Ryo Kanada
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View article: Conversion of an agonistic anti-TNFR2 biparatopic antibody into an antagonist by insertion of peptide linkers into the hinge region
Conversion of an agonistic anti-TNFR2 biparatopic antibody into an antagonist by insertion of peptide linkers into the hinge region Open
Biparatopic antibodies (BpAbs) bind two different antigen epitopes to form characteristic immunocomplexes. Many BpAbs have been developed for enhanced crosslinking to induce signal transduction or cell internalization, whereas few have bee…
View article: Precision spatiotemporal analysis of large-scale compound–protein interactions through molecular dynamics simulation
Precision spatiotemporal analysis of large-scale compound–protein interactions through molecular dynamics simulation Open
Biological systems are composed of and regulated by intricate and diverse biomolecular interactions. Experimental and computational approaches have been developed to elucidate the mechanisms of these interactions; however, owing to cost, t…
View article: Receptor-independent regulation of Gα13 by alpha-1-antitrypsin C-terminal peptides
Receptor-independent regulation of Gα13 by alpha-1-antitrypsin C-terminal peptides Open
Alpha-1-antitrypsin (AAT), a circulating serine protease inhibitor, is an acute inflammatory response protein with anti-inflammatory functions. The C-terminal peptides of AAT are found in various tissues and have been proposed as putative …
View article: A thermodynamically consistent monte carlo cross-bridge model with a trapping mechanism reveals the role of stretch activation in heart pumping
A thermodynamically consistent monte carlo cross-bridge model with a trapping mechanism reveals the role of stretch activation in heart pumping Open
Changes in intracellular calcium concentrations regulate heart beats. However, the decline in the left ventricular pressure during early diastole is much sharper than that of the Ca 2+ transient, resulting in a rapid supply of blood to the…
View article: Enhanced Conformational Sampling with an Adaptive Coarse-Grained Elastic Network Model Using Short-Time All-Atom Molecular Dynamics
Enhanced Conformational Sampling with an Adaptive Coarse-Grained Elastic Network Model Using Short-Time All-Atom Molecular Dynamics Open
Compared to all-atom molecular dynamics (AA-MD) simulations, coarse-grained (CG) MD simulations can significantly reduce calculation costs. However, existing CG-MD methods are unsuitable for sampling structures that depart significantly fr…
View article: Semi-Implicit Time Integration with Hessian Eigenvalue Corrections for a Larger Time Step in Molecular Dynamics Simulations
Semi-Implicit Time Integration with Hessian Eigenvalue Corrections for a Larger Time Step in Molecular Dynamics Simulations Open
In molecular dynamics simulations, the limited time step size has been a barrier to simulating long-time behaviors. Implicit time integration methods allow markedly larger time steps than the standard explicit time method, although they ha…
View article: Microsecond-timescale MD simulation of EGFR minor mutation predicts the structural flexibility of EGFR kinase core that reflects EGFR inhibitor sensitivity
Microsecond-timescale MD simulation of EGFR minor mutation predicts the structural flexibility of EGFR kinase core that reflects EGFR inhibitor sensitivity Open
Approximately 15–30% of patients with lung cancer harbor mutations in the EGFR gene. Major EGFR mutations (>90% of EGFR-mutated lung cancer) are highly sensitive to EGFR tyrosine kinase inhibitors (TKIs). Many uncommon EGFR mutations have …
View article: High-Precision Atomic Charge Prediction for Protein Systems Using Fragment Molecular Orbital Calculation and Machine Learning
High-Precision Atomic Charge Prediction for Protein Systems Using Fragment Molecular Orbital Calculation and Machine Learning Open
Here, we have constructed neural network-based models that predict atomic partial charges with high accuracy at low computational cost. The models were trained using high-quality data acquired from quantum mechanics calculations using the …
View article: Coarse-Grained Diffraction Template Matching Model to Retrieve Multiconformational Models for Biomolecule Structures from Noisy Diffraction Patterns
Coarse-Grained Diffraction Template Matching Model to Retrieve Multiconformational Models for Biomolecule Structures from Noisy Diffraction Patterns Open
Biomolecular imaging using X-ray free-electron lasers (XFELs) has been successfully applied to serial femtosecond crystallography. However, the application of single-particle analysis for structure determination using XFELs with 100 nm or …
View article: Exploring Successful Parameter Region for Coarse-Grained Simulation of Biomolecules by Bayesian Optimization and Active Learning
Exploring Successful Parameter Region for Coarse-Grained Simulation of Biomolecules by Bayesian Optimization and Active Learning Open
Accompanied with an increase of revealed biomolecular structures owing to advancements in structural biology, the molecular dynamics (MD) approach, especially coarse-grained (CG) MD suitable for macromolecules, is becoming increasingly imp…
View article: Stabilization Mechanism for a Nonfibrillar Amyloid β Oligomer Based on Formation of a Hydrophobic Core Determined by Dissipative Particle Dynamics
Stabilization Mechanism for a Nonfibrillar Amyloid β Oligomer Based on Formation of a Hydrophobic Core Determined by Dissipative Particle Dynamics Open
Neurotoxicity caused by nonfibrillar amyloid β (Aβ) oligomers in the brain is suggested to be associated with the onset of Alzheimer's disease (AD). Elucidating the structural features of Aβ oligomers is critical for promoting drug discove…
View article: Nucleosome Crowding in Chromatin Slows the Diffusion but Can Promote Target Search of Proteins
Nucleosome Crowding in Chromatin Slows the Diffusion but Can Promote Target Search of Proteins Open
View article: Molecular dynamics simulation-guided drug sensitivity prediction for lung cancer with rare <i>EGFR</i> mutations
Molecular dynamics simulation-guided drug sensitivity prediction for lung cancer with rare <i>EGFR</i> mutations Open
Significance A variety of rare mutations account for 10–20% of EGFR mutations in nonsmall cell lung cancer. However, due to high diversity, proper medication for patients with such mutations is impossible in daily clinic. To appropriately …
View article: Prediction of ALK mutations mediating ALK-TKIs resistance and drug re-purposing to overcome the resistance
Prediction of ALK mutations mediating ALK-TKIs resistance and drug re-purposing to overcome the resistance Open
View article: Diffusion enhancement of Brownian motors revealed by a solvable model
Diffusion enhancement of Brownian motors revealed by a solvable model Open
A solvable model is proposed and analyzed to reveal the mechanism underlying\nthe diffusion enhancement recently reported for a model of molecular motors and\npredicted to be observed in the biological rotary motor $\\rm F_1$-ATPase. It\nt…
View article: Coupling Langevin Dynamics With Continuum Mechanics: Exposing the Role of Sarcomere Stretch Activation Mechanisms to Cardiac Function
Coupling Langevin Dynamics With Continuum Mechanics: Exposing the Role of Sarcomere Stretch Activation Mechanisms to Cardiac Function Open
High-performance computing approaches that combine molecular-scale and macroscale continuum mechanics have long been anticipated in various fields. Such approaches may enrich our understanding of the links between microscale molecular mech…
View article: Prediction of ALK Mutations Mediating ALK-TKIs Resistance and Drug Re-Purposing to Overcome the Resistance
Prediction of ALK Mutations Mediating ALK-TKIs Resistance and Drug Re-Purposing to Overcome the Resistance Open
View article: Allosterically Regulated Structural Fluctuation and Microtubule-Binding Affinity of KiF1A -- A Simulation Study of Coarse-Grained Model --
Allosterically Regulated Structural Fluctuation and Microtubule-Binding Affinity of KiF1A -- A Simulation Study of Coarse-Grained Model -- Open