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| http://dx.doi.org/10.1073/pnas.2411135121 | DOI Listing |
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FlowPacker: Protein side-chain packing with torsional flow matching.
Bioinformatics
January 2025
Department of Molecular Genetics, University of Toronto, Ontario, M5S 3K3, Canada.
Motivation: Accurate prediction of protein side-chain conformations is necessary to understand protein folding, protein-protein interactions and facilitate de novo protein design.
Results: Here we apply torsional flow matching and equivariant graph attention to develop FlowPacker, a fast and performant model to predict protein side-chain conformations conditioned on the protein sequence and backbone. We show that FlowPacker outperforms previous state-of-the-art baselines across most metrics with improved runtime.
Drug Development.
Alzheimers Dement
December 2024
Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
Background: Protein misfolding is a key pathological phenomenon driving neurodegenerative diseases that affect millions of people. Visualizing this misfolding process with smart imaging probes would greatly facilitate early diagnosis, etiology elucidation, disease progression monitoring, and drug discovery of neurodegeneration. Although numerous probes have been reported, several unmet needs still exist.
View Article and Find Full Text PDFEndoplasmic reticulum stress causes long bone shortening in P4hb mice: A mouse model exhibiting significant features of cole-carpenter syndrome driven by P4HB mutations.
Biochim Biophys Acta Mol Basis Dis
January 2025
Shanghai Clinical Research Center of Bone Disease, Department of Osteoporosis and Bone Diseases, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China. Electronic address:
Cole-Carpenter syndrome (CCS) is a rare autosomal-dominant genetic disease characterized by craniosynostosis, ocular proptosis, hydrocephalus, distinctive facial features, and bone fragility. Previous cases of CCS are associated with genetic variations in P4HB, which encodes the protein disulfide isomerase (PDI), a key enzyme in protein folding. Patients with CCS caused by P4HB mutations often present with short stature, limb deformities, and abnormal epiphyseal plates.
View Article and Find Full Text PDFAnalytical Characterization of Aberrant Trisulfide Bond Formation in Therapeutic Proteins and Their Impact on Product Quality.
J Pharm Sci
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Laboratory of Applied Biochemistry, Division of Biotechnology Review and Research III, Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA.. Electronic address:
Post translational modifications (PTMs) of proteins play an integral role in maintaining the overall structure and function of proteins including their proper folding, binding, and potency. However, not all PTMs play a positive role in protein drugs as some can lead to product-related impurities that negatively impact protein function. One example of a PTM is trisulfide formation, which appears as a product related species in multiple biologic drug products.
View Article and Find Full Text PDFUbiquitin-like modifier-activating enzyme 1 interacts with Zika virus NS5 and promotes viral replication in the infected cell.
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Unidad de Medicina Molecular, Instituto de Biomedicina de UCLM (IB-UCLM), Universidad de Castilla-La Mancha (UCLM), Albacete, Spain.
Translation errors, impaired folding or environmental stressors (e.g. infection) can all lead to an increase in the presence of misfolded proteins.
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