Utility of B-factors in protein science: interpreting rigidity, flexibility, and internal motion and engineering thermostability

Z Sun, Q Liu, G Qu, Y Feng, MT Reetz - Chemical reviews, 2019 - ACS Publications
The term B-factor, sometimes called the Debye–Waller factor, temperature factor, or atomic
displacement parameter, is used in protein crystallography to describe the attenuation of X …

Protein flexibility in the light of structural alphabets

P Craveur, AP Joseph, J Esque, TJ Narwani… - Frontiers in molecular …, 2015 - frontiersin.org
Protein structures are valuable tools to understand protein function. Nonetheless, proteins
are often considered as rigid macromolecules while their structures exhibit specific flexibility …

[HTML][HTML] Essential site scanning analysis: A new approach for detecting sites that modulate the dispersion of protein global motions

BT Kaynak, I Bahar, P Doruker - Computational and Structural …, 2020 - Elsevier
Despite the wealth of methods developed for exploring the molecular basis of allostery in
biomolecular systems, there is still a need for structure-based predictive tools that can …

Hydration of proteins and nucleic acids: advances in experiment and theory. A review

L Biedermannová, B Schneider - Biochimica et Biophysica Acta (BBA) …, 2016 - Elsevier
Background Most biological processes involve water, and the interactions of biomolecules
with water affect their structure, function and dynamics. Scope of review This review …

BANΔIT: B'‐factor analysis for drug design and structural biology

F Barthels, T Schirmeister, C Kersten - Molecular Informatics, 2021 - Wiley Online Library
The analysis of B‐factor profiles from X‐ray protein structures can be utilized for structure‐
based drug design since protein mobility changes have been associated with the quality of …

QStatin, a Selective Inhibitor of Quorum Sensing in Vibrio Species

BS Kim, SY Jang, Y Bang, J Hwang, Y Koo, KK Jang… - MBio, 2018 - Am Soc Microbiol
Pathogenic Vibrio species cause diseases in diverse marine animals reared in aquaculture.
Since their pathogenesis, persistence, and survival in marine environments are regulated by …

Structural insights into the interaction of clinically relevant phosphorothioate mRNA cap analogs with translation initiation factor 4E reveal stabilization via electrostatic …

M Warminski, J Kowalska, E Nowak… - ACS Chemical …, 2021 - ACS Publications
mRNA-based therapies and vaccines constitute a disruptive technology with the potential to
revolutionize modern medicine. Chemically modified 5′ cap structures have provided …

Discovery of Nonretinoid Inhibitors of CRBP1: Structural and Dynamic Insights for Ligand-Binding Mechanisms

J Plau, CE Morgan, Y Fedorov, S Banerjee… - ACS Chemical …, 2023 - ACS Publications
The dysregulation of retinoid metabolism has been linked to prevalent ocular diseases
including age-related macular degeneration and Stargardt disease. Modulating retinoid …

Ligand binding induces conformational changes in human cellular retinol-binding protein 1 (CRBP1) revealed by atomic resolution crystal structures

JA Silvaroli, JM Arne, S Chelstowska, PD Kiser… - Journal of Biological …, 2016 - ASBMB
Important in regulating the uptake, storage, and metabolism of retinoids, cellular retinol-
binding protein 1 (CRBP1) is essential for trafficking vitamin A through the cytoplasm …

Molecular dynamics of photosystem II embedded in the thylakoid membrane

FJ Van Eerden, T Van Den Berg… - The Journal of …, 2017 - ACS Publications
Photosystem II (PSII) is one of the key protein complexes in photosynthesis. We introduce a
coarse grained model of PSII and present the analysis of 60 μs molecular dynamics …