K. Lindorff-Larsen

Predicting absolute protein folding stability using generative models

The paper uses generative models to predict absolute protein stability, achieving a mean error of 1.5 kcal/mol and a correlation coefficient of 0.7.

A coarse-grained model for disordered and multi-domain proteins

The paper introduces a coarse-grained model for multi-domain proteins that accurately simulates conformational properties and phase separation behavior.

Activation and substrate specificity of the human P4-ATPase ATP8B1

This study presents cryo-EM structures and functional analysis of the human ATP8B1-CDC50A complex, revealing its mechanism of action, substrate specificity, and regulation by phosphoinositides.

MolecularWebXR: Multiuser discussions about chemistry and biology in immersive and inclusive VR

MolecularWebXR enables multiuser VR/AR discussions about chemistry and biology in immersive environments accessible via web browsers and consumer devices.

Design of intrinsically disordered protein variants with diverse structural properties

This paper introduces a physics-based algorithm to design intrinsically disordered proteins with specified structural properties, demonstrating high accuracy in predicting compaction and phase separation behavior.

A mutational atlas for Parkin proteostasis

This study maps Parkin missense variants' abundance and degradation mechanisms, showing most low-abundance variants are degraded via the ubiquitin-proteasome system and stabilized at lower temperatures.

Revisiting the use of dioxane as a reference compound for determination of the hydrodynamic radius of proteins by pulsed field gradient NMR spectroscopy

The paper revisits the use of dioxane as a reference compound in PFG NMR to determine protein hydrodynamic radius, finding the current reference value underestimated and proposing a new value.

The effect of linker conformation on performance and stability of a two-domain lytic polysaccharide monooxygenase

This study investigates how linker conformation affects the performance and stability of a two-domain lytic polysaccharide monooxygenase by analyzing wild-type and engineered variants.

Rescaling protein-protein interactions improves Martini 3 for flexible proteins in solution

This study improves the Martini 3 model by reducing protein-protein interaction strength, enhancing accuracy for flexible proteins in solution and with lipid membranes.

Characterizing glucokinase variant mechanisms using a multiplexed abundance assay

The paper characterizes mechanisms of human glucokinase variants by analyzing their abundance and stability, identifying residues that affect metabolic stability and conformational dynamics.

Conformational ensembles of the human intrinsically disordered proteome: Bridging chain compaction with function and sequence conservation

The paper develops a model to predict conformational ensembles of human intrinsically disordered regions (IDRs) from sequence, showing correlations between chain compaction, function, localization, and sequence conservation across orthologs.

Kinetic stabilization of translation-repression condensates by a neuron-specific microexon

The paper shows that a neuron-specific microexon in CPEB4 stabilizes translation-repression condensates by competing with aggregation, enabling reversible regulation of gene expression in neurons.

Combining experiments and simulations to examine the temperature-dependent behaviour of a disordered protein

The paper combines molecular dynamics simulations and experimental data to study temperature effects on Histatin 5's conformational behavior, finding agreement with some data but not all.

Fitting Force Field parameters to NMR Relaxation Data

This paper optimizes force field parameters using NMR relaxation data from T4 lysozyme and shows improved agreement with experimental data and better MD trajectory reweighting.

FRETpredict: A Python package for FRET efficiency predictions using rotamer libraries

FRETpredict predicts FRET efficiencies from protein conformations using rotamer libraries, validated on various systems and available as open-source software.

Rare catechol-O-methyltransferase (COMT) missense variants are structurally unstable proteasome targets

The paper shows two rare COMT missense variants are structurally unstable, leading to proteasomal degradation and reduced enzyme levels, with degradation independent of COMT isoform.

Slow conformational changes in the rigid and highly stable chymotrypsin inhibitor 2

The paper investigates how mutations affect slow conformational dynamics and stability in chymotrypsin inhibitor 2, finding that the excited state population correlates with protein stability.

Lysine deserts prevent adventitious ubiquitylation of ubiquitin-proteasome components

The paper identifies lysine deserts in UPS proteins and shows that introducing lysines increases ubiquitylation, with functional consequences for protein stability and function.

The prolactin receptor scaffolds Janus kinase 2 via co-structure formation with phosphoinositide-4,5-bisphosphate

This study shows that the prolactin receptor forms a co-structure with JAK2 and PI(4,5)P2, enabling signal transduction by stabilizing the receptor's disordered domain.

Conformational and oligomeric states of SPOP from small-angle X-ray scattering and molecular dynamics simulations

This study characterizes SPOP's conformational and oligomeric states using SAXS and molecular dynamics simulations, revealing rigid helical structures with flexible linker regions.

Effect of naturally-occurring mutations on the stability and function of cancer-associated NQO1: comparison of experiments and computation.

The paper compares computational predictions and experimental analysis of NQO1 variants to assess their stability and function, finding good correlation but noting outliers.

Deciphering the alphabet of disorder -- Glu and Asp act differently on local but not global properties

This study compares the functional and structural differences between glutamate and aspartate in intrinsically disordered proteins using experimental and computational methods.

Rapid protein stability prediction using deep learning representations

This paper introduces RaSP, a deep learning method for rapid protein stability prediction, showing it matches biophysics-based methods and reveals population-level patterns in stability changes.

Discovering functionally important sites in proteins

This paper introduces a machine learning method to predict functional sites in proteins by integrating sequence conservation and biophysical stability models, validated through experimental data on missense variants.

Accurate protein stability predictions from homology models

This study evaluates the accuracy of protein stability predictions from homology models compared to crystal structures, finding they perform equally well when sequence identity is at least 40%.

Interpreting the molecular mechanisms of disease variants in human membrane proteins

This paper investigates missense variants in human membrane proteins, finding that loss of stability is a common mechanism for pathogenicity in over half of the studied variants.

Improved Predictions of Phase Behaviour of Intrinsically Disordered Proteins by Tuning the Interaction Range

The paper improves predictions of phase behaviour in intrinsically disordered proteins by refining interaction range and model parameters.

Assessment of models for calculating the hydrodynamic radius of intrinsically disordered proteins

The paper evaluates models for calculating the hydrodynamic radius of intrinsically disordered proteins using conformational ensembles validated by small-angle X-ray scattering and finds the Kirkwood-Riseman equation to be the most accurate.

Increasing protein stability by inferring substitution effects from high-throughput experiments

The paper uses a computational model to infer substitution effects from high-throughput experiments, increasing protein stability through targeted amino acid changes.

Conserved degronome features governing quality control-associated proteolysis

The paper identifies conserved degron features in yeast, viruses, and humans that govern quality control proteolysis, showing transmembrane domain-like sequences are key determinants of protein half-life.