Probing the Energetics of Dynactin Filament Assembly and the Binding of Cargo Adaptor Proteins Using Molecular Dynamics Simulation and Electrostatics-Based Structural Modeling

Dynactin, a large multiprotein complex, binds with the cytoplasmic dynein-1 motor and various adaptor proteins to allow recruitment and transportation of cellular cargoes toward the minus end of microtubules. The structure of the dynactin complex is built around an actin-like minifilament with a defined length, which has been visualized in a high-resolution structure of the dynactin filament determined by cryo-electron microscopy (cryo-EM). To understand the energetic basis of dynactin filament assembly, we used molecular dynamics simulation to probe the intersubunit interactions among the actin-like proteins, various capping proteins, and four extended regions of the dynactin shoulder. Our simulations revealed stronger intersubunit interactions at the barbed and pointed ends of the filament and involving the extended regions (compared with the interactions within the filament), which may energetically drive filament termination by the capping proteins and recruitment of the actin-like proteins by the extended regions, two key features of the dynactin filament assembly process. Next, we modeled the unknown binding configuration among dynactin, dynein tails, and a number of coiled-coil adaptor proteins (including several Bicaudal-D and related proteins and three HOOK proteins), and predicted a key set of charged residues involved in their electrostatic interactions. Our modeling is consistent with previous findings of conserved regions, functional sites, and disease mutations in the adaptor proteins and will provide a structural framework for future functional and mutational studies of these adaptor proteins. In sum, this study yielded rich structural and energetic information about dynactin and associated adaptor proteins that cannot be directly obtained from the cryo-EM structures with limited resolutions

All-Atom Molecular Dynamics Simulations of Actin–Myosin Interactions: A Comparative Study of Cardiac α Myosin, β Myosin, and Fast Skeletal Muscle Myosin

Myosins are a superfamily of actin-binding motor proteins with significant variations in kinetic properties (such as actin binding affinity) between different isoforms. It remains unknown how such kinetic variations arise from the structural and dynamic tuning of the actin–myosin interface at the amino acid residue level. To address this key issue, we have employed molecular modeling and simulations to investigate, with atomistic details, the isoform dependence of actin–myosin interactions in the rigor state. By combining electron microscopy-based docking with homology modeling, we have constructed three all-atom models for human cardiac α and β and rabbit fast skeletal muscle myosin in complex with three actin subunits in the rigor state. Starting from these models, we have performed extensive all-atom molecular dynamics (MD) simulations (total of 100 ns per system) and then used the MD trajectories to calculate actin–myosin binding free energies with contributions from both electrostatic and nonpolar forces. Our binding calculations are in good agreement with the experimental finding of isoform-dependent differences in actin binding affinity between these myosin isoforms. Such differences are traced to changes in actin–myosin electrostatic interactions (i.e., hydrogen bonds and salt bridges) that are highly dynamic and involve several flexible actin-binding loops. By partitioning the actin–myosin binding free energy to individual myosin residues, we have also identified key myosin residues involved in the actin–myosin interactions, some of which were previously validated experimentally or implicated in cardiomyopathy mutations, and the rest make promising targets for future mutational experiments

All-Atom Molecular Dynamics Simulations of Actin–Myosin Interactions: A Comparative Study of Cardiac α Myosin, β Myosin, and Fast Skeletal Muscle Myosin

Myosins are a superfamily of actin-binding motor proteins with significant variations in kinetic properties (such as actin binding affinity) between different isoforms. It remains unknown how such kinetic variations arise from the structural and dynamic tuning of the actin–myosin interface at the amino acid residue level. To address this key issue, we have employed molecular modeling and simulations to investigate, with atomistic details, the isoform dependence of actin–myosin interactions in the rigor state. By combining electron microscopy-based docking with homology modeling, we have constructed three all-atom models for human cardiac α and β and rabbit fast skeletal muscle myosin in complex with three actin subunits in the rigor state. Starting from these models, we have performed extensive all-atom molecular dynamics (MD) simulations (total of 100 ns per system) and then used the MD trajectories to calculate actin–myosin binding free energies with contributions from both electrostatic and nonpolar forces. Our binding calculations are in good agreement with the experimental finding of isoform-dependent differences in actin binding affinity between these myosin isoforms. Such differences are traced to changes in actin–myosin electrostatic interactions (i.e., hydrogen bonds and salt bridges) that are highly dynamic and involve several flexible actin-binding loops. By partitioning the actin–myosin binding free energy to individual myosin residues, we have also identified key myosin residues involved in the actin–myosin interactions, some of which were previously validated experimentally or implicated in cardiomyopathy mutations, and the rest make promising targets for future mutational experiments

All-Atom Structural Investigation of Kinesin–Microtubule Complex Constrained by High-Quality Cryo-Electron-Microscopy Maps

In this study, we have performed a comprehensive structural investigation of three major biochemical states of a kinesin complexed with microtubule under the constraint of high-quality cryo-electron-microscopy (EM) maps. In addition to the ADP and ATP state which were captured by X-ray crystallography, we have also modeled the nucleotide-free or APO state for which no crystal structure is available. We have combined flexible fitting of EM maps with regular molecular dynamics simulations, hydrogen-bond analysis, and free energy calculation. Our APO-state models feature a subdomain rotation involving loop L2 and α6 helix of kinesin, and local structural changes in active site similar to a related motor protein, myosin. We have identified a list of hydrogen bonds involving key residues in the active site and the binding interface between kinesin and microtubule. Some of these hydrogen bonds may play an important role in coupling microtubule binding to ATPase activities in kinesin. We have validated our models by calculating the binding free energy between kinesin and microtubule, which quantitatively accounts for the observation of strong binding in the APO and ATP state and weak binding in the ADP state. This study will offer promising targets for future mutational and functional studies to investigate the mechanism of kinesin motors

All-Atom Molecular Dynamics Simulations of Actin–Myosin Interactions: A Comparative Study of Cardiac α Myosin, β Myosin, and Fast Skeletal Muscle Myosin

Myosins are a superfamily of actin-binding motor proteins with significant variations in kinetic properties (such as actin binding affinity) between different isoforms. It remains unknown how such kinetic variations arise from the structural and dynamic tuning of the actin–myosin interface at the amino acid residue level. To address this key issue, we have employed molecular modeling and simulations to investigate, with atomistic details, the isoform dependence of actin–myosin interactions in the rigor state. By combining electron microscopy-based docking with homology modeling, we have constructed three all-atom models for human cardiac α and β and rabbit fast skeletal muscle myosin in complex with three actin subunits in the rigor state. Starting from these models, we have performed extensive all-atom molecular dynamics (MD) simulations (total of 100 ns per system) and then used the MD trajectories to calculate actin–myosin binding free energies with contributions from both electrostatic and nonpolar forces. Our binding calculations are in good agreement with the experimental finding of isoform-dependent differences in actin binding affinity between these myosin isoforms. Such differences are traced to changes in actin–myosin electrostatic interactions (i.e., hydrogen bonds and salt bridges) that are highly dynamic and involve several flexible actin-binding loops. By partitioning the actin–myosin binding free energy to individual myosin residues, we have also identified key myosin residues involved in the actin–myosin interactions, some of which were previously validated experimentally or implicated in cardiomyopathy mutations, and the rest make promising targets for future mutational experiments

Decrypting the Structural, Dynamic, and Energetic Basis of a Monomeric Kinesin Interacting with a Tubulin Dimer in Three ATPase States by All-Atom Molecular Dynamics Simulation

We have employed molecular dynamics (MD) simulation to investigate, with atomic details, the structural dynamics and energetics of three major ATPase states (ADP, APO, and ATP state) of a human kinesin-1 monomer in complex with a tubulin dimer. Starting from a recently solved crystal structure of ATP-like kinesin–tubulin complex by the Knossow lab, we have used flexible fitting of cryo-electron-microscopy maps to construct new structural models of the kinesin–tubulin complex in APO and ATP state, and then conducted extensive MD simulations (total 400 ns for each state), followed by flexibility analysis, principal component analysis, hydrogen bond analysis, and binding free energy analysis. Our modeling and simulation have revealed key nucleotide-dependent changes in the structure and flexibility of the nucleotide-binding pocket (featuring a highly flexible and open switch I in APO state) and the tubulin-binding site, and allosterically coupled motions driving the APO to ATP transition. In addition, our binding free energy analysis has identified a set of key residues involved in kinesin–tubulin binding. On the basis of our simulation, we have attempted to address several outstanding issues in kinesin study, including the possible roles of β-sheet twist and neck linker docking in regulating nucleotide release and binding, the structural mechanism of ADP release, and possible extension and shortening of α4 helix during the ATPase cycle. This study has provided a comprehensive structural and dynamic picture of kinesin’s major ATPase states, and offered promising targets for future mutational and functional studies to investigate the molecular mechanism of kinesin motors

Особенности плечевой артерии и ее ветвей

Актуальность. В настоящее время большое внимание уделяется индивидуальным особенностям человека. В практике современного врача чаще встречаются не типичные проявления какой-либо патологии или средние значения какого-либо показателя. По данным некоторых исследователей около 20% крупных артериальных стволов верхней конечности имеют нетипичное расположение и ветвление. Материалы и методы: Обзор литературы

Ni/Ni₃C Core/Shell Hierarchical Nanospheres with Enhanced Electrocatalytic Activity for Water Oxidation

Developing efficient and low-cost catalysts with high activity and excellent electrochemical and structural stability toward the oxygen evolution reaction (OER) is of great significance for both energy and environment sustainability. Herein, Ni/Ni₃C core/shell hierarchical nanospheres have been in situ synthesized via an ionic liquid-assisted hydrothermal method at relatively low temperature. Ionic liquid 1-butyl-3-methylimidazolium acetate has played multiple roles in the whole synthesis process. Benefiting from the high electrical conductivity, more exposed active sites and the core/shell interface effect, the obtained Ni/Ni₃C core/shell hierarchical nanospheres exhibit an outstanding OER performance with lower overpotential, small Tafel slope, and excellent stability. This fundamental method and insights with in situ coupling high conductivity metal support and metal carbide in a core/shell nanoarchitecture by an ionic liquid-assisted hydrothermal method would open up a new pathway to achieve high-performance electrocatalysts toward the OER

A Novel PbS Hierarchical Superstructure Guided by the Balance between Thermodynamic and Kinetic Control via a Single-Source Precursor Route

In this work, a novel lead sulfide (PbS) hierarchical superstructure, denoted as octapodal dendrites with a cubic center, has been synthesized employing a simple single-source precursor route. Our experimental results demonstrate that the novel hierarchical superstructure was generated through the delicate balance between the kinetic growth and thermodynamic growth regimes. Moreover, the morphology of PbS crystals can be controlled by adjusting the solvent under a thermodynamically or kinetically controlled growth regime. It is highly expected that these findings will be useful in understanding the formation of PbS nanocrystals with different morphologies, which are also applicable to other face-centered cubic nanocrystals

A Sandwich Zwitterionic Ruthenium Complex Bearing a Cyanamido Group

A sandwich zwitterionic ruthenium complex (<b>4</b>) was prepared by an intramolecular 1,3-dipolar cycloaddition of the ruthenium azido isocyanide [CpMe₅Ru­(CNAr)₂N₃] (<b>2</b>). The reaction involved a formal 1,3-migration mechanism along a highly conjugated system linking to a cyanamido group