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Selenomethionine incorporation has proven useful in X-ray crystallography of proteins to obtain phase information. In nucleic acids, the introduction of selenium to different positions is beneficial for solving the phase problem as well, but its addition to the 2' position also significantly enhances the crystal formation. The selenium modification in a single nucleotide shows a preference towards 2'-endo sugar puckering, which is in conflict with existing crystal structures where the duplex incorporated 2'-selenium-modified nucleotide is exclusively found in a 3'-endo conformation. Our work provides a rationale why 2'-selenium modifications facilitate crystallization despite this contradictory behavior.
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http://dx.doi.org/10.1080/07391102.2014.880944 | DOI Listing |
Cell Res
September 2025
Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
The γ-carboxylation state of osteocalcin determines its essential functions in bone mineralization or systemic metabolism and serves as a prominent biomarker for bone health and vitamin K nutrition. This post-translational modification of glutamate residues is catalyzed by the membrane-embedded vitamin K-dependent γ-carboxylase (VKGC), which typically recognizes protein substrates through their tightly bound propeptide that triggers γ-carboxylation. However, the osteocalcin propeptide exhibits negligible affinity for VKGC.
View Article and Find Full Text PDFIEEE J Biomed Health Inform
August 2025
Epilepsy is a prevalent neurological disorder marked by sudden, brief episodes of excessive neuronal activity caused by abnormal electrical discharges, which may lead to some mental disorders. Most existing deep learning methods for epilepsy detection rely solely on unimodal EEG signals, neglecting the potential benefits of multimodal information. To address this, we propose a novel multimodal model, DistilCLIP-EEG, based on the CLIP framework, which integrates both EEG signals and text descriptions to capture comprehensive features of epileptic seizures.
View Article and Find Full Text PDFJ Phys Chem B
August 2025
Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States.
Developing accurate force fields for biomolecules remains a significant challenge due to the subtle energetic differences between various conformational states. We present a novel force field model for polyalanine, ALAMP2_25, developed using adaptive force matching (AFM) with Møller-Plesset perturbation theory at the second order (MP2) as the reference method. By fitting smaller model compounds and transferring parameters to larger peptides, we overcome the limitations of traditional AFM approaches and enable the use of more accurate electronic structure methods.
View Article and Find Full Text PDFJ Chem Inf Model
August 2025
Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-0002, United States.
Noncanonical amino acids (NCAAs) occupy an important place, both in natural biology and in synthetic applications. However, modeling these amino acids still lies outside the capabilities of most deep learning methods due to sparse training data sets for this task. Instead, biophysical methods such as Rosetta can excel in modeling NCAAs.
View Article and Find Full Text PDFJ Chem Theory Comput
August 2025
Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560 064, India.
Delineating the conformer populations in neat liquid ethylene glycol (EG) has been challenging as experiments lack sufficient resolution, while simulations suffer from low accuracy and/or high computational demand. Ab initio MD (AIMD) simulations of liquid EG at ambient conditions have reported that about 20% of the molecules have their central (OCCO) dihedral in the conformation. Yet, adequate conformational sampling is an issue with AIMD simulations, given the limited duration of the trajectory.
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