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Structural Dynamics
Scopus
ISSN 2329-7778 · AIP Publishing LLC and ACA · 935 artikel di indeks
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Integrating neutron vibrational spectroscopy and computer simulation to elucidate structure and dynamics of hydrogen
Understanding the structure and dynamics of hydrogen is critically important, yet direct experimental measurements are often challenging. Hydrogen interacts only weakly with common probing particles such as photons and electrons, and strong nuclear quantum effects can produce large nonthermal and…
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Photoelectron spectroscopy and circular dichroism of an open-shell organometallic camphor complex
We present an investigation of one-photon valence-shell photoelectron spectroscopy and photoelectron circular dichroism (PECD) for the chiral molecule (1R,4R)-3-(heptafluorobutyryl)-(+)-camphor (HFC) and its europium complex Eu(III) tris[3-(heptafluorobutyryl)-(1R,4R)-camphorate] (Eu-HFC3), the…
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Putrescine-bound structure and multi-temperature crystallography provide new insights into ligand binding and conformational heterogeneity in spermidine synthase
Spermidine synthase (SPDS) is an important enzyme in the pathway for the biosynthesis of polyamines, and it synthesizes the polyamine spermidine from putrescine (PUT) and decarboxylated S-adenosylmethionine. This pathway is a promising target for antiproliferative therapies because of the functions…
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Bayesian model comparison of type-I and type-II ultrafast demagnetization dynamics
Ultrafast demagnetization dynamics are often phenomenologically classified into type-I and type-II responses according to their temporal evolution following femtosecond laser excitation. However, finite experimental temporal resolution and noise can substantially obscure the intrinsic dynamics and…
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Directional sensitivity of the A1g phonon in biaxially strained bismuth heterofilms studied by transient white light reflectivity
Strain engineering in epitaxial Bi(111) films on Si(111) enables temperature-tunable phonon frequencies through thermal expansion mismatch. Using in situ low-energy electron diffraction combined with broadband femtosecond transient reflectivity on the same samples, we directly correlate anisotropic…
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Bromodomain dimers: A case study of BRD4 and family-wide AlphaFold predictions
Bromodomains are conserved acetyl-lysine reader domains that play a central role in the assembly of transcriptional regulatory complexes. While generally presumed to function as monomers, bromodomain homo-dimers have been identified, and several bromodomain-containing proteins have been linked to…
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Integrating metabolomics and histopathology: A method for metabolite recovery from fixed tissue specimens
Combined histopathological and metabolomic analysis of the same tissue specimen can reduce biological variability compared to independent analyses of similar samples. However, conventional workflows are incompatible: tissue fixation leads to metabolite loss through dilution and chemical reactions…
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A role of protein conformational dynamics in mammalian DNA methylation
DNA methylation at the C-5 position of cytosine is an important epigenetic mechanism underpinning various cellular functions, such as heterochromatin assembly, gene expression, and cell fate determination. In mammals, DNA methylation mainly occurs in the context of CpG dinucleotide contexts…
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Structural basis of the oligomerization of anti-silencer Ler from enterohemorrhagic E. coli (EHEC)
The locus of enterocyte effacement-encoded regulator (Ler) is a master transcriptional activator essential for the virulence of enterohemorrhagic and enteropathogenic Escherichia coli. Although Ler shares homology with the global silencer H-NS, it functions uniquely as an anti-silencer, a role…
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Report of high data rate macromolecular crystallography (HDRMX) meeting, 23 July 2025
This paper is a report of the High Data Rate Macromolecular Crystallography workshop held on 23 July 2025 as part of the 2025 meeting of the American Crystallographic Association in Lombard, IL, USA, 18–23 July 2025. This report summarizes the discussions, questions, action items, and…
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Slowly exchanging bound states of SARS-CoV-2 3CLpro-inhibitor complexes revealed by 19F NMR
The SARS-CoV-2 virus causes COVID-19, and several of its gene products have been successfully targeted for antiviral drug development, including the 3C-like protease (3CLpro). The substrate-binding site of 3CLpro exhibits significant conformational plasticity. While available X-ray crystal…
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John L. Markley, a legacy of service in structural biology
John L. Markley was an early pioneer of the application of nuclear magnetic resonance (NMR) spectroscopy to investigate the structure, dynamics, and function of biological macromolecules by NMR. A recurring theme of his career is the development of standards and shared resources that have enabled…
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Prospects for direct electron detectors in ultrafast electron diffraction and scattering experiments
Ultrafast electron diffraction and phonon-diffuse scattering [UED(S)] experiments make use of photo-induced changes to electron scattering intensity across 2D detectors to report on a very wide range of dynamic structural phenomena in molecules and materials. Hybrid pixel counting detectors (HPCDs)…
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Structural heterogeneity of iron–sulfur cluster scaffold protein IscU: Metamorphic or partially folded?
The scaffold protein IscU plays a central role in iron–sulfur (Fe–S) cluster assembly and transfer. Despite extensive structural and biochemical research, the conformational nature of IscU remains unclear. IscU has been proposed as a metamorphic protein that interconverts between structured (S) and…
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Simultaneous two-color absorption dynamics in the van der Waals ferromagnet Fe3GeTe2
For the integration of two-dimensional materials in future devices, a fundamental understanding of their response to external stimuli is needed. Toward this goal, we have investigated the electron and spin dynamics in the metallic van der Waals material Fe3GeTe2 (FGT) in its paramagnetic state…
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13C NMR as a foundation for machine learning models of polysaccharides
Polysaccharide structural assignment via nuclear magnetic resonance (NMR) spectroscopy remains an analytical challenge due to spectral overlap because of limited chemical shift dispersion. This challenge is exacerbated by the wide-spread use of proton (1H) detection. Progress has also been hindered…
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Coherent phonon-driven band renormalizations in 1T′-MoTe2
Here, we investigate phonon mode- and electron band-selective electron–phonon couplings in centrosymmetric 1T′-MoTe2 using time- and angle-resolved photoemission spectroscopy combined with frequency-domain analysis. Femtosecond near-infrared pulses excite coherent Ag-symmetric phonon modes at 2.34…
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Solution characterization of TraW, a regulatory protein of the F plasmid type 4 secretion system
Bacterial conjugation facilitates horizontal gene transfer through the Type IV Secretion System (T4SS), a complex nanomachine central to antibiotic resistance dissemination. This study investigates the structure and dynamics of TraW, a key F-plasmid conjugative protein. TraW, in conjugation with…
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Poplar: A polarized neutron development beamline for polarization analysis and Larmor labeling techniques
A thermal neutron development beamline equipped with a Si monochromator has been commissioned at the HB-2D beam port of the High Flux Isotope Reactor at Oak Ridge National Laboratory. This instrument is dedicated to the development of neutron scattering methods and instrumentation, serving as a…
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Crystal structure of apo human spermidine synthase reveals dynamic rearrangement at the active site
Polyamines are polycations involved in both differentiation and proliferation of cells. Highly conserved polyamine biosynthetic enzymes are involved in the synthesis of polyamines. Spermidine synthase (SPDS) is an important enzyme in the polyamine biosynthetic pathway, and it is an…