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Protein Multimerization

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Editorial-Sequences and topology.

Current opinion in structural biology 28587734
Animals Binding Sites Computational Biology Humans Machine Learning Molecular Docking Simulation Protein Binding Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Protein Interaction Domains and Motifs Protein Interaction Mapping Protein Multimerization Proteins Thermodynamics
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modeling of the cryptic E2∼ubiquitin-binding site of E6-associated protein (E6AP)/UBE3A reveals the mechanism of polyubiquitin chain assembly.

The Journal of biological chemistry 28924046
To understand the mechanism for assembly of Lys-linked polyubiquitin degradation signals, we previously demonstrated that the E6AP/UBE3A ligase harbors two functionally distinct E2∼ubiquitin-binding sites: a high-affinity Site 1 required for E6AP Cys...
Amino Acid Substitution Animals Binding Sites Biocatalysis Cattle Computational Biology Cysteine Expert Systems Humans Iodine Radioisotopes Isoenzymes Models, Molecular Molecular Docking Simulation Mutagenesis, Site-Directed Point Mutation Protein Conformation Protein Multimerization Recombinant Fusion Proteins Ubiquitin Ubiquitin-Conjugating Enzymes Ubiquitin-Protein Ligases Ubiquitination
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Integrated structural modeling and super-resolution imaging resolve GPCR oligomers.

Progress in molecular biology and translational science 31952685
Formation of G protein-coupled receptors (GPCRs) dimers and higher order oligomers represents a key mechanism in pleiotropic signaling, yet how individual protomers function within oligomers remains poorly understood. For the Class A/rhodopsin subfam...
Algorithms Allosteric Site Animals Computational Biology Crystallography, X-Ray Fluorescence Resonance Energy Transfer Humans Ligands Machine Learning Molecular Dynamics Simulation Mutation Neural Networks, Computer Protein Binding Protein Interaction Mapping Protein Multimerization Protein Structure, Secondary Receptors, G-Protein-Coupled Software Support Vector Machine
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Computational Models for Self-Interacting Proteins Prediction.

Protein and peptide letters 31880240
Self-Interacting Proteins (SIPs), whose two or more copies can interact with each other, have significant roles in cellular functions and evolution of Protein Interaction Networks (PINs). Knowing whether a protein can act on itself is important to un...
Computer Simulation Databases, Protein Drug Design Machine Learning Models, Molecular Protein Binding Protein Interaction Maps Protein Multimerization Proteins
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Energy-based graph convolutional networks for scoring protein docking models.

Proteins 32144844
Structural information about protein-protein interactions, often missing at the interactome scale, is important for mechanistic understanding of cells and rational discovery of therapeutics. Protein docking provides a computational alternative for su...
Amino Acid Sequence Benchmarking Binding Sites Computer Graphics Deep Learning Humans Ligands Molecular Docking Simulation Peptides Protein Binding Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Protein Interaction Domains and Motifs Protein Interaction Mapping Protein Multimerization Proteins Research Design Software Structural Homology, Protein Thermodynamics
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A Two-Layer SVM Ensemble-Classifier to Predict Interface Residue Pairs of Protein Trimers.

Molecules (Basel, Switzerland) 32977371
Study of interface residue pairs is important for understanding the interactions between monomers inside a trimer protein-protein complex. We developed a two-layer support vector machine (SVM) ensemble-classifier that considers physicochemical and ge...
Computational Biology Protein Multimerization Protein Structure, Quaternary Proteins Support Vector Machine
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Machine Learning Enables Selection of Epistatic Enzyme Mutants for Stability Against Unfolding and Detrimental Aggregation.

Chembiochem : a European journal of chemical biology 33094545
Machine learning (ML) has pervaded most areas of protein engineering, including stability and stereoselectivity. Using limonene epoxide hydrolase as the model enzyme and innov'SAR as the ML platform, comprising a digital signal process, we achieved h...
Epoxide Hydrolases Limonene Machine Learning Molecular Dynamics Simulation Mutation Protein Engineering Protein Folding Protein Multimerization Rhodococcus
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Accurate prediction of inter-protein residue-residue contacts for homo-oligomeric protein complexes.

Briefings in bioinformatics 33693482
Protein-protein interactions play a fundamental role in all cellular processes. Therefore, determining the structure of protein-protein complexes is crucial to understand their molecular mechanisms and develop drugs targeting the protein-protein inte...
Binding Sites Datasets as Topic Deep Learning Humans Molecular Docking Simulation Protein Binding Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Protein Interaction Domains and Motifs Protein Multimerization Proteins Software
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Integrating deep learning with microfluidics for biophysical classification of sickle red blood cells adhered to laminin.

PLoS computational biology 34843453
Sickle cell disease, a genetic disorder affecting a sizeable global demographic, manifests in sickle red blood cells (sRBCs) with altered shape and biomechanics. sRBCs show heightened adhesive interactions with inflamed endothelium, triggering painfu...
Anemia, Sickle Cell Biophysical Phenomena Computational Biology Deep Learning Diagnosis, Computer-Assisted Erythrocyte Deformability Erythrocytes, Abnormal Hemoglobin, Sickle High-Throughput Screening Assays Humans Image Interpretation, Computer-Assisted In Vitro Techniques Lab-On-A-Chip Devices Laminin Microfluidics Neural Networks, Computer Protein Multimerization
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Machine learning-driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins.

Proceedings of the National Academy of Sciences of the United States of America 34983849
RAS is a signaling protein associated with the cell membrane that is mutated in up to 30% of human cancers. RAS signaling has been proposed to be regulated by dynamic heterogeneity of the cell membrane. Investigating such a mechanism requires near-at...
Cell Membrane Humans Lipids Machine Learning Molecular Dynamics Simulation Protein Multimerization Proto-Oncogene Proteins p21(ras) Signal Transduction
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