Carbon Atoms Speaking Out: How the Geometric Sensitivity of 13C Chemical Shifts Leads to Understanding the Colour Tuning of Phycocyanobilin in Cph1 and AnPixJ
Abstract
:1. Introduction
2. Results
2.1. How Bond Alternation and Thermal Fluctuations Determine 13C-NMR Chemical Shifts
2.2. Correlations of 13C Chemical Shifts and Their Geometric Sensitivity
2.3. Inversion of the Geometric Sensitivity Points to Pg and Pfr States
3. Discussion
3.1. Pg: Short Conjugation
3.2. Pfr: Long Conjugation
4. Conclusions
5. Materials and Methods
5.1. Preparations
5.2. Force Field Molecular Dynamics Simulations
5.3. QM/MM Molecular Dynamics Simulations
5.4. Calculation of Nuclear Shieldings
5.5. Statistical Analysis
6. Other
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
AIMD | Ab initio molecular dynamics |
AnPixJg2 | Second GAF domain (out of four) of a phototaxis regulator found in heterocyst-forming |
cyanobacteria Anabaena (Nostoc) sp. PCC 7120 (all1069) [13,67]. Pix, originally pis (PhototaxIS), | |
is a class of regulatory genes required for positive phototactic movement (PositIve phototaXis), | |
whereas J is a serial letter [15] | |
BLYP | Becke/Lee-Yang-Parr (exchange/correlation) |
CBCR | Cyanobacteriochrome |
CHARMM | Chemistry at Harvard macromolecular mechanics |
Cph12 | “Cyanobacterial phytochrome 1”, i.e., the first phytochrome found in cyanobacteria, more |
precisely Synechocystis sp. PCC 6803 (slr0473) [10,46,47]. It functions as light-regulated histidine | |
protein kinase [10,35]. Δ2 denotes the sensory module of the protein comprising 514 N-terminal | |
residues; Δ1 comprises 492 N-terminal residues [48] | |
CSGT | Continuous set of gauge transformations |
DFT | Density functional theory |
FFMD | Force field molecular dynamics |
GAF | cGMP phosphodiesterase/adenylyl cyclase/FhlA |
GAPW | Gaussian-augmented plane waves |
GEEP | Gaussian expansion of the electrostatic potential |
GPW | Gaussian and plane waves |
GTH | Goedecker-Teter-Hutter (pseudopotential) |
IGAIM | Individual Gauges for Atoms in Molecules |
IR | Infrared |
MAS | Magic angle spinning |
MD | Molecular dynamics |
MM | Molecular mechanics |
NMR | Nuclear magnetic resonance |
NVT | Canonical (ensemble) |
PAS | period circadian/aryl hydrocarbon receptor nuclear translocator/single-minded |
PBC | Periodic boundary conditions |
PCA | Principal component analysis |
PCB | Phycocyanobilin |
PHY | Phytochrome specific |
PP | Pseudopotential |
QM | Quantum mechanics |
QM/MM | (Hybrid) Quantum mechanics/molecular mechanics |
QMP | QM part |
RMSE | Root mean square error |
UV | Ultraviolett |
Appendix A
Appendix A.1. Size of the QM Part and Convergence
Appendix A.2. Statistical Data
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C–C | C–C | C–C | C–C | C–C | C–C | |||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
C | C | C | C | C | C | |||||||
(P–P) * | ||||||||||||
(P–P) * | ||||||||||||
(P–P) * | ||||||||||||
(P–P) * | ||||||||||||
d(P) ** | 143 | 144 | 137 | 148 | 137 | 149 | ||||||
(P–P) ** | ||||||||||||
(P–P) ** | ||||||||||||
(P–P) ** | ||||||||||||
(P–P) ** |
C–C | C–C | C–C | C–C | C–C | C–C | |
---|---|---|---|---|---|---|
double | single | double | (single) | single | double | |
single | double | single | (single) | double | single |
Parameter | FFMD | AIMD | NMR |
---|---|---|---|
Ensemble | NPT | NVT | NVT |
No. of atoms | 37,651/104,960 * | ≈100 | ≈280 |
Temperature | 300 K | 300 K | – |
Pressure | 1.01325 bar | – | – |
Barostat | Langevin | – | – |
Thermostat | Nosé–Hoover | Nosé–Hoover | – |
ABC (Å) | – ** | 30.0, 30.0, 30.0 | 35.0, 35.0, 35.0 |
Force Field/Functional | CHARMM22 | BLYP-D3 | BLYP-D3 |
Basis Set | – | TZVP-GTH | pcS2/3 |
Density Cutoff | – | 320 Ry | 400 Ry |
No. of Snapshots | – | – | 405 |
/ | ≈1 s | >20 ps | – |
Other | SHAKE [81] |
AnPixJg2 | Cph12 | ||||||
---|---|---|---|---|---|---|---|
Residue | AIMD | NMR | Capping Atom | Residue | AIMD | NMR | Capping Atom |
PCB | x | x | – | PCB | x | x | – |
Trp289 | x | x | CA | Asp207 | x | x | CB/CA ** |
Asp291 | x | x | CA | Ile208 | x | x | C/C,CB ** |
His293 | – | x | CA | Arg222 | – | x | CB |
Arg301 | – | x | CA | Arg254 | – | x | CB |
Tyr302 | – | x | CA | Ala256 | – | x | CA |
Phe308 | – | x | CA | Tyr257 | – | x | – |
His318 | – | x | CA | His258 | x | x | CA/CB ** |
Phe319 | – | x | CA | Cys259 | x | x | – |
Ser320 | x | x | CA | His260 | x | x | C |
Cys321 | x | x | – | Tyr263 | – | x | CA |
His322 | x | x | C | His290 | – | x | CA |
Tyr334 | – | x | CA | Water * | x | x | – |
Water * | – | x | – |
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Jähnigen, S.; Sebastiani, D. Carbon Atoms Speaking Out: How the Geometric Sensitivity of 13C Chemical Shifts Leads to Understanding the Colour Tuning of Phycocyanobilin in Cph1 and AnPixJ. Molecules 2020, 25, 5505. https://doi.org/10.3390/molecules25235505
Jähnigen S, Sebastiani D. Carbon Atoms Speaking Out: How the Geometric Sensitivity of 13C Chemical Shifts Leads to Understanding the Colour Tuning of Phycocyanobilin in Cph1 and AnPixJ. Molecules. 2020; 25(23):5505. https://doi.org/10.3390/molecules25235505
Chicago/Turabian StyleJähnigen, Sascha, and Daniel Sebastiani. 2020. "Carbon Atoms Speaking Out: How the Geometric Sensitivity of 13C Chemical Shifts Leads to Understanding the Colour Tuning of Phycocyanobilin in Cph1 and AnPixJ" Molecules 25, no. 23: 5505. https://doi.org/10.3390/molecules25235505