Fluctuating Atlantic inflows modulate Arctic atlantification.

Enhanced warm, salty subarctic inflows drive high-latitude atlantification, which weakens oceanic stratification, amplifies heat fluxes, and reduces sea ice. In this work, we show that the atmospheric Arctic Dipole (AD) associated with anticyclonic winds over North America and cyclonic winds over Eurasia modulates inflows from the North Atlantic across the Nordic Seas. The alternating AD phases create a "switchgear mechanism." From 2007 to 2021, this switchgear mechanism weakened northward inflows and enhanced sea-ice export across Fram Strait and increased inflows throughout the Barents Sea. By favoring stronger Arctic Ocean circulation, transferring freshwater into the Amerasian Basin, boosting stratification, and lowering oceanic heat fluxes there after 2007, AD+ contributed to slowing sea-ice loss. A transition to an AD- phase may accelerate the Arctic sea-ice decline, which would further change the Arctic climate system.

Multiscale Simulations of the Covalent Inhibition of the SARS-CoV-2 Main Protease: Four Compounds and Three Reaction Mechanisms.

We report the results of computational modeling of the reactions of the SARS-CoV-2 main protease (MPro) with four potential covalent inhibitors. Two of them, carmofur and nirmatrelvir, have shown experimentally the ability to inhibit MPro. Two other compounds, X77A and X77C, were designed computationally in this work. They were derived from the structure of X77, a non-covalent inhibitor forming a tight surface complex with MPro. We modified the X77 structure by introducing warheads capable of reacting with the catalytic cysteine residue in the MPro active site. The reaction mechanisms of the four molecules with MPro were investigated by quantum mechanics/molecular mechanics (QM/MM) simulations. The results show that all four compounds form covalent adducts with the catalytic cysteine Cys 145 of MPro. From the chemical perspective, the reactions of these four molecules with MPro follow three distinct mechanisms. The reactions are initiated by a nucleophilic attack of the thiolate group of the deprotonated cysteine residue from the catalytic dyad Cys145-His41 of MPro. In the case of carmofur and X77A, the covalent binding of the thiolate to the ligand is accompanied by the formation of the fluoro-uracil leaving group. The reaction with X77C follows the nucleophilic aromatic substitution SNAr mechanism. The reaction of MPro with nirmatrelvir (which has a reactive nitrile group) leads to the formation of a covalent thioimidate adduct with the thiolate of the Cys145 residue in the enzyme active site. Our results contribute to the ongoing search for efficient inhibitors of the SARS-CoV-2 enzymes.

Modeling Light-Induced Chromophore Hydration in the Reversibly Photoswitchable Fluorescent Protein Dreiklang.

We report the results of a computational study of the mechanism of the light-induced chemical reaction of chromophore hydration in the fluorescent protein Dreiklang, responsible for its switching from the fluorescent ON-state to the dark OFF-state. We explore the relief of the charge-transfer excited-state potential energy surface in the ON-state to locate minimum energy conical intersection points with the ground-state energy surface. Simulations of the further evolution of model systems allow us to characterize the ground-state reaction intermediate tentatively suggested in the femtosecond studies of the light-induced dynamics in Dreiklang and finally to arrive at the reaction product. The obtained results clarify the details of the photoswitching mechanism in Dreiklang, which is governed by the chemical modification of its chromophore.

Quantum-based Modeling of Protein-ligand Interaction: The Complex of RutA with Uracil and Molecular Oxygen.

Modern quantum-based methods are employed to model interaction of the flavin-dependent enzyme RutA with the uracil and oxygen molecules. This complex presents the structure of reactants for the chain of chemical reactions of monooxygenation in the enzyme active site, which is important in drug metabolism. In this case, application of quantum-based approaches is an essential issue, unlike conventional modeling of protein-ligand interaction with force fields using molecular mechanics and classical molecular dynamics methods. We focus on two difficult problems to characterize the structure of reactants in the RutA-FMN-O2 -uracil complex, where FMN stands for the flavin mononucleotide species. First, location of a small O2 molecule in the triplet spin state in the protein cavities is required. Second, positions of both ligands, O2 and uracil, must be specified in the active site with a comparable accuracy. We show that the methods of molecular dynamics with the interaction potentials of quantum mechanics/molecular mechanics theory (QM/MM MD) allow us to characterize this complex and, in addition, to surmise possible reaction mechanism of uracil oxygenation by RutA.

Protonation States of Molecular Groups in the Chromophore-Binding Site Modulate Properties of the Reversibly Switchable Fluorescent Protein rsEGFP2.

The role of protonation states of the chromophore and its neighboring amino acid side chains of the reversibly switching fluorescent protein rsEGFP2 upon photoswitching is characterized by molecular modeling methods. Numerous conformations of the chromophore-binding site in computationally derived model systems are obtained using the quantum chemistry and QM/MM approaches. Excitation energies are computed using the extended multiconfigurational quasidegenerate perturbation theory (XMCQDPT2). The obtained structures and absorption spectra allow us to provide an interpretation of the observed structural and spectral properties of rsEGFP2 in the active ON and inactive OFF states. The results demonstrate that in addition to the dominating anionic and neutral forms of the chromophore, the cationic and zwitterionic forms may participate in the photoswitching of rsEGFP2. Conformations and protonation forms of the Glu223 and His149 side chains in the chromophore-binding site play an essential role in stabilizing specific protonation forms of the chromophore.

Stalling chromophore synthesis of the fluorescent protein Venus reveals the molecular basis of the final oxidation step.

Fluorescent proteins (FPs) have revolutionised the life sciences, but the mechanism of chromophore maturation is still not fully understood. Here we show that incorporation of a photo-responsive non-canonical amino acid within the chromophore stalls maturation of Venus, a yellow FP, at an intermediate stage; a crystal structure indicates the presence of O2 located above a dehydrated enolate form of the imidazolone ring, close to the strictly conserved Gly67 that occupies a twisted conformation. His148 adopts an "open" conformation so forming a channel that allows O2 access to the immature chromophore. Absorbance spectroscopy supported by QM/MM simulations suggests that the first oxidation step involves formation of a hydroperoxyl intermediate in conjunction with dehydrogenation of the methylene bridge. A fully conjugated mature chromophore is formed through release of H2O2, both in vitro and in vivo. The possibility of interrupting and photochemically restarting chromophore maturation and the mechanistic insights open up new approaches for engineering optically controlled fluorescent proteins.

Modeling photophysical properties of the bacteriophytochrome-based fluorescent protein IFP1.4.

An enhanced interest in the phytochrome-based fluorescent proteins is explained by their ability to absorb and emit light in the far-red and infra-red regions particularly suitable for bioimaging. The fluorescent protein IFP1.4 was engineered from the chromophore-binding domain of a bacteriophytochrome in attempts to increase the fluorescence quantum yield. We report the results of simulations of structures in the ground S0 and excited S1 electronic states of IFP1.4 using the methods of quantum chemistry and quantum mechanics/molecular mechanics. We construct different protonation states of the biliverdin (BV) chromophore in the red-absorbing form of the protein by moving protons from the BV pyrrole rings to a suitable acceptor within the system and show that these structures are close in energy but differ by absorption bands. For the first time, we report structures of the minimum energy conical intersection points S1/S0 on the energy surfaces of BV in the protein environment and describe their connection to the local minima in the excited S1 state. These simulations allow us to characterize the deactivation routes in IFP1.4.

Interplay between Locally Excited and Charge Transfer States Governs the Photoswitching Mechanism in the Fluorescent Protein Dreiklang.

We present the results of high-level electronic structure and dynamics simulations of the photoactive protein Dreiklang. With the goal of understanding the details of the Dreiklang photocycle, we carefully characterize the excited states of the ON- and OFF-forms of Dreiklang. The key finding of our study is the existence of a low-lying excited state of a charge-transfer character in the neutral ON form and that population of this state, which is nearly isoenergetic with the locally excited bright state, initiates a series of steps that ultimately lead to the formation of the hydrated dark chromophore (OFF state). These results allow us to refine the mechanistic picture of Dreiklang's photocycle and photoactivation.

Arctic tidal current atlas.

Tidal and wind-driven near-inertial currents play a vital role in the changing Arctic climate and the marine ecosystems. We compiled 429 available moored current observations taken over the last two decades throughout the Arctic to assemble a pan-Arctic atlas of tidal band currents. The atlas contains different tidal current products designed for the analysis of tidal parameters from monthly to inter-annual time scales. On shorter time scales, wind-driven inertial currents cannot be analytically separated from semidiurnal tidal constituents. Thus, we include 10-30 h band-pass filtered currents, which include all semidiurnal and diurnal tidal constituents as well as wind-driven inertial currents for the analysis of high-frequency variability of ocean dynamics. This allows for a wide range of possible uses, including local case studies of baroclinic tidal currents, assessment of long-term trends in tidal band kinetic energy and Arctic-wide validation of ocean circulation models. This atlas may also be a valuable tool for resource management and industrial applications such as fisheries, navigation and offshore construction.

Structure of the Brain N-Acetylaspartate Biosynthetic Enzyme NAT8L Revealed by Computer Modeling.

We report the results of computational modeling of a three-dimensional all-atom structure of the membrane-associated protein encoded by the NAT8L gene, aspartate N-acetyltransferase, which is essential for brain synthesis of N-acetyl-l-aspartate (NAA). The lack of experimentally derived three-dimensional structures of NAT8L poses one of the obstacles in studies of the mechanism of NAA formation and understanding the precise role of NAA in neurological disorders. We apply a computational protocol employing the contact map prediction, ab initio folding, homology modeling, and refinement to obtain a structure of NAT8L with the aspartate and acetyl coenzyme A cofactors in the protein molecule. To verify the computational protocol, we check its predictive power by reproducing the crystal structure of a related N-acetyltransferase domain, specifically, that from the bacterial N-acetylglutamate synthase. We show that the constructed NAT8L model correlates with structural features of the protein revealed in rare experimental studies. The obtained structure of the enzyme active site with the trapped reactants suggests a mechanism of the acetyl transfer upon NAA formation.

Computational Modeling Reveals the Mechanism of Fluorescent State Recovery in the Reversibly Photoswitchable Protein Dreiklang.

The unique properties of the photoswitchable protein Dreiklang are attributed to a reversible hydration/dehydration reaction at the imidazolinone ring of the chromophore. Recovery of the fluorescent state, which is associated with a chemical reaction of the chromophore's dehydration, is an important part of the photocycle of this protein. Here we characterize the fluorescent (ON) and nonfluorescent (OFF) states of Dreiklang and simulate the thermal recovery reaction OFF → ON using computational approaches. By using molecular modeling methods including the quantum mechanics/molecular mechanics (QM/MM) technique, we characterize the structures and spectra of the ON- and OFF-states. The results are consistent with available experimental data. The computed reaction profile explains the observed recovery reaction and clarifies the mechanism of chemical transformations in the chromophore-containing pocket in Dreiklang.

Improving the Design of the Triple-Decker Motif in Red Fluorescent Proteins.

We characterize computationally a red fluorescent protein (RFP) with the chromophore (Chro) sandwiched between two aromatic tyrosine rings in a triple-decker motif. According to the original proposal [ J. Phys. Chem. Lett. 2013 , 4 , 1743 ], such a tyrosine-chromophore-tyrosine π-stacked construct can be accommodated in the green fluorescent protein (GFP). A recent study [ ACS Chem. Biol. 2016 , 11 , 508 ] attempted to realize the triple-decker motif and obtained an RFP variant called mRojoA-VYGV with two tyrosine residues surrounding the chromophore. The crystal structure showed that only a tyrosine-chromophore pair was involved in π-stacking, whereas the second tyrosine was oriented perpendicularly, edge-to-face with respect to the chromophore. We propose a more promising variant of this RFP with a perfect triple-decker unit achieved by introducing additional mutations in mRojoA-VYGV. The structures and optical properties of model proteins based on the structures of mCherry and mRojoA are characterized computationally by QM(DFT)/MM. The electronic transitions in the protein-bound chromophores are computed by high-level quantum chemical methods. According to our calculations, the triple-decker chromophore unit in the new RFP variant is stable within the protein and its optical bands are red-shifted with respect to the parent mCherry and mRojoA species.

Greater role for Atlantic inflows on sea-ice loss in the Eurasian Basin of the Arctic Ocean.

Arctic sea-ice loss is a leading indicator of climate change and can be attributed, in large part, to atmospheric forcing. Here, we show that recent ice reductions, weakening of the halocline, and shoaling of the intermediate-depth Atlantic Water layer in the eastern Eurasian Basin have increased winter ventilation in the ocean interior, making this region structurally similar to that of the western Eurasian Basin. The associated enhanced release of oceanic heat has reduced winter sea-ice formation at a rate now comparable to losses from atmospheric thermodynamic forcing, thus explaining the recent reduction in sea-ice cover in the eastern Eurasian Basin. This encroaching "atlantification" of the Eurasian Basin represents an essential step toward a new Arctic climate state, with a substantially greater role for Atlantic inflows.

Everolimus-eluting stents stabilize plaque inflammation in vivo: assessment by intravascular fluorescence molecular imaging.

AIMS: Inflammation drives atherosclerosis complications and is a promising therapeutic target for plaque stabilization. At present, it is unknown whether local stenting approaches can stabilize plaque inflammation in vivo. Here, we investigate whether everolimus-eluting stents (EES) can locally suppress plaque inflammatory protease activity in vivo using intravascular near-infrared fluorescence (NIRF) molecular imaging. METHODS AND RESULTS: Balloon-injured, hyperlipidaemic rabbits with atherosclerosis received non-overlapping EES and bare metal stents (BMS) placement into the infrarenal aorta (n = 7 EES, n = 7 BMS, 3.5 mm diameter x 12 mm length). Four weeks later, rabbits received an injection of the cysteine protease-activatable NIRF imaging agent Prosense VM110. Twenty-four hours later, co-registered intravascular 2D NIRF, X-ray angiography and intravascular ultrasound imaging were performed. In vivo EES-stented plaques contained substantially reduced NIRF inflammatory protease activity compared with untreated plaques and BMS-stented plaques (P = 0.006). Ex vivo macroscopic NIRF imaging of plaque protease activity corroborated the in vivo results (P = 0.003). Histopathology analyses revealed that EES-treated plaques showed reduced neointimal and medial arterial macrophage and cathepsin B expression compared with unstented and BMS-treated plaques. CONCLUSIONS: EES-stenting stabilizes plaque inflammation as assessed by translational intravascular NIRF molecular imaging in vivo. These data further support that EES may provide a local approach for stabilizing inflamed plaques.

A Light-Induced Reaction with Oxygen Leads to Chromophore Decomposition and Irreversible Photobleaching in GFP-Type Proteins.

Photobleaching and photostability of proteins of the green fluorescent protein (GFP) family are crucially important for practical applications of these widely used biomarkers. On the basis of simulations, we propose a mechanism for irreversible bleaching in GFP-type proteins under intense light illumination. The key feature of the mechanism is a photoinduced reaction of the chromophore with molecular oxygen (O2) inside the protein barrel leading to the chromophore's decomposition. Using quantum mechanics/molecular mechanics (QM/MM) modeling we show that a model system comprising the protein-bound Chro(-) and O2 can be excited to an electronic state of the intermolecular charge-transfer (CT) character (Chro(•)···O2(-•)). Once in the CT state, the system undergoes a series of chemical reactions with low activation barriers resulting in the cleavage of the bridging bond between the phenolic and imidazolinone rings and disintegration of the chromophore.

First-principles characterization of the energy landscape and optical spectra of green fluorescent protein along the A→I→B proton transfer route.

Structures and optical spectra of the green fluorescent protein (GFP) forms along the proton transfer route A→I→B are characterized by first-principles calculations. We show that in the ground electronic state the structure representing the wild-type (wt) GFP with the neutral chromophore (A-form) is lowest in energy, whereas the systems with the anionic chromophore (B- and I-forms) are about 1 kcal/mol higher. In the S65T mutant, the structures with the anionic chromophore are significantly lower in energy than the systems with the neutral chromophore. The role of the nearby amino acid residues in the chromophore-containing pocket is re-examined. Calculations reveal that the structural differences between the I- and B-forms (the former has a slightly red-shifted absorption relative to the latter) are based not on the Thr203 orientation, but on the Glu222 position. In the case of wt-GFP, the hydrogen bond between the chromophore and the His148 residue stabilizes the structures with the deprotonated phenolic ring in the I- and B-forms. In the S65T mutant, concerted contributions from the His148 and Thr203 residues are responsible for a considerable energy gap between the lowest energy structure of the B type with the anionic chromophore from other structures.

Unusual emitting states of the kindling fluorescent protein: appearance of the cationic chromophore in the GFP family.

The kindling fluorescent protein (KFP), the Ala143Gly variant of the natural chromoprotein asFP595, is a prospective biomarker in live cells. Following the results of QM/MM calculations, we predict that excitation of the protein under certain conditions, favoring formation of KFP fractions with the neutral chromophore, should result in fluorescence from the cationic form of the chromophore which is unusual for the members of the green fluorescent protein family. Occurrence of the neutral form is due to a water wire connecting the chromophore with the exterior of the protein. Occurrence of the cationic form is due to the excited-state proton transfer from the conserved Glu215 to the imidazolinone ring nitrogen of the chromophore. The emission band from conformations with the trans cationic chromophore should be noticeably shifted to the blue side around 520 nm compared to the well-known red fluorescence around 600 nm arising from the cis anionic species.

Triple-Decker Motif for Red-Shifted Fluorescent Protein Mutants.

Among fluorescent proteins (FPs) used as genetically encoded fluorescent tags, the red-emitting FPs are of particular importance as suitable markers for deep tissue imaging. Using electronic structure calculations, we predict a new structural motif for achieving red-shifted absorption and emission in FPs from the GFP family. By introducing four point mutations, we arrive to the structure with the conventional anionic GFP chromophore sandwiched between two tyrosine residues. Contrary to the existing red FPs in which the red shift is due to extended conjugation of the chromophore, in the triple-decker motif, the chromophore is unmodified and the red shift is due to π-stacking interactions. The absorption/emission energies of the triple-decker FP are 2.25/2.16 eV, respectively, which amounts to shifts of ∼40 (absorption) and ∼25 nm (emission) relative to the parent species, the I form of wtGFP. Using a different structural motif based on a smaller chromophore may help to improve optical output of red FPs by reducing losses due to radiationless relaxation and photobleaching.

Recent oceanic changes in the Arctic in the context of long-term observations.

This synthesis study assesses recent changes of Arctic Ocean physical parameters using a unique collection of observations from the 2000s and places them in the context of long-term climate trends and variability. Our analysis demonstrates that the 2000s were an exceptional decade with extraordinary upper Arctic Ocean freshening and intermediate Atlantic water warming. We note that the Arctic Ocean is characterized by large amplitude multi-decadal variability in addition to a long-term trend, making the link of observed changes to climate drivers problematic. However, the exceptional magnitude of recent high-latitude changes (not only oceanic, but also ice and atmospheric) strongly suggests that these recent changes signify a potentially irreversible shift of the Arctic Ocean to a new climate state. These changes have important implications for the Arctic Ocean's marine ecosystem, especially those components that are dependent on sea ice or that have temperature-dependent sensitivities or thresholds. Addressing these and other questions requires a carefully orchestrated combination of sustained multidisciplinary observations and advanced modeling.

Trajectory of the Arctic as an integrated system.

Although much remains to be learned about the Arctic and its component processes, many of the most urgent scientific, engineering, and social questions can only be approached through a broader system perspective. Here, we address interactions between components of the Arctic system and assess feedbacks and the extent to which feedbacks (1) are now underway in the Arctic and (2) will shape the future trajectory of the Arctic system. We examine interdependent connections among atmospheric processes, oceanic processes, sea-ice dynamics, marine and terrestrial ecosystems, land surface stocks of carbon and water, glaciers and ice caps, and the Greenland ice sheet. Our emphasis on the interactions between components, both historical and anticipated, is targeted on the feedbacks, pathways, and processes that link these different components of the Arctic system. We present evidence that the physical components of the Arctic climate system are currently in extreme states, and that there is no indication that the system will deviate from this anomalous trajectory in the foreseeable future. The feedback for which the evidence of ongoing changes is most compelling is the surface albedo-temperature feedback, which is amplifying temperature changes over land (primarily in spring) and ocean (primarily in autumn-winter). Other feedbacks likely to emerge are those in which key processes include surface fluxes of trace gases, changes in the distribution of vegetation, changes in surface soil moisture, changes in atmospheric water vapor arising from higher temperatures and greater areas of open ocean, impacts of Arctic freshwater fluxes on the meridional overturning circulation of the ocean, and changes in Arctic clouds resulting from changes in water vapor content.