K. Lindorff-Larsen

The paper identifies two PQC degrons in DHFR that become exposed in disease-linked missense variants, leading to proteasomal degradation.

This study assesses AlphaFold 2's applications in structural biology, finding it outperforms existing tools in predicting disorder, complexes, and structural features with high confidence.

This study investigates the conformational dynamics of CorA, revealing Mg2+-dependent conformational equilibria and dynamic behavior through SANS, MD simulations, and NMR.

The paper predicts and interprets large-scale mutagenesis data by analyzing protein stability and conservation, finding that sequence conservation provides more accurate variant effect predictions than stability calculations.

The paper develops a coarse-grained model of intrinsically disordered proteins using data-driven optimization to accurately predict phase behaviour and self-association.

The paper assesses computational protein design templates using Rosetta Design and experimental validation, finding that the cart_bonded energy term improves template selection for successful designs.

This paper presents a protocol to refine conformational ensembles of flexible proteins using SAXS data and a Bayesian/Maximum Entropy framework, identifying robust parameter sets for accurate modeling.

This study investigates how an inhibitory domain of Vav1 autoinhibits by transiently exposing a phosphorylation site through conformational changes.

This study determines the NMR structures of two chitin-binding domains from CjLPMO10A and shows functional differences in their chitin-binding affinities and substrate specificity.

The paper compares force fields and methods for refining α-synuclein ensembles using SAXS data, showing that accurate ensembles require compatible simulations and experimental integration.

This study predicts the 3D structures and dynamics of five RNA stem loops in the SARS-CoV-2 5' UTR using molecular dynamics simulations and enhanced sampling techniques.

This paper introduces GMMA, a method to identify beneficial amino acid substitutions in proteins using multi-mutant data, and applies it to GFP variants to find stabilizing and functional improvements.

The paper identifies two stabilizing variants of barley chymotrypsin inhibitor 2, showing synergistic effects in a double mutant.

This study shows properdin oligomers adopt rigid extended conformations that are essential for their function in the complement cascade.

The paper uses molecular dynamics simulations to study how phosphorylation of buried residues in p27 occurs through transient exposure facilitated by protein dynamics.

The paper analyzes variant effects on protein activity and abundance in NUDT15 and PTEN, finding that a third of variants cause loss of function and half of these also reduce abundance.

This paper introduces a dual-reporter system to assess protein translation and folding in E. coli, validated on five proteins with good correlation between reporter signals and protein expression/solubility.

This study investigates the degradation pathway of a disease-linked ASPA variant, finding it is degraded via the proteasome and dependent on Hsp70 and Hsp110.

The paper integrates side-chain NMR relaxation data with molecular dynamics simulations to improve the accuracy of protein dynamics models.

DEER-PREdict calculates EPR and NMR data from protein conformational ensembles to validate models and interpret experiments.

This study integrates NMR, SAXS, SANS, and molecular dynamics simulations to characterize the structure and dynamics of two nanodiscs, revealing conformational heterogeneity and lipid ordering differences.

This study investigates charge interactions in a charge-depleted protein using simulations and experiments, revealing context-dependent residue interactions and their impact on protein stability.

This study determines the structure of the full-length human growth hormone receptor using integrated SAXS, X-ray diffraction, NMR, and molecular dynamics simulations, revealing a flexible ensemble of domains.

The paper uses molecular dynamics simulations to study phospholipid transport and specificity in a flippase, revealing a preference for phosphatidylserine and insights into substrate selectivity mechanisms.

The paper determines how two mitochondrial chaperones bind different membrane proteins by analyzing their structural interactions and identifies factors that influence client specificity.

The paper integrates NMR and simulations to study UUCG RNA stem-loop dynamics, identifying two states and showing MD simulations overestimate a non-native conformation.

This study investigates how folded domains of hnRNPA1 modulate phase separation behavior of its disordered low-complexity domain, showing salt-dependent effects through electrostatic interactions and solubility changes.

The paper combines molecular dynamics simulations with small-angle scattering data to study multi-domain proteins, showing how refining simulations against SAXS data improves agreement with experiments.

This paper introduces a method to assess protein stability using combined temperature and denaturant unfolding with minimal protein requirements, demonstrating its applicability for small-scale protein purification.

The paper derives a structural model of the TIM9{middle dot}10{middle dot}12 complex using NMR, X-ray scattering, and MD simulations, revealing dynamic subunit exchange and conformational changes.