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Showing 1 to 12 of 12 for “"Protein Flexibility"”.
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Modeling protein flexibility using collective modes of motion: Applications to drug design
… shows how to decrease the complexity of modeling flexibility in proteins by reducing the number of dimensions necessary to model important macromolecular motions such as the induced fit process. Induced fit occurs during the binding of a protein to other proteins, nucleic acids or small molecules …
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Enhancing protein-protein docking by new approaches to protein flexibility and scoring of docking hypotheses
… Verständnis von biologischen Funktionen können Proteindockingverfahren angewandt werden. Die Simulation der Interaktion von Proteinen ermöglicht einen Einblick in die Mechanismen dieser Funktionen. Viele Dockingansätze modellieren Proteine als feste Körper. Proteine sind jedoch flexibel. …
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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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Investigating the Role of Conformational Flexibility in tRNA Aminoacylation
Proteins are dynamic macromolecules. According to Koshland's classical "induced fit" model of enzyme regulation, proteins have essential conformational flexibility for ligand binding, which promotes catalysis by structural rearrangement. Proteins undergo structural rearrangements to bind ligands, …
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Fluorescence Depolarization Study of Internal Tryptophan Mobility in Hydrated Azurin Films
The effect of hydration on protein dynamics was investigated using steady state fluorescence depolarization on azurin, which has a single tryptophan residue well-buried in the hydrophobic interior. Azurin was imbedded in a thin, solid, water-permeable polymer film. This procedure inhibited …
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Fluorenscence depolarization study of internal tryptophan mobility in hydrated azurin films
The effect of hydration on protein dynamics was investigated using steady state fluorescence depolarization on azurin, which has a single tryptophan residue well-buried in the hydrophobic interior. Azurin was imbedded in a thin, solid, water-permeable polymer film. This procedure inhibited …
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Mapping Ligand Binding Sites in hERG1 Channel with Biomolecular Simulations
… generated affinity maps from SILCS account for protein flexibility, solutes desolvation effects, and protein-fragments interaction. Using SILCS, we mapped the binding sites of the hERG1 channel including the intracellular cavity, lipid phasing domains, and voltage sensor domains. Our SILCS- …
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Novel Bio-Imaging Techniques Based on Molecular Switching
… genetically-encoded microviscosity sensor using protein-flexibility mediated photochromism, deep tissue imaging with super-nonlinear fluorescence microscopy, and light-driven fluorescent timer for simultaneous spatial-temporal mapping of protein dynamics in live cells. The first technique, dark …
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Kinesin-1 mechanical flexibility and motor cooperation
… (151±46nm/s). Due to the similar value of flexibility for both short construct (8±11 kBT/rad vs 7±1 1 kBT/rad) and their different behavior at high density (700±16 nm/s vs. 151±46 nm/s) a new hypothesis is presented, the swivel might have a strain dependent conformation. Using Circular …
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Evolution of protein structure, function, and dynamics in biological systems
… respectively. Intrinsic disorder analysis at the protein domain level revealed that early protein domains were ordered and therefore, disorder is a benefit that was acquired later in evolution. In contrast, at the more granular level of protein secondary structure, we found that protein loops of …
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STRUCTURE-BASED COMPUTATIONAL MODELING OF PROTEIN-LIGAND INTERACTIONS - APPLIED TO PROTEINS INVOLVED IN HUMAN DISEASES
Protein structure-based virtual screening of large chemical libraries is commonly performed against static X-ray and NMR structures. However, proteins are dynamic macromolecules occupying different conformational spaces. Consequently, different protein structures of the same protein could exhibit …
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Thermal adaptation of conformational dynamics in ribonuclease H
Structural changes are critical to the ability of proteins, particularly enzymes, to carry out their biological function. However, flexibility also leaves proteins vulnerable to denaturation and degradation; thus a balance must be struck between the dynamics required for function and the rigidity …