The intrinsic plasticity of protein residues, along with the occurrence of transitions between distinct residue conformations, plays a pivotal role in a variety of molecular recognition events in the cell. Analysis aimed at identifying both of these features has been limited so far to protein-complex structures. We present a computationally efficient tool (T-pad), which quantitatively analyzes protein residues' flexibility and detects backbone conformational transitions. T-pad is based on directional statistics of NMR structural ensembles or molecular dynamics trajectories. T-pad is here applied to human ubiquitin (hU), a paradigmatic cellular interactor. The calculated plasticity is compared to hU's Debye-Waller factors from the literature as well as those from experimental work carried out for this paper. T-pad is able to identify most of the key residues involved in hU's molecular recognition, also in the absence of its cellular partners. Indeed, T-pad identified as many as 90% of ubiquitin residues interacting with their cognate proteins. Hence, T-pad might be a useful tool for the investigation of interactions between proteins and their cellular partners at the genome-wide level.
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Proteins
January 2025
Institute of Transformative bio-Molecules, Nagoya University, Nagoya, Japan.
In plants, sugar will eventually be exported transporters (SWEETs) facilitate the translocation of mono- and disaccharides across membranes and play a critical role in modulating responses to gibberellin (GA3), a key growth hormone. However, the dynamic mechanisms underlying sucrose and GA3 binding and transport remain elusive. Here, we employed microsecond-scale molecular dynamics (MD) simulations to investigate the influence of sucrose and GA3 binding on SWEET13 transporter motions.
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January 2025
Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.
Argonaute proteins are categorized into AGO and PIWI clades. Across most animal species, AGO-clade proteins are widely expressed in various cell types, and regulate normal gene expression. By contrast, PIWI-clade proteins predominantly function during gametogenesis to suppress transposons and ensure fertility.
View Article and Find Full Text PDFInt J Biol Macromol
January 2025
College of Food Science and Engineering, Henan University of Technology, Zhengzhou, Henan Province, PR China. Electronic address:
The aim of this study was to investigate the mechanism of protein digestibility improvement by exploring the changes in structural characteristics of proteins in noodles with varying levels of mechanically activated starch. Therefore, different levels of mechanically activated wheat starch were mixed with refined wheat flour to produce noodles. Results showed that moderately mechanically activated starch could significantly improve protein digestibility and noodles containing 8.
View Article and Find Full Text PDFLangmuir
January 2025
School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China.
The antifreeze mechanism of antifreeze glycoproteins (AFGPs) remains incompletely understood, which limits the design of new antifreeze molecules for practical applications. For instance, the ice growth inhibition of AFGP8 (the shortest AFGPs) is primarily driven by hydrophobic methyl and hydrogen-bonding hydroxyl groups. However, altering the C3-β linkage in the disaccharide moiety of AFGP8, denoted as variant GP8-LacNAc, significantly reduces its antifreeze activity.
View Article and Find Full Text PDFNat Commun
January 2025
Department of Polymer Science and Engineering, Key Laboratory of High-Performance Polymer Materials and Technology of MOE, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing, China.
Overheating remains a major barrier to chip miniaturization, leading to device malfunction. Addressing the urgent need for thermal management promotes the development of solid-state electrocaloric cooling. However, enhancing passive heat dissipation through two-dimensional materials in electrocaloric polymers typically compromises the electrocaloric effect.
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