Water models for biomolecular simulations

AV Onufriev, S Izadi - Wiley Interdisciplinary Reviews …, 2018 - Wiley Online Library
Modern simulation and modeling approaches to investigation of biomolecular structure and
function rely heavily on a variety of methods—water models—to approximate the influence …

NAD+ cleavage activity by animal and plant TIR domains in cell death pathways

S Horsefield, H Burdett, X Zhang, MK Manik, Y Shi… - Science, 2019 - science.org
SARM1 (sterile alpha and TIR motif containing 1) is responsible for depletion of
nicotinamide adenine dinucleotide in its oxidized form (NAD+) during Wallerian …

Improvements to the APBS biomolecular solvation software suite

E Jurrus, D Engel, K Star, K Monson, J Brandi… - Protein …, 2018 - Wiley Online Library
Abstract The Adaptive Poisson–Boltzmann Solver (APBS) software was developed to solve
the equations of continuum electrostatics for large biomolecular assemblages that have …

Structure of the mechanically activated ion channel Piezo1

K Saotome, SE Murthy, JM Kefauver, T Whitwam… - Nature, 2018 - nature.com
Piezo1 and Piezo2 are mechanically activated ion channels that mediate touch perception,
proprioception and vascular development. Piezo proteins are distinct from other ion …

[HTML][HTML] Protein electrostatics: From computational and structural analysis to discovery of functional fingerprints and biotechnological design

F Vascon, M Gasparotto, M Giacomello… - Computational and …, 2020 - Elsevier
Computationally driven engineering of proteins aims to allow them to withstand an extended
range of conditions and to mediate modified or novel functions. Therefore, it is crucial to the …

Structure of the yeast mitochondrial large ribosomal subunit

A Amunts, A Brown, X Bai, JL Llácer, T Hussain… - Science, 2014 - science.org
Mitochondria have specialized ribosomes that have diverged from their bacterial and
cytoplasmic counterparts. We have solved the structure of the yeast mitoribosomal large …

Molecular architecture of SF3b and structural consequences of its cancer-related mutations

C Cretu, J Schmitzová, A Ponce-Salvatierra, O Dybkov… - Molecular cell, 2016 - cell.com
SF3b is a heptameric protein complex of the U2 small nuclear ribonucleoprotein (snRNP)
that is essential for pre-mRNA splicing. Mutations in the largest SF3b subunit …

Molecular characterization of AIFM2/FSP1 inhibition by iFSP1-like molecules

TN Xavier da Silva, C Schulte, AN Alves… - Cell Death & …, 2023 - nature.com
Ferroptosis is a form of cell death characterized by phospholipid peroxidation, where
numerous studies have suggested that the induction of ferroptosis is a therapeutic strategy …

MyD88 TIR domain higher-order assembly interactions revealed by microcrystal electron diffraction and serial femtosecond crystallography

MTB Clabbers, S Holmes, TW Muusse… - Nature …, 2021 - nature.com
MyD88 and MAL are Toll-like receptor (TLR) adaptors that signal to induce pro-inflammatory
cytokine production. We previously observed that the TIR domain of MAL (MALTIR) forms …

Manipulation of GES and ERG20 for geraniol overproduction in Saccharomyces cerevisiae

GZ Jiang, MD Yao, Y Wang, L Zhou, TQ Song, H Liu… - Metabolic …, 2017 - Elsevier
Manipulation of monoterpene synthases to maximize flux towards targeted products from
GPP (geranyl diphosphate) is the main challenge for heterologous monoterpene …