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Multidisciplinary Sciences
Yunbeom Lee, Jong Goo Kim, Sang Jin Lee, Srinivasan Muniyappan, Tae Wu Kim, Hosung Ki, Hanui Kim, Junbeom Jo, So Ri Yun, Hyosub Lee, Kyung Won Lee, Seong Ok Kim, Marco Cammarata, Hyotcherl Ihee
Summary: Researchers utilized femtosecond time-resolved X-ray solution scattering (fs-TRXSS) to visualize the ultrafast structural changes of homodimeric hemoglobin, and tracked the time-dependent change of electron density of the hydration shell. Analysis of protein structural dynamics in solution using fs-TRXSS provides critical information in understanding protein behavior.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
F. Trinter, T. Miteva, M. Weller, A. Hartung, M. Richter, J. B. Williams, A. Gatton, B. Gaire, J. Sartor, B. Berry, I. Ben-Itzhak, N. Sisourat, V Stumpf, K. Gokhberg, R. Doerner, T. Jahnke, T. Weber
Summary: Interatomic Coulombic decay in NeKr dimers was investigated after neon inner-valence photoionization using a synchrotron light source. The temporal evolution of the state was probed by carefully tracing the post-collision interaction between the photoelectron and the emitted ICD electron, revealing the lifetime of the intermediate dimer cation state and the contraction of the nuclear structure on the femtosecond time scale.
Article
Chemistry, Physical
Jie Yang, Yifei Zhang, Yangyi Lu, Lijuan Wang, Faming Lu, Dongping Zhong
Summary: Short-range protein electron transfer is crucial in light-induced biological processes, and this study demonstrates how the dynamics are coupled with protein fluctuations. Comparison with a different flavodoxin shows the importance of electronic coupling in ET rates.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Yo-ichi Yamamoto, Yoshi-Ichi Suzuki, Toshinori Suzuki
Summary: Charge transfer reactions from I- to solvent water, methanol, and ethanol were investigated using extreme ultraviolet time-resolved photoelectron spectroscopy (EUV-TRPES). This technique overcomes the spectral broadening issue caused by electron inelastic scattering in liquids, allowing for clear observation of the spectral evolution. The changes in peak position, width, and intensity reveal electron detachment and subsequent solvation and thermalization processes. Geminate recombination between detached electrons and iodine atoms is analyzed using a diffusion equation and a kinetic model-based global fitting analysis.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Biochemistry & Molecular Biology
Marco van den Noort, Marijn de Boer, Bert Poolman
Summary: This study demonstrates that different ligands induce distinct bound conformations, and by changing the free energies of available conformations, ligand affinity can be adjusted. Experimental data on the maltose-binding protein (MBP) from Escherichia coli reveals that ligand affinity can be modulated through altering conformations.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biophysics
Yihan Huang, Bradley S. Harris, Shiaki A. Minami, Seongwon Jung, Priya S. Shah, Somen Nandi, Karen A. McDonald, Roland Faller
Summary: Highly detailed steered molecular dynamics simulations were conducted on differently glycosylated receptor binding domains of the SARS-CoV-2 spike protein. Glycosylation increased the binding strength and range, and a catch-slip behavior was observed during protein pulling, where new interactions replaced broken interactions. Hydrogen bonds were the dominant interaction mode, while Lennard-Jones and electrostatic interactions were also relevant.
BIOPHYSICAL JOURNAL
(2022)
Article
Chemistry, Medicinal
Hamid Reza Kalhor, Elham Taghikhani
Summary: The study investigated the effect of commonly used drugs on the release of warfarin bound to HSA in silico. Both s-ibuprofen and ascorbic acid were found to exhibit allosteric effects on the release of warfarin from HSA, with ibuprofen showing a stabilizing effect and ascorbic acid aiding in the release through destabilization of HSA. Molecular dynamics simulations provided valuable insights into the interactions of drugs with the protein and the mechanism of anticoagulant release.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Chemistry, Physical
Jie Yang, Yifei Zhang, Ting-Fang He, Yangyi Lu, Lijuan Wang, Bei Ding, Dongping Zhong
Summary: The study focused on short-range protein electron transfer (ET) processes, specifically investigating the photoinduced redox cycle using femtosecond spectroscopy. Ultrafast dynamics were observed including initial charge separation, subsequent charge recombination, and final vibrational cooling of products. Active-site solvation characteristics were further characterized, revealing nonergodic ET dynamics.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Biology
Remy A. Yovanno, Tsung Han Chou, Sarah J. Brantley, Hiro Furukawa, Albert Y. Lau
Summary: This study investigated the mechanisms of D-serine in receptor activation and found that D-serine competes with glutamate for binding to GluN2A. The inhibitory effect of D-serine at high concentrations was confirmed through electrophysiology experiments.
Article
Multidisciplinary Sciences
Giorgos Gouridis, Yusran A. Muthahari, Marijn de Boer, Douglas A. Griffith, Alexandra Tsirigotaki, Konstantinos Tassis, Niels Zijlstra, Ruixue Xu, Nikolaos Eleftheriadis, Yovin Sugijo, Martin Zacharias, Alexander Domling, Spyridoula Karamanou, Charalambos Pozidis, Anastassios Economou, Thorben Cordes
Summary: Novel biophysical tools have allowed exploration of protein structural dynamics and evolution, revealing how modifications of structural cores can lead to diversification of protein functions. The mechanism uncovered in this study provides insights into the emergence of functional promiscuity during long periods of evolution, with implications for a wide range of domain architectures.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Enrico Rennella, Danny D. Sahtoe, David Baker, Lewis E. Kay
Summary: With recent advancements in calculating protein structures from amino acid sequences using AI algorithms, the next important step is to understand how dynamics is encoded in the primary protein sequence to improve function prediction. This study emphasizes the significance of dynamics in modulating the function of a designed protein called C34, which binds β-strands. By investigating the structural dynamics of C34 using NMR spectroscopy, the researchers show that manipulating conformations can enhance functionality in protein design.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Chemistry, Medicinal
Shuhei Yoshida, Shota Uehara, Noriyasu Kondo, Yu Takahashi, Shiho Yamamoto, Atsushi Kameda, Soichiro Kawagoe, Naoko Inoue, Masami Yamada, Norito Yoshimura, Yuki Tachibana
Summary: This article proposes a novel small molecule lead discovery strategy, combining peptide display screening and pharmacophore-guided de novo design, to identify high-affinity macrocyclic peptides and further optimize them into cell-active small molecules, showing potential value in drug discovery.
JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Chemistry, Physical
Yifei Zhang, Jie Yang, Na Liu, Lijuan Wang, Faming Lu, Jie Chen, Dongping Zhong
Summary: This study provides a thorough investigation of the understanding of ultrafast short-range electron transfer in proteins, and conducts systematic studies on well-defined biological systems by utilizing two types of flavodoxins and designing mutants. The research identifies a position with a favorable orientation and distance for ultrafast electron transfer, and reveals that all forward and back electron transfer dynamics are ultrafast nonequilibrium processes.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Multidisciplinary Sciences
Ding Xu, Arkajit Mandal, James M. Baxter, Shan-Wen Cheng, Inki Lee, Haowen Su, Song Liu, David R. Reichman, Milan Delor
Summary: Semiconductor excitations can form exciton-polaritons with light-like energy flow and matter-like interactions. By using nonlinear momentum-resolved optical approach, the authors directly image the exciton-polaritons in real space on femtosecond scales. It is found that exciton-phonon interactions result in a renormalization of exciton-polariton velocities, but ballistic transport can be maintained for half-exciton polaritons. Upon increasing the excitonic character, rapid decoherence leads to diffusive transport.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Jonathan Alexis Cordova, Juan Cruz Palermo, Dario A. Estrin, Sara E. Bari, Luciana Capece
Summary: The interactions between the heme iron of hemeproteins and sulfide and disulfide compounds have potential interest as physiological signaling processes. While the interaction with hydrogen sulfide has been studied computationally and experimentally, the reaction with disulfide and the molecular mechanism for ligand binding have not been thoroughly investigated. In this study, the association process for disulfane and its conjugate base disulfanide at different pH conditions was examined using advanced sampling techniques. The study also investigated the ligand interchange reaction using hybrid quantum mechanics-molecular mechanics calculations and provided a molecular explanation for the experimental information.
JOURNAL OF INORGANIC BIOCHEMISTRY
(2023)