Browsing by Subject "protein folding"

Now showing 1 - 6 of 6
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    Chaperonins keeping a lid on folding proteins
    (2001-09) Kusmierczyk, Andrew R; Martin, Jörg
    Two classes of chaperonins are known in all groups of organisms to participate in the folding of newly synthesized proteins. Whereas bacterial type I chaperonins use a reversibly binding cofactor to temporarily sequester folding substrate proteins within the cylindrical chaperonin cavity, type II chaperonins in archaea and the eukaryotic cytosol appear to have evolved a built-in lid for this purpose. Not entirely surprisingly, this has consequences for the folding modes of the two types of chaperonins.
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    From sequence to structure, to function, and back again: Integrating knowledge-based approaches with physical intuitions for protein folding, binding, and design
    (Office of the Vice Chancellor for Research, 2010-04-09) Zhou, Yaoqi
    By combining physical and knowledge-based approaches, state-of-the-art bioinformatics tools are developed for protein structure prediction, function prediction (DNA binding) and structurebased protein and ligand design.
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    From sequence to structure, to function, and back again: Integrating knowledge-based approaches with physical intuitions for protein folding, binding, and design
    (Office of the Vice Chancellor for Research, 2011-04-08) Zhou, Yaoqi
    Most biological activities are directed and/or regulated by proteins made of a gene-specified sequence of 20 amino-acid residue types. As a result, function or malfunction of specific proteins is responsible for almost all diseases. Proteins perform their function through their unique, self-assembled (folded) three-dimensional structures and through their specific binding to small molecules, to DNA/RNA (e.g. transcription factors that regulate gene expressions), or to other proteins (e.g. molecular recognition in signal transduction). Thus, how to predict the structure of a protein from its amino-acid sequence, discover the function from its structure and, then, design the sequence from its function or structure are the most essential problems in structural biology. In this poster, we will illustrate how the coupling of physical intuitions with learning from structural databases can go a long way toward untangling the complex relation between sequence, structure and function of proteins.
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    High salt-induced conversion of Escherichia coli GroEL into a fully functional thermophilic chaperonin
    (2000-08) Kusmierczyk, Andrew R; Martin, Jörg
    The GroE chaperonin system can adapt to and function at various environmental folding conditions. To examine chaperonin-assisted protein folding at high salt concentrations, we characterized Escherichia coli GroE chaperonin activity in 1.2 M ammonium sulfate. Our data are consistent with GroEL undergoing a conformational change at this salt concentration, characterized by elevated ATPase activity and increased exposure of hydrophobic surface, as indicated by increased binding of the fluorophore bis-(5,5′)-8-anilino-1-naphthalene sulfonic acid to the chaperonin. The presence of the salt results in increased substrate stringency and dependence on the full GroE system for release and productive folding of substrate proteins. Surprisingly, GroEL is fully functional as a thermophilic chaperonin in high concentrations of ammonium sulfate and is stable at temperatures up to 75 °C. At these extreme conditions, GroEL can suppress aggregation and mediate refolding of non-native proteins.
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    Online protein unfolding characterized by ion mobility electron capture dissociation mass spectrometry: Cytochrome C from neutral and acidic solutions
    (Springer, 2023-02) Cain, Rebecca L.; Webb, Ian K.; Chemistry and Chemical Biology, School of Science
    Electrospray ionization mass spectrometry (ESI-MS) experiments, including ion mobility spectrometry mass spectrometry (ESI-IMS-MS) and electron capture dissociation (ECD) of proteins ionized from aqueous solutions, have been used for the study of solution-like structures of intact proteins. By mixing aqueous proteins with denaturants online before ESI, the amount of protein unfolding can be precisely controlled and rapidly analyzed, permitting the characterization of protein folding intermediates in protein folding pathways. Herein, we mixed various pH solutions online with aqueous cytochrome C for unfolding and characterizing its unfolding intermediates with ESI-MS charge state distribution measurements, IMS, and ECD. The presence of folding intermediates and unfolded cytochrome c structures were detected from changes in charge states, arrival time distributions (ATDs), and ECD. We also compared structures from nondenaturing and denaturing solution mixtures measured under “gentle” (i.e., low energy) ion transmission conditions with structures measured under “harsh” (i.e., higher energy) transmission. This work confirms that when using “gentle” instrument conditions, the gas-phase cytochrome c ions reflect attributes of the various solution-phase structures. However, “harsh” conditions that maximize ion transmission produce extended structures that no longer correlate with changes in solution structure.
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    Thermodynamics of Protein Folding Studied by Umbrella Sampling along a Reaction Coordinate of Native Contacts
    (ACS, 2017) Meshkin, Hamed; Zhu, Fangqiang; Physics, School of Science
    Spontaneous transitions between the native and non-native protein conformations are normally rare events that hardly take place in typical unbiased molecular dynamics simulations. It was recently demonstrated that such transitions can be well described by a reaction coordinate, Q, that represents the collective fraction of the native contacts between the protein atoms. Here we attempt to use this reaction coordinate to enhance the conformational sampling. We perform umbrella sampling simulations with biasing potentials on Q for two model proteins, Trp-Cage and BBA, using the CHARMM force field. Hamiltonian replica exchange is implemented in these simulations to further facilitate the sampling. The simulations appear to have reached satisfactory convergence, resulting in unbiased free energies as a function of Q. In addition to the native structure, multiple folded conformations are identified in the reconstructed equilibrium ensemble. Some conformations without any native contacts nonetheless have rather compact geometries and are stabilized by hydrogen bonds not present in the native structure. Whereas the enhanced sampling along Q reasonably reproduces the equilibrium conformational space, we also find that the folding of an α-helix in Trp-Cage is a slow degree of freedom orthogonal to Q and therefore cannot be accelerated by biasing the reaction coordinate. Overall, we conclude that whereas Q is an excellent parameter to analyze the simulations, it is not necessarily a perfect reaction coordinate for enhanced sampling, and better incorporation of other slow degrees of freedom may further improve this reaction coordinate.