Alexander Jussupow
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View article: Author response: Protein-Induced Membrane Strain Drives Supercomplex Formation
Author response: Protein-Induced Membrane Strain Drives Supercomplex Formation Open
View article: Protein-Induced Membrane Strain Drives Supercomplex Formation
Protein-Induced Membrane Strain Drives Supercomplex Formation Open
Mitochondrial membranes harbor the electron transport chain (ETC) that powers oxidative phosphorylation (OXPHOS) and drives the synthesis of ATP. Yet, under physiological conditions, the OXPHOS proteins operate as higher-order supercomplex…
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: Protein-Induced Membrane Strain Drives Supercomplex Formation
Protein-Induced Membrane Strain Drives Supercomplex Formation Open
Mitochondrial membranes harbor the electron transport chain (ETC) that powers oxidative phosphorylation (OXPHOS) and drives the synthesis of ATP. Yet, under physiological conditions, the OXPHOS proteins operate as higher-order supercomplex…
View article: Author response: Protein-Induced Membrane Strain Drives Supercomplex Formation
Author response: Protein-Induced Membrane Strain Drives Supercomplex Formation 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 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: 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: 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: Protein-Induced Membrane Strain Drives Supercomplex Formation
Protein-Induced Membrane Strain Drives Supercomplex Formation Open
Mitochondrial membranes harbor the electron transport chain (ETC) that powers oxidative phosphorylation (OXPHOS) and drives the synthesis of ATP. Yet, under physiological conditions, the OXPHOS proteins operate as higher-order supercomplex…
View article: Protein-Induced Membrane Strain Drives Supercomplex Formation
Protein-Induced Membrane Strain Drives Supercomplex Formation Open
Mitochondrial membranes harbor the electron transport chain (ETC) that powers oxidative phosphorylation (OXPHOS) and drives the synthesis of ATP. Yet, under physiological conditions, the OXPHOS proteins operate as higher-order supercomplex…
View article: Evolution of the conformational dynamics of the molecular chaperone Hsp90
Evolution of the conformational dynamics of the molecular chaperone Hsp90 Open
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: Effective Molecular Dynamics from Neural Network-Based Structure Prediction Models
Effective Molecular Dynamics from Neural Network-Based Structure Prediction Models Open
Recent breakthroughs in neural network-based structure prediction methods, such as AlphaFold2 and RoseTTAFold, have dramatically improved the quality of computational protein structure prediction. These models also provide statistical conf…
View article: Effective Molecular Dynamics from Neural-Network Based Structure Prediction Models
Effective Molecular Dynamics from Neural-Network Based Structure Prediction Models Open
Recent breakthroughs in neural-network based structure prediction methods, such as AlphaFold2 and RoseTTAFold, have dramatically improved the quality of computational protein structure prediction. These models also provide statistical conf…
View article: Effective Molecular Dynamics from Neural-Network Based Structure Prediction Models
Effective Molecular Dynamics from Neural-Network Based Structure Prediction Models Open
Molecular dynamics simulation (61.5 us) data of 28 one- and two-domain proteins from Jussupow & Kaila: Effective Molecular Dynamics from Neural-Network Based Structure Prediction Models
View article: Effective Molecular Dynamics from Neural-Network Based Structure Prediction Models
Effective Molecular Dynamics from Neural-Network Based Structure Prediction Models Open
Molecular dynamics simulation (61.5 us) data of 28 one- and two-domain proteins from Jussupow & Kaila: Effective Molecular Dynamics from Neural-Network Based Structure Prediction Models
View article: Extended conformational states dominate the Hsp90 chaperone dynamics
Extended conformational states dominate the Hsp90 chaperone dynamics Open
aMD and cgMD simulation trajectories for publication "Extended conformational states dominate the Hsp90 chaperone dynamics" Jussupow et al. doi: 10.1016/j.jbc.2022.102101
View article: Extended conformational states dominate the Hsp90 chaperone dynamics
Extended conformational states dominate the Hsp90 chaperone dynamics Open
aMD and cgMD simulation trajectories for publication "Extended conformational states dominate the Hsp90 chaperone dynamics" Jussupow et al. doi: 10.1016/j.jbc.2022.102101
View article: Extended conformational states dominate the Hsp90 chaperone dynamics
Extended conformational states dominate the Hsp90 chaperone dynamics Open
View article: Deactivation blocks proton pathways in the mitochondrial complex I
Deactivation blocks proton pathways in the mitochondrial complex I Open
Significance The electron transport chain of mitochondria is initiated by the respiratory complex I that converts chemical energy into a proton motive force to power synthesis of adenosine triphosphate. On a chemical level, complex I catal…
View article: Refinement of α-Synuclein Ensembles Against SAXS Data: Comparison of Force Fields and Methods
Refinement of α-Synuclein Ensembles Against SAXS Data: Comparison of Force Fields and Methods Open
The inherent flexibility of intrinsically disordered proteins (IDPs) makes it difficult to interpret experimental data using structural models. On the other hand, molecular dynamics simulations of IDPs often suffer from force-field inaccur…
View article: Refinement of<i>α</i>-synuclein ensembles against SAXS data: Comparison of force fields and methods
Refinement of<i>α</i>-synuclein ensembles against SAXS data: Comparison of force fields and methods Open
The inherent flexibility of intrinsically disordered proteins (IDPs) makes it difficult to interpret experimental data using structural models. On the other hand, molecular dynamics simulations of IDPs often suffer from force-field inaccur…
View article: Structure of inhibitor-bound mammalian complex I
Structure of inhibitor-bound mammalian complex I Open
View article: The dynamics of linear polyubiquitin
The dynamics of linear polyubiquitin Open
A new efficient method for SAXS-driven simulations allows researchers to explain the dynamics of linear polyubiquitin.
View article: Molecular recognition and dynamics of linear poly-ubiquitins: integrating coarse-grain simulations and experiments
Molecular recognition and dynamics of linear poly-ubiquitins: integrating coarse-grain simulations and experiments Open
Poly-ubiquitin chains are flexible multidomain proteins, whose conformational dynamics enable their molecular recognition by a large number of partners in multiple biological pathways. By using alternative linkage, it is possible to obtain…