Analysis of Potential Amino Acid Biomarkers in Brain Tissue and the Effect of Galangin on Cerebral Ischemia
Abstract
:1. Introduction
2. Results
2.1. Method Validation
2.2. Assessment of Neurological Defects
2.3. Effect of Galangin on the Level Changes of AAs in Rat Brain Tissue and Identification of Biomarkers
2.4. Metabolite-Protein Interaction Networks
3. Discussion
4. Materials and Methods
4.1. Chemicals and Reagents
4.2. Animals
4.3. Animal Models and Experimental Protocol
4.4. Assessment of Neurological Defects
4.5. Brain Tissue Homogenate Sampling and Preparation
4.6. Instrumentation (Chromatographic and MS Spectrum Conditions)
4.7. Identification of the Endogenous AAs
4.8. Data Analysis
4.9. Network Analysis
4.10. Molecule Docking
5. Conclusions
Acknowledgments
Author Contributions
Conflicts of Interest
References
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- Sample Availability: Not available.
AAs + I.S. | m/z | Ion Transition | Dwell Time (s) | FV (V) | CE (eV) | Mean RT |
---|---|---|---|---|---|---|
Naa | 176.1 | 176.1 > 134.3 | 20 | 80 | 0 | 6.176 |
176.1 > 88.1 | 20 | 80 | 10 | 6.176 | ||
Ala | 90.1 | 90.1 > 44.2 | 10 | 45 | 10 | 4.466 |
GABA | 104.1 | 104.1 > 87.2 | 20 | 80 | 10 | 4.077 |
Phe | 166.3 | 166.3 > 120.3 | 10 | 90 | 10 | 8.833 |
166.3 > 103.2 | 10 | 90 | 20 | 8.833 | ||
Tyr | 182.3 | 182.3 > 165 | 10 | 110 | 4 | 5.579 |
182.3 > 136.3 | 10 | 110 | 10 | 5.579 | ||
Gly | 76.2 | 76.2 > 48.2 | 10 | 50 | 3 | 4.432 |
76.2 > 30.2 | 10 | 50 | 4 | 4.432 | ||
Met | 150.2 | 150.2 > 133 | 10 | 55 | 4 | 5.432 |
150.2 > 104.2 | 10 | 55 | 5 | 5.432 | ||
Trp | 205.2 | 205.2 > 188.3 | 10 | 90 | 7 | 10.535 |
205.2 > 146.2 | 10 | 90 | 17 | 10.535 | ||
Asp | 134.2 | 134.2 > 88.2 | 10 | 60 | 5 | 4.620 |
134.2 > 74.2 | 10 | 60 | 12 | 4.620 | ||
Ser | 106.1 | 106.1 > 60.2 | 10 | 70 | 10 | 4.478 |
106.1 > 42.2 | 10 | 70 | 10 | 4.478 | ||
Glu | 148.2 | 148.2 > 102 | 10 | 90 | 4 | 4.570 |
148.2 > 84.2 | 10 | 90 | 10 | 4.570 | ||
Hcy | 136.1 | 136.1 > 90.2 | 20 | 80 | 10 | 4.966 |
136.1 > 56.2 | 20 | 80 | 20 | 4.966 | ||
acrylamide-d3 | 75.1 | 75.1 > 58.1 | 10 | 40 | 8 | 6.505 |
75.1 > 30.2 | 10 | 40 | 8 | 6.505 |
Chemicals | Equations | Correlation Coefficient (r2) | Linear Range a (ng·mL−1) | LOD b (ng·mL−1) | LOQ c (ng·mL−1) |
---|---|---|---|---|---|
Ala | y = 3.0611x + 0.0165 | 0.9999 | 10–5000 | 0.53 | 1.79 |
GABA | y = 1.1833x − 0.0018 | 0.9991 | 10–5000 | 0.31 | 1.05 |
Ser | y = 1. 0241x + 0.0230 | 0.9997 | 10–5000 | 0.49 | 1.67 |
Asp | y = 0.6314x + 0.0040 | 0.9997 | 10–5000 | 0.49 | 1.67 |
Gly | y = 0.5793x + 0.0018 | 0.9990 | 10–5000 | 0.51 | 1.73 |
Hcy | y = 0.3371x + 07.73583 × 10−4 | 0.9966 | 1–500 | 0.10 | 0.35 |
Glu | y = 1.5217x + 0.0102 | 0.9999 | 20–10000 | 0.47 | 1.59 |
Met | y = 1.7855x + 0.0055 | 0.9993 | 1–500 | 0.05 | 0.18 |
Phe | y = 7.4569x + 0.0922 | 0.9981 | 1–500 | 0.02 | 0.07 |
Naa | y = 0.0789x − 2.50132 × 10−4 | 0.9994 | 20–10000 | 0.64 | 2.17 |
Tyr | y = 0.8392x + 0.0126 | 0.9981 | 1–500 | 0.05 | 0.18 |
Trp | y = 4.6319x + 0.0199 | 0.9996 | 1–500 | 0.13 | 0.43 |
Chemicals | Intra-Day Precision RSD (%, n = 6) | Inter-Day Precision RSD (%, n = 6) | Recovery (%, n = 6) | ||||
---|---|---|---|---|---|---|---|
Low | Mid | High | Low | Mid | High | ||
GABA | 0.54 | 1.69 | 8.03 | 1.69 | 3.25 | 8.18 | 98.80 |
Gly | 3.64 | 1.81 | 6.22 | 4.31 | 3.13 | 6.13 | 97.46 |
Ala | 2.95 | 1.72 | 8.10 | 3.62 | 2.90 | 6.36 | 96.21 |
Ser | 3.43 | 1.64 | 8.39 | 4.55 | 3.29 | 8.20 | 108.58 |
Glu | 1.60 | 2.47 | 8.35 | 2.33 | 3.51 | 7.05 | 100.38 |
Asp | 6.63 | 2.39 | 8.65 | 5.32 | 4.07 | 6.62 | 85.11 |
Hcy | 3.78 | 3.99 | 7.56 | 4.66 | 4.91 | 9.42 | 114.87 |
Met | 7.86 | 3.02 | 7.02 | 7.89 | 4.03 | 8.91 | 78.78 |
Tyr | 10.97 | 4.11 | 7.52 | 9.73 | 6.60 | 9.58 | 69.71 |
Naa | 3.07 | 1.69 | 9.16 | 2.87 | 3.41 | 9.25 | 107.96 |
Phe | 5.70 | 3.36 | 8.43 | 6.16 | 3.24 | 6.77 | 72.10 |
Trp | 8.72 | 6.57 | 7.99 | 6.41 | 7.20 | 9.83 | 75.72 |
Chemicals | Stability RSD (%, n = 6) | Repeatability RSD (%, n = 6) | |||
---|---|---|---|---|---|
−80 °C Freeze | Freeze-Thaw | Room Temperature | 4 °C | ||
GABA | 6.44 | 9.37 | 11.22 | 9.54 | 5.72 |
Gly | 11.53 | 7.16 | 15.32 | 5.08 | 3.75 |
Ala | 12.20 | 6.45 | 15.42 | 4.33 | 3.65 |
Ser | 12.72 | 6.73 | 15.98 | 6.13 | 3.48 |
Glu | 6.19 | 6.89 | 13.82 | 3.63 | 3.62 |
Asp | 9.49 | 6.66 | 13.60 | 3.43 | 2.88 |
Hcy | 16.90 | 8.07 | 6.51 | 8.75 | 8.35 |
Met | 14.59 | 5.54 | 13.51 | 4.81 | 3.00 |
Tyr | 11.85 | 9.48 | 15.07 | 7.28 | 6.61 |
Naa | 12.52 | 6.60 | 6.70 | 4.61 | 3.22 |
Phe | 9.47 | 4.87 | 13.70 | 3.90 | 3.26 |
Trp | 8.95 | 5.63 | 7.84 | 5.02 | 2.90 |
Proteins | MOE Docking of Endogenous Ligands | MOE Docking Scores of Galangin | Interacting Residues | |
---|---|---|---|---|
RMSD | Scores | |||
GLUD1 | 1.256284 | −22.78383 | −26.44535 | Arg 211, Val 255, Met 111, Asn 349, Lys 126, Met 169 |
GLUL | 0.9439976 | −35.19292 | −18.74692 | Arg 355 |
GLS | 1.326625 | −21.21566 | −17.68718 | Tyr A394, Leu A321, Phe A322, Leu A323 |
GAD1 | 3.128657 | −16.44727 | ||
CTH | 1.960125 | −16.61392 | −10.80142 | Lys 210, Tyr 111, Arg 372, Tyr 338 |
ATP1B3 | 3.068527 | −13.54975 | ||
GOT2 | 1.691135 | −21.93334 | −19.29626 | Arg 258, Lys 250, Trp 133 |
HP | 1.764202 | −15.15395 | −19.11285 | Ser 557, Tyr 646, Val 564, Val 635 |
Proteins | Full Name | Pdb Number |
---|---|---|
GLUD1 | Glutamate dehydrogenase 1, mitochondrial | 3ETD |
GLUL | Glutamine synthetase | 1FPY |
GLS | Glutaminase | 3VOZ |
GAD1 | Glutamate decarboxylase 1 | 4HKP |
CTH | cystathionase | 2FQ6 |
ATP1B3 | ATPase | 3N23 |
GOT2 | Aspartate aminotransferase | 1IVR |
HP | haptoglobin | 3QUG |
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Yang, R.; Chen, K.; Zhao, Y.; Tian, P.; Duan, F.; Sun, W.; Liu, Y.; Yan, Z.; Li, S. Analysis of Potential Amino Acid Biomarkers in Brain Tissue and the Effect of Galangin on Cerebral Ischemia. Molecules 2016, 21, 438. https://doi.org/10.3390/molecules21040438
Yang R, Chen K, Zhao Y, Tian P, Duan F, Sun W, Liu Y, Yan Z, Li S. Analysis of Potential Amino Acid Biomarkers in Brain Tissue and the Effect of Galangin on Cerebral Ischemia. Molecules. 2016; 21(4):438. https://doi.org/10.3390/molecules21040438
Chicago/Turabian StyleYang, Ruocong, Kun Chen, Yanyan Zhao, Pengpeng Tian, Feipeng Duan, Wenli Sun, Yuxin Liu, Zhiyong Yan, and Shaojing Li. 2016. "Analysis of Potential Amino Acid Biomarkers in Brain Tissue and the Effect of Galangin on Cerebral Ischemia" Molecules 21, no. 4: 438. https://doi.org/10.3390/molecules21040438
APA StyleYang, R., Chen, K., Zhao, Y., Tian, P., Duan, F., Sun, W., Liu, Y., Yan, Z., & Li, S. (2016). Analysis of Potential Amino Acid Biomarkers in Brain Tissue and the Effect of Galangin on Cerebral Ischemia. Molecules, 21(4), 438. https://doi.org/10.3390/molecules21040438