Results 101 to 110 of about 170,997 (257)

A light‐triggered Time‐Resolved X‐ray Solution Scattering (TR‐XSS) workflow with application to protein conformational dynamics

FEBS Open Bio, EarlyView.
Time‐resolved X‐ray solution scattering captures how proteins change shape in real time under near‐native conditions. This article presents a practical workflow for light‐triggered TR‐XSS experiments, from data collection to structural refinement. Using a calcium‐transporting membrane protein as an example, the approach can be broadly applied to study ...
Fatemeh Sabzian‐Molaei, Fredrik Orädd, Konstantinos Magkakis, Magnus Andersson   +3 more
wiley   +1 more source

Single‐molecule DNA flow‐stretch assays for high‐throughput DNA–protein interaction studies

FEBS Open Bio, EarlyView.
We describe an optimised single‐molecule DNA flow‐stretch assay that visualises DNA–protein interactions in real time. Linear DNA fragments are tethered to a surface and stretched by buffer flow for fluorescence imaging. Using λ and φX174 DNA, this protocol enhances reproducibility and accessibility, providing a versatile approach for studying diverse ...
Ayush Kumar Ganguli, Mohammad Nour Alsamsam, Ugnė Bagdonaitė, Van Truc Vu, Chun‐Jen Huang, Polina Kuzhir, Mindaugas Zaremba, Aurimas Kopūstas, Marijonas Tutkus   +8 more
wiley   +1 more source

Analysing the significance of small conformational changes and low occupancy states in serial crystallographic data

FEBS Open Bio, EarlyView.
This protocol paper outlines methods to establish the success of a time‐resolved serial crystallographic experiment, by means of statistical analysis of timepoint data in reciprocal space and models in real space. We show how to amplify the signal from excited states to visualise structural changes in successful experiments.
Jake Hill, Yelyzaveta Pulnova, Elke De Zitter, Helen M. Ginn, Briony A. Yorke   +4 more
wiley   +1 more source

Molecular dynamics simulations of positively selected codons in FcγRI reveal novel biochemical binding properties

FEBS Open Bio, EarlyView.
Evolutionary analysis across 32 placental mammals identified positive selection at residues H148 and W149 in the immune receptor FcγR1. Ancestral reconstruction combined with molecular dynamics simulations reveals how these mutations may influence receptor structure and dynamics, providing insight into the evolution of antibody recognition and immune ...
David A. Young, Omar Arias‐Gaguancela, Fiona Gibson, Morgan Grainger, Jodie Score, Amit Nathubhai, Mauricio Cafiero, Lee Richard Machado   +7 more
wiley   +1 more source

Refinement of amino‐acid conformation vs. difference density maps in time‐resolved serial femtosecond crystallography data analysis

FEBS Open Bio, EarlyView.
The dFoCC pipeline starts with observed DED and resting‐state coordinates, which are then used to generate a library of triggered states. Correlation analysis of the calculated DED features of each candidate vs observed DED permits quantitative evaluation of candidate structural quality.
Meng Iao Fong, Yuhei Hosokawa, Lars Oliver Essen, Manuel Maestre‐Reyna   +3 more
wiley   +1 more source

Acute caffeine treatment protects the developing retina from ischemia‐induced cell death

FEBS Open Bio, EarlyView.
Caffeine reduces cell death in the developing retina under ischemia (OGD). This effect does not involve BDNF upregulation or antioxidant pathways (NRF2/VEGF). Neuroprotection occurs mainly through adenosine A2A receptor antagonism, decreasing glutamate release and excitotoxicity, highlighting caffeine's potential as an acute neuroprotective agent in ...
Amanda Alves Nascimento, Danniel Pereira‐Figueiredo, Gabriella Grossi de Lima Dias, Gabriel Ferreira dos Santos, Mariana Rodrigues Pereira, Rafael Brito, Karin C Calaza   +6 more
wiley   +1 more source

RoundMi: A quantitative method to analyze mitochondrial morphology in mitotic cells

FEBS Open Bio, EarlyView.
RoundMi is a workflow for rapid analysis of mitochondrial morphology in mitotic cells. By combining adaptive preprocessing with automated segmentation and quantification, it enables accurate measurements from single focal plane images, reducing acquisition time and computational demands while remaining compatible with high‐throughput fixed and live ...
Elmira Parvindokht Bararpour, Christine Volmert, Valentina Piano   +2 more
wiley   +1 more source

Versatile vector tools for efficient protein screening across multiple expression systems

FEBS Open Bio, EarlyView.
A unified vector toolkit enables rapid protein expression screening across E. coli, insect, and mammalian cells. A single primer pair amplifies the target gene, which is inserted into any vector via a standardized interface. This streamlined workflow eliminates repeated cloning steps, accelerating the identification of optimal expression conditions for
Zhimin Zhu, Yaqing Liu, Lei Qin, Feng Yu, Qisheng Wang, Yahui Liu   +5 more
wiley   +1 more source

UiO‐66 metal–organic frameworks in biomedicine: From structural tunability to bioimaging, photodiagnostics, and photodynamic cancer therapy

FEBS Open Bio, EarlyView.
UiO‐66(Zr) metal–organic frameworks are chemically stable, biocompatible, and highly tunable nanomaterials. Their modular structure enables controlled drug delivery, multimodal bioimaging, and light‐activated photodynamic therapy, supporting integrated diagnostic and therapeutic (theranostic) applications in cancer and biomedical research.
Veronika Huntošová, Grigorii Rakhalskii, Miroslav Almáši   +2 more
wiley   +1 more source

Analysis of 'Investigating an extended multiphase flow model that includes specific interfacial area', Computer Methods in Applied Mechanics and Engineering, 418:116594, 2024. [PDF]

Comput Methods Appl Mech Eng
Gray WG, Miller CT.
europepmc   +1 more source