Protein Structure and Dynamics

This study shows that Ca2+ binding regulates trypsin's biomolecular condensation, preventing autolysis and preserving esterase activity over time.

The paper uses computational methods to analyze the mutational landscape of GB1's binding to IgG-Fc, identifying key hydrogen bonds and structural features that influence binding affinity.

This paper introduces a machine learning-guided directed evolution framework using large language models to improve protein design efficiency and effectiveness.

This paper fine-tunes a large language model to predict protein phase transitions from sequence data and shows its utility in assessing sequence variants' effects on aggregation and droplet formation.

This paper identifies frustration-free topologies in pure parallel beta-sheet structures, showing their designability and connection to protein superfolds.

This paper surveys chemical and geometric patterns on protein surfaces and compares them to nanoparticle ligand patterns, finding similarities and differences that inform synthetic nanoparticle design.

DeepPBS predicts protein-DNA binding specificity using geometric deep learning, showing alignment with experimental mutagenesis data and enabling analysis of molecular dynamics simulations.

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

This paper presents the crystal structure and molecular dynamics simulations of KCTD1 and its P20S mutant, revealing structural insights into its function and disease mechanisms.

The paper investigates the structural basis for the distinct conformational landscapes of tyrosine and serine/threonine kinases using sequence and structure-based models.

This study characterizes the DNA-binding Myb domain of TTF1 using computational modeling and experimental validation, confirming its predominantly helical structure.

This study reveals a pH-induced conformational switching mechanism in Betanodavirus protrusions that governs infectivity through dynamic structural changes.

This study investigates how TFE concentration and salt affect the aggregation and secondary structure transitions of the amyloidogenic peptide Uperin 3.5 in TFE:water mixtures.

This study investigates the structural properties of the N-terminal region of TFIP11, showing it behaves as a polyampholytic intrinsically disordered protein with salt-dependent conformational changes.

The paper identifies protein surface chemistry as a determinant of desiccation tolerance and shows that modifying surface amino acids can confer tolerance to otherwise sensitive proteins.

The paper describes Affilin proteins that bind oncofetal fibronectin's EDB domain, revealing structural plasticity through beta-strand slippage in the ubiquitin scaffold.

The paper improves protein complex prediction by denoising the MSA profile using gradient descent through AlphaFold-multimer, increasing accuracy on difficult targets.

The paper introduces ECSA, an electrophoretic crosslinking shift assay, to detect low-affinity peptide-protein interactions, demonstrating its effectiveness with MAP kinase and D-motif peptides.

This paper introduces a geometric transformer model that predicts protein sequences from backbone scaffolds while considering molecular environment restraints.

This paper develops a computational method to identify stabilizing disulfide bonds for prefusion class I fusion proteins, demonstrating its effectiveness in stabilizing the RSV F protein and providing protection in a cotton rat model.

The paper uses coarse-grained simulations and unsupervised learning to study protein-mediated DNA compaction, finding that protein-protein interactions are critical for forming looped structures observed experimentally.

This paper fine-tunes a protein language model on a large dataset to predict protein folding stability, showing reasonable performance on small domains but limitations in generalizing to larger scaffolds.

This study uses AlphaFold and RosettaCM to model 18 uncharacterized delta-conotoxins, providing structural insights and implications for drug development.

The paper compares pore structure and dynamics in bacterial microcompartment shell proteins under different geometries using molecular modeling and simulations.

The paper identifies a missing-link fold, DZBB, that connects RNA polymerase and ribosomal proteins, showing rapid diversification from a common ancestor.

This study analyzes two engineered biosensors based on PYR1 to recognize different ligands, revealing binding mechanisms and computational methods for biosensor design.

The paper systematically compares conformational movements in LeuT-fold transporters using distance difference matrices, identifying common and distinct motions across nine proteins.

WEDAP is a Python package that simplifies plotting molecular simulation data from conventional MD and weighted ensemble simulations, with examples using HIV-1 capsid protein data.

The paper uses molecular dynamics simulations to show that ATP binding free energy in CDK1 is affected by acetylation at the active site and reveals non-local entropy changes linked to protein-protein interactions.

The paper characterizes how disease mutations in intrinsically disordered regions modulate protein interactions mediated by short linear motifs, identifying both loss and gain of interactions.