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Protein Target Search Diffusion-association/dissociation Free Energy Landscape around DNA Binding Site with Flanking Sequences.
Biophys J
January 2025
Department of Physics and Astronomy, Department of Chemistry, NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, California, USA. Electronic address:
In this work we present a minimal structure-based model of protein diffusional search along local DNA amid protein binding and unbinding events on the DNA, taking into account protein-DNA electrostatic interactions and hydrogen-bonding (HB) interactions or contacts at the interface. We accordingly constructed the protein diffusion-association/dissociation free energy surface and mapped it to 1D as the protein slides along DNA, maintaining the protein-DNA interfacial HB contacts that presumably dictate the DNA sequence information detection. Upon DNA helical path correction, the protein 1D diffusion rates along local DNA can be physically derived to be consistent with experimental measurements.
View Article and Find Full Text PDFCorrection: Zhang et al. GL-1196 Suppresses the Proliferation and Invasion of Gastric Cancer Cells via Targeting PAK4 and Inhibiting PAK4-Mediated Signaling Pathways. 2016, , 470.
Int J Mol Sci
December 2024
Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110122, China.
In the original publication [...
View Article and Find Full Text PDFA novel dual filtering mechanism for laser safety eyewear with polycarbonate lens coated by zirconium dioxide and silicon dioxide.
Lasers Med Sci
January 2025
Department of Physics, Shabestar Branch, Islamic Azad University, Shabestar, Iran.
In laser safety eyewear, due to the lack of complete blocking of ultraviolet and infrared rays, we proposed a structure based on one-dimensional multilayer composed of several layers of silicon dioxide and zirconium dioxide materials alternately behind polycarbonate lens. It is find out that the acceptance angle range to the photonic crystal is 0 to 39°. This incident angle range corresponds to the band gap of the photonic crystal.
View Article and Find Full Text PDFRobust STAP with coprime sampling structure based on optimal singular value thresholding.
Sci Rep
January 2025
Postdoctoral Innovation Practice Base, Chengdu Textile College, Chengdu, 611731, China.
In radar systems, element gain-phase errors can degrade the performance of space-time adaptive processing (STAP), and even cause complete failure. To address this issue, the STAP with the coprime sampling structure based on optimal singular value thresholding is proposed. The algorithm corrects errors by adding four calibrated auxiliary elements and auxiliary pulses to the original array and pulse sequence, while maintaining the coprime sampling structure.
View Article and Find Full Text PDFLeveraging the Thermodynamics of Protein Conformations in Drug Discovery.
J Chem Inf Model
January 2025
Schrödinger Inc., 1540 Broadway, 24th Floor, New York, New York 10036-4041, United States.
As the name implies, structure-based drug design requires confidence in the holo complex structure. The ability to clarify which protein conformation to use when ambiguity arises would be incredibly useful. We present a large scale validation of the computational method Protein Reorganization Free Energy Perturbation (PReorg-FEP) and demonstrate its quantitative accuracy in selecting the correct protein conformation among candidate models in apo or ligand induced states for 14 different systems.
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