Results 121 to 130 of about 3,454,137 (301)

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

NMR RELAXATION METHODS TO DETECT PROTEIN DYNAMICS: EVALUATION OF ACCURACY, IMPROVEMENT OF THE METHODOLOGY, AND ITS APPLICATION [PDF]

, 2013
Proteins are dynamic molecules whose ability to undergo conformational changes and fluctuations can impact their biological function, such as enzyme catalysis and substrate recognition. Mutations or perturbations that do not significantly change protein
Myint, Wazo
core  

Conformational Dynamics and Energetics of Carbon Nanohoops and their Ring-In-Ring Complexes [PDF]

Carbon nanohoops are promising precursors for the bottom-up synthesis of carbon nanotubes, whose structural dynamics are not well understood despite their desirable materials properties. Here, we investigate the conformational landscape and energetics of
Stefan, Frühwald, Andreas, Görling, Perdita, Barran, Niklas, Geue, Markus, Freiberger, Thomas, Drewello   +5 more
core   +2 more sources

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

Protein Dynamics and its Correlation to Protein Activity and Stability [PDF]

, 2009
The aim of this thesis is to investigate the role of fast protein dynamics (picosecond timescale) in enzyme activity and stability, and specifically to test the hypothesis that enzyme activity and stability are inversely related by their internal ...
Clement, David
core  

Multi-state Targeting Machinery Govern the Fidelity and Efficiency of Protein Localization

, 2014
Proper localization of newly synthesized proteins is essential to cellular function. Among different protein localization modes, the signal recognition particle (SRP) and SRP receptor (SR) constitute the conserved targeting machinery in all three life ...
Han, KL, Pang, Xueqin, Yang, MJ, Han, Keli, Yang, Mingjun, Zhang, X   +5 more
core   +1 more source

Molecular Mechanism of Phosphorylation-Mediated Impacts on the Conformation Dynamics of GTP-Bound KRAS Probed by GaMD Trajectory-Based Deep Learning

Molecules
The phosphorylation of different sites produces a significant effect on the conformational dynamics of KRAS. Gaussian accelerated molecular dynamics (GaMD) simulations were combined with deep learning (DL) to explore the molecular mechanism of the ...
Jianzhong Chen, Jian Wang, Wanchun Yang, Lu Zhao, Juan Zhao, Guodong Hu   +5 more
doaj   +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

Cortisol Recognition by a Conformationally Responsive DNA Aptamer

Advanced Sensor Research
Cortisol‐binding DNA aptamers have emerged as promising recognition elements for non‐invasive cortisol biosensing. However, the molecular basis of cortisol recognition and signal generation remains poorly understood.
Lakshitha Jasin Arachchige, Nayoon Kwon, Isoo Youn, Chang‐Seuk Lee, Tiffany R. Walsh   +4 more
doaj   +1 more source

Molecular characterization of covRS mutations in M1UK Streptococcus pyogenes

FEBS Open Bio, EarlyView.
Group A Streptococcus (GAS) acquires covRS mutations driving a hypervirulent bacterial state, frequently associated with invasive disease‐like necrotizing fasciitis. We demonstrate that the newly emerged M1UK GAS lineage can also acquire these mutations.
Jarrad Pritchard, Emma‐Jayne Proctor, Jiawa Wang, Nikolas P. Johnston, Andrew Hayes, Georgia McCorkell, Haibo Yu, Jai Tree, Mark R. Davies, Mark J. Walker, Ronald Sluyter, Stephan Brouwer, Martina L. Sanderson‐Smith   +12 more
wiley   +1 more source