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Hypoxia-inducible factor 1 (HIF-1), recognized as a master transcription factor for adaptation to hypoxia, is associated with malignant characteristics and therapy resistance in cancers. It has become clear that cofactors such as ZBTB2 are critical for the full activation of HIF-1; however, the mechanisms downregulating the ZBTB2-HIF-1 axis remain poorly understood. In this study, we identified ZBTB7A as a negative regulator of ZBTB2 by analyzing protein sequences and structures. We found that ZBTB7A forms a heterodimer with ZBTB2, inhibits ZBTB2 homodimerization necessary for the full expression of ZBTB2-HIF-1 downstream genes, and ultimately delays the proliferation of cancer cells under hypoxic conditions. The Cancer Genome Atlas (TCGA) analyses revealed that overall survival is better in patients with high ZBTB7A expression in their tumor tissues. These findings highlight the potential of targeting the ZBTB7A-ZBTB2 interaction as a novel therapeutic strategy to inhibit HIF-1 activity and improve treatment outcomes in hypoxia-related cancers., Competing Interests: Declaration of competing interest The authors declare no competing interests., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

The maintenance of lipid asymmetry on the plasma membrane is regulated by flippases, such as ATP8A2, ATP11A, and ATP11C, which translocate phosphatidylserine and phosphatidylethanolamine from the outer leaflet to the inner leaflet. We previously identified a patient-derived point mutation (Q84E) in ATP11A at the phospholipid entry site, which acquired the ability to flip phosphatidylcholine (PtdCho). This mutation led to elevated levels of sphingomyelin (SM) in the outer leaflet of the plasma membrane. We herein present two de novo ATP11A dominant mutations (E114G and S399L) in heterozygous patients exhibiting neurological and developmental disorders. These mutations, situated near the predicted phospholipid exit site, similarly confer the ability for ATP11A to recognize PtdCho as a substrate, resulting in its internalization into cells. Cells expressing these mutants had increased SM levels on their surface, attributed to the up-regulated expression of the sphingomyelin synthase-1 gene, rendering them more susceptible to SM phosphodiesterase-mediated cell lysis. Corresponding mutations in ATP11C and ATP8A2, paralogs of ATP11A, exerted similar effects on PtdCho-flipping activity and increased SM levels on the cell surface. Molecular dynamics simulations, based on the ATP11C structure, suggest that the E114G and S399L mutations enhance ATP11C's affinity toward PtdCho. These findings underscore the importance of the well-conserved exit and entry sites in determining phospholipid substrate specificity and indicate that aberrant flipping of PtdCho contributes to neurological disorders., Competing Interests: Competing interests statement:The authors declare no competing interest.

Phycocyanobilin (PCB)-binding proteins, including cyanobacteriochromes and phytochromes, function as photoreceptors and exhibit a wide range of absorption maximum wavelengths. To elucidate the color-tuning mechanisms among these proteins, we investigated seven crystal structures of six PCB-binding proteins: Anacy_2551g3, AnPixJg2, phosphorylation-responsive photosensitive histidine kinase, RcaE, Sb.phyB(PG)-PCB, and Slr1393g3. Employing a quantum chemical/molecular mechanical approach combined with a polarizable continuum model, our analysis revealed that differences in absorption wavelengths among PCB-binding proteins primarily arise from variations in the shape of the PCB molecule itself, accounting for a ∼150 nm difference. Remarkably, calculated excitation energies sufficiently reproduced the absorption wavelengths of these proteins spanning ∼200 nm, including 728 nm for Anacy_2551g3. However, assuming the hypothesized lactim conformation resulted in a significant deviation from the experimentally measured absorption wavelength for Anacy_2551g3. The significantly red-shifted absorption wavelength of Anacy_2551g3 can unambiguously be explained by the significant overlap of molecular orbitals between the two pyrrole rings at both edges of the PCB chromophore without the need to hypothesize lactim formation., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

In type-II reaction centers, such as photosystem II (PSII) and reaction centers from purple bacteria (PbRC), light-induced charge separation involves electron transfer from pheophytin (Pheo D1 ) to quinone (Q A ), occurring near a conserved tryptophan residue (D2-Trp253 in PSII and Trp-M252 in PbRC). This study investigates the route of the Pheo D1 -to-Q A electron transfer, focusing on the superexchange coupling (| H PheoD1···QA |) in the PSII protein environment. | H PheoD1···QA | is significantly larger for the Pheo D1 -like intermediate state, 0.73 meV) compared to direct electron transfer (0.13 meV), suggesting that superexchange is the dominant mechanism in the PSII protein environment. While the overall impact of the protein environment is limited, local interactions, particularly H-bonds, enhance superexchange electron transfer by directly affecting the delocalization of molecular orbitals. The D2-W253F mutation significantly decreases the electron transfer rate. The conservation of D2-Trp253/D1-Phe255 (Trp-M252/Phe-L216 in PbRC) in the two branches appears to differentiate superexchange coupling, contributing to the branches being either active or inactive in electron transfer.A electron transfer via the unoccupied molecular orbitals of D2-Trp253 ([Trp] •- -like intermediate state, 0.73 meV) compared to direct electron transfer (0.13 meV), suggesting that superexchange is the dominant mechanism in the PSII protein environment. While the overall impact of the protein environment is limited, local interactions, particularly H-bonds, enhance superexchange electron transfer by directly affecting the delocalization of molecular orbitals. The D2-W253F mutation significantly decreases the electron transfer rate. The conservation of D2-Trp253/D1-Phe255 (Trp-M252/Phe-L216 in PbRC) in the two branches appears to differentiate superexchange coupling, contributing to the branches being either active or inactive in electron transfer.

Deprotonation or suppression of the p K a of the amino group of a lysine sidechain is a widely recognized phenomenon whereby the sidechain amino group transiently can act as a nucleophile at the active site of enzymatic reactions. However, a deprotonated lysine and its molecular interactions have not been directly experimentally detected. Here, we demonstrate a deprotonated lysine stably serving as an "acceptor" in a H-bond between the photosensor protein RcaE and its chromophore. Signal splitting and trans-H-bond J coupling observed by NMR spectroscopy provide direct evidence that Lys261 is deprotonated and serves as a H-bond acceptor for the chromophore NH group. Quantum mechanical/molecular mechanical calculations also indicate that this H-bond exists stably. Interestingly, the sidechain amino group of the lysine can act as both donor and acceptor. The remarkable shift in the H-bond characteristics arises from a decrease in solvation, triggered by photoisomerization. Our results provide insights into the dual role of this lysine. This mechanism has broad implications for other biological reactions in which lysine plays a role., Competing Interests: Competing interests statement:The authors declare no competing interest.

Structural differences between illuminated and unilluminated crystal structures led to the proposal that the charge-separated state was stabilized by structural changes in its membrane extrinsic protein subunit H in a bacterial photosynthetic reaction center [Katona, G. et al. Nat. Struct. Mol. Biol. 2005, 12, 630-631]. Here, we explored the proposal by titrating all titratable sites and calculating the redox potential (E m ) values in these crystal structures. Contrary to the expected charge-separated states, E m for quinone, E m (Q A /Q A ), is even lower in the proposed charge-separated structure than in the ground-state structure. The subunit-H residues, which were proposed to exhibit electron-density changes in the two crystal structures, contribute to an E •- ), is even lower in the proposed charge-separated structure than in the ground-state structure. The subunit-H residues, which were proposed to exhibit electron-density changes in the two crystal structures, contribute to an E m (Q A /Q A •- ) difference of only <0.5 mV. Furthermore, the protonation states of the titratable residues in the entire reaction center are practically identical in the two structures. These findings indicate that the proposed structural differences are irrelevant to explaining the significant prolongation of the charge-separated-state lifetime., (© 2024. The Author(s).)

In photosystem II (PSII), D1-Tyr246 and D2-Tyr244 are symmetrically located at the binding site of the bicarbonate ligand of the non-heme Fe complex. Here, we investigated the role of the symmetrically arranged tyrosine pair, D1-Tyr246 and D2-Tyr244, in the function of PSII, by generating four chloroplast mutants of PSII from Chlamydomonas reinhardtii: D1-Y246F, D1-Y246T, D2-Y244F, and D2-Y244T. The mutants exhibited altered photoautotrophic growth, reduced PSII protein accumulation, and impaired O 2 -evolving activity. Flash-induced fluorescence yield decay kinetics indicated a significant slowdown in electron transfer from Q A •- to Q B in all mutants. Bicarbonate reconstitution resulted in enhanced O 2 -evolving activity, suggesting destabilization of bicarbonate binding in the mutants. Structural analyses based on a quantum mechanical/molecular mechanical approach identified the existence of a water channel that leads to incorporation of bulk water molecules and destabilization of the bicarbonate binding site. The water intake channels, crucial for bicarbonate stability, exhibited distinct paths in the mutants. These findings shed light on the essential role of the tyrosine pair in maintaining bicarbonate stability and facilitating efficient electron transfer in native PSII., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Exiguobacterium sibiricum rhodopsin (ESR) functions as a light-driven proton pump utilizing Lys96 for proton uptake and maintaining its activity over a wide pH range. Using a combination of methodologies including the linear Poisson-Boltzmann equation and a quantum mechanical/molecular mechanical approach with a polarizable continuum model, we explore the microscopic mechanisms underlying its pumping activity. Lys96, the primary proton uptake site, remains deprotonated owing to the loss of solvation in the ESR protein environment. Asp85, serving as a proton acceptor group for Lys96, does not form a low-barrier H-bond with His57. Instead, deprotonated Asp85 forms a salt-bridge with protonated His57, and the proton is predominantly located at the His57 moiety. Glu214, the only acidic residue at the end of the H-bond network exhibits a p K value of ∼6, slightly elevated due to solvation loss. It seems likely that the H-bond network [Asp85···His57···H a value of ∼6, slightly elevated due to solvation loss. It seems likely that the H-bond network [Asp85···His57···H 2 O···Glu214] serves as a proton-conducting pathway toward the protein bulk surface.

The Mn 4 CaO 5 cluster, featuring four ligand water molecules (W1 to W4), serves as the water-splitting site in photosystem II (PSII). X-ray free electron laser (XFEL) structures exhibit an additional oxygen site (O6) adjacent to the O5 site in the fourth lowest oxidation state, S 3 , forming Mn 4 CaO 6 . Here, we investigate the mechanism of the second water ligand molecule at the dangling Mn (W2) as a potential incorporating species, using a quantum mechanical/molecular mechanical (QM/MM) approach. Previous QM/MM calculations demonstrated that W1 releases two protons through a low-barrier H-bond toward D1-Asp61 and subsequently releases an electron during the S 2 to S 3 transition, resulting in O •- at W1 and protonated D1-Asp61. During the process of Mn 4 CaO 6 formation, O •- , rather than H 2 O or OH - , best reproduced the O5···O6 distance. Although the catalytic cluster with O •- at O6 is more stable than that with O •- at W1 in S 3 , it does not occur spontaneously due to the significantly uphill deprotonation process. Assuming O •- at W2 incorporates into the O6 site, an exergonic conversion from Mn1(III)Mn2(IV)Mn3(IV)Mn4(IV) (equivalent to the open-cubane S 2 valence state) to Mn1(IV)Mn2(IV)Mn3(IV)Mn4(III) (equivalent to the closed-cubane S 2 valence state) occurs. These findings provide energetic insights into the deprotonation and structural conversion events required for the Mn 4 CaO 6 formation.

Quinone analogue molecules, functioning as herbicides, bind to the secondary quinone site, Q B , in type-II photosynthetic reaction centers, including those from purple bacteria (PbRC). Here, we investigated the impact of herbicide binding on electron transfer branches, using herbicide-bound PbRC crystal structures and employing the linear Poisson-Boltzmann equation. In contrast to urea and phenolic herbicides [Fufezan, C. Biochemistry 2005, 44, 12780-12789], binding of atrazine and triazine did not cause significant changes in the redox-potential ( E m ) values of the primary quinone (Q A difference at the bacteriopheophytin in the electron transfer inactive branch (H E m difference at the bacteriopheophytin in the electron transfer inactive branch (H M ) was observed between the S -mediated link between the electron transfer inactive H R (+)-triazine-bound PbRC structures. This discrepancy is linked to variations in the protonation pattern of the tightly coupled Glu-L212 and Glu-H177 pairs, crucial components of the proton uptake pathway in native PbRC. These findings suggest the existence of a Q B -mediated link between the electron transfer inactive H M and the proton uptake pathway in PbRCs.

Blue light using flavin (BLUF) domain proteins are photoreceptors in various organisms. The PixD BLUF domain can adopt two conformations, W91 out and W91 in , with Trp91 either proximal or distal to flavin (FMN). Using a quantum mechanical/molecular mechanical/polarizable continuum model approach, the energetics of charge-separated and biradical states in the two conformations were investigated. In the W91 out conformation, the charge-separated state (FMN •- ) is more stable than the photoexcited state (FMN*), whereas it is less stable due to an electrostatic repulsive interaction with the Ser28 side chain in the W91 in conformation. This leads to a lower activation energy for the charge separation in the W91 out conformation, resulting in a faster charge separation compared to that in the W91 in conformation. In the W91 out conformation, the radical state (FMNH • ) is more stable than FMN •- and forms from FMN •- , leading to reorientation of the Gln50 side chain adjacent to FMN and formation of a hydrogen bond between Gln50 and FMN. Subsequently, a signaling state forms through charge recombination. In contrast, in the W91 in conformation, FMN •- cannot proceed further, returning to the dark-adapted state, as FMNH • is less stable. Thus, formation of the signaling state exclusively occurs in the W91 out conformation.

D1-Tyr161 (TyrZ) forms a low-barrier H-bond with D1-His190 and functions as a redox-active group in photosystem II. When oxidized to the radical form (TyrZ-O • ), it accepts an electron from the oxygen-evolving Mn 4 CaO 5 cluster, facilitating an increase in the oxidation state (S n ; n = 0-3). In this study, we investigated the mechanism of how TyrZ-O • drives proton-coupled electron transfer during the S 2 to S 3 transition using a quantum mechanical/molecular mechanical approach. In response to TyrZ-O • formation and subsequent loss of the low-barrier H-bond, the ligand water molecule at the Ca 2+ site (W4) reorients away from TyrZ and donates an H-bond to D1-Glu189 at Mn4 of Mn 4 CaO 5 together with an adjacent water molecule. The H-bond donation to the Mn 4 CaO 5 cluster triggers the release of the proton from the lowest p K site (W1 at Mn4) along the W1…D1-Asp61 low-barrier H-bond, leading to protonation of D1-Asp61. The interplay of the two low-barrier H-bonds, involving the Ca a site (W1 at Mn4) along the W1…D1-Asp61 low-barrier H-bond, leading to protonation of D1-Asp61. The interplay of the two low-barrier H-bonds, involving the Ca 2+ interface and forming the extended Grotthuss-like network [TyrZ…D1-His190]-[Mn 4 CaO 5 ]-[W1…D1-Asp61], rather than the direct electrostatic interaction, is likely a basis of the apparent long-distance interaction (11.4 Å) between TyrZ-O • formation and D1-Asp61 protonation., (© The Author(s) 2023. Published by Oxford University Press on behalf of National Academy of Sciences.)

Photosynthesis is one of the most important reactions for sustaining our environment. Photosystem II (PSII) is the initial site of photosynthetic electron transfer by water oxidation. Light in excess, however, causes the simultaneous production of reactive oxygen species (ROS), leading to photo-oxidative damage in PSII. To maintain photosynthetic activity, the PSII reaction center protein D1, which is the primary target of unavoidable photo-oxidative damage, is efficiently degraded by FtsH protease. In PSII subunits, photo-oxidative modifications of several amino acids such as Trp have been indeed documented, whereas the linkage between such modifications and D1 degradation remains elusive. Here, we show that an oxidative post-translational modification of Trp residue at the N-terminal tail of D1 is correlated with D1 degradation by FtsH during high-light stress. We revealed that Arabidopsis mutant lacking FtsH2 had increased levels of oxidative Trp residues in D1, among which an N-terminal Trp-14 was distinctively localized in the stromal side. Further characterization of Trp-14 using chloroplast transformation in Chlamydomonas indicated that substitution of D1 Trp-14 to Phe, mimicking Trp oxidation enhanced FtsH-mediated D1 degradation under high light, although the substitution did not affect protein stability and PSII activity. Molecular dynamics simulation of PSII implies that both Trp-14 oxidation and Phe substitution cause fluctuation of D1 N-terminal tail. Furthermore, Trp-14 to Phe modification appeared to have an additive effect in the interaction between FtsH and PSII core in vivo. Together, our results suggest that the Trp oxidation at its N-terminus of D1 may be one of the key oxidations in the PSII repair, leading to processive degradation by FtsH., Competing Interests: YK, HK, SO, KS, VD, MS, GZ, Cd, HI, CK, MH, YT, WS No competing interests declared, (© 2023, Kato, Kuroda, Ozawa et al.)

The experimentally measured stretching vibrational frequencies of O-D [ν O-D (donor)] and C=O [ν C=O (donor)] H-bond donor groups can provide valuable information about the H-bonds in proteins. Here, using a quantum mechanical/molecular mechanical approach, the relationship between these vibrational frequencies and the difference in pK a values between H-bond donor and acceptor groups [ΔpK a (donor … acceptor)] in bacteriorhodopsin and photoactive yellow protein environments was investigated. The results show that ν O-D (donor) is correlated with ΔpK a (donor … acceptor), regardless of the specific protein environment. ν C=O (donor) is also correlated with ΔpK a (donor … acceptor), although the correlation is weak because the C=O bond does not have a proton. Importantly, the shifts in ν O-D (donor) and ν C=O (donor) are not caused by changes in pK a (donor) alone, but rather by changes in ΔpK a (donor … acceptor). Specifically, a decrease in ΔpK a (donor … acceptor) can lead to proton release from the H-bond donor group toward the acceptor group, resulting in shifts in the vibrational frequencies of the protein environment. These findings suggest that changes in the stretching vibrational frequencies, in particular ν O-D (donor), can be used to monitor proton transfer in protein environments., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

Using the X-ray free-electron laser (XFEL) structures of the photosynthetic reaction center from Blastochloris viridis that show light-induced time-dependent structural changes (Dods et al., (2021) Nature 589 , 310-314), we investigated time-dependent changes in the energetics of the electron-transfer pathway, considering the entire protein environment of the protein structures and titrating the redox-active sites in the presence of all fully equilibrated titratable residues. In the dark and charge separation intermediate structures, the calculated redox potential ( E m and H L and H L and H M and H M ). However, the stabilization of the charge-separated [P L P M H •+ H L (H • - state owing to protein reorganization is not clearly observed in the E m H L state) structure. Furthermore, the expected chlorin ring deformation upon formation of H L (saddling mode) is absent in the H M ] •+ H L • - state) structure. Furthermore, the expected chlorin ring deformation upon formation of H L • - (saddling mode) is absent in the H L geometry of the original 5 ps structure. These findings suggest that there is no clear link between the time-dependent structural changes and the electron-transfer events in the XFEL structures., Competing Interests: GN, YS, KS, HI No competing interests declared, (© 2023, Nishikawa et al.)

The high-resolution structure of heliorhodopsin crystallized at low pH reveals the presence of a planar triangle molecule, acetate, in the inner water cavity. Here, we investigate how the acetate molecule is stabilized at the counterion Glu107 moiety, using molecular dynamics (MD) simulations and a quantum mechanical/molecular mechanical (QM/MM) approach. QM/MM calculations indicate that the density is best described as acetate among triangle acids, including nitric acid and bicarbonate. The calculated protonation state indicates that protonated acetate donates an H-bond to deprotonated Glu107 in the low-pH crystal structure. The observed red-shift of ∼30 nm in the absorption wavelength with p K a ≈ 4 is likely due to the His23/His80 protonation, rather than the Glu107 protonation. MD simulations also show that acetate can exist at the Glu107 moiety only when it is protonated. When ionized, acetate is released from the Glu107 moiety via Asn101 at the channel bottleneck and Arg91 on the intracellular protein surface. These observations could explain how acetate binds at low pH and releases at high pH.

In photosystem II (PSII), one-electron oxidation of the most stable oxidation state of the Mn 4 CaO 5 cluster (S 1 ) leads to formation of two distinct states, the open-cubane S 2 conformation [Mn1(III)Mn2(IV)Mn3(IV)Mn4(IV)] with low spin and the closed-cubane S 2 conformation [Mn1(IV)Mn2(IV)Mn3(IV)Mn4(III)] with high spin. In electron paramagnetic resonance (EPR) spectroscopy, the open-cubane S 2 conformation exhibits a g = 2 multiline signal. However, its protonation state remains unclear. Here, we investigated the protonation state of the open-cubane S 2 conformation by calculating exchange couplings in the presence of the PSII protein environment and simulating the pulsed electron-electron double resonance (PELDOR). When a ligand water molecule, which forms an H-bond with D1-Asp61 (W1), is deprotonated at dangling Mn4(IV), the first-exited energy (34 cm -1 ) in manifold spin excited states aligns with the observed value in temperature-dependent pulsed EPR analyses, and the PELDOR signal is best reproduced. Consequently, the g = 2 multiline signal observed in EPR corresponds to the open-cubane S 2 conformation with the deprotonated W1 (OH - )., (© The Author(s) 2023. Published by Oxford University Press on behalf of National Academy of Sciences.)

Manganese (Mn) serves as the catalytic center for water splitting in photosystem II (PSII), despite the abundance of iron (Fe) on earth. As a first step toward why Mn and not Fe is employed by Nature in the water oxidation catalyst, we investigated the Fe 4 CaO 5 cluster in the PSII protein environment using a quantum mechanical/molecular mechanical (QM/MM) approach, assuming an equivalence between Mn(III/IV) and Fe(II/III). Substituting Mn with Fe resulted in the protonation of μ -oxo bridges at sites O2 and O3 by Arg357 and D1-His337, respectively. While the Mn 4 CaO 5 cluster exhibits distinct open- and closed-cubane S 2 conformations, the Fe 4 CaO 5 cluster lacks this variability due to an equal spin distribution over sites Fe1 and Fe4. The absence of a low-barrier H-bond between a ligand water molecule (W1) and D1-Asp61 in the Fe 4 CaO 5 cluster may underlie its incapability for ligand water deprotonation, highlighting the relevance of Mn in natural water splitting., Competing Interests: The authors declare no competing interest., (© 2023 The Authors.)

The electron transfer pathways in type I photosynthetic reaction centers, such as photosystem I (PSI) and reaction centers from green sulfur bacteria (GsbRC), are terminated by two Fe 4 S 4 clusters, F A and F B . The protein structures are the basis of understanding how the protein electrostatic environment interacts with the Fe 4 S 4 clusters and facilitates electron transfer. Using the protein structures, we calculated the redox potential ( E m ) values for F A and F B in PSI and GsbRC, solving the linear Poisson-Boltzmann equation. The F A -to-F B electron transfer is energetically downhill in the cyanobacterial PSI structure, while it is isoenergetic in the plant PSI structure. The discrepancy arises from differences in the electrostatic influences of conserved residues, including PsaC-Lys51 and PsaC-Arg52, located near F A . The F A -to-F B electron transfer is slightly downhill in the GsbRC structure. E m (F A ) and E m (F B ) exhibit similar levels upon isolation of the membrane-extrinsic PsaC and PscB subunits from the PSI and GsbRC reaction centers, respectively. The binding of the membrane-extrinsic subunit at the heterodimeric/homodimeric reaction center plays a key role in tuning E m (F A ) and E m (F B ).

In photosynthetic reaction centers from purple bacteria (PbRCs), light-induced charge separation leads to the reduction of the terminal electron acceptor quinone, Q B . The reduction of Q B to Q B •- is followed by protonation via Asp-L213 and Ser-L223 in PbRC from Rhodobacter sphaeroides . However, Asp-L213 is replaced with nontitratable Asn-L222 and Asn-L213 in PbRCs from Thermochromatium tepidum , respectively. Here, we investigated the energetics of proton transfer along the asparagine-involved H-bond network using a quantum mechanical/molecular mechanical approach. The potential energy profile for the H-bond between H Blastochloris viridis , respectively. Here, we investigated the energetics of proton transfer along the asparagine-involved H-bond network using a quantum mechanical/molecular mechanical approach. The potential energy profile for the H-bond between H 3 O + and the carbonyl O site of Asn-L222 shows that the proton is predominantly localized at the Asn-L222 moiety in the T. tepidum site toward Ser-L232 via tautomerization suffers from the energy barrier. Upon reorientation of Asn-L222, the enol -OH site forms a short low-barrier H-bond with Ser-L232, facilitating protonation of Q 2 site toward Ser-L232 via tautomerization suffers from the energy barrier. Upon reorientation of Asn-L222, the enol -OH site forms a short low-barrier H-bond with Ser-L232, facilitating protonation of Q B •- in a Grotthuss-like mechanism. This is a basis of how asparagine or glutamine side chains function as acceptors/donors in proton transfer pathways.

In photosystem II (PSII), the O3 and O4 sites of the Mn 4 CaO 5 cluster form hydrogen bonds with D1-His337 and a water molecule (W539), respectively. The low-dose X-ray structure shows that these hydrogen bond distances differ between the two homogeneous monomer units (A and B) [Tanaka et al., J. Am Chem. Soc. 2017, 139, 1718]. We investigated the origin of the differences using a quantum mechanical/molecular mechanical (QM/MM) approach. QM/MM calculations show that the short O4-O W539 hydrogen bond (~2.5 Å) of the B monomer is reproduced when O4 is protonated in the S 1 state. The short O3-Nε His337 hydrogen bond of the A monomer is due to the formation of a low-barrier hydrogen bond between O3 and doubly-protonated D1-His337 in the overreduced states (S -1 or S -2 ). It seems plausible that the oxidation state differs between the two monomer units in the crystal., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Saito, Nakao and Ishikita.)

Ca 2+ , which provides binding sites for ligand water molecules W3 and W4 in the Mn 4 CaO 5 cluster, is a prerequisite for O 2 evolution in photosystem II (PSII). We report structural changes in the H-bond network and the catalytic cluster itself upon the replacement of Ca 2+ with other alkaline earth metals, using a quantum mechanical/molecular mechanical approach. The small radius of Mg 2+ makes W3 donate an H-bond to D1-Glu189 in Mg 2+ -PSII. If an additional water molecule binds at the large surface of Ba 2+ , it donates H-bonds to D1-Glu189 and the ligand water molecule at the dangling Mn, altering the H-bond network. The potential energy profiles of the H-bond between D1-Tyr161 (TyrZ) and D1-His190 and the interconversion between the open- and closed-cubane S 2 conformations remain substantially unaltered upon the replacement of Ca 2+ . Remarkably, the O5⋯Ca 2+ distance is shortest among all O5⋯metal distances irrespective of the radius being larger than that of Mg 2+ . Furthermore, Ca 2+ is the only alkaline earth metal that equalizes the O5⋯metal and O2⋯metal distances and facilitates the formation of the symmetric cubane structure.

Photosynthetic reaction centers from heliobacteria (HbRC) and green sulfur bacteria (GsbRC) are homodimeric proteins and share a common ancestor with photosystem I (PSI), classified as type I reaction centers. Using the HbRC crystal structure, we calculated the redox potential ( E m ) values in the electron-transfer branches, solving the linear Poisson-Boltzmann equation and considering the protonation states of all titratable sites in the entire protein-pigment complex. E m (A -1 ) for bacteriochlorophyll g at the secondary site in HbRC (-1157 mV) is as low as E m (A -1 ) for chlorophyll a in PSI (-1173 mV). E m (A 0 /HbRC) is at the same level as E m (A 0 /GsbRC) and is 200 mV higher than E m (A 0 /PSI) due to the replacement of PsaA-Trp697/PsaB-Trp677 in PSI with PshA-Arg554 in HbRC. In contrast, E m (F X ) for the Fe 4 S 4 cluster in HbRC (-420 mV) is significantly higher than E m (F X ) in GsbRC (-719 mV) and PSI (-705 mV) due to the absence of acidic residues that correspond to PscA-Asp634 in GsbRC and PsaB-Asp575 in PSI. It seems likely that type I reaction centers have evolved, adopting (bacterio)chlorophylls suitable for their light environments while maintaining electron-transfer cascades.

We evaluated excitation energy transfer (EET) coupling (J) between all pairs of chlorophylls (Chls) and pheophytins (Pheos) in the protein environment of photosystem II based on the time-dependent density functional theory with a quantum mechanical/molecular mechanics approach. In the reaction center, the EET coupling between Chls P D1 and P D2 is weaker (|J(P D1 /P D2 )| = 79 cm -1 ), irrespective of a short edge-to-edge distance of 3.6 Å (Mg-to-Mg distance of 8.1 Å), than the couplings between P D1 and the accessory Chl D1 (|J(P D1 /Chl D2 )| = 104 cm -1 ) and between P D2 and Chl D2 (|J(P D2 /Chl D1 )| = 101 cm -1 ), suggesting that P D1 and P D2 are two monomeric Chls rather than a "special pair". There exist strongly coupled Chl pairs (|J| > ∼100 cm -1 ) in the CP47 and CP43 core antennas, which may be candidates for the red-shifted Chls observed in spectroscopic studies. In CP47 and CP43, Chls ligated to CP47-His26 and CP43-His56, which are located in the middle layer of the thylakoid membrane, play a role in the "hub" that mediates the EET from the lumenal to stromal layers. In the stromal layer, Chls ligated to CP47-His466, CP43-His441, and CP43-His444 mediate the EET from CP47 to Chl D2 /Pheo D2 and from CP43 to Chl D1 /Pheo D1 in the reaction center. Thus, the excitation energy from both CP47 and CP43 can always be utilized for the charge-separation reaction in the reaction center., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

Diatoms can use light in the blue-green region because they have chlorophyll c (Chl c ) in light-harvesting antenna proteins, fucoxanthin and chlorophyll a / c -binding protein (FCP). Chl c has a protonatable acrylate group (-CH═CH-COOH/COO - ) conjugated to the porphyrin ring. As the absorption wavelength of Chl c changes upon the protonation of the acrylate group, Chl c is a candidate component that is responsible for photoprotection in diatoms, which switches the FCP function between light-harvesting and energy-dissipation modes depending on the light intensity. Here, we investigate the mechanism by which the absorption wavelength of Chl c changes owing to the change in the protonation state of the acrylate group, using a quantum mechanical/molecular mechanical approach. The calculated absorption wavelength of the Soret band of protonated Chl c is ∼25 nm longer than that of deprotonated Chl c , which is due to the delocalization of the lowest (LUMO) and second lowest (LUMO+1) unoccupied molecular orbitals toward the acrylate group. These results suggest that in FCP, the decrease in pH on the lumenal side under high-light conditions leads to protonation of Chl c and thereby a red shift in the absorption wavelength.

The electron transfer from the oxygen-evolving Mn 4 CaO 5 cluster to the electron acceptor D1-Tyr161 (TyrZ) is a prerequisite for water oxidation and O 2 evolution. Here, we analyzed the electronic coupling in the rate-limiting electron-transfer transitions using a combined quantum mechanical/molecular mechanical/polarizable continuum model approach. In the S 0 to S 1 transition, the electronic coupling between the electron-donor Mn3(III) and TyrZ is small (2 meV). In contrast, the electronic coupling between the dangling Mn4(III) and TyrZ is significantly large (172 meV), which suggests that the electron transfer proceeds from Mn3(III) to TyrZ via Mn4(III). In the S 1 to S 2 transition, the electronic coupling between Mn4(III) and TyrZ is also larger (124 meV) than that between Mn1(III) and TyrZ (1 meV), which favors the formation of the open-cubane S 2 conformation with Mn4(IV) over the formation of the closed-cubane S 2 conformation with Mn1(IV). In the S 0 to S 1 and S 1 to S 2 transitions, the Mn4 d -orbital and the TyrZ π-orbital are hybridized via D1-Asp170, which suggests that D1-Asp170 commonly provides a dominant electron-transfer route.

Aberrant activation of the hypoxia-inducible transcription factor HIF-1 and dysfunction of the tumor suppressor p53 have been reported to induce malignant phenotypes and therapy resistance of cancers. However, their mechanistic and functional relationship remains largely unknown. Here, we reveal a mechanism by which p53 deficiency triggers the activation of HIF-1-dependent hypoxia signaling and identify zinc finger and BTB domain-containing protein 2 (ZBTB2) as an important mediator. ZBTB2 forms homodimers via its N-terminus region and increases the transactivation activity of HIF-1 only when functional p53 is absent. The ZBTB2 homodimer facilitates invasion, distant metastasis, and growth of p53-deficient, but not p53-proficient, cancers. The intratumoral expression levels of ZBTB2 are associated with poor prognosis in lung cancer patients. ZBTB2 N-terminus-mimetic polypeptides competitively inhibit ZBTB2 homodimerization and significantly suppress the ZBTB2-HIF-1 axis, leading to antitumor effects. Our data reveal an important link between aberrant activation of hypoxia signaling and loss of a tumor suppressor and provide a rationale for targeting a key mediator, ZBTB2, to suppress cancer aggressiveness., (© 2022 The Authors.)

Bacteriorhodopsin, a light-driven proton pump, alters the absorption wavelengths in the range of 410-617 nm during the photocycle. Here, we report the absorption wavelengths, calculated using 12 bacteriorhodopsin crystal structures (including the BR, BR 13- cis , J, K 0 , K E , K L , L, M, N, and O state structures) and a combined quantum mechanical/molecular mechanical/polarizable continuum model (QM/MM/PCM) approach. The QM/MM/PCM calculations reproduced the experimentally measured absorption wavelengths with a standard deviation of 4 nm. The shifts in the absorption wavelengths can be explained mainly by the following four factors: (i) retinal Schiff base deformation/twist induced by the protein environment, leading to a decrease in the electrostatic interaction between the protein environment and the retinal Schiff base; (ii) changes in the protonation state of the protein environment, directly altering the electrostatic interaction between the protein environment and the retinal Schiff base; (iii) changes in the protonation state; or (iv) isomerization of the retinal Schiff base, where the absorption wavelengths of the isomers originally differ.

Heliorhodopsin releases a proton from the Schiff base during the L-state to M-state transition but not toward the protein bulk surface. Here we investigate proton transfer and induced structural changes along the H-bond network in heliorhodopsin using a quantum mechanical/molecular mechanical approach and molecular dynamics simulations. Light-induced proton transfer could occur from the Schiff base toward Glu107, reorienting Ser76, followed by subsequent proton transfer toward His80. His80 protonation induces the reorientation of Trp246 on the extracellular surface, originating from the electrostatic interaction that propagates along the transmembrane H-bond network [His80…His23…H 2 O [H23/Q26] …Gln26…Trp246] over a distance of 15 Å. Furthermore, it induces structural fluctuation on the intracellular side in the H-bond network [His80…Asn16…Tyr92…Glu230…Arg104…Glu149], opening the inner cavity at the Tyr92 moiety. These may be a basis of how light-induced proton transfer causes conformational changes during the M-state to O-state transition., (© 2022. The Author(s).)

In photosynthetic reaction centers from purple bacteria (PbRCs) and photosystem II (PSII), the photoinduced charge separation is terminated by an electron transfer between the primary (Q A ) and secondary (Q B ) quinones. Here, we investigate the electron transfer route, calculating the superexchange coupling ( H QA-QB ) for electron transfer from Q A to Q B in the protein environment. H QA-QB is significantly larger in PbRC than in PSII. In superexchange electron tunneling, the electron transfer via unoccupied molecular orbitals of the nonheme Fe complex (Q A → Fe → Q B ) is pronounced in PbRC, whereas the electron transfer via occupied molecular orbitals (Fe → Q B is caused by a water molecule that donates the H-bond to the ligand Glu-M234 in PbRC. The corresponding water molecule is absent in PSII due to the existence of D1-Tyr246. A → Fe) is pronounced in PSII. The significantly large H H-bond formation caused by an extension of the H-bond network, which facilitates charge delocalization over the Q QA-QB is caused by a water molecule that donates the H-bond to the ligand Glu-M234 in PbRC. The corresponding water molecule is absent in PSII due to the existence of D1-Tyr246. H QA-QB increases in response to the Ser-L223···Q B H-bond formation caused by an extension of the H-bond network, which facilitates charge delocalization over the Q B site. This explains the observed discrepancy in the Q A -to-Q B electron transfer between PbRC and PSII, despite their structural similarity.

Photosynthetic reaction centers from a green sulfur bacterium (GsbRC), the PscA/PscA proteins, and photosystem I (PSI), PsaA/PsaB proteins, share structural similarities. Here, we report the redox potential ( E m ) values of GsbRC by solving the linear Poisson-Boltzmann equation and considering the protonation states of all titratable sites in the entire GsbRC protein and identify the factors that shift the E m values with respect to PSI. The E m values for one-electron reduction of the accessory (A -1 ) and adjacent (A 0 ) chlorophylls in GsbRC are 100-250 mV higher than those in PSI, whereas the E m values for the Fe 4 S 4 cluster (F X ) are at the same level. The PsaA-Trp697/PsaB-Trp677 pair in PSI, which forms the A 1 -quinone binding site, is replaced with PscA-Arg638 in GsbRC. PsaB-Asp575 in PSI, which is responsible for the E m difference between A 1A and A 1B quinones in PSI, is absent in GsbRC. These discrepancies also contribute to the upshift in E m (A -1 ) and E m (A 0 ) in GsbRC with respect to PSI. It seems likely that the upshifted E m for chlorophylls in GsbRC ultimately originates from the characteristics of the electrostatic environment that corresponds to the A 1 site of PSI.

In photosystem II (PSII), one-electron oxidation of the most stable state of the oxygen-evolving Mn 4 CaO 5 cluster (S 1 ) leads to the S 2 state formation, Mn1(III)Mn2(IV)Mn3(IV)Mn4(IV) (open-cubane S 2 ) or Mn1(IV)Mn2(IV)Mn3(IV)Mn4(III) (closed-cubane S 2 ). In electron paramagnetic resonance (EPR) spectroscopy, the g  = 4.1 signal is not observed in cyanobacterial PSII but in plant PSII, whereas the g  = 4.8 signal is observed in cyanobacterial PSII and extrinsic-subunit-depleted plant PSII. Here, we investigated the closed-cubane S 2 conformation, a candidate for a higher spin configuration that accounts for g  > 4.1 EPR signal, considering all pairwise exchange couplings in the PSII protein environment (i.e. instead of considering only a single exchange coupling between the [Mn 3 (CaO 4 )] cubane region and the dangling Mn4 site). Only when a ligand water molecule that forms an H-bond with D1-Asp61 (W1) is deprotonated at dangling Mn4(IV), the g  = 4.1 EPR spectra can be reproduced using the cyanobacterial PSII crystal structure. The closed-cubane S 2 is less stable than the open-cubane S 2 in cyanobacterial PSII, which may explain why the g  = 4.1 EPR signal is absent in cyanobacterial PSII., (© The Author(s) 2022. Published by Oxford University Press on behalf of the National Academy of Sciences.)

Self-assembled coordination cages composed of metal cations and ligands can enhance the hydrolysis of non-covalently trapped amides in mild conditions as demonstrated in recent experiments. Here, we reveal the mechanism that accelerates base-catalyzed amide hydrolysis inside the octahedral coordination cage, by means of a quantum mechanics/molecular mechanics/polarizable continuum model. The calculated activation barrier of the nucleophilic OH - addition to a planar diaryl amide drastically decreases in the cage because of mechanical bond-twisting due to host-guest π-stacking. By contrast, the OH - addition to an N -acylindole, which possesses a twisted amide bond in bulk water, is not enhanced in the cage. Even though the cage hinders OH - collisions with the confined amide, the cage can twist the dihedral angle of the planar amide so as to mimic the transition state of OH - addition.

Photo-induced charge separation, which is terminated by electron transfer from the primary quinone Q A to the secondary quinone Q B , provides the driving force for O 2 evolution in photosystem II (PSII). However, the backward charge recombination using the same electron-transfer pathway leads to the triplet chlorophyll formation, generating harmful singlet-oxygen species. Here, we investigated the molecular mechanism of proton-mediated Q A stabilization. Quantum mechanical/molecular mechanical (QM/MM) calculations show that in response to the loss of the bicarbonate ligand, a low-barrier H-bond forms between D2-His214 and Q ⋅- stabilization. Quantum mechanical/molecular mechanical (QM/MM) calculations show that in response to the loss of the bicarbonate ligand, a low-barrier H-bond forms between D2-His214 and Q A ⋅- . The migration of the proton from D2-His214 toward Q A ⋅- stabilizes Q A ⋅- H 2+ site is an energetically uphill process, whereas the bidentate-to-monodentate reorientation is almost isoenergetic. These suggest that the bicarbonate protonation and decomposition may be a basis of the mechanism of photoprotection via Q A ⋅- /Q A H ⋅ stabilization, increasing the Q A redox potential and activating a charge-recombination pathway that does not generate the harmful singlet oxygen., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Sugo and Ishikita.)

In photosystem II (PSII) and photosynthetic reaction centers from purple bacteria (PbRC), the electron released from the electronically excited chlorophyll is transferred to the terminal electron acceptor quinone, Q B . Q B accepts two electrons and two protons before leaving the protein. We investigated the molecular mechanism of quinone exchange in PSII, conducting molecular dynamics (MD) simulations and quantum mechanical/molecular mechanical (QM/MM) calculations. MD simulations suggest that the release of Q B leads to the transformation of the short helix (D1-Phe260 to D1-Ser264), which is adjacent to the stromal helix de (D1-Asn247 to D1-Ile259), into a loop and to the formation of a water-intake channel. Water molecules enter the Q B binding pocket via the channel and form an H-bond network. QM/MM calculations indicate that the H-bond network serves as a proton-transfer pathway for the reprotonation of D1-His215, the proton donor during Q B H - /Q B H 2 conversion. Together with the absence of the corresponding short helix but the presence of Glu-L212 in PbRC, it seems likely that the two type-II reaction centers undergo quinone exchange via different mechanisms.

Photosystem II (PSII) is a multisubunit membrane protein complex that catalyzes light-driven oxidation of water to molecular oxygen. The chloride ion (Cl - ) has long been known as an essential cofactor for oxygen evolution by PSII, and two Cl - ions (Cl-1 and Cl-2) have been found to specifically bind near the Mn 4 CaO 5 cluster within the oxygen-evolving center (OEC). However, despite intensive studies on these Cl - ions, little is known about the function of Cl-2, the Cl - ion that is associated with the backbone nitrogens of D1-Asn338, D1-Phe339, and CP43-Glu354. In green plant PSII, the membrane extrinsic subunits-PsbP and PsbQ-are responsible for Cl - retention within the OEC. The Loop 4 region of PsbP, consisting of highly conserved residues Thr135-Gly142, is inserted close to Cl-2, but its importance has not been examined to date. Here, we investigated the importance of PsbP-Loop 4 using spinach PSII membranes reconstituted with spinach PsbP proteins harboring mutations in this region. Mutations in PsbP-Loop 4 had remarkable effects on the rate of oxygen evolution by PSII. Moreover, we found that a specific mutation, PsbP-D139N, significantly enhances the oxygen-evolving activity in the absence of PsbQ, but not significantly in its presence. The D139N mutation increased the Cl - retention ability of PsbP and induced a unique structural change in the OEC, as indicated by light-induced Fourier transform infrared (FTIR) difference spectroscopy and theoretical calculations. Our findings provide insight into the functional significance of Cl-2 in the water-oxidizing reaction of PSII., (© The Author(s) 2022. Published by Oxford University Press on behalf of National Academy of Sciences.)

Identifying the p K a values of aspartic acid (Asp) and glutamic acid (Glu) in active sites is essential for understanding enzyme reaction mechanisms. In this study, we investigated the correlation between the C═O stretching vibrational frequency (ν C═O ) of protonated carboxylic acids and the p K a values using density functional theory calculations. In unsaturated carboxylic acids (e.g., benzoic acid analogues), ν C═O decreases as the p K increases (the positive correlation) as long as the structure of the H-bond network around the acid is identical. The negative/positive correlation between ν a increases (the negative correlation), whereas in saturated carboxylic acids (e.g., acetic acid analogues, Asp, and Glu), ν C═O increases as the p K a increases (the positive correlation) as long as the structure of the H-bond network around the acid is identical. The negative/positive correlation between ν C═O and p K a can be rationalized by the presence or absence of the C═C double bond. The p K a shift was estimated from the ν C═O shift of Asp and Glu in proteins on the basis of the negative correlation derived from benzoic acids. The previous estimations should be revisited by using the positive correlation derived in this study, as demonstrated by quantum mechanical/molecular mechanical calculations of ν C═O and electrostatic calculations of p K a on a key Asp85 in the proton-transfer pathway of bacteriorhodopsin.

In photosystem II (PSII), the second-lowest oxidation state (S 1 ) of the oxygen-evolving Mn 4 CaO 5 cluster is the most stable, as the radical form of the redox-active D2-Tyr160 is considered to be a candidate that accepts an electron from the lowest oxidation state (S 0 ) in the dark. Using quantum mechanical/molecular mechanical calculations, we investigated the redox potential ( E ) of TyrD and its H-bond partner, D2-His189. The potential energy profile indicates that the release of a proton from the TyrD...D2-His189 pair leads to the formation of a low-barrier H-bond. The m depends on the H E position along the low-barrier H-bond, e.g., 680 mV when the H m is at the D2-His189 moiety and 800 mV when the H + position along the low-barrier H-bond, e.g., 680 mV when the H + is at the D2-His189 moiety and 800 mV when the H + is at the TyrD moiety, which can explain why TyrD mediates both the S 0 to S 1 oxidation and the S 2 to S 1 reduction., Competing Interests: The authors declare no competing financial interest., (© 2022 The Authors. Published by American Chemical Society.)

Most low-potential Fe 4 S 4 clusters exist in the conserved binding sequence CxxCxxC (C n C n +3 C n +6 ). Fe(II) and Fe(III) at the first (C n ) and third (C n +6 ) cysteine ligand sites form a mixed-valence Fe 2.5+ ···Fe 2.5+ pair in the reduced Fe(II) 3 Fe(III) cluster. Here, we investigate the mechanism of how the conserved protein environment induces mixed-valence pair formation in the Fe 4 S 4 clusters, F X , F A , and F B in photosystem I, using a quantum mechanical/molecular mechanical approach. Exchange coupling between Fe sites is predominantly determined by the shape of the Fe 4 S 4 cluster, which is stabilized by the preorganized protein electrostatic environment. The backbone NH and CO groups in the conserved CxxCxxC and adjacent helix regions orient along the Fe C n ···Fe C( n +6) axis, generating an electric field and stabilizing the Fe C n (II)Fe C( n +6) (III) state in F A and F B . The overlap of the d orbitals via -S- (superexchange) is observed for the single Fe C n (II)···Fe C( n +6) (III) pair, leading to the formation of the mixed-valence Fe 2.5+ ···Fe 2.5+ pair. In contrast, several superexchange Fe(II)···Fe(III) pairs are observed in F X due to the highly symmetric pair of the CDGPGRGGTC sequences. This is likely the origin of F X serving as an electron acceptor in the two electron transfer branches.

In low-barrier hydrogen bonds (H-bonds), the p K values for the H-bond donor and acceptor moieties are nearly equal, whereas the redox potential values depend on the H a position. Spectroscopic details of low-barrier H-bonds remain unclear. Here, we report the absorption wavelength along low-barrier H-bonds in protein environments, using a quantum mechanical/molecular mechanical approach. Low-barrier H-bonds form between Glu46 and + position. Spectroscopic details of low-barrier H-bonds remain unclear. Here, we report the absorption wavelength along low-barrier H-bonds in protein environments, using a quantum mechanical/molecular mechanical approach. Low-barrier H-bonds form between Glu46 and p -coumaric acid ( p state of photoactive yellow protein and between Asp116 and the retinal Schiff base in the intermediate M-state of the sodium-pumping rhodopsin KR2. The H CW displacement of only ∼0.4 Å, which does not easily occur without low-barrier H-bonds, is responsible for the ∼50 nm-shift in the absorption wavelength. This may be a basis of how photoreceptor proteins have evolved to proceed photocycles using abundant protons.+ displacement of only ∼0.4 Å, which does not easily occur without low-barrier H-bonds, is responsible for the ∼50 nm-shift in the absorption wavelength. This may be a basis of how photoreceptor proteins have evolved to proceed photocycles using abundant protons., Competing Interests: The authors declare no competing interest., (© 2022 The Author(s).)

Dynamic nuclear polarization (DNP) is a cutting-edge technique that markedly enhances the detection sensitivity of molecules using nuclear magnetic resonance (NMR)/magnetic resonance imaging (MRI). This methodology enables real-time imaging of dynamic metabolic status in vivo using MRI. To expand the targetable metabolic reactions, there is a demand for developing exogenous, i.e., artificially designed, DNP-NMR molecular probes; however, complying with the requirements of practical DNP-NMR molecular probes is challenging because of the lack of established design guidelines. Here, we report Ala-[1- 13 C]Gly- d 2 -NMe 2 as a DNP-NMR molecular probe for in vivo detection of aminopeptidase N activity. We developed this probe rationally through precise structural investigation, calculation, biochemical assessment, and advanced molecular design to achieve rapid and detectable responses to enzyme activity in vivo. With the fabricated probe, we successfully detected enzymatic activity in vivo. This report presents a comprehensive approach for the development of artificially derived, practical DNP-NMR molecular probes through structure-guided molecular design.

In photosystem II (PSII), Cl - is a prerequisite for the second flash-induced oxidation of the Mn 4 CaO 5 cluster (the S 2 to S 3 transition). We report proton transfer from the substrate water molecule via D1-Asp61 and electron transfer via redox-active D1-Tyr161 (TyrZ) to the chlorophyll pair in Cl - -depleted PSII using a quantum mechanical/molecular mechanical approach. The low-barrier H-bond formation between the substrate water molecule and D1-Asp61 remained unaffected upon the depletion of Cl - . However, the binding site, D2-Lys317, formed a salt bridge with D1-Asp61, leading to the inhibition of the subsequent proton transfer. Remarkably, the redox potential ( E m ) of S 2 /S 3 increased significantly, making electron transfer from S 2 to TyrZ energetically uphill, as observed in Ca 2+ -depleted PSII. The uphill electron transfer pathway was induced by the significant increase in E m (S 2 /S 3 ) caused by the loss of charge compensation for D2-Lys317 upon the depletion of Cl - , whereas it was induced by the significant decrease in E m (TyrZ) caused by the rearrangement of the water molecules at the Ca 2+ binding moiety upon the depletion of Ca 2+ .

Anion channelrhodopsin from Guillardia theta ( Gt ACR1) has Asp234 (3.2 Å) and Glu68 (5.3 Å) near the protonated Schiff base. Here, we investigate mutant Gt ACR1s (e.g., E68Q/D234N) expressed in HEK293 cells. The influence of the acidic residues on the absorption wavelengths was also analyzed using a quantum mechanical/molecular mechanical approach. The calculated protonation pattern indicates that Asp234 is deprotonated and Glu68 is protonated in the original crystal structures. The D234E mutation and the E68Q/D234N mutation shorten and lengthen the measured and calculated absorption wavelengths, respectively, which suggests that Asp234 is deprotonated in the wild-type Gt ACR1. Molecular dynamics simulations show that upon mutation of deprotonated Asp234 to asparagine, deprotonated Glu68 reorients toward the Schiff base and the calculated absorption wavelength remains unchanged. The formation of the proton transfer pathway via Asp234 toward Glu68 and the disconnection of the anion conducting channel are likely a basis of the gating mechanism., Competing Interests: MT, KK, SK, YS, HI No competing interests declared, (© 2021, Tsujimura et al.)

Rhodopsins act as photoreceptors with their chromophore retinal (vitamin-A aldehyde) and they regulate light-dependent biological functions. Archaerhodopsin-3 (AR3) is an outward proton pump that has been widely utilized as a tool for optogenetics, a method for controlling cellular activity by light. To characterize the retinal binding cavity of AR3, we synthesized a dimethyl phenylated retinal derivative, (2E,4E,6E,8E)-9-(2,6-Dimethylphenyl)-3,7-dimethylnona-2,4,6,8-tetraenal (DMP-retinal). QM/MM calculations suggested that DMP-retinal can be incorporated into the opsin of AR3 (archaeopsin-3, AO3). Thus, we introduced DMP-retinal into AO3 to obtain the non-natural holoprotein (AO3-DMP) and compared some molecular properties with those of AO3 with the natural A1-retinal (AO3-A1) or AR3. Light-induced pH change measurements revealed that AO3-DMP maintained slow outward proton pumping. Noteworthy, AO3-DMP had several significant changes in its molecular properties compared with AO3-A1 as follows; 1) spectroscopic measurements revealed that the absorption maximum was shifted from 556 to 508 nm and QM/MM calculations showed that the blue-shift was due to the significant increase in the HOMO-LUMO energy gap of the chromophore with the contribution of some residues around the chromophore, 2) time-resolved spectroscopic measurements revealed the photocycling rate was significantly decreased, and 3) kinetical spectroscopic measurements revealed the sensitivity of the chromophore binding Schiff base to attack by hydroxylamine was significantly increased. The QM/MM calculations show that a cavity space is present at the aromatic ring moiety in the AO3-DMP structure whereas it is absent at the corresponding β -ionone ring moiety in the AO3-A1 structure. We discuss these alterations of the difference in interaction between the natural A1-retinal and the DMP-retinal with binding cavity residues., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Tsuneishi, Takahashi, Tsujimura, Kojima, Ishikita, Takeuchi and Sudo.)

The mechanisms governing the long-range electron tunneling from the primary (Q A ) to secondary (Q B ) quinones in photosystem II are clarified by analyzing superexchange pathways through a nonheme Fe complex, using a quantum mechanics/molecular mechanics/polarizable continuum model approach. The electron tunneling rate is evaluated using the Marcus-Levich-Jortner theory considering electronic coupling, energy difference, and Franck-Condon factor. The superexchange Q A → Q B electron tunneling is enhanced by hybridized σ/σ* orbitals of histidines (D2-His214 and D1-His215) via penetration of the wave function into hydrogen bonds with both Q A and Q B . Despite a large energy gap to the intermediate states, the contributions of the histidine σ/σ* orbitals to the superexchange coupling are larger than those of π/π* orbitals. Fe 2+ is not an essential component for the Q A → Q B electron tunneling because hybridized histidine molecular orbitals can be coupled with both Q A and Q B simultaneously in the absence of Fe d orbitals.

Silicon (Si), the most abundant mineral element in the earth's crust, is taken up by plant roots in the form of silicic acid through Low silicon rice 1 (Lsi1). Lsi1 belongs to the Nodulin 26-like intrinsic protein subfamily in aquaporin and shows high selectivity for silicic acid. To uncover the structural basis for this high selectivity, here we show the crystal structure of the rice Lsi1 at a resolution of 1.8 Å. The structure reveals transmembrane helical orientations different from other aquaporins, characterized by a unique, widely opened, and hydrophilic selectivity filter (SF) composed of five residues. Our structural, functional, and theoretical investigations provide a solid structural basis for the Si uptake mechanism in plants, which will contribute to secure and sustainable rice production by manipulating Lsi1 selectivity for different metalloids., (© 2021. The Author(s).)

ATP11A translocates phosphatidylserine (PtdSer), but not phosphatidylcholine (PtdCho), from the outer to the inner leaflet of plasma membranes, thereby maintaining the asymmetric distribution of PtdSer. Here, we detected a de novo heterozygous point mutation of ATP11A in a patient with developmental delays and neurological deterioration. Mice carrying the corresponding mutation died perinatally of neurological disorders. This mutation caused an amino acid substitution (Q84E) in the first transmembrane segment of ATP11A, and mutant ATP11A flipped PtdCho. Molecular dynamics simulations revealed that the mutation allowed PtdCho binding at the substrate entry site. Aberrant PtdCho flipping markedly decreased the concentration of PtdCho in the outer leaflet of plasma membranes, whereas sphingomyelin (SM) concentrations in the outer leaflet increased. This change in the distribution of phospholipids altered cell characteristics, including cell growth, cholesterol homeostasis, and sensitivity to sphingomyelinase. Matrix-assisted laser desorption ionization-imaging mass spectrometry (MALDI-IMS) showed a marked increase of SM levels in the brains of Q84E-knockin mouse embryos. These results provide insights into the physiological importance of the substrate specificity of plasma membrane flippases for the proper distribution of PtdCho and SM.

In photosystem I, two electron-transfer pathways via quinones (A 1A and A 1B ) are merged at the iron-sulfur Fe 4 S 4 cluster F X into a single pathway toward the other two Fe 4 S 4 clusters F A and F B . Using a quantum mechanical/molecular mechanical approach, we identify the redox-active Fe sites in the clusters. In F A and F B , the Fe site, which does not belong to the CxxCxxCxxxCP motif, serves as an electron acceptor/donor. F X has two independent electron acceptor Fe sites for A- and B-branch electron transfers, depending on the Asp-B575 protonation state, which causes the A 1A -to-F X electron transfer to be uphill and the A 1B -to-F X electron transfer to be downhill. The two asymmetric electron-transfer pathways from A 1 to F X and the separation of the electron acceptor and donor Fe sites are likely associated with the specific role of F X in merging the two electron transfer pathways into the single pathway.

In photosynthetic reaction centers from purple bacteria (PbRCs) from Rhodobacter sphaeroides , the secondary quinone Q B accepts two electrons and two protons via electron-coupled proton transfer (PT). Here, we identify PT pathways that proceed toward the Q B binding site, using a quantum mechanical/molecular mechanical approach. As the first electron is transferred to Q B , the formation of the Grotthuss-like pre-PT H-bond network is observed along Asp-L213, Ser-L223, and the distal Q B carbonyl O site. As the second electron is transferred, the formation of a low-barrier H-bond is observed between His-L190 at Fe and the proximal Q B carbonyl O site, which facilitates the second PT. As Q B H 2 leaves PbRC, a chain of water molecules connects protonated Glu-L212 and deprotonated His-L190 forms, which serves as a pathway for the His-L190 reprotonation. The findings of the second pathway, which does not involve Glu-L212, and the third pathway, which proceeds from Glu-L212 to His-L190, provide a mechanism for PT commonly used among PbRCs., Competing Interests: The authors declare no competing interest., (Copyright © 2021 the Author(s). Published by PNAS.)