K. E. Johansson

GMMA can stabilize proteins across different functional constraints

The paper identifies 5 stabilizing mutations for PYR1 variants using GMMA that increase thermal stability without affecting functionality across different ligand-binding capabilities.

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.

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.

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.

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.

HSP70-binding motifs function as protein quality control degrons

The paper shows that Hsp70-binding motifs can function as PQC degrons, targeting misfolded proteins for degradation in yeast and human cells.

Computational and experimental assessment of backbone templates for computational protein design

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.

Global analysis of multi-mutants to improveprotein function

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.

Understanding the origins of loss of protein function by analyzing the effects of thousands of variants on activity and abundance

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.

Charge Interactions in a Highly Charge-depleted Protein

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.

Global analysis of protein stability by temperature and chemical denaturation

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.