E. Papaleo

Data-driven discovery of gene expression markers distinguishing pediatric acute lymphoblastic leukemia subtypes

This study identifies gene expression markers that distinguish pediatric B-cell and T-cell acute lymphoblastic leukemia subtypes and shows their association with patient survival.

Decoding Phospho-Regulation and Flanking Regions in Autophagy-Associated Short Linear Motifs: A Case Study of Optineurin-LC3B Interaction

This study investigates phospho-regulation and flanking regions in autophagy-related SLiMs using optineurin-LC3B as a case, revealing structural mechanisms and disease mutation impacts.

TRAP1 S-nitrosylation as a model of population-shift mechanism to study the effects of nitric oxide on redox-sensitive oncoproteins.

The paper investigates how TRAP1 S-nitrosylation induces conformational changes and explores its implications for redox-sensitive oncoproteins through simulations and bioinformatics.

MIADE metadata guidelines: Minimum Information About a Disorder Experiment

The paper introduces MIADE guidelines to standardize metadata for experiments studying intrinsically disordered proteins, improving data interpretation and reproducibility.

A dual-reporter system for investigating and optimizing protein translation and folding in E. coli

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.

S-nitrosylation affects TRAP1 structure and ATPase activity and modulates cell response to apoptotic stimuli

This study shows that S-nitrosylation of TRAP1 at Cys501 alters its structure and ATPase activity, affecting cell response to apoptotic stimuli.

Computational and cellular studies reveal structural destabilization and degradation of MLH1 variants in Lynch syndrome

The paper identifies structural destabilization and degradation of MLH1 variants in Lynch syndrome, linking reduced cellular levels to loss-of-function and suggesting stability predictions for diagnostic use.

The conformational and mutational landscape of the ubiquitin-like marker for the autophagosome formation in cancer

The paper evaluates molecular dynamics models of LC3B and analyzes 26 missense mutations to understand their impact on structure and function in cancer.

Conformational gating in ammonia lyases

This study uses molecular dynamics to investigate conformational changes in a 3-methylaspartate ammonia lyase, showing how structural elements regulate active site accessibility.

Molecular dynamics ensemble refinement of the heterogeneous native state of NCBD using chemical shifts and NOEs

This study refines the native state ensemble of NCBD using chemical shifts and NOEs to accurately model its conformational dynamics.

How well do force fields capture the strength of salt bridges in proteins?

This study benchmarks molecular dynamics simulations of salt bridge stability in GB1 using NMR data, finding that simulations overestimate salt bridge stability compared to experimental results.