Interfacial Modeling of Fibrinogen Adsorption onto LiNbO3 Single Crystal–Single Domain Surfaces
Abstract
:1. Introduction
2. Results and Discussion
2.1. Experimental Results
2.2. Simulation Results and Discussion
2.2.1. Charge Distribution Calculation for the FBG Protein Structure
2.2.2. Facet Area Using a Monte Carlo Method to Find the Best Surface Conducive to Crystal Growth
2.2.3. Calculated Adsorption Energy of FBG Fragment on LNO Surface
2.2.4. Surface Electrostatic Potential and Charge Calculation Using the DFT Method
2.3. Dynamics Calculation Is Performed Using Molecular Mechanics Method with Water Molecules
3. Experimental Section
3.1. Material Preparation and Interfacial Analysis
3.2. FBG Adsorption
4. Molecular Model and Simulation Methods
4.1. Molecular Model
4.1.1. LNO Surface Simulation
4.1.2. Protein Model
4.2. Simulation Methods
4.2.1. Surface Electrostatic Potential Calculation
4.2.2. Morphology Method
4.2.3. Adsorption Calculation
4.2.4. Amorphous Packing
4.2.5. Molecular Dynamics Method
4.2.6. Density Functional Theory Method
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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h k l | Multiplicity | D hkl (Å) | % Total Facet Area |
---|---|---|---|
0 0 1 | 1 | 2.3105 | 49.5433 |
0 0 −1 | 1 | 2.3105 | 49.5433 |
−1 1 −2 | 3 | 3.7498 | 0 |
1 −1 2 | 3 | 3.7498 | 0 |
−3 2 1 | 6 | 1.6728 | 0.456671 |
−3 2 2 | 6 | 1.6374 | 0.456671 |
Fragment Nature | Adsorption Energies (kcal/mol) | Average Adsorption Energy/Per Atom for Protein Fragment (kcal/mol) |
---|---|---|
Positive | −906.3 | −4.89 (185) |
Negative | −718.1 | −4.10 (175) |
Fragment Nature | Adsorption Energies (kcal/mol) | Average Adsorption Energy/Per Atom of Protein Fragment (kcal/mol) |
---|---|---|
Positive | −713.2 | −3.85 (185) |
Negative | −856.1 | −4.89 (175) |
System | Total Energy (kcal/mol) | Average Binding Energy of Protein Fragment ΔE (kcal/mol) |
---|---|---|
Blank (001) surface | −13,428.29 | |
Blank (00−1) surface | −13,425.67 | |
Positive Protein Fragment | −10,651.34 | |
Negative Protein fragment | −10,548.28 | |
Positive fragment + (001) | −24,085.78 | −6.15 |
Negative fragment + (001) | −23,980.18 | −3.61 |
Positive fragment + (00−1) | −24,080.34 | −3.33 |
Negative fragment + (00−1) | −23,978.23 | −4.28 |
System | Total Energy (kcal/mol) | Average Binding Energy of Protein Fragment ΔE (kcal/mol) |
---|---|---|
Blank (001) surface | −13,428.29 | |
Blank (00−1) surface | −13,425.67 | |
Positive Protein Fragment | −10,651.34 | |
Negative Protein fragment | −10,548.28 | |
1701 Water Molecules | −85,896.09 | |
Positive fragment + (001) | −109,993.21 | −17.49 |
Negative fragment + (001) | −109,879.38 | −6.72 |
Positive fragment + (00−1) | −109,980.21 | −7.11 |
Negative fragment + (00−1) | −109,878.12 | −8.08 |
System | Diffusion Coefficient A^2/ps | R^2 |
---|---|---|
Protein Fragment with Nb rich surface (00−1) | 3.634 × 10−6 | 0.9972 |
Protein Fragment with Nb poor surface (001) | 2.284 × 10−6 | 0.9965 |
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Cross, J.S.; Kubota, Y.; Chatterjee, A.; Unni, S.; Ikoma, T.; Tagaya, M. Interfacial Modeling of Fibrinogen Adsorption onto LiNbO3 Single Crystal–Single Domain Surfaces. Int. J. Mol. Sci. 2021, 22, 5946. https://doi.org/10.3390/ijms22115946
Cross JS, Kubota Y, Chatterjee A, Unni S, Ikoma T, Tagaya M. Interfacial Modeling of Fibrinogen Adsorption onto LiNbO3 Single Crystal–Single Domain Surfaces. International Journal of Molecular Sciences. 2021; 22(11):5946. https://doi.org/10.3390/ijms22115946
Chicago/Turabian StyleCross, Jeffrey S., Yasuhiro Kubota, Abhijit Chatterjee, Samir Unni, Toshiyuki Ikoma, and Motohiro Tagaya. 2021. "Interfacial Modeling of Fibrinogen Adsorption onto LiNbO3 Single Crystal–Single Domain Surfaces" International Journal of Molecular Sciences 22, no. 11: 5946. https://doi.org/10.3390/ijms22115946
APA StyleCross, J. S., Kubota, Y., Chatterjee, A., Unni, S., Ikoma, T., & Tagaya, M. (2021). Interfacial Modeling of Fibrinogen Adsorption onto LiNbO3 Single Crystal–Single Domain Surfaces. International Journal of Molecular Sciences, 22(11), 5946. https://doi.org/10.3390/ijms22115946