Design of buried charged networks in artificial proteins

Baumgart, Mona; Röpke, Michael; Mühlbauer, Max E.; Asami, Sam; Mader, Sophie L.; Fredriksson, Kai; Groll, M.; Gámiz‐Hernández, Ana P.; Kaila, Ville R. I.

doi:10.1038/s41467-021-21909-7

Cited by 11 publications

(9 citation statements)

References 46 publications

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“…Finally, we note that in a recent study, Kaila and co-workers have used computational design to engineer one or multiple ion-pairs into the interior of a set of highly stable helical bundles. Structural characterizations using crystallography and NMR along with thermodynamic measurements supported the overall stability of these mutants with buried ion-pairs; in fact, one of the mutants exhibited impressive thermodynamic stability comparable to the original protein background.…”

Section: Discussionmentioning

confidence: 98%

“…31 Along this line, it is worth stressing that, in general, a destabilizing charged ion-pair relative to nonpolar isosteres 7 does not necessarily suggest that the ion-pair prefers the charge-neutral ionization state; as evident from Figure 6c, the charge-neutral ionization state is favored (i.e., ΔG PT F < 0) only when the folding stability difference between the two ionization states (ΔG f ′ N − ΔG f C ) offsets the pK a difference between the two titratable residues in solution (ΔG ΔpK U ). Finally, we note that in a recent study, 84 Kaila and coworkers have used computational design to engineer one or multiple ion-pairs into the interior of a set of highly stable helical bundles. Structural characterizations using crystallography and NMR along with thermodynamic measurements supported the overall stability of these mutants with buried ion-pairs; in fact, one of the mutants exhibited impressive thermodynamic stability comparable to the original protein background.…”

Section: Free Energy Simulations Strongly Reverse Protonation For The...mentioning

confidence: 96%

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Reverse Protonation of Buried Ion-Pairs in Staphylococcal Nuclease Mutants

Deng

Cui

2021

J. Chem. Theory Comput.

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Although buried titratable residues in protein cavities are often of major functional importance, it is generally challenging to understand their properties such as the ionization state and factors of stabilization based on experimental studies alone. A specific set of examples involve buried Glu–Lys pairs in a series of variants of Staphylococcal nuclease, for which recent structural and thermodynamic studies appeared to suggest that both the stability and the ionization state of the buried Glu–Lys pair are sensitive to its orientation (i.e., Glu23–Lys36 vs Lys23–Glu36). To further clarify the situation, especially ionization states of the buried Glu–Lys pairs, we have conducted extensive molecular dynamics simulations and free energy computations. Microsecond molecular dynamics simulations show that the hydration level of the cavity depends on the orientation of the buried ion-pair therein as well as its ionization state; free energy simulations recapitulate the relative stability of Glu23–Lys36 (EK) vs Lys23–Glu36 (KE) mutants measured experimentally, although the difference is similar in magnitude regardless of the ionization state of the Glu–Lys pair. A complementary set of free energy simulations strongly suggests that, in contrast to the original suggestion in the experimental analysis, the Glu and Lys residues prefer to adopt their charge-neutral rather than the ionized states. This result is consistent with the low dielectric constant computed for water in the cavity, which makes it difficult for the protein cavity to stabilize a pair of charged Glu–Lys residues, even with water penetration. The current study highlights the role of free energy simulations in understanding the ionization state of buried titratable residues and the relevant energetic contributions, forming the basis for the rational design of buried charge networks in proteins.

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Section: Discussionmentioning

confidence: 98%

Section: Free Energy Simulations Strongly Reverse Protonation For The...mentioning

confidence: 96%

Reverse Protonation of Buried Ion-Pairs in Staphylococcal Nuclease Mutants

Deng

Cui

2021

J. Chem. Theory Comput.

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“… 58 , 62 Similar effects are also found in cytochrome c oxidase, where redox-driven dissociation of a propionate-arginine (Δ-propionate/Arg438 in bovine numbering) ion-pair modulates the proton transfer barriers across the membrane. 63 , 64 Conformational changes in ion-pairs have also been suggested to trigger ion-transport and/or catalysis in bacterial light-driven Na + pumps, 65 molecular chaperones, 66 and in artificial designer proteins, 67 suggesting that the described key functional motifs are generally applied also in other proteins.…”

Section: Discussionmentioning

confidence: 99%

Molecular Principles of Redox-Coupled Protonation Dynamics in Photosystem II

et al. 2022

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Photosystem II (PSII) catalyzes light-driven water oxidization, releasing O 2 into the atmosphere and transferring the electrons for the synthesis of biomass. However, despite decades of structural and functional studies, the water oxidation mechanism of PSII has remained puzzling and a major challenge for modern chemical research. Here, we show that PSII catalyzes redox-triggered proton transfer between its oxygen-evolving Mn 4 O 5 Ca cluster and a nearby cluster of conserved buried ion-pairs, which are connected to the bulk solvent via a proton pathway. By using multi-scale quantum and classical simulations, we find that oxidation of a redox-active Tyr z (Tyr161) lowers the reaction barrier for the water-mediated proton transfer from a Ca 2+ -bound water molecule (W3) to Asp61 via conformational changes in a nearby ion-pair (Asp61/Lys317). Deprotonation of this W3 substrate water triggers its migration toward Mn1 to a position identified in recent X-ray free-electron laser (XFEL) experiments [Ibrahim et al. Proc. Natl. Acad. Sci. USA 2020, 117, 12,624–12,635]. Further oxidation of the Mn 4 O 5 Ca cluster lowers the proton transfer barrier through the water ligand sphere of the Mn 4 O 5 Ca cluster to Asp61 via a similar ion-pair dissociation process, while the resulting Mn-bound oxo/oxyl species leads to O 2 formation by a radical coupling mechanism. The proposed redox-coupled protonation mechanism shows a striking resemblance to functional motifs in other enzymes involved in biological energy conversion, with an interplay between hydration changes, ion-pair dynamics, and electric fields that modulate the catalytic barriers.

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“… 69 Similar electrostatic effects have also recently been described in the molecular chaperone Hsp90 ( Figure 6 d), where an IP dissociation (Glu33/Arg32) modulates the reaction barrier for ATP hydrolysis 66 and which further triggers large-scale conformational changes in the chaperone structure. The conservation of such functional elements has recently inspired us to design buried ion pairs using artificial minimal protein frameworks, 67 that could help to dissect and probe the conformational dynamics and intriguing mechanistic principles in simplified biochemical model systems from a bottom-up approach ( Figure 6 e).…”

Section: Long-range Pcet Reactions In Complex Imentioning

confidence: 99%

Section: Long-range Pcet Reactions In Complex Imentioning

confidence: 99%

Resolving Chemical Dynamics in Biological Energy Conversion: Long-Range Proton-Coupled Electron Transfer in Respiratory Complex I

Kaila

2021

Acc. Chem. Res.

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Conspectus Biological energy conversion is catalyzed by membrane-bound proteins that transduce chemical or light energy into energy forms that power endergonic processes in the cell. At a molecular level, these catalytic processes involve elementary electron-, proton-, charge-, and energy-transfer reactions that take place in the intricate molecular machineries of cell respiration and photosynthesis. Recent developments in structural biology, particularly cryo-electron microscopy (cryoEM), have resolved the molecular architecture of several energy transducing proteins, but detailed mechanistic principles of their charge transfer reactions still remain poorly understood and a major challenge for modern biochemical research. To this end, multiscale molecular simulations provide a powerful approach to probe mechanistic principles on a broad range of time scales (femtoseconds to milliseconds) and spatial resolutions (10 1 –10 6 atoms), although technical challenges also require balancing between the computational accuracy, cost, and approximations introduced within the model. Here we discuss how the combination of atomistic (aMD) and hybrid quantum/classical molecular dynamics (QM/MM MD) simulations with free energy (FE) sampling methods can be used to probe mechanistic principles of enzymes responsible for biological energy conversion. We present mechanistic explorations of long-range proton-coupled electron transfer (PCET) dynamics in the highly intricate respiratory chain enzyme Complex I, which functions as a redox-driven proton pump in bacterial and mitochondrial respiratory chains by catalyzing a 300 Å fully reversible PCET process. This process is initiated by a hydride (H – ) transfer between NADH and FMN, followed by long-range (>100 Å) electron transfer along a wire of 8 FeS centers leading to a quinone biding site. The reduction of the quinone to quinol initiates dissociation of the latter to a second membrane-bound binding site, and triggers proton pumping across the membrane domain of complex I, in subunits up to 200 Å away from the active site. Our simulations across different size and time scales suggest that transient charge transfer reactions lead to changes in the internal hydration state of key regions, local electric fields, and the conformation of conserved ion pairs, which in turn modulate the dynamics of functional steps along the reaction cycle. Similar functional principles, which operate on much shorter length scales, are also found in some unrelated proteins, suggesting that enzymes may employ conserved principles in the catalysis of biological energy transduction processes.

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Design of buried charged networks in artificial proteins

Cited by 11 publications

References 46 publications

Reverse Protonation of Buried Ion-Pairs in Staphylococcal Nuclease Mutants

Reverse Protonation of Buried Ion-Pairs in Staphylococcal Nuclease Mutants

Molecular Principles of Redox-Coupled Protonation Dynamics in Photosystem II

Resolving Chemical Dynamics in Biological Energy Conversion: Long-Range Proton-Coupled Electron Transfer in Respiratory Complex I

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