Molecular Recognition Patterns between Vitamin B12 and Proteins Explored through STD-NMR and In Silico Studies
Abstract
:1. Introduction
2. Hypotheses
3. Materials and Methods
3.1. Reagents
3.2. Characterization of Cobalamin
3.3. Saturation Transfer Difference via Nuclear Magnetic Resonance (STD–NMR)
3.4. Molecular Docking
4. Results and Discussion
4.1. Cyanocobalamin Structure after the 1H Scan in NMR
4.2. Interaction between Vitamin B12 and Protein Identified Using STD–NMR
4.3. Binding Capability Judgment Based on Cyanocobalamin
4.4. Binding Conformation Simulation
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
DMB | Dimethyl benzimidazole |
STD–NMR | Saturation transfer difference by nuclear magnetic resonance |
CNBL | Cyanocobalamin |
OHBL | Aqua cobalamin |
Kα | Binding constant |
KD | Dissociation constant |
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Binding Constant—Kα (L/mol) | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
C20 | C25 | C35 | C53 | C10 | B10/11 | B4 | B2 | B7 | ||||||||||
Cyanocobalamin | Aqua Cobalamin | Cyanocobalamin | Aqua Cobalamin | Cyanocobalamin | Aqua Cobalamin | Cyanocobalamin | Aqua Cobalamin | Cyanocobalamin | Aqua Cobalamin | Cyanocobalamin | Aqua Cobalamin | Cyanocobalamin | Aqua Cobalamin | Cyanocobalamin | Aqua Cobalamin | Cyanocobalamin | Aqua Cobalamin | |
Gluten | 2.88 × 104 | 3.21 × 104 | 3.03 × 104 | 3.59 × 104 | 3.7 × 103 | 2.78 × 103 | 1.99 × 104 | 4.65 × 103 | 2.77 × 103 | 2.83 × 103 | 3.02 × 104 | 3.46 × 104 | 3.16 × 103 | 3.65 × 103 | 3.77 × 103 | 3.09 × 103 | 2.76 × 103 | 2.40 × 103 |
Myoglobin | 3.16 × 103 | 4.04 × 104 | 4.82 × 104 | 3.04 × 104 | 4.34 × 104 | 4.39 × 104 | 3.16 × 104 | 3.51 × 104 | 4.33 × 104 | 3.86 × 104 | 3.96 × 104 | 4.67 × 104 | 3.74 × 104 | 4.86 × 104 | 3.05 × 104 | 4.37 × 104 | 2.48 × 104 | 4.20 × 104 |
Casein | 4.24 × 104 | 3.04 × 104 | 4.88 × 104 | 2.71 × 104 | 2.47 × 104 | 4.27 × 104 | 3.42 × 104 | 5.52 × 103 | 3.01 × 104 | 3.11 × 104 | 3.19 × 104 | 4.72 × 104 | 2.29 × 104 | 3.75 × 104 | 2.92 × 104 | 3.11 × 104 | 3.16 × 104 | 3.04 × 104 |
Egg albumin | 2.35 × 104 | 3.73 × 104 | 3.04 × 104 | 3.20 × 104 | 2.33 × 104 | 3.44 × 104 | 2.43 × 104 | 2.66 × 104 | 1.87 × 104 | 3.28 × 104 | 1.61 × 104 | 2.60 × 104 | 2.48 × 104 | 4.16 × 104 | 1.60 × 104 | 6.46 × 104 | 2.41 × 104 | 8.03 × 104 |
Pea | 7.29 × 103 | 4.10 × 104 | 2.96 × 104 | 1.48 × 104 | 1.13 × 104 | 3.06 × 104 | 3.85 × 104 | 3.04 × 104 | 1.08 × 104 | 3.21 × 104 | 7.65 × 103 | 3.80 × 104 | 1.28 × 104 | 4.54 × 104 | 1.09 × 104 | 4.54 × 104 | 1.01 × 104 | 4.97 × 104 |
Rice | 3.13 × 104 | 3.43 × 104 | 3.84 × 104 | 2.46 × 104 | 3.52 × 104 | 2.46 × 104 | 2.21 × 104 | 3.91 × 104 | 2.44 × 104 | 2.60 × 104 | 2.49 × 104 | 4.28 × 104 | 2.01 × 104 | 2.41 × 104 | 2.31 × 103 | 2.56 × 103 | 4.81 × 104 | 2.95 × 104 |
KD (mM) | Kα (L/mol)-Binding Constant | |||
---|---|---|---|---|
Cyanocobalamin | Aqua Cobalamin | Cyanocobalamin | Aqua Cobalamin | |
Gluten | 0.23469 | 0.25545 | 4261.01 | 3914.70 |
Myoglobin | 0.02911 | 0.02315 | 34,353.06 | 43,189.09 |
Casein | 0.03401 | 0.02876 | 29,399.73 | 34,772.23 |
Egg albumin | 0.04926 | 0.02527 | 20,301.11 | 39,573.24 |
Pea | 0.10247 | 0.02554 | 9758.70 | 39,159.15 |
Rice | 0.09200 | 0.08544 | 10,869.40 | 11,703.72 |
Cyanocobalamin | Aqua Cobalamin | |||
---|---|---|---|---|
Vina Score | Amino Acids Interacting | Vina Score | Amino Acids Interacting | |
Casein | −5.9 | ASP184, VAL186, ILE187, ARG189, PRO214, THR219, ALA220, GLU223, ASP284, ILE351, LYS358, TYR359, PRO389, ASP390, LEU393, ASP394 | −4.4 | SER344, VAL345, ARG346, VAL349, ARG353, VAL373, GLN377, GLY629, ASN633, ASP634, GLU635, GLU792, GLU793, ARG794, PHE795, GLU796, GLN797, ASN798 |
myoglobin | −5.1 | PHE44, LYS46, PHE47, ASP61, HIS65, THR68, ALA72, ALA85, HIS89, HIS98 | −5.2 | ARG32, LEU33, GLY36, HIS37, LYS103, GLU106, PHE107, ILE108, ASP110, ALA111, ILE113, HIS114, HIS117, GLN129 |
Egg Albumin | −6.5 | VAL222, LYS223, TYR246, MET319, GLU320, GLU322, PHE323, LYS457, LYS464, LEU468, ARG472, ALA475, TYR480, ILE483, VAL484 | −5.6 | GLU43, GLU44, LYS47, MET51, TYR63, SER67, LYS68, VAL70, LYS71, ASP75, GLN78, ASN158, VAL160, SER161, HIS165 |
Gluten | −7.1 | PRO46, ASP174, VAL177, LEU46, ARG123, VAL168, LEU170, PRO187, GLN188, PRO189, LEU190, LYS191 | −7.5 | HIS10, GLN44, LEU101, PHE103, PRO120, ARG123, ASP166, HIS167, VAL168, GLU169, LEU170, SER171, GLU178, VAL179, HIS180, SER181, GLY182, VAL183, CYS184, THR185, ASP186, PRO187, GLN188, PRO189, LEU203, TYR228 |
Rice | −8.1 | ARG199, HIS200, ARG201, PHE203, PHE204, ILE211, LEU215, GLU219, ASP222, SER224, ASN226, VAL227 | −6.7 | TRP34, GLN35, SER36, SER37, ARG38, ARG39, GLY40, SER41, GLU44, CYS45, ARG46, PHE47, CYS78, THR79, TYR190, ILE371, ASN372, HIS374, ASN391, GLN411, HIS412, HIS413 |
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Ghosh, R.; Thomas, D.S.; Arcot, J. Molecular Recognition Patterns between Vitamin B12 and Proteins Explored through STD-NMR and In Silico Studies. Foods 2023, 12, 575. https://doi.org/10.3390/foods12030575
Ghosh R, Thomas DS, Arcot J. Molecular Recognition Patterns between Vitamin B12 and Proteins Explored through STD-NMR and In Silico Studies. Foods. 2023; 12(3):575. https://doi.org/10.3390/foods12030575
Chicago/Turabian StyleGhosh, Ruchira, Donald S. Thomas, and Jayashree Arcot. 2023. "Molecular Recognition Patterns between Vitamin B12 and Proteins Explored through STD-NMR and In Silico Studies" Foods 12, no. 3: 575. https://doi.org/10.3390/foods12030575