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Alternative low-populated conformations prompt phase transitions in polyalanine repeat expansions
Abnormal trinucleotide repeat expansions alter protein conformation causing malfunction and contribute to a significant number of incurable human...
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CryoEM-sampling of metastable conformations appearing in cofactor-ligand association and catalysis of glutamate dehydrogenase
Kinetic aspects of enzymatic reactions are described by equations based on the Michaelis–Menten theory for the initial stage. However, the kinetic...
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Applying atomistic neural networks to bias conformer ensembles towards bioactive-like conformations
Identifying bioactive conformations of small molecules is an essential process for virtual screening applications relying on three-dimensional...
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Intermediate conformations of CD4-bound HIV-1 Env heterotrimers
HIV-1 envelope (Env) exhibits distinct conformational changes in response to host receptor (CD4) engagement. Env, a trimer of gp120 and gp41...
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Conformations of Cycloalkanes
Cycloalkanes, as we know, are cyclic compounds and contain carbon-carbon single bonds as in the case of alkanes. Examples include cyclopropane...
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Influence of Lipid Conformations on the Interaction Energy between a Membrane and a Peripheral Protein
Peripheral membrane proteins are temporarily coupled to the surface of a membrane, penetrating into the lipid layer. In this work, it has been shown...
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Terminus-immobilization effect on peptide conformations and peptide–peptide interactions
Peptide-modified delivery systems are enabling the improvement of the targeting specificity, biocompatibility, stability, etc. However, the precise...
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Predicting multiple conformations via sequence clustering and AlphaFold2
AlphaFold2 (ref.
1 ) has revolutionized structural biology by accurately predicting single structures of proteins. However, a protein’s biological...
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Conformations of Bcs1L undergoing ATP hydrolysis suggest a concerted translocation mechanism for folded iron-sulfur protein substrate
The human AAA-ATPase Bcs1L translocates the fully assembled Rieske iron-sulfur protein (ISP) precursor across the mitochondrial inner membrane,...
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Exploration of Conformations for an Intrinsically Disordered Protein
Intrinsically disordered proteins (IDP) are at the center of numerous biological processes, and attract consequently extreme interest in structural...
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Single cell Hi-C identifies plastic chromosome conformations underlying the gastrulation enhancer landscape
Embryonic development involves massive proliferation and differentiation of cell lineages. This must be supported by chromosome replication and...
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Polymer chain conformations in hybrid composites of UHMWPE incorporated by GNP/MWCNT
A great many of important physical/chemical properties, containing thermal behavior and dynamic properties, are determined by polymer chain...
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Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter
Here we used cryo-electron microscopy (cryo-EM), double electron-electron resonance spectroscopy (DEER), and molecular dynamics (MD) simulations, to...
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Chromophore carbonyl twisting in fluorescent biosensors encodes direct readout of protein conformations with multicolor switching
Fluorescent labeling of proteins is a powerful tool for probing structure-function relationships with many biosensing applications. Structure-based...
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Self-assembled Conformations of a Core-shell Comb-like Chain with Adjustable Architectural Parameters
Combining Brownian dynamics simulations and self-consistent field theory, we demonstrate that the architectural parameters of core-shell comb-like...
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3D genome map** identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma
Ependymoma is a tumor of the brain or spinal cord. The two most common and aggressive molecular groups of ependymoma are the supratentorial ZFTA -fusio...
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The Amazing DNA Macromolecule: Computer Modeling of its 3D Structure and the Diversity of Watson–Crick Conformations in the Duplex
AbstractThe development of ideas about the 3D structure of DNA and the mechanisms of its formation, from the discovery of the double helix to the...
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Kinetics and map** of Ca-driven calmodulin conformations on skeletal and cardiac muscle ryanodine receptors
Calmodulin transduces [Ca 2+ ] information regulating the rhythmic Ca 2+ cycling between the sarcoplasmic reticulum and cytoplasm during contraction and...
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Does AlphaFold2 model proteins’ intracellular conformations? An experimental test using cross-linking mass spectrometry of endogenous ciliary proteins
A major goal in structural biology is to understand protein assemblies in their biologically relevant states. Here, we investigate whether AlphaFold2...
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Asymmetric conformations of cleaved HIV-1 envelope glycoprotein trimers in styrene-maleic acid lipid nanoparticles
During virus entry, the pretriggered human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer initially transits into a default...
