Y. Sugita

Structural and Dynamic Insights into the Biased Signaling Mechanism of the Human Kappa Opioid Receptor

This study investigates the structural dynamics of the human KOR-Gi signaling complex with G-protein-biased and balanced agonists, identifying key residues involved in signaling bias.

Structural basis of Ebola virus nucleocapsid assembly and functions

This study determines the structure of the Ebola virus nucleocapsid using cryo-EM and identifies VP24's role in assembly and function.

GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamicload balancing for heterogeneous biomolecular systems

The paper introduces GENESIS CGDYN, a large-scale coarse-grained MD simulation tool with dynamic load balancing for heterogeneous biomolecular systems, demonstrating its application to IDP droplet fusions and large droplet formation.

Micelle-like clusters in phase-separated Nanog condensates: A molecular simulation study

This study uses molecular simulations to show that Nanog forms micelle-like clusters in condensates via hydrophobic interactions, with surface domains mediating condensate bridging and DNA recruitment.

Repulsive interaction and secondary structure of highly charged proteins in regulating biomolecular condensation

This study uses molecular dynamics simulations to investigate how Hero11 proteins regulate TDP-43 condensation through repulsive and attractive interactions, proposing three mechanisms for preventing pathological aggregation.

The impact of inhibitor size and flexibility on the binding pathways to c-Src kinase

This study uses molecular dynamics simulations to show that inhibitor size and flexibility affect binding pathways and energetics to c-Src kinase, influencing residence time.

Hidden Markov Modeling of Molecular Orientations and Structures from High-Speed Atomic Force Microscopy Time-Series Images

This paper introduces a hidden Markov model to estimate molecular orientations from HS-AFM time-series data, showing improved robustness compared to frame-by-frame analysis.

Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations

The paper implements residue-level coarse-grained models in GENESIS to enable large-scale molecular dynamics simulations of biomolecules, improving computational efficiency and handling heterogeneous systems.

Structural Ramifications of Spike Protein D614G Mutation in SARS-CoV-2

This study investigates the structural impact of the D614G mutation in SARS-CoV-2 Spike protein using molecular dynamics simulations, revealing its role in enhancing infectivity and stabilizing the protein structure.

A nano-liquid hub integrating growth and immune-evasion signaling to promote cell survival

The paper identifies GEM, a nano-liquid hub that integrates growth and immune-evasion signaling to enhance cell survival in mice.

The Inherent Flexibility of Receptor Binding Domains in SARS-CoV-2 Spike Protein

This study identifies multiple conformational states of the SARS-CoV-2 Spike protein's receptor binding domain through molecular dynamics simulations, highlighting structural flexibility important for drug and vaccine design.

Structural insight into Marburg virus nucleoprotein-RNA complex formation

This study determines the structure of the Marburg virus NP-RNA complex using cryo-EM, revealing conserved residues critical for nucleocapsid formation and RNA synthesis between MARV and EBOV.

Molecular basis for two stereoselective Diels-Alderases that produce decalin skeletons

This study determines the molecular mechanisms of two Diels-Alderases that produce enantiomeric decalin scaffolds through structural and computational analyses.

Glycosylphosphatidylinositol-anchoring is required for the proper transport and glycosylation of classical arabinogalactan protein precursor in tobacco BY-2 cells

This study shows that GPI-anchoring is essential for the correct transport and glycosylation of an AGP precursor in tobacco cells.

Implicit micelle model for membrane proteins using super-ellipsoid approximation

The paper introduces an implicit micelle model (IMIC) for MD simulations of membrane proteins, showing it provides accurate structure predictions with lower computational cost than explicit models.

Chemo-mechanical Coupling in the Transport Cycle of a Type II ABC Transporter

This study uses molecular dynamics simulations to uncover new conformations and the role of LSGG[Q/E] motifs in ATPase activity regulation in an ABC transporter.

Structure of APP-C991-99 and Implications for Role of Extra-Membrane Domains in Function and Oligomerization

This study investigates the structure of APP-C99 in model membranes, revealing how extra-membrane domains influence Aβ oligomerization and γ-secretase processing.