De novo design of proteins housing excitonically coupled chlorophyll special pairs.

Natural photosystems couple light harvesting to charge separation using a 'special pair' of chlorophyll molecules that accepts excitation energy from the antenna and initiates an electron-transfer cascade. To investigate the photophysics of special pairs independently of the complexities of native photosynthetic proteins, and as a first step toward creating synthetic photosystems for new energy conversion technologies, we designed C2-symmetric proteins that hold two chlorophyll molecules in closely juxtaposed arrangements. X-ray crystallography confirmed that one designed protein binds two chlorophylls in the same orientation as native special pairs, whereas a second designed protein positions them in a previously unseen geometry. Spectroscopy revealed that the chlorophylls are excitonically coupled, and fluorescence lifetime imaging demonstrated energy transfer. The cryo-electron microscopy structure of a designed 24-chlorophyll octahedral nanocage with a special pair on each edge closely matched the design model. The results suggest that the de novo design of artificial photosynthetic systems is within reach of current computational methods.

Generalized biomolecular modeling and design with RoseTTAFold All-Atom.

Deep-learning methods have revolutionized protein structure prediction and design but are presently limited to protein-only systems. We describe RoseTTAFold All-Atom (RFAA), which combines a residue-based representation of amino acids and DNA bases with an atomic representation of all other groups to model assemblies that contain proteins, nucleic acids, small molecules, metals, and covalent modifications, given their sequences and chemical structures. By fine-tuning on denoising tasks, we developed RFdiffusion All-Atom (RFdiffusionAA), which builds protein structures around small molecules. Starting from random distributions of amino acid residues surrounding target small molecules, we designed and experimentally validated, through crystallography and binding measurements, proteins that bind the cardiac disease therapeutic digoxigenin, the enzymatic cofactor heme, and the light-harvesting molecule bilin.

In memoriam Liv Hatle 1936-2023, pioneering echocardiologist.

Professor Liv Hatle died in June 2023. In Trondheim, Norway, in the mid-1970s she was the first cardiologist to be given access to a PEDOF Doppler ultrasound system for clinical examinations, which she used to investigate cardiovascular haemodynamics non-invasively. She went on to establish methods for estimating valve gradients, pulmonary arterial pressure, and left ventricular diastolic function, that are still used today in millions of patients worldwide.

Twisted Carotenoids Do Not Support Efficient Intramolecular Singlet Fission in the Orange Carotenoid Protein.

Singlet exciton fission is the spin-allowed generation of two triplet electronic excited states from a singlet state. Intramolecular singlet fission has been suggested to occur on individual carotenoid molecules within protein complexes provided that the conjugated backbone is twisted out of plane. However, this hypothesis has been forwarded only in protein complexes containing multiple carotenoids and bacteriochlorophylls in close contact. To test the hypothesis on twisted carotenoids in a "minimal" one-carotenoid system, we study the orange carotenoid protein (OCP). OCP exists in two forms: in its orange form (OCPo), the single bound carotenoid is twisted, whereas in its red form (OCPr), the carotenoid is planar. To enable room-temperature spectroscopy on canthaxanthin-binding OCPo and OCPr without laser-induced photoconversion, we trap them in a trehalose glass. Using transient absorption spectroscopy, we show that there is no evidence of long-lived triplet generation through intramolecular singlet fission despite the canthaxanthin twist in OCPo.

De novo design of energy transfer proteins housing excitonically coupled chlorophyll special pairs.

Natural photosystems couple light harvesting to charge separation using a "special pair" of chlorophyll molecules that accepts excitation energy from the antenna and initiates an electron-transfer cascade. To investigate the photophysics of special pairs independent of complexities of native photosynthetic proteins, and as a first step towards synthetic photosystems for new energy conversion technologies, we designed C2-symmetric proteins that precisely position chlorophyll dimers. X-ray crystallography shows that one designed protein binds two chlorophylls in a binding orientation matching native special pairs, while a second positions them in a previously unseen geometry. Spectroscopy reveals excitonic coupling, and fluorescence lifetime imaging demonstrates energy transfer. We designed special pair proteins to assemble into 24-chlorophyll octahedral nanocages; the design model and cryo-EM structure are nearly identical. The design accuracy and energy transfer function of these special pair proteins suggest that de novo design of artificial photosynthetic systems is within reach of current computational methods.

Zeta-Carotene Isomerase (Z-ISO) Is Required for Light-Independent Carotenoid Biosynthesis in the Cyanobacterium Synechocystis sp. PCC 6803.

Carotenoids are crucial photosynthetic pigments utilized for light harvesting, energy transfer, and photoprotection. Although most of the enzymes involved in carotenoid biosynthesis in chlorophototrophs are known, some are yet to be identified or fully characterized in certain organisms. A recently characterized enzyme in oxygenic phototrophs is 15-cis-zeta(ζ)-carotene isomerase (Z-ISO), which catalyzes the cis-to-trans isomerization of the central 15-15' cis double bond in 9,15,9'-tri-cis-ζ-carotene to produce 9,9'-di-cis-ζ-carotene during the four-step conversion of phytoene to lycopene. Z-ISO is a heme B-containing enzyme best studied in angiosperms. Homologs of Z-ISO are present in organisms that use the multi-enzyme poly-cis phytoene desaturation pathway, including algae and cyanobacteria, but appear to be absent in green bacteria. Here we confirm the identity of Z-ISO in the model unicellular cyanobacterium Synechocystis sp. PCC 6803 by showing that the protein encoded by the slr1599 open reading frame has ζ-carotene isomerase activity when produced in Escherichia coli. A Synechocystis Δslr1599 mutant synthesizes a normal quota of carotenoids when grown under illumination, where the photolabile 15-15' cis double bond of 9,15,9'-tri-cis-ζ-carotene is isomerized by light, but accumulates this intermediate and fails to produce 'mature' carotenoid species during light-activated heterotrophic growth, demonstrating the requirement of Z-ISO for carotenoid biosynthesis during periods of darkness. In the absence of a structure of Z-ISO, we analyze AlphaFold models of the Synechocystis, Zea mays (maize), and Arabidopsis thaliana enzymes, identifying putative protein ligands for the heme B cofactor and the substrate-binding site.

Engineering purple bacterial carotenoid biosynthesis to study the roles of carotenoids in light-harvesting complexes.

Carotenoids are important photosynthetic pigments that play key roles in light harvesting and energy transfer, photoprotection, and in the folding, assembly, and stabilization of light-harvesting pigment-protein complexes. The genetically tractable purple phototrophic bacteria have been useful for investigating the biosynthesis and function of photosynthetic pigments and cofactors, including carotenoids. Here, we give an overview of the roles of carotenoids in photosynthesis and of their biosynthesis, focusing on the extensively studied purple bacterium Rhodobacter sphaeroides as a model organism. We provide detailed procedures for manipulating carotenoid biosynthesis, and for the preparation and analysis of the light-harvesting and photosynthetic reaction center complexes that bind them. Using appropriate examples from the literature, we discuss how such approaches have enhanced our understanding of the biosynthesis of carotenoids and the photosynthesis-related functions of these fascinating molecules.

A concise history of echocardiography: timeline, pioneers, and landmark publications.

Echocardiography is less than 70 years old, and many major advances have occurred within living memory, but already some pioneering contributions may be overlooked. In order to consider what circumstances have been common to the most successful innovations, we have studied and here provide a timeline and summary of the most important developments in transthoracic and transoesophageal ultrasound imaging and Doppler techniques, as well as in intravascular ultrasound and imaging in paediatric cardiology. The entries are linked to a comprehensive list of first publications and to a collection of first-hand historical accounts published by early investigators. Review of the original manuscripts highlights that it is difficult to establish unequivocal precedence for many new imaging methods, since engineers were often working independently but simultaneously on similar problems. Many individuals who are prominently linked with particular developments were not the first in their field. Developments in echocardiography have been highly dependent on technological advances, and most likely to be successful when engineers and clinicians were able to collaborate with open exchange between centres and disciplines. As with many other new medical technologies, initial responses were sceptical and introduction into clinical practice required persistence and substantial energy from the first adopters. Current developments involve advances in software as much as in equipment, and progress will depend on continuing collaborations between engineers and clinical scientists, for example to identify unmet needs and to investigate the clinical impact of particular imaging approaches.

The terminal enzymes of (bacterio)chlorophyll biosynthesis.

(Bacterio)chlorophylls are modified tetrapyrroles that are used by phototrophic organisms to harvest solar energy, powering the metabolic processes that sustain most of the life on Earth. Biosynthesis of these pigments involves enzymatic modification of the side chains and oxidation state of a porphyrin precursor, modifications that differ by species and alter the absorption properties of the pigments. (Bacterio)chlorophylls are coordinated by proteins that form macromolecular assemblies to absorb light and transfer excitation energy to a special pair of redox-active (bacterio)chlorophyll molecules in the photosynthetic reaction centre. Assembly of these pigment-protein complexes is aided by an isoprenoid moiety esterified to the (bacterio)chlorin macrocycle, which anchors and stabilizes the pigments within their protein scaffolds. The reduction of the isoprenoid 'tail' and its addition to the macrocycle are the final stages in (bacterio)chlorophyll biosynthesis and are catalysed by two enzymes, geranylgeranyl reductase and (bacterio)chlorophyll synthase. These enzymes work in conjunction with photosynthetic complex assembly factors and the membrane biogenesis machinery to synchronize delivery of the pigments to the proteins that coordinate them. In this review, we summarize current understanding of the catalytic mechanism, substrate recognition and regulation of these crucial enzymes and their involvement in thylakoid biogenesis and photosystem repair in oxygenic phototrophs.

The Southern California Extracorporeal Membrane Oxygenation Consortium During the Coronavirus Disease 2019 Pandemic.

In March 2020, at the onset of the coronavirus disease 2019 (COVID-19) pandemic in the United States, the Southern California Extracorporeal Membrane Oxygenation (ECMO) Consortium was formed. The consortium included physicians and coordinators from the 4 ECMO centers in San Diego County. Guidelines were created to ensure that ECMO was delivered equitably and in a resource effective manner across the county during the pandemic. A biomedical ethicist reviewed the guidelines to ensure ECMO use would provide maximal community benefit of this limited resource. The San Diego County Health and Human Services Agency further incorporated the guidelines into its plans for the allocation of scarce resources. The consortium held weekly video conferences to review countywide ECMO capacity (including census and staffing), share data, and discuss clinical practices and difficult cases. Equipment exchanges between ECMO centers maximized regional capacity. From March 1 to November 30, 2020, consortium participants placed 97 patients on ECMO. No eligible patients were denied ECMO due to lack of resources or capacity. The Southern California ECMO Consortium may serve as a model for other communities seeking to optimize ECMO resources during the current COVID-19 or future pandemics.

A Thermostable Protein Matrix for Spectroscopic Analysis of Organic Semiconductors.

Advances in protein design and engineering have yielded peptide assemblies with enhanced and non-native functionalities. Here, various molecular organic semiconductors (OSCs), with known excitonic up- and down-conversion properties, are attached to a de novo-designed protein, conferring entirely novel functions on the peptide scaffolds. The protein-OSC complexes form similarly sized, stable, water-soluble nanoparticles that are robust to cryogenic freezing and processing into the solid-state. The peptide matrix enables the formation of protein-OSC-trehalose glasses that fix the proteins in their folded states under oxygen-limited conditions. The encapsulation dramatically enhances the stability of protein-OSC complexes to photodamage, increasing the lifetime of the chromophores from several hours to more than 10 weeks under constant illumination. Comparison of the photophysical properties of astaxanthin aggregates in mixed-solvent systems and proteins shows that the peptide environment does not alter the underlying electronic processes of the incorporated materials, exemplified here by singlet exciton fission followed by separation into weakly bound, localized triplets. This adaptable protein-based approach lays the foundation for spectroscopic assessment of a broad range of molecular OSCs in aqueous solutions and the solid-state, circumventing the laborious procedure of identifying the experimental conditions necessary for aggregate generation or film formation. The non-native protein functions also raise the prospect of future biocompatible devices where peptide assemblies could complex with native and non-native systems to generate novel functional materials.

Probing the quality control mechanism of the Escherichia coli twin-arginine translocase with folding variants of a de novo-designed heme protein.

Protein transport across the cytoplasmic membrane of bacterial cells is mediated by either the general secretion (Sec) system or the twin-arginine translocase (Tat). The Tat machinery exports folded and cofactor-containing proteins from the cytoplasm to the periplasm by using the transmembrane proton motive force as a source of energy. The Tat apparatus apparently senses the folded state of its protein substrates, a quality-control mechanism that prevents premature export of nascent unfolded or misfolded polypeptides, but its mechanistic basis has not yet been determined. Here, we investigated the innate ability of the model Escherichia coli Tat system to recognize and translocate de novo-designed protein substrates with experimentally determined differences in the extent of folding. Water-soluble, four-helix bundle maquette proteins were engineered to bind two, one, or no heme b cofactors, resulting in a concomitant reduction in the extent of their folding, assessed with temperature-dependent CD spectroscopy and one-dimensional 1H NMR spectroscopy. Fusion of the archetypal N-terminal Tat signal peptide of the E. coli trimethylamine-N-oxide (TMAO) reductase (TorA) to the N terminus of the protein maquettes was sufficient for the Tat system to recognize them as substrates. The clear correlation between the level of Tat-dependent export and the degree of heme b-induced folding of the maquette protein suggested that the membrane-bound Tat machinery can sense the extent of folding and conformational flexibility of its substrates. We propose that these artificial proteins are ideal substrates for future investigations of the Tat system's quality-control mechanism.

The hydrological functioning of a constructed fen wetland watershed.

Mine reclamation requires the reconstruction of entire landforms and drainage systems. The hydrological regime of reclaimed landscapes will be a manifestation of the processes operating within the individual landforms that comprise it. Hydrology is the most important process regulating wetland function and development, via strong controls on chemical and biotic processes. Accordingly, this research addresses the growing and immediate need to understand the hydrological processes that operate within reconstructed landscapes following resource extraction. In this study, the function of a constructed fen watershed (the Nikanotee Fen watershed) is evaluated for the first two years following construction (2013-2014) and is assessed and discussed within the context of the construction-level design. The system design was capable of sustaining wet conditions within the Nikanotee Fen during the snow-free period in 2013 and 2014, with persistent ponded water in some areas. Evapotranspiration dominated the water fluxes from the system. These losses were partially offset by groundwater discharge from the upland aquifer, which demonstrated strong hydrologic connectivity with the fen in spite of most construction materials having lower than targeted saturated hydraulic conductivities. However, the variable surface infiltration rates and thick placement of a soil-capping layer constrained recharge to the upland aquifer, which remained below designed water contents in much of the upland. These findings indicate that it is possible to engineer the landscape to accommodate the hydrological functions of a fen peatland following surface oil sands extraction. Future research priorities should include understanding the storage and release of water within coarse-grained reclaimed landforms as well as evaluating the relative importance of external water sources and internal water conservation mechanisms for the viability of fen ecosystems over the longer-term.

Sudden cardiac death: the pro-arrhythmic interaction of an acute loading with an underlying substrate.

Sudden cardiac death (SCD) is a complex phenomenon, occurring either in apparently normal individuals or in those where there is a recognized underlying cardiac abnormality. In both groups, the lethal arrhythmia has frequently been related to the physiologic trigger of either exercise or stress. Prior research into SCD has focused mainly on a combination of identifying either vulnerable myocardial substrates; pharmacological approaches to altering electrical activation/repolarisation in substrates; or the suppression of induced lethal arrhythmias with implantable defibrillators. However, it has been suggested that in a significant number of cases, the interaction of a transient induced trigger with a pre-existing electrical or mechanical substrate is the basis for the induction of the sustained lethal arrhythmia. In this manuscript we will discuss the precise mechanisms whereby one of such potential physiologic trigger: an acute change in systolic blood pressure, can induce a sequence of alterations in global and local cardiac mechanics which in turn result in regional left ventricular post-systolic deformation which, mediated (through stretch-induced changes in local mechano-electrical coupling) provokes local electrical after-depolarisations which can spill over into complex runs of premature ventricular beats. These local acute pressure/stretch induced runs of ventricular ectopy originate in either basal or apical normal myocardium and, in combination with a co-existing distal pro-arrhymic substrate, can interact to induce a lethal arrhythmia.

Further insights into blood pressure induced premature beats: Transient depolarizations are associated with fast myocardial deformation upon pressure decline.

BACKGROUND: An acute increase in blood pressure is associated with the occurrence of premature ventricular complexes (PVCs). OBJECTIVE: We aimed to study the timing of these PVCs with respect to afterload-induced changes in myocardial deformation in a controlled, preclinically relevant, novel closed-chest pig model. METHODS: An acute left ventricular (LV) afterload challenge was induced by partial balloon inflation in the descending aorta, lasting 5-10 heartbeats (8 pigs; 396 inflations). RESULTS: Balloon inflation enhanced the reflected wave (augmentation index 30% ± 8% vs 59% ± 6%; P < .001), increasing systolic central blood pressure by 35% ± 4%. This challenge resulted in a more abrupt LV pressure decline, which was delayed beyond ventricular repolarization (rate of pressure decline 0.16 ± 0.01 mm Hg/s vs 0.27 ± 0.04 mm Hg/ms; P < .001 and interval T-wave to peak pressure 1 ± 12 ms vs 36 ± 9 ms; P = .008), during which the velocity of myocardial shortening at the basal septum increased abruptly (ie, postsystolic shortening) (peak strain rate -0.6 ± 0.5 s(-1) vs -2.5 ± 0.8 s(-1); P < .001). It is exactly at this time of LV pressure decline, with increased postsystolic shortening, and not at peak pressure, that PVCs occur (22% of inflations). These PVCs preferentially occurred at the basal and apical segments. In the same regions, monophasic action potentials demonstrated the appearance of delayed afterdepolarization-like transient depolarizations as origin of PVCs. CONCLUSION: An acute blood pressure increase results in a more abrupt LV pressure decline, which is delayed after ventricular repolarization. This has a profound effect on myocardial mechanics with enhanced postsystolic shortening. Coincidence with induced transient depolarizations and PVCs provides support for the mechanoelectrical origin of pressure-induced premature beats.

Control of histone H3 phosphorylation by CaMKIIδ in response to haemodynamic cardiac stress.

Heart failure is associated with the reactivation of a fetal cardiac gene programme that has become a hallmark of cardiac hypertrophy and maladaptive ventricular remodelling, yet the mechanisms that regulate this transcriptional reprogramming are not fully understood. Using mice with genetic ablation of calcium/calmodulin-dependent protein kinase II δ (CaMKIIδ), which are resistant to pathological cardiac stress, we show that CaMKIIδ regulates the phosphorylation of histone H3 at serine-10 during pressure overload hypertrophy. H3 S10 phosphorylation is strongly increased in the adult mouse heart in the early phase of cardiac hypertrophy and remains detectable during cardiac decompensation. This response correlates with up-regulation of CaMKIIδ and increased expression of transcriptional drivers of pathological cardiac hypertrophy and of fetal cardiac genes. Similar changes are detected in patients with end-stage heart failure, where CaMKIIδ specifically interacts with phospho-H3. Robust H3 phosphorylation is detected in both adult ventricular myocytes and in non-cardiac cells in the stressed myocardium, and these signals are abolished in CaMKIIδ-deficient mice after pressure overload. Mechanistically, fetal cardiac genes are activated by increased recruitment of CaMKIIδ and enhanced H3 phosphorylation at hypertrophic promoter regions, both in mice and in human failing hearts, and this response is blunted in CaMKIIδ-deficient mice under stress. We also document that the chaperone protein 14-3-3 binds phosphorylated H3 in response to stress, allowing proper elongation of fetal cardiac genes by RNA polymerase II (RNAPII), as well as elongation of transcription factors regulating cardiac hypertrophy. These processes are impaired in CaMKIIδ-KO mice after pathological stress. The findings reveal a novel in vivo function of CaMKIIδ in regulating H3 phosphorylation and suggest a novel epigenetic mechanism by which CaMKIIδ controls cardiac hypertrophy.

Ultrafast cardiac ultrasound imaging: technical principles, applications, and clinical benefits.

Several recent technical advances in cardiac ultrasound allow data to be acquired at a very high frame rate. Retrospective gating, plane/diverging wave imaging, and multiline transmit imaging all improve the temporal resolution of the conventional ultrasound system. The main drawback of such high frame rate data acquisition is that it typically has reduced image quality. However, for given clinical applications, the acquisition of temporally-resolved data might outweigh the reduction in image quality. It is the aim of this paper to provide an overview of the technical principles behind these new ultrasound imaging modalities, to review the current evidence of their potential clinical added value, and to forecast how they might influence daily clinical practice.