Structural and functional consequences of the H180A mutation of the light-driven sodium pump KR2

Kriebel, Clara Nassrin; Asido, Marvin; Kaur, Jagdeep; Orth, Jennifer; Braun, Philipp; Becker‐Baldus, Johanna; Wachtveitl, Josef; Glaubitz, Clemens

doi:10.1016/j.bpj.2022.12.023

Cited by 8 publications

(21 citation statements)

References 52 publications

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“…In this work, the KR2 pentamer contains 273 residues per protomer, of which 201 residues per protomer have experimental NMR chemical shift results . In the pentamer system, 22.89% of the 201 residues contain cross-protomer interactions.…”

Section: Resultsmentioning

confidence: 98%

“…This result is consistent with the solid-state NMR experiment. 85 It was found in the experiment that the signal change/ loss occurred in residues 83Thr, 86Phe, and 87Thr in the presence of NaCl (Table S5). Moreover, retinal plays an important role in sodium ion (or a proton in the absence of sodium) translocation across the membrane.…”

Section: Influence Of the Local Chemical Environmentmentioning

confidence: 96%

“…−2.00 ppm). 85 In contrast, there is no substantial effect on the retinal 13 C chemical shifts in the NMR experiments caused by the presence of NaCl. 85 Our theoretical calculations show that the perturbations of the 13 C chemical shifts of the retinal are all lower than 0.80 ppm, and the average perturbation is 0.40 ppm (see Table S7).…”

Section: Influence Of the Local Chemical Environmentmentioning

confidence: 97%

“…The lipid was chosen to be compatible with the experimental NMR studies. 85 Besides, 5 sodium ions and 541 crystallographic water molecules in the crystal structure as well as 41 sodium ions and 31 chloride ions were added to neutralize the entire system along with 11,459 TIP3P water molecules. The structures were first optimized using the AMBER18 program.…”

Section: Computational Approachesmentioning

confidence: 99%

“…In this work, the KR2 pentamer contains 273 residues per protomer, of which 201 residues per protomer have experimental NMR chemical shift results. 85 In the pentamer system, 22.89% of the 201 residues contain cross-protomer interactions. Comparing the results of these 22.89% residues with the monomer system (see Figure 13a), we find that the RMSE, MUE, and maxD are all decreased, from 6.21 to 5.67 ppm, from 4.64 to 4.18 ppm, and from 17.78 to 12.71 ppm, respectively, which indicates that the interaction of the crossprotomer between the residues in the pentameric environment can improve the prediction accuracy of the 15 N chemical shift calculation.…”

Section: Influence Of the Local Chemical Environmentmentioning

confidence: 99%

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Automated Fragmentation Quantum Mechanical Calculation of ¹⁵N and ¹³C Chemical Shifts in a Membrane Protein

Zhang,

Kriebel,

Wan

et al. 2023

J. Chem. Theory Comput.

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In this work, we developed an accurate and costeffective automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) method to calculate the chemical shifts of 15 N and 13 C of membrane proteins. The convergence of the AF-QM/ MM method was tested using Krokinobacter eikastus rhodopsin 2 as a test case. When the distance threshold of the QM region is equal to or larger than 4.0 Å, the results of the AF-QM/MM calculations are close to convergence. In addition, the effects of selected density functionals, basis sets, and local chemical environment of target atoms on the chemical shift calculations were systematically investigated. Our results demonstrate that the predicted chemical shifts are more accurate when important environmental factors including crossprotomer interactions, lipid molecules, and solvent molecules are taken into consideration, especially for the 15 N chemical shift prediction. Furthermore, with the presence of sodium ions in the environment, the chemical shift of residues, retinal, and retinal Schiff base are affected, which is consistent with the results of the solid-state nuclear magnetic resonance (NMR) experiment. Upon comparing the performance of various density functionals (namely, B3LYP, B3PW91, M06-2X, M06-L, mPW1PW91, OB95, and OPBE), the results show that mPW1PW91 is a suitable functional for the 15 N and 13 C chemical shift prediction of the membrane proteins. Meanwhile, we find that the improved accuracy of the 13 C β chemical shift calculations can be achieved by the employment of the triple-ζ basis set. However, the employment of the triple-ζ basis set does not improve the accuracy of the 15 N and 13 C α chemical shift calculations nor does the addition of a diffuse function improve the overall prediction accuracy of the chemical shifts. Our study also underscores that the AF-QM/MM method has significant advantages in predicting the chemical shifts of key ligands and nonstandard residues in membrane proteins than most widely used empirical models; therefore, it could be an accurate computational tool for chemical shift calculations on various types of biological systems.

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Section: Resultsmentioning

confidence: 98%

Section: Influence Of the Local Chemical Environmentmentioning

confidence: 96%

Section: Influence Of the Local Chemical Environmentmentioning

confidence: 97%

Section: Computational Approachesmentioning

confidence: 99%

Section: Influence Of the Local Chemical Environmentmentioning

confidence: 99%

See 3 more Smart Citations

Automated Fragmentation Quantum Mechanical Calculation of ¹⁵N and ¹³C Chemical Shifts in a Membrane Protein

Zhang,

Kriebel,

Wan

et al. 2023

J. Chem. Theory Comput.

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A Detailed View on the (Re)isomerization Dynamics in Microbial Rhodopsins Using Complementary Near‐UV and IR Readouts

Asido,

Lamm,

Lienert

et al. 2024

Angewandte Chemie

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Isomerization is a key process in many (bio)chemical systems. In microbial rhodopsins, the photoinduced isomerization of the all‐trans retinal to the 13‐cis isomer initiates a cascade of structural changes of the protein. The interplay between these changes and the thermal relaxation of the isomerized retinal is one of the crucial determinants for rhodopsin functionality. It is therefore important to probe this dynamic interplay with chromophore specific markers that combine gapless temporal observation with spectral sensitivity. Here we utilize the near‐UV and mid‐IR fingerprint region in the framework of a systematic (time‐resolved) spectroscopic study on H+‐ (HsBR, (G)PR), Na+‐ (KR2, ErNaR) and Cl‐‐ (NmClR) pumps. We demonstrate that the near‐UV region is an excellent probe for retinal configuration and ‐ being sensitive to the electrostatic environment of retinal ‐ even transient ion binding, which allows us to pinpoint protein specific mechanistic nuances and chromophore‐charge interactions. The combination of the near‐UV and mid‐IR fingerprint region hence provides a spectroscopic analysis tool that allows a detailed, precise and temporally fully resolved description of retinal configurations during all stages of the photocycle.

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A Detailed View on the (Re)isomerization Dynamics in Microbial Rhodopsins Using Complementary Near‐UV and IR Readouts

Asido,

Lamm,

Lienert

et al. 2024

Angew Chem Int Ed

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Structural and functional consequences of the H180A mutation of the light-driven sodium pump KR2

Cited by 8 publications

References 52 publications

Automated Fragmentation Quantum Mechanical Calculation of ¹⁵N and ¹³C Chemical Shifts in a Membrane Protein

Automated Fragmentation Quantum Mechanical Calculation of ¹⁵N and ¹³C Chemical Shifts in a Membrane Protein

A Detailed View on the (Re)isomerization Dynamics in Microbial Rhodopsins Using Complementary Near‐UV and IR Readouts

A Detailed View on the (Re)isomerization Dynamics in Microbial Rhodopsins Using Complementary Near‐UV and IR Readouts

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Structural and functional consequences of the H180A mutation of the light-driven sodium pump KR2

Cited by 8 publications

References 52 publications

Automated Fragmentation Quantum Mechanical Calculation of 15N and 13C Chemical Shifts in a Membrane Protein

Automated Fragmentation Quantum Mechanical Calculation of 15N and 13C Chemical Shifts in a Membrane Protein

A Detailed View on the (Re)isomerization Dynamics in Microbial Rhodopsins Using Complementary Near‐UV and IR Readouts

A Detailed View on the (Re)isomerization Dynamics in Microbial Rhodopsins Using Complementary Near‐UV and IR Readouts

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Automated Fragmentation Quantum Mechanical Calculation of ¹⁵N and ¹³C Chemical Shifts in a Membrane Protein

Automated Fragmentation Quantum Mechanical Calculation of ¹⁵N and ¹³C Chemical Shifts in a Membrane Protein