Protein Structure and Dynamics

Topological Entanglement in Intrinsically Disordered Proteins: Sequence, Structural, and Functional Determinants

The paper uses entanglement measures from knot theory to analyze sequence and structural features of intrinsically disordered proteins and identifies functionally enriched regions in entanglement space.

Electrostatic interactions compensate energetic frustration in the coupled folding and binding of intrinsically disordered proteins

The paper investigates the energy landscape of coupled folding and binding in intrinsically disordered proteins, finding that electrostatic interactions compensate for energetic frustration.

Inferring Dynamic Information from Protein Structures by Gaussian Integrals and Deep Learning

This paper develops a deep learning framework to predict protein flexibility from static structural data, achieving moderate accuracy and identifying key structural features associated with flexibility.

A structure-derived contact-network responsiveness atlas of human proteins

The paper introduces CNR, a framework to quantify how protein contact networks respond to stabilizing interaction changes, using human AlphaFold models to analyze 22,167 structures.

Simulation of cell-size systems at long timescales with flexible protein structures

The paper introduces a docking-based simulation method that combines rigid-body approximations with flexible protein structures to model macromolecular interactions in crowded cellular environments over long timescales.

kontakteUR: transforming coordinates to chemical intuition to focus on essential interactions in biomolecular systems

kontakteUR transforms structural coordinates into a chemically informed contact space to analyze biomolecular interactions and their changes, enabling systematic comparison and functional insights.

Sequence-encoded differences in the conformational ensembles of CITED transcriptional activation domains impact coactivator binding

The paper investigates how sequence differences in CITED CTADs affect their conformational ensembles and TAZ1 binding, showing that minor sequence changes impact IDP structure and function.

Ovo, an Open-Source Ecosystem for De Novo Protein Design

Ovo provides an open-source platform for de novo protein design, integrating tools, workflows, and visualization to simplify and scale the design process.

Physical Confinement Modulates the Rate-Limiting Transition in the Release of Phosphate from Actin Filaments

The paper uses molecular dynamics simulations to show that phosphate release from actin filaments is limited by dissociation from Mg2+ and varies with subunit position and water molecule count.

AFM-Fold: Rapid Reconstruction of Protein Conformations from AFM Images

AFM-Fold reconstructs 3D protein conformations from AFM images using a generative AI framework, outperforming rigid-body fitting and capturing conformational dynamics.

SteerAF: Distogram-based Steering of AlphaFold2 toward Alternative Conformations

SteerAF improves AlphaFold2's ability to predict alternative protein conformations by using distogram information from MSAs, achieving better results than existing methods.

Functional importance of a structurally encoded succinimide modification in a high-affinity solute-binding protein

The paper shows that a spontaneous post-translational succinimide modification in a bacterial solute-binding protein enhances its thermostability and binding affinity for 5-oxoproline.

Highly diverged non-vertebrate Ki-67 proteins with conserved biophysical and functional properties

The paper identifies Ki-67-like proteins in non-vertebrate eukaryotes, showing conserved biophysical and functional properties despite low sequence homology.

Crowder induced conformational fluctuations modulate the phase separation of yeast SUP35 NM domain

This study shows that crowder shape affects Sup35NM conformation and phase separation, with rod-like crowders promoting phase separation while spherical ones do not.

Zero-shot design of a de novo metalloenzyme

This paper introduces dEVA, a framework for de novo metalloenzyme design, achieving high catalytic activity without natural templates.

DNA-binding specificity recognition from predicted homologous protein-DNA structures

This paper introduces HomoDSP, a method for DNA-binding specificity prediction using homologous protein-DNA structures, showing improved accuracy and generalization over existing methods.

A histidine switch controls the pH-responsive self-assembly of a helical protein filament

The paper identifies a histidine switch that regulates pH-responsive self-assembly of a helical protein filament through electrostatic interactions.

Blocking protein quality control degradation leads to structural stabilization of DHFR indel variants

The paper shows that blocking protein quality control degradation stabilizes DHFR indel variants, suggesting a therapeutic approach for protein misfolding diseases.

MartiniSurf: Automated Simulations of Surface-Immobilized Biomolecular Systems with Martini

MartiniSurf automates the setup of surface-immobilized biomolecular systems for Martini simulations, enabling systematic in silico studies of immobilization strategies.

Strategic template filtering accelerates fragment-based peptide docking

PatchMAN2 improves peptide-protein docking efficiency by filtering fragments and focusing sampling on relevant regions, reducing computational cost while maintaining accuracy.

When can AlphaFold predict the oligomeric states of proteins?

This study evaluates AlphaFold2-Multimer and AlphaFold3's ability to predict oligomeric states of proteins, showing their utility but also highlighting limitations for proteins without structural representatives in the training set.

Customizing the Structure of Minimal TIM Barrels to Craft Efficient De Novo Enzymes

The paper designs de novo TIM barrels with structural lids to create active sites for enzymatic function, achieving high catalytic efficiency.

Large datasets and machine learning models fail to capture extremophile enzyme melting and optimum temperatures

The paper shows that machine learning models and large datasets fail to accurately predict extremophile enzyme melting and optimum temperatures, due to biased and error-laden training data.

Protein-Solvent Shape Complementarity as a Unifying Principle in Excipient-Mediated Protein Thermal Stability

The paper uses molecular dynamics simulations to identify a unifying mechanism for excipient-mediated protein thermal stability based on shape complementarity between proteins and solvents.

Transposable elements as evolutionary substrates of proteindisorder in the human proteome

The paper identifies transposable elements as a source of intrinsic disorder in human proteins, showing that TE insertions are enriched in disordered regions and their conformational fate depends on their age and TE class.

Differences between protein fitness models can be used to design variants of altered specificity

The paper evaluates how protein fitness models predict and design variants with altered specificity, finding that models biased against such changes can be leveraged by using weighted differences in model scores.

Testing the reliability of AI-generated protein structures

The paper tests AlphaFold2 and ColabFold's reliability by using false protein sequences and finds a low false positive rate, while also discovering new pseudogenes in the human genome.

Membrane-dependent structural organization of cowpox virus CPXV012 and its recognition of TAP

This study investigates the membrane-dependent structure of CPXV012 and its interaction with TAP, revealing a two-helical organization and flexible ER-luminal region critical for TAP recognition.

Predicting molecular recognition features in protein sequences with MoRFchibi 2.0

MoRFchibi 2.0 predicts Molecular Recognition Features in protein sequences, outperforming existing tools and models including AlphaFold and protein language models.

Tightly Knotted Enzymes Inhibit Protein-Protein Aggregation

This study shows that knotted protein structures inhibit aggregation by limiting expanded states and suppressing liquid-liquid phase separation.