Michael Feig
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View article: Deep generative modeling of temperature-dependent structural ensembles of proteins
Deep generative modeling of temperature-dependent structural ensembles of proteins Open
View article: Molecular Modeling and Molecular Dynamics Simulation of a Packed and Intact Bacterial Microcompartment
Molecular Modeling and Molecular Dynamics Simulation of a Packed and Intact Bacterial Microcompartment Open
Bacterial microcompartments (BMCs) are protein-bound organelles found in some bacteria which encapsulate enzymes for enhanced catalytic activity. These compartments spatially sequester enzymes within semipermeable shell proteins and are pa…
View article: Molecular Modeling and Molecular Dynamics Simulation of a Packed and Intact Bacterial Microcompartment
Molecular Modeling and Molecular Dynamics Simulation of a Packed and Intact Bacterial Microcompartment Open
Bacterial microcompartments (BMCs) are protein-bound organelles found in some bacteria which encapsulate enzymes for enhanced catalytic activity. These compartments spatially sequester enzymes within semi-permeable shell proteins, and are …
View article: Abstract 2321 Molecular Modeling and Molecular Dynamics Simulation of a Packed Bacterial Microcompartment
Abstract 2321 Molecular Modeling and Molecular Dynamics Simulation of a Packed Bacterial Microcompartment Open
View article: Accurate Predictions of Molecular Properties of Proteins via Graph Neural Networks and Transfer Learning
Accurate Predictions of Molecular Properties of Proteins via Graph Neural Networks and Transfer Learning Open
Machine learning has emerged as a promising approach for predicting molecular properties of proteins, as it addresses limitations of experimental and traditional computational methods. Here, we introduce GSnet, a graph neural network (GNN)…
View article: Towards a Unified Framework for Determining Conformational Ensembles of Disordered Proteins
Towards a Unified Framework for Determining Conformational Ensembles of Disordered Proteins Open
Disordered proteins play essential roles in myriad cellular processes, yet their structural characterization remains a major challenge due to their dynamic and heterogeneous nature. We here present a community-driven initiative to address …
View article: Deep generative modeling of temperature-dependent structural ensembles of proteins
Deep generative modeling of temperature-dependent structural ensembles of proteins Open
Deep learning has revolutionized protein structure prediction, but capturing conformational ensembles and structural variability remains an open challenge. While molecular dynamics (MD) is the foundation method for simulating biomolecular …
View article: Controlled Enzyme Cargo Loading in Engineered Bacterial Microcompartment Shells
Controlled Enzyme Cargo Loading in Engineered Bacterial Microcompartment Shells Open
Bacterial microcompartments (BMCs) are nanometer-scale organelles with a protein-based shell that serve to colocalize and encapsulate metabolic enzymes. They may provide a range of benefits to improve pathway catalysis, including substrate…
View article: COCOMO2: A Coarse-Grained Model for Interacting Folded and Disordered Proteins
COCOMO2: A Coarse-Grained Model for Interacting Folded and Disordered Proteins Open
Biomolecular interactions are essential in many biological processes, including complex formation and phase separation processes. Coarse-grained computational models are especially valuable for studying such processes via simulation. Here,…
View article: Accurate Predictions of Molecular Properties of Proteins via Graph Neural Networks and Transfer Learning
Accurate Predictions of Molecular Properties of Proteins via Graph Neural Networks and Transfer Learning Open
Machine learning has emerged as a promising approach for predicting molecular properties of proteins, as it addresses limitations of experimental and traditional computational methods. Here, we introduce GSnet, a graph neural network (GNN)…
View article: Diffusion and Viscosity in Mixed Protein Solutions
Diffusion and Viscosity in Mixed Protein Solutions Open
The viscosity and diffusion properties of crowded protein systems were investigated with molecular dynamics simulations of SH3 mixtures with different crowders, and results were compared with experimental data. The simulations accurately r…
View article: Structure Characterization of Bacterial Microcompartment Shells via X-ray Scattering and Coordinate Modeling: Evidence for adventitious capture of cytoplasmic proteins
Structure Characterization of Bacterial Microcompartment Shells via X-ray Scattering and Coordinate Modeling: Evidence for adventitious capture of cytoplasmic proteins Open
Bacterial microcompartments (BMCs) are self-assembling, protein shell structures that are widely investigated across a broad range of biological and abiotic chemistry applications. A central challenge in BMC research is the targeted captur…
View article: COCOMO2: A coarse-grained model for interacting folded and disordered proteins
COCOMO2: A coarse-grained model for interacting folded and disordered proteins Open
Biomolecular interactions are essential in many biological processes, including complex formation and phase separation processes. Coarse-grained computational models are especially valuable for studying such processes via simulation. Here,…
View article: Controlled enzyme cargo loading in engineered bacterial microcompartment shells
Controlled enzyme cargo loading in engineered bacterial microcompartment shells Open
Bacterial microcompartments (BMCs) are nanometer-scale organelles with a protein-based shell that serve to co-localize and encapsulate metabolic enzymes. They may provide a range of benefits to improve pathway catalysis, including substrat…
View article: Diffusion and Viscosity in Mixed Protein Solutions
Diffusion and Viscosity in Mixed Protein Solutions Open
The viscosity and diffusion properties of crowded protein systems were investigated with molecular dynamics simulations of SH3 mixtures with different crowders, and results were compared with experimental data. The simulations accurately r…
View article: CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed
CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed Open
Since its inception nearly a half century ago, CHARMM has been playing a central role in computational biochemistry and biophysics. Commensurate with the developments in experimental research and advances in computer hardware, the range of…
View article: Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser
Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser Open
Catalysis and translocation of multisubunit DNA-directed RNA polymerases underlie all cellular mRNA synthesis. RNA polymerase II (Pol II) synthesizes eukaryotic pre-mRNAs from a DNA template strand buried in its active site. Structural det…
View article: <i>In Vitro</i> Encapsulation of Functionally Active Abiotic Photosensitizers Inside a Bacterial Microcompartment Shell
<i>In Vitro</i> Encapsulation of Functionally Active Abiotic Photosensitizers Inside a Bacterial Microcompartment Shell Open
Bacterial microcompartments (BMCs) are self-assembling, selectively permeable protein shells that encapsulate enzymes to enhance catalytic efficiency of segments of metabolic pathways through means of confinement. The modular nature of BMC…
View article: De Novo Synthesis and Structural Elucidation of CDR-H3 Loop Mimics
De Novo Synthesis and Structural Elucidation of CDR-H3 Loop Mimics Open
The binding affinity of antibodies to specific antigens stems from a remarkably broad repertoire of hypervariable loops known as complementarity-determining regions (CDRs). While recognizing the pivotal role of the heavy-chain 3 CDRs (CDR-…
View article: De Novo Synthesis and Structural Elucidation of CDR-H3 Loop Mimics
De Novo Synthesis and Structural Elucidation of CDR-H3 Loop Mimics Open
The binding affinity of antibodies to specific antigens stems from a remarkably broad repertoire of hypervariable loops known as complementarity-determining regions (CDRs). While recognizing the pivotal role of the heavy-chain 3 CDRs (CDR-…
View article: Transferable deep generative modeling of intrinsically disordered protein conformations
Transferable deep generative modeling of intrinsically disordered protein conformations Open
Intrinsically disordered proteins have dynamic structures through which they play key biological roles. The elucidation of their conformational ensembles is a challenging problem requiring an integrated use of computational and experimenta…
View article: Transferable deep generative modeling of intrinsically disordered protein conformations
Transferable deep generative modeling of intrinsically disordered protein conformations Open
Intrinsically disordered proteins have dynamic structures through which they play key biological roles. The elucidation of their conformational ensembles is a challenging problem requiring an integrated use of computational and experimenta…
View article: One bead per residue can describe all-atom protein structures
One bead per residue can describe all-atom protein structures Open
View article: PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins
PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins Open
The Protein Ensemble Database (PED) (URL: https://proteinensemble.org) is the primary resource for depositing structural ensembles of intrinsically disordered proteins. This updated version of PED reflects advancements in the field, denoti…
View article: Structural basis of transcription: RNA Polymerase II substrate binding and metal coordination at 3.0 Å using a free-electron laser
Structural basis of transcription: RNA Polymerase II substrate binding and metal coordination at 3.0 Å using a free-electron laser Open
Catalysis and translocation of multi-subunit DNA-directed RNA polymerases underlie all cellular mRNA synthesis. RNA polymerase II (Pol II) synthesizes eukaryotic pre-mRNAs from a DNA template strand buried in its active site. Structural de…
View article: One particle per residue is sufficient to describe all-atom protein structures
One particle per residue is sufficient to describe all-atom protein structures Open
Atomistic resolution is considered the standard for high-resolution biomolecular structures, but coarse-grained models are often necessary to reflect limited experimental resolution or to achieve feasibility in computational studies. It is…
View article: The effect of polymer length in liquid-liquid phase separation
The effect of polymer length in liquid-liquid phase separation Open
Understanding the thermodynamics that drive liquid-liquid phase separation (LLPS) is quite important given the number of diverse biomolecular systems undergoing this phenomenon. Many studies have focused on condensates of long polymers, bu…
View article: Varying molecular interactions explain aspects of crowder-dependent enzyme function of a viral protease
Varying molecular interactions explain aspects of crowder-dependent enzyme function of a viral protease Open
Biochemical processes in cells, including enzyme-catalyzed reactions, occur in crowded conditions with various background macromolecules occupying up to 40% of cytoplasm’s volume. Viral enzymes in the host cell also encounter such crowded …
View article: Characterization of RNA polymerase II trigger loop mutations using molecular dynamics simulations and machine learning
Characterization of RNA polymerase II trigger loop mutations using molecular dynamics simulations and machine learning Open
Catalysis and fidelity of multisubunit RNA polymerases rely on a highly conserved active site domain called the trigger loop (TL), which achieves roles in transcription through conformational changes and interaction with NTP substrates. Th…
View article: Direct generation of protein conformational ensembles via machine learning
Direct generation of protein conformational ensembles via machine learning Open
Dynamics and conformational sampling are essential for linking protein structure to biological function. While challenging to probe experimentally, computer simulations are widely used to describe protein dynamics, but at significant compu…