The ManifoldEM method for cryo-EM: a step-by-step breakdown accompanied by a modern Python implementation.

Resolving continuous conformational heterogeneity in single-particle cryo-electron microscopy (cryo-EM) is a field in which new methods are now emerging regularly. Methods range from traditional statistical techniques to state-of-the-art neural network approaches. Such ongoing efforts continue to enhance the ability to explore and understand the continuous conformational variations in cryo-EM data.

Protein dynamics underlying allosteric regulation.

Allostery is the mechanism by which information and control are propagated in biomolecules. It regulates ligand binding, chemical reactions, and conformational changes. An increasing level of experimental resolution and control over allosteric mechanisms promises a deeper understanding of the molecular basis for life and powerful new therapeutics.

Q1291H-CFTR molecular dynamics simulations and theratyping in nasal epithelial models and clinical response to elexacaftor/tezacaftor/ivacaftor in a Q1291H/F508del patient.

Cystic fibrosis (CF) is caused by a wide spectrum of mutations in the CF transmembrane conductance regulator () gene, with some leading to non-classical clinical presentations. We present an integrated and investigation of an individual with CF carrying the rare Q1291H allele and the common F508del allele. At age 56 years, the participant had obstructive lung disease and bronchiectasis, qualifying for Elexacaftor/Tezacaftor/Ivacaftor (ETI) CFTR modulator treatment due to their F508del allele.

S945L-CFTR molecular dynamics, functional characterization and tezacaftor/ivacaftor efficacy and in matched pediatric patient-derived cell models.

Cystic Fibrosis (CF) results from over 400 different disease-causing mutations in the CF Transmembrane Conductance Regulator () gene. These mutations lead to numerous defects in CFTR protein function. A novel class of targeted therapies (CFTR modulators) have been developed that can restore defects in CFTR folding and gating.

Molecular Dynamics and Theratyping in Airway and Gut Organoids Reveal R352Q-CFTR Conductance Defect.

A significant challenge to making targeted cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapies accessible to all individuals with cystic fibrosis (CF) are many mutations in the gene that can cause CF, most of which remain uncharacterized. Here, we characterized the structural and functional defects of the rare mutation R352Q, with a potential role contributing to intrapore chloride ion permeation, in patient-derived cell models of the airway and gut. CFTR function in differentiated nasal epithelial cultures and matched intestinal organoids was assessed using an ion transport assay and forskolin-induced swelling assay, respectively.

Molecular dynamics and functional characterization of I37R-CFTR lasso mutation provide insights into channel gating activity.

Characterization of I37R, a mutation located in the lasso motif of the CFTR chloride channel, was conducted by theratyping several CFTR modulators from both potentiator and corrector classes. Intestinal current measurements in rectal biopsies, forskolin-induced swelling (FIS) in intestinal organoids, and short circuit current measurements in organoid-derived monolayers from an individual with I37R/F508del CFTR genotype demonstrated that the I37R-CFTR results in a residual function defect amenable to treatment with potentiators and type III, but not type I, correctors. Molecular dynamics of I37R using an extended model of the phosphorylated, ATP-bound human CFTR identified an altered lasso motif conformation which results in an unfavorable strengthening of the interactions between the lasso motif, the regulatory (R) domain, and the transmembrane domain 2 (TMD2).