A Dynamical Approach to Protein Folding [PDF]
Journal of Biological Physics, 2001 In this paper we show that a dynamical description of the protein folding process provides an effective representation of equilibrium properties and it allows for a direct investigation of the mechanisms ruling the approach towards the native configuration.
A. TORCINI, LIVI, ROBERTO, A. POLITI
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Dynamics in unfolded polypeptide chains as model for elementary steps in protein folding [PDF]
, 2004 This thesis deals with the dynamics of unfolded polypeptide chains as model for the earliest steps in protein folding. Starting from an ensemble of unfolded conformations a folding polypeptide chain has to form specific backbone and side-chain ...
Krieger, Florian
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Lasso-grafting of macrocyclic peptide pharmacophores yields multi-functional proteins
Nature Communications, 2021 RaPID (Random non-standard Peptides Integrated Discovery) enables discovery of small macrocyclic peptides binding desired targets. Here, the authors propose lasso-grafting: the RaPID-derived peptides are implanted onto diverse proteins and maintain both ...
Emiko Mihara +12 more
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gbabbitt/DROIDS-1.0---free-software-project-for-comparative-protein-dynamics: DROIDS 1.0 software for comparative protein dynamics [PDF]
, 2017 <p>Our main goal is to try to visualize the impact of one of the longest time scale processes in the universe (i.e molecular evolution over 100s millions of years) on one of the shortest time scale processes (i.e. molecular motion over femtoseconds)
gbabbitt
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COMPARISONS OF PROTEIN FAMILY DYNAMICS [PDF]
Biocomputing 2008, 2007 Similarities between different protein structures have led to the identification of protein families based upon some measure of structural similarity. Using these similarities one can classify proteins into structural families and higher-order groupings from which inferred function can be transferred.
A. J. Radar, Joshua T. Harrell
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Are Protein Shape-Encoded Lowest-Frequency Motions a Key Phenotype Selected by Evolution?
Applied Sciences, 2023 At the very deepest molecular level, the mechanisms of life depend on the operation of proteins, the so-called “workhorses” of the cell. Proteins are nanoscale machines that transform energy into useful cellular work, such as ion or nutrient transport ...
Laura Orellana
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Neutron frequency windows and the protein dynamical transition [PDF]
, 2004 Proteins undergo an apparent dynamical transition on temperature variation that has been correlated with the onset of function. The transition in the mean-square displacement, ∆r2 , that is observed using a spectrometer or computer simulation, depends on
Becker, Torsten +4 more
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Release factor-dependent ribosome rescue by BrfA in the Gram-positive bacterium Bacillus subtilis
Nature Communications, 2019 In bacteria, the conserved trans-translation system serves as the primary pathway of ribosome rescue, but many species can also use alternative rescue pathways. Here the authors report that in B. subtilis, the rescue factor BrfA binds to non-stop stalled
Naomi Shimokawa-Chiba +6 more
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Epigenetic mechanisms to propagate histone acetylation by p300/CBP
Nature Communications, 2023 Histone acetylation is important for the activation of gene transcription but little is known about its direct read/write mechanisms. Here, we report cryogenic electron microscopy structures in which a p300/CREB-binding protein (CBP) multidomain monomer ...
Masaki Kikuchi +8 more
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Two domains of Tim50 coordinate translocation of proteins across the two mitochondrial membranes
Life Science Alliance, 2023 Biochemical and genetic experiments identify distinct roles of the two domains of Tim50 in the intermembrane space during translocation of proteins into the mitochondria via the TOM and TIM23 complexes.
Marcel G Genge +7 more
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