CageCavityCalc (C3): A Computational Tool for Calculating and Visualizing Cavities in Molecular Cages

V Martí-Centelles, TK Piskorz… - Journal of Chemical …, 2024 - ACS Publications
Organic (porous) and metal–organic cages are promising biomimetic platforms with diverse
applications spanning recognition, sensing, and catalysis. The key to the emergence of …

Cryo-EM structures of human SPCA1a reveal the mechanism of Ca2+/Mn2+ transport into the Golgi apparatus

Z Chen, S Watanabe, H Hashida, M Inoue… - Science …, 2023 - science.org
Secretory pathway Ca2+/Mn2+ ATPase 1 (SPCA1) actively transports cytosolic Ca2+ and
Mn2+ into the Golgi lumen, playing a crucial role in cellular calcium and manganese …

Accelerating the discovery of alkyl halide-derived natural products using halide depletion

NR Glasser, D Cui, DD Risser, CD Okafor… - Nature Chemistry, 2024 - nature.com
Even in the genomic era, microbial natural product discovery workflows can be laborious
and limited in their ability to target molecules with specific structural features. Here we …

The switch states of the GDP-bound HRAS affected by point mutations: A study from Gaussian accelerated molecular dynamics simulations and free energy …

H Bao, W Wang, H Sun, J Chen - Journal of Biomolecular Structure …, 2024 - Taylor & Francis
Point mutations play a vital role in the conformational transformation of HRAS. In this work,
Gaussian accelerated molecular dynamics (GaMD) simulations followed by constructions of …

AI-enabled pipeline for virus detection, validation, and SNP discovery from next-generation sequencing data

A Ghorbani, M Rostami, PH Guzzi - Frontiers in Genetics, 2024 - frontiersin.org
Background and Aims The rapid and accurate detection of viruses and the discovery of
single nucleotide polymorphisms (SNPs) are critical for disease management and …

[HTML][HTML] Structural and functional features of a broad-spectrum prophage-encoded enzybiotic from Enterococcus faecium

GE Premetis, A Stathi, AC Papageorgiou… - Scientific Reports, 2023 - nature.com
Multidrug-resistant (MDR) bacteria have become a growing threat to public health. The gram-
positive Enterococcus faecium is classified by WHO as a high-priority pathogen among the …

Variability in phenylalanine side chain conformations facilitates broad substrate tolerance of fatty acid binding in cockroach milk proteins

PR Santhakumari, KV Dhanabalan, S Virani… - PLoS …, 2023 - journals.plos.org
Diploptera punctata, also known as the Pacific beetle cockroach, is a viviparous cockroach
that gives birth to live offspring and secretes a highly concentrated mixture of glycosylated …

Cavity Characterization in Supramolecular Cages

JVS Guerra, LFG Alves, D Bourissou… - Journal of Chemical …, 2023 - ACS Publications
Confining molecular guests within artificial hosts has provided a major driving force in the
rational design of supramolecular cages with tailored properties. Over the last 30 years, a …

Antimicrobial Peptide Recognition Motif of the Substrate Binding Protein SapA from Nontypeable Haemophilus influenzae

KG Rivera, KJ Tanaka, ER Buechel, O Origel Jr… - Biochemistry, 2024 - ACS Publications
Nontypeable Haemophilus influenzae (NTHi) is an opportunistic pathogen associated with
respiratory diseases, including otitis media and exacerbations of chronic obstructive …

Engineering rice Nramp5 modifies cadmium and manganese uptake selectivity using yeast assay system

J Inoue, T Teramoto, T Kazama… - Frontiers in Plant …, 2024 - frontiersin.org
Cd is a seriously hazardous heavy metal for both plants and humans and international
regulations regarding Cd intake have become stricter in recent years. Three-quarters of the …