Crystal structures, at 1.7 A resolution, were solved for complexes between each of two chemically synthesized partially folded analogues of bovine pancreatic trypsin inhibitor (BPTI) with the proteolytically inactive rat trypsin mutant S195A. The BPTI analogue termed [14-38](Abu) retains only the disulfide bond between Cys14 and Cys38, while Cys5, Cys30, Cys51, and Cys55 are replaced by isosteric alpha-amino-n-butyric acid residues. The analogue K26P,A27D[14-38](Abu) contains two further replacements, by statistically favored residues, in the type I beta-turn that has been suggested to be a main site for initiation of BPTI folding. As a control, the structure of the complex between S195A trypsin and wild-type BPTI was also solved. Despite significant differences in the degree of structure detected among these three BPTIs in solution by several biophysical techniques, their tertiary folds once bound to S195A trypsin in a crystalline lattice are essentially superimposable.
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http://dx.doi.org/10.1016/j.jmb.2007.10.084 | DOI Listing |
Proc Natl Acad Sci U S A
January 2025
Department of Computer Science, University of Haifa, Haifa 3303221, Israel.
Selective pressure acts on the codon use, optimizing multiple, overlapping signals that are only partially understood. We trained AI models to predict codons given their amino acid sequence in the eukaryotes and and the bacteria and to study the extent to which we can learn patterns in naturally occurring codons to improve predictions. We trained our models on a subset of the proteins and evaluated their predictions on large, separate sets of proteins of varying lengths and expression levels.
View Article and Find Full Text PDFJ Biol Chem
December 2024
Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA. Electronic address:
Glutathione (GSH) is an abundant thiol-containing tripeptide that functions in redox homeostasis, protein folding, and iron metabolism. In Saccharomyces cerevisiae, GSH depletion leads to increased sensitivity to oxidants and other toxic compounds, disruption of Fe-S cluster biogenesis, and eventually cell death. GSH pools are supplied by intracellular biosynthesis and GSH import from the extracellular environment.
View Article and Find Full Text PDFLife Sci
December 2024
Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy. Electronic address:
Aims: Osteogenesis imperfecta (OI) is a collagen I-related heritable family of skeletal diseases associated to extreme bone fragility and deformity. Its classical forms are caused by dominant mutations in COL1A1 and COL1A2, which encode for the protein α chains, and are characterized by impairment in collagen I structure, folding, and secretion. Mutant collagen I assembles in an altered extracellular matrix affecting mineralization and bone properties and partially accumulating inside the cells, leading to impaired trafficking and cellular stress.
View Article and Find Full Text PDFAnnu Rev Biophys
December 2024
1Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA; email:
A complete understanding of protein function and dynamics requires the characterization of the multiple thermodynamic states, including the denatured state ensemble (DSE). Whereas residual structure in the DSE (as well as in partially folded states) is pertinent in many biological contexts, here we are interested in how such structure affects protein thermodynamics. We examine issues related to chain collapse in light of new developments, focusing on potential complications arising from differences in the DSE's properties under various conditions.
View Article and Find Full Text PDFJ Clin Endocrinol Metab
December 2024
Research Centre for Medical Genetics, Moscow, Russian Federation.
Context: Pathogenic variants in the TBCE gene, encoding tubulin-specific chaperone E crucial for tubulin folding, are linked to three severe neurodevelopmental disorders: Hypoparathyroidism-retardation-dysmorphism (HRD) syndrome, Kenny-Caffey syndrome type 1, and progressive encephalopathy with amyotrophy and optic atrophy.
Objective: We identified patients with a novel, milder TBCE-associated phenotype and aimed to characterize it at the clinical and molecular levels.
Materials And Methods: We conducted splicing analysis using deep NGS sequencing of RT-PCR products and detected TBCE through Western blotting.
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