The MIR algorithm provides an ab initio prediction of a protein's core residues. An improved version, the MIR2, is presented and validated on 3203 proteins from PDB. Structures are decomposed in Closed Loops, their limits constituting the observed core residues. They are predicted by MIR2 with an accuracy approaching 80%.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.2174/092986609789353673 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Structural insights into the role of reduced cysteine residues in SOD1 amyloid filament formation.
Proc Natl Acad Sci U S A
February 2025
Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Republic of Korea.
The formation of superoxide dismutase 1 (SOD1) filaments has been implicated in amyotrophic lateral sclerosis (ALS). Although the disulfide bond formed between Cys57 and Cys146 in the active state has been well studied, the role of the reduced cysteine residues, Cys6 and Cys111, in SOD1 filament formation remains unclear. In this study, we investigated the role of reduced cysteine residues by determining and comparing cryoelectron microscopy (cryo-EM) structures of wild-type (WT) and C6A/C111A SOD1 filaments under thiol-based reducing and metal-depriving conditions, starting with protein samples possessing enzymatic activity.
View Article and Find Full Text PDFTranscriptome-scale analysis uncovers conserved residues in the hydrophobic core of the bacterial RNA chaperone Hfq required for small regulatory RNA stability.
Nucleic Acids Res
January 2025
Centre for Bacterial Resistance Biology, Imperial College London, LondonSW7 2AZ, United Kingdom.
The RNA chaperone Hfq plays crucial roles in bacterial gene expression and is a major facilitator of small regulatory RNA (sRNA) action. The toroidal architecture of the Hfq hexamer presents three well-characterized surfaces that allow it to bind sRNAs to stabilize them and engage target transcripts. Hfq-interacting sRNAs are categorized into two classes based on the surfaces they use to bind Hfq.
View Article and Find Full Text PDFPrevalence and determinants of nasal carriage of penicillin non-susceptible : a cross-sectional household survey in northern Vietnam.
Lancet Reg Health West Pac
January 2025
Oxford University Clinical Research Unit (OUCRU), National Hospital for Tropical Diseases, 78 Giai Phong, Dong Da District, Hanoi, Viet Nam.
Background: Beta-lactams remain the first-line treatment of infections despite the increasing global prevalence of penicillin-resistant/non-susceptible strains. We conducted a cross-sectional household survey in a rural community in northern Vietnam in 2018-2019 to provide prevalence estimates of penicillin non-susceptible (PNSP) carriage and to investigate behavioural and environmental factors associated with PNSP colonization. The data presented will inform the design of a large trial of population-based interventions targeting inappropriate antibiotic use.
View Article and Find Full Text PDFExogenous L-fucose attenuates depression induced by chronic unpredictable stress: implicating core fucosylation has an antidepressant potential.
J Biol Chem
January 2025
Division of Regulatory Glycobiology, Graduate School of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University; Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi 981-8558, Japan. Electronic address:
Core fucosylation is one of the most essential modifications of the N-glycans, catalyzed by α1,6-fucosyltransferase (Fut8), which transfers fucose from guanosine 5'-diphosphate (GDP)-fucose to the innermost N-acetylglucosamine residue of N-glycans in an α1-6 linkage. Our previous studies demonstrated that lipopolysaccharide (LPS) can induce a more robust neuroinflammatory response in Fut8 homozygous knockout (KO) (Fut8) and heterozygous KO (Fut8) mice contrasted to the wild-type (Fut8) mice. Exogenous administration of L-fucose suppressed LPS-induced neuroinflammation.
View Article and Find Full Text PDFA quantitative intracellular peptide binding assay reveals recognition determinants and context dependence of short linear motifs.
J Biol Chem
January 2025
Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA. Electronic address:
Transient protein-protein interactions play key roles in controlling dynamic cellular responses. Many examples involve globular protein domains that bind to peptide sequences known as Short Linear Motifs (SLiMs), which are enriched in intrinsically disordered regions of proteins. Here we describe a novel functional assay for measuring SLiM binding, called Systematic Intracellular Motif Binding Analysis (SIMBA).
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!