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Characterization and quantification of iron species in the banded iron formations (BIFs) in China Craton to explore the potential for H2 production using XRD and Mössbauer spectroscopy.
PLoS One
January 2025
Ocean Georesources Research Department, Korea Institute of Ocean Science and Technology, Busan, Republic of Korea.
Banded iron formations (BIFs), significant iron ore deposits formed approximately 2.3 billion years ago under low-oxygen conditions, have recently gained attention as potential geological sources for evaluating hydrogen (H₂) production. BIFs are characterized by high concentrations of iron oxide (20 to 40 wt.
View Article and Find Full Text PDFMethods for detecting, building, and improving tryptophan mannosylation in glycoprotein structures.
Protein Sci
February 2025
York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.
Tryptophan mannosylation, the covalent addition of an α-ᴅ-mannose sugar to a tryptophan side chain, is a post-translational modification (PTM) that can affect protein stability, folding, and interactions. Compared to other forms of protein glycosylation, it is relatively uncommon but is affected by conformational anomalies and modeling errors similar to those seen in N- and O-glycans in the Protein Data Bank (PDB). In this work, we report methods for detecting, building, and improving mannose structures linked to tryptophans.
View Article and Find Full Text PDFBenchmarking protein language models for protein crystallization.
Sci Rep
January 2025
Biotechnology Research Center, Technology Innovation Institute, P.O. Box 9639, Abu Dhabi, United Arab Emirates.
The problem of protein structure determination is usually solved by X-ray crystallography. Several in silico deep learning methods have been developed to overcome the high attrition rate, cost of experiments and extensive trial-and-error settings, for predicting the crystallization propensities of proteins based on their sequences. In this work, we benchmark the power of open protein language models (PLMs) through the TRILL platform, a be-spoke framework democratizing the usage of PLMs for the task of predicting crystallization propensities of proteins.
View Article and Find Full Text PDFExamining Gravettian and Magdalenian mobility and technological organization with IR spectroscopy.
Sci Rep
January 2025
Department of Early Prehistory and Quaternary Ecology, Institute of Prehistory, Early History and Medieval Archeology, University of Tübingen, Tübingen, Germany.
Archaeologists can use the provenance of lithic raw materials to examine the movements, territories, and settlement dynamics of hunter-gatherers. Several studies have used macroscopic analyses to propose the long-distance transport of raw material during the Gravettian and the Magdalenian of the Swabian Jura in Central Europe. Until now hypotheses about raw material transport in this region were not based on reproducible analyses.
View Article and Find Full Text PDFAlphaFold-guided molecular replacement for solving challenging crystal structures.
Acta Crystallogr D Struct Biol
January 2025
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
Molecular replacement (MR) is highly effective for biomolecular crystal structure determination, increasingly so as the database of known structures has increased. For candidates without recognizable similarity to known structures, however, crystal structure analyses have nearly always required experiments for de novo phase evaluation. Now, with the unprecedented accuracy of AlphaFold predictions of protein structures from amino-acid sequences, an appreciable expansion of the reach of MR for proteins is realized.
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