Hierarchical Coarse-Grained Strategy for Macromolecular Self-Assembly: Application to Hepatitis B Virus-Like Particles
Abstract
:1. Introduction
2. Methods and Materials
2.1. Framework Overview
2.2. Reference Structure HBcAg Dimer
2.3. Intermolecular Interaction Potential
2.3.1. Molecular Dynamics Simulations
2.3.2. Spatial Descriptors
2.3.3. Multivariant Estimation using Universal Kriging
2.3.4. Molecular Collisions
2.3.5. 2D Example of Kriging and Sampling Algorithm
2.3.6. Biased MD Sampling and Insertion of Empirical Data
2.3.7. Summary and Implementation
- 1.
- Molecular reference structure of all involved molecules from, e.g., a protein data bank. This reference structure has to be the same as used for the parameterization of the diffusion model [65].
- 2.
- Initial interaction potential sampling using MD and the outlined sampling methodology. (For large interaction spaces proximity sampling might be required for sufficient correlation data.)
- 3.
- Trend fitting in a lower dimensional interaction space of for all potential components.
- 4.
- Correlation analysis and sectional variogram fitting of trend-compensated residual R for all potential components. Identification of potential components with reasonable spatial continuity besides trend (only fulfilled by A-B potential).
- 5.
- Grid design based on interaction distance and memory size constraints.
- 6.
- Universal Kriging for multivariant estimation of interaction potential component residual R.
- 7.
- Molecular collision accounting as a function of molecular overlap and flexibility with increasing interaction potential.
- 8.
- Iterative refinement of field estimate based on estimation variance and extrema (potential minima/maxima, gradient maxima) localization and specification.
2.4. Diffusion Model
2.5. Usage and Implementation within the Molecular Discrete Element Method
2.5.1. Simulation Procedure
VLP Binding Agreement and Stability (SP1)
VLP Capsid Stability (SP2)
VLP Self-Assembly (SP3)
2.5.2. Postprocessing
3. Results and Discussion
3.1. HBcAg Interaction Potential and VLP Stability
3.1.1. Pure MD-Based Interaction Potential
MD Data
Convergence
Resulting Field
3.1.2. Biased MD Interaction Potential
3.1.3. MD-Based Interaction Potential with Empirical Data
3.2. VLP Self-Assembly
3.2.1. Assembly Properties
3.2.2. Assembly Kinetics
3.2.3. Assembly Pathways
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
AA-MD | All-Atom Molecular Dynamics |
ANN | Artificial Neural Networks |
BD | Brownian Dynamics |
BLUE | Best Linear Unbiased Estimate |
CG-MD | Coarse-Grained Molecular Dynamics |
CPU | Central Processing Unit |
DEM | Discrete Element Method |
DOF | Degree of Freedom |
DPD | Dissipative Particle Dynamics |
FF | Force Field |
GPR | Gaussian Process Regression |
GPU | Graphics Processing Unit |
HBcAg | Hepatitis B Core Antigen |
HBcAg | HBcAg Dimer |
HBV | Hepatitis B Virus |
LD | Langevin Dynamics |
MDEM | Molecular Discrete Element Method |
MD | Molecular Dynamics |
NPT | Isothermal-Isobaric Ensemble |
PBC | Periodic Boundary Conditions |
PDB | Protein Data Bank |
PME | Particle Mesh Ewald |
PW | Polarizable Water |
QM/MM | Quantum Mechanics/Molecular Mechanics |
RMS | Root-Mean-Square |
RMSD | Root-Mean-Square Distance |
SAS | Self-Assembled Structure |
SI | Supplementary Information |
SPX | Simulation Procedure X |
SVD | Singular Value Decomposition |
UK | Universal Kriging |
VLP | Virus-Like Particles |
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# | x | y | z | |||
---|---|---|---|---|---|---|
1 | −2.74 | −0.74 | −3.10 | −0.48 | 0.98 | −0.32 |
2 | 1.47 | −0.91 | −4.14 | −0.88 | −1.05 | 0.67 |
3 | −3.01 | −0.70 | −3.08 | −2.72 | −1.05 | 3.03 |
4 | −0.65 | −0.77 | 4.25 | 2.72 | 0.92 | 2.76 |
[m s] | [Mrad s] | ||||
---|---|---|---|---|---|
x | y | z | |||
87.69 | 72.27 | 71.48 | 12.05 | 7.46 | 7.00 |
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Depta, P.N.; Dosta, M.; Wenzel, W.; Kozlowska, M.; Heinrich, S. Hierarchical Coarse-Grained Strategy for Macromolecular Self-Assembly: Application to Hepatitis B Virus-Like Particles. Int. J. Mol. Sci. 2022, 23, 14699. https://doi.org/10.3390/ijms232314699
Depta PN, Dosta M, Wenzel W, Kozlowska M, Heinrich S. Hierarchical Coarse-Grained Strategy for Macromolecular Self-Assembly: Application to Hepatitis B Virus-Like Particles. International Journal of Molecular Sciences. 2022; 23(23):14699. https://doi.org/10.3390/ijms232314699
Chicago/Turabian StyleDepta, Philipp Nicolas, Maksym Dosta, Wolfgang Wenzel, Mariana Kozlowska, and Stefan Heinrich. 2022. "Hierarchical Coarse-Grained Strategy for Macromolecular Self-Assembly: Application to Hepatitis B Virus-Like Particles" International Journal of Molecular Sciences 23, no. 23: 14699. https://doi.org/10.3390/ijms232314699