Protein Structure and Dynamics

This paper provides a tutorial on using ShapeGMM to cluster and sample biomolecular conformations from molecular dynamics simulations.

This study uses molecular dynamics and correlated motion analysis to reveal distal thermal activation pathways in soybean lipoxygenase, showing preferential communication through Leu546 over Leu754.

This paper determines the 3D structure of four disulfide-rich modules of CREMP, a structural protein in avian eggshell membrane, using NMR and compares it to other tandem repeat proteins.

The paper evaluates AlphaFold models' ability to predict phosphorylation-induced structural changes in proteins using experimentally derived conformational ensembles.

The paper compares structural networks of remote homologous protein domains from different architectures to assess how domain combinations influence structural and evolutionary changes.

This study uses molecular dynamics simulations to show how the S810L mutation in the MR alters ligand-specific agonist/antagonist behavior by changing side-chain network interactions.

The paper analyzes distantly evolved fish orthologues of titin kinase to identify conserved sequence motifs and classify titin gene duplicates into isoforms.

This study shows glycopolymers stabilize protein folding and interactions through enthalpic interactions, challenging simple volume exclusion models of crowding.

DynamicGT improves protein binding interface prediction by incorporating dynamic features and conformational changes, outperforming static models on flexible and disordered regions.

This paper designs globular proteins that drive biomolecular condensation and demonstrates their use in forming dynamic condensates in cells.

ProFam is an open-source protein family language model that improves fitness prediction and design by leveraging evolutionary context through homologous sequences.

The paper introduces SPURS, a deep learning framework for protein stability prediction that integrates generative models and achieves accurate, scalable, and generalizable results.

This study identifies a sequence-encoded mechanism in plant proteins that enables thermoresponsive phase separation through low-complexity domains.

This paper uses computational methods to study the structural disorder of Dsup and its interaction with the human nucleosome, revealing dynamic electrostatic shielding effects.

This study uses alanine scanning and computational methods to map sequence-function relationships in the yeast killer toxin K2, revealing key residues for activity and enabling engineering of enhanced toxicity and specificity.

The paper investigates MALT1 activation dynamics using a combination of AlphaFold, MD simulations, and NMR analyses, revealing how ionic strength influences its conformational states.

This study investigates the conformational transitions of Rep helicase using single-molecule techniques, revealing two intermediate states influenced by salt concentration.

This study designs a protein that precisely controls Gremlin-1 antagonism by releasing BMPs, revealing the role of interface rigidity in antagonist function.

LoMuS improves protein stability prediction using a multimodal deep learning model that combines physicochemical descriptors with low-rank adapted embeddings from a protein language model.

This study identifies helix III destabilization as the initial trigger for SAA1-76 misfolding by exposing its amyloidogenic core through computational simulations.

This study uses molecular dynamics simulations to show that CDRs significantly influence antibody framework dynamics through CDR-FW correlation networks, highlighting their impact on structure and function.

This paper introduces PS and IIOS, AI tools for analyzing and engineering molecular interactions by decomposing binding interfaces with stage-resolved force-wise insights.

The paper shows that structural divergence in enzymes correlates with residue flexibility and distance from the active site, arising from non-functional and functional evolutionary constraints.

This study reveals the conformational dynamics of Tom70 through structural and computational analyses, showing how its allosteric network coordinates mitochondrial protein import and is modulated by viral interactions.

This study uses SAXS and simulations to show that protein hydration shells shrink with increasing temperature, revealing temperature-sensitive structural changes in the hydration shell.

This paper describes an engineered archaeal PTP with enhanced thermostability and unique biochemical properties, revealing insights into enzyme evolution and biotechnological potential.

This paper evaluates AlphaFold 3 and other methods in predicting α-synuclein polymorphs using a reference set of known structures and finds they can generate fibril-like models, though performance varies with template use.

This paper shows how oppositely charged IDPPs can form synthetic condensates with tunable properties through sequence-encoded phase behavior and micropolarity.

The paper engineers a covalent linkage into a de novo enzyme, revealing that the modified protein rescues cells through upregulating siderophore biosynthesis rather than catalyzing iron release.

The paper shows that full-length Staphylococcal protein A fails to fold stably despite its individual domains being stable, challenging assumptions about modular protein folding and AI prediction accuracy.