristics. Implicit solvent molecular dynamics CHARMM simulations demonstrated details inaccessible by AFM and OT methods, such as the linkage dependency of …
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Comparing Solution-Phase and Gas-Phase Protein Stability Using Ion Mobility and Differential Mobility Mass Spectrometry
A critical quality attribute for many proteins concerning biopharmaceutical products is the proteins stability. Current stability assays are lengthy but some quick stability assays to determine the proteins melting temperature include thermal ramps of a protein using a fluorescent dye to monitor …
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Cooperativity and communication in archaeal Cdc48·20S, an ancient proteolytic machine
… use the energy of ATP hydrolysis to power the unfolding and translocation of protein substrates into compartmentalized peptidases for regulated proteolysis. Cdc48 is a highly conserved AAA+ homohexameric unfoldase which is made up of two AAA+ rings. Each ring can, in principle, bind and …
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Unique Features of PTB RRMs: Insight into Protein Motions and RNA Binding
Polypyrimidine tract binding protein: PTB) is a highly conserved RNA binding protein comprised of four RRMs: RNA recognition motifs). RRMs are extremely prevalent in all kingdoms of life, and have been very well characterized in terms of structure and RNA binding properties. However, all four RRMs …
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Mechanistic studies of the AAA+ molecular motor ClpXP
… motor for the ClpXP protease system. ClpX binds protein substrates via an amino acid sequence known as a tag, denatures them, and translocates them into the associated peptidase, ClpP. ClpX utilizes the energy from ATP hydrolysis to pull on bound substrates, destabilizing folded substrates and …
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Physicochemical Aspects of the Two-Step Mechanism of Nucleation in Protein Solutions
Protein-rich liquid clusters exist in solutions of numerous proteins. They play the role of nucleation precursors of ordered solids of both folded proteins and partially misfolded chains. Examples include protein crystals, sickle-cell hemoglobin polymers, and amyloid fibrils. The clusters hold the …
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Advancing fast relaxation imaging to determine protein stability and folding kinetics on poly(n-isopropyl acrylamide) films
… polymer PNIPAM to capture and release cells or proteins for medical purposes; however, this assumes that PNIPAM does not perturb the stability of biomolecules. Previous analytical and spectroscopic techniques have not been able to confirm this assumption due to limitations in detection of …
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Mechanistic studies of a AAA+ protease
… energy-dependent degradation of most cytosolic proteins. Substrates for AAA+ proteases are unfolded and translocated into a compartmental peptidase. The requirement for protein unfolding raises several questions. How easily are proteins unfolded within the native environment of a cell? Are some …
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Role of communication between subunits and enzymes in ClpXP-mediated substrate unfolding and degradation
… important roles in quality control by helping proteins fold, by dismantling hyper-stable complexes, and by degrading unwanted proteins. The highly conserved AAA+ Clp/Hsp100 proteins are ATPases which function as disassembly chaperones as well as essential components of energy-dependent …
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Structure and activity of protein-nanoparticle conjugates: towards a strategy for optimizing the interface
Nanoparticle-protein conjugates have a variety of applications in imaging, sensing, assembly and control. The nanoparticle-protein interface is made of numerous complex interactions between protein side-chains and the nanoparticle surface, which are likely to affect protein structure and compromise …
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Mass spectrometric indentification of formaldehyde-induced modifications of peptides and proteins under in vivo protein cross-linking conditions
Formaldehyde cross-linking has been used to study protein-protein interactions in cells. Its short spacer arm, ability to permeate through cell membrane and the reversibility of the cross-linking reaction makes this a desirable cross-linker for in vivo studies. Although it has been widely used as a …
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Investigating the Electrostatic Properties and Dynamics of Amyloidogenic Proteins with Polarizable Molecular Dynamics Simulations
… sequences, the underlying amyloidogenic proteins form similar supramolecular fibril structures that are highly stable and resistant to physical and chemical denaturation. AD is characterized by two toxic lesions: extracellular amyloid β-peptide (Aβ) plaques and intracellular …
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Energy Stress Causes Chaperones to Assemble Into Cytoplasmic Complexes
<p>The majority of proteins require molecular chaperones to assist their folding into tertiary and quaternary structures. Certain stresses can compromise the weak hydrophobic forces responsible for these structures and lead to protein unfolding, misfolding, and aggregation. Aggregates of proteins …
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Lysozyme encapsulated gold nanocluster for studying protein denaturation
Protein denaturation is a change in a protein's structure from its native folded state to a non-native misfolded state. Protein denaturation is the cause of many diseases. Current methods used for protein denaturation studies have provided useful information regarding protein structures, but have …
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Mechanisms of substrate recognition by the AAA+ protease HslUV
Protein degradation is a central component of all biological processes. The proteome must constantly change in response to environmental stimuli. As a result, protein synthesis and regulated proteolysis are vital to cell survival. In Escherichia coli, the protease HslUV is one of five ATP-dependent …
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