Spectral Tuning and Excitation-Energy Transfer by Unique Carotenoids in Diatom Light-Harvesting Antenna.

The light-harvesting antennae of diatoms and spinach are composed of similar chromophores; however, they exhibit different absorption wavelengths. Recent advances in cryoelectron microscopy have revealed that the diatom light-harvesting antenna fucoxanthin chlorophyll a/c-binding protein (FCPII) forms a tetramer and differs from the spinach antenna in terms of the number of protomers; however, the detailed molecular mechanism remains elusive. Herein, we report the physicochemical factors contributing to the characteristic light absorption of the diatom light-harvesting antenna based on spectral calculations using an exciton model. Spectral analysis reveals the significant contribution of unique fucoxanthin molecules (fucoxanthin-S) in FCPII to the diatom-specific spectrum, and further analysis determines their essential role in excitation-energy transfer to chlorophyll. It was revealed that the specificity of these fucoxanthin-S molecules is caused by the proximity between protomers associated with the tetramerization of FCPII. The findings of this study demonstrate that diatoms employ fucoxanthin-S to harvest energy under the ocean in the absence of long-wavelength sunlight and can provide significant information about the survival strategies of photosynthetic organisms to adjust to their living environment.

In Silico Screening and Experimental Verification of Near-Infrared-Emissive Two-Boron-Doped Polycyclic Aromatic Hydrocarbons.

Embedding two boron atoms into a polycyclic aromatic hydrocarbon (PAH) leads to the formation of a neutral analogue that is isoelectronic to the corresponding dicationic PAH skeleton, which can significantly alter its electronic structure. Based on this concept, we explore herein the identification of near-infrared (NIR)-emissive PAHs with the aid of an in silico screening method. Using perylene as the PAH scaffold, we embedded two boron atoms and fused two thiophene rings to it. Based on this design concept, all possible structures (ca. 2500 entities) were generated using a comprehensive structure generator. Time-dependent DFT calculations were conducted on all these structures, and promising candidates were extracted based on the vertical excitation energy, transition dipole moment, and atomization energy per bond. One of the extracted dithieno-diboraperylene candidates was synthesized and indeed exhibited emission at 724 nm with a quantum yield of 0.40 in toluene, demonstrating the validity of this screening method. This modification was further applied to other PAHs, and a series of thienobora-modified PAHs was synthesized.

A quantum chemical study on the anti-SARS-CoV-2 activity of TMPRSS2 inhibitors.

Nafamostat and camostat are known to inhibit the spike protein-mediated fusion of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by forming a covalent bond with the human transmembrane serine protease 2 (TMPRSS2) enzyme. Previous experiments revealed that the TMPRSS2 inhibitory activity of nafamostat surpasses that of camostat, despite their structural similarities; however, the molecular mechanism of TMPRSS2 inhibition remains elusive. Herein, we report the energy profiles of the acylation reactions of nafamostat, camostat, and a nafamostat derivative by quantum chemical calculations using a combined molecular cluster and polarizable continuum model (PCM) approach. We further discuss the physicochemical relevance of their inhibitory activity in terms of thermodynamics and kinetics. Our analysis attributes the strong inhibitory activity of nafamostat to the formation of a stable acyl intermediate and its low activation energy during acylation with TMPRSS2. The proposed approach is also promising for elucidating the molecular mechanisms of other covalent drugs.

Impact of Hydrophobic/Hydrophilic Balance on Aggregation Pathways, Morphologies, and Excited-State Dynamics of Amphiphilic Diketopyrrolopyrrole Dyes in Aqueous Media.

We report the thermodynamic and kinetic aqueous self-assembly of a series of amide-functionalized dithienyldiketopyrrolopyrroles (TDPPs) that bear various hydrophilic oligoethylene glycol (OEG) and hydrophobic alkyl chains. Spectroscopic and microscopic studies showed that the TDPP-based amphiphiles with an octyl group form sheet-like aggregates with J-type exciton coupling. The effect of the alkyl chains on the aggregated structure and the internal molecular orientation was examined via computational studies combining MD simulations and TD-DFT calculations. Furthermore, solvent and thermal denaturation experiments provided a state diagram that indicates the formation of unexpected nanoparticles during the self-assembly into nanosheets when longer OEG side chains are introduced. A kinetic analysis revealed that the nanoparticles were obtained selectively as an on-pathway intermediate state toward the formation of thermodynamically controlled nanosheets. The metastable aggregates were used for seed-initiated supramolecular assembly, which allowed establishing control over the assembly kinetics and the aggregate size. The sheet-like aggregates prepared using the seeding method exhibited coherent vibration in the excited state, indicating a well-ordered orientation of the TDPP units. These results underline the significance of fine tuning of the hydrophobic/hydrophilic balance in the molecular design to kinetically control the assembly of amphiphilic π-conjugated molecules into two-dimensional nanostructures in aqueous media.

Structure-Function Study of a Novel Inhibitor of Cyclin-Dependent Kinase C in Arabidopsis.

The circadian clock, an internal time-keeping system with a period of about 24 h, coordinates many physiological processes with the day-night cycle. We previously demonstrated that BML-259 [N-(5-isopropyl-2-thiazolyl) phenylacetamide], a small molecule with mammal CYCLIN DEPENDENT KINASE 5 (CDK5)/CDK2 inhibition activity, lengthens Arabidopsis thaliana (Arabidopsis) circadian clock periods. BML-259 inhibits Arabidopsis CDKC kinase, which phosphorylates RNA polymerase II in the general transcriptional machinery. To accelerate our understanding of the inhibitory mechanism of BML-259 on CDKC, we performed structure-function studies of BML-259 using circadian period-lengthening activity as an estimation of CDKC inhibitor activity in vivo. The presence of a thiazole ring is essential for period-lengthening activity, whereas acetamide, isopropyl and phenyl groups can be modified without effect. BML-259 analog TT-539, a known mammal CDK5 inhibitor, did not lengthen the period nor did it inhibit Pol II phosphorylation. TT-361, an analog having a thiophenyl ring instead of a phenyl ring, possesses stronger period-lengthening activity and CDKC;2 inhibitory activity than BML-259. In silico ensemble docking calculations using Arabidopsis CDKC;2 obtained by a homology modeling indicated that the different binding conformations between these molecules and CDKC;2 explain the divergent activities of TT539 and TT361.

Phosphorylation of RNA Polymerase II by CDKC;2 Maintains the Arabidopsis Circadian Clock Period.

The circadian clock is an internal timekeeping system that governs about 24 h biological rhythms of a broad range of developmental and metabolic activities. The clocks in eukaryotes are thought to rely on lineage-specific transcriptional-translational feedback loops. However, the mechanisms underlying the basic transcriptional regulation events for clock function have not yet been fully explored. Here, through a combination of chemical biology and genetic approaches, we demonstrate that phosphorylation of RNA polymerase II by CYCLIN DEPENDENT KINASE C; 2 (CDKC;2) is required for maintaining the circadian period in Arabidopsis. Chemical screening identified BML-259, the inhibitor of mammalian CDK2/CDK5, as a compound lengthening the circadian period of Arabidopsis. Short-term BML-259 treatment resulted in decreased expression of most clock-associated genes. Development of a chemical probe followed by affinity proteomics revealed that BML-259 binds to CDKC;2. Loss-of-function mutations of cdkc;2 caused a long period phenotype. In vitro experiments demonstrated that the CDKC;2 immunocomplex phosphorylates the C-terminal domain of RNA polymerase II, and BML-259 inhibits this phosphorylation. Collectively, this study suggests that transcriptional activity maintained by CDKC;2 is required for proper period length, which is an essential feature of the circadian clock in Arabidopsis.

Chemical biology to dissect molecular mechanisms underlying plant circadian clocks.

Circadian clocks regulate the diel rhythmic physiological activities of plants, enabling them to anticipate and adapt to day-night and seasonal changes. Genetic and biochemical approaches have suggested that transcription-translation feedback loops (TTFL) are crucial for Arabidopsis clock function. Recently, the study of chemical chronobiology has emerged as a discipline within the circadian clock field, with important and complementary discoveries from both plant and animal research. In this review, we introduce recent advances in chemical biology using small molecules to perturb plant circadian clock function through TTFL components. Studies using small molecule clock modulators have been instrumental for revealing the role of post-translational modification in the clock, or the metabolite-dependent clock input pathway, as well as for controlling clock-dependent flowering time.

Fluorescent Organic π-Radicals Stabilized with Boron: Featuring a SOMO-LUMO Electronic Transition.

We report on the fluorescence properties of a new class of emissive and stable π-radicals that contain a boron atom at a position distant from the radical center. A fully planarized derivative exhibited an intense red fluorescence with high fluorescence quantum yields (ΦF >0.67) even in polar solvents. To elucidate the origin of this phenomenon, we synthesized another boron-stabilized radical that contains a bulky aryl group on the boron atom. A comparison of these derivatives, as well as with conventional donor-π-acceptor (D-π-A)-type emissive π-radicals, unveiled several characteristic features in their photophysical properties. A theoretical analysis revealed that the SOMO-LUMO electronic transition generates an emissive D1 state. Unlike conventional D-π-A-type π-radicals, this state does not undergo significant structural relaxation. The boron-stabilized π-radicals demonstrated promising potential for organic light-emitting diodes as an emitting material.

Excitonic coupling effect on the circular dichroism spectrum of sodium-pumping rhodopsin KR2.

We investigate the role of excitonic coupling between retinal chromophores of Krokinobacter eikastus rhodopsin 2 (KR2) in the circular dichroism (CD) spectrum using an exciton model combined with the transition density fragment interaction (TDFI) method. Although the multimer formation of retinal protein commonly induces biphasic negative and positive CD bands, the KR2 pentamer shows only a single positive CD band. The TDFI calculation reveals the dominant contribution of the Coulomb interaction and negligible contributions of exchange and charge-transfer interactions to the excitonic coupling energy. The exciton model with TDFI successfully reproduces the main features of the experimental absorption and CD spectra of KR2, which allow us to investigate the mechanism of the CD spectral shape observed in the KR2 pentamer. The results clearly show that the red shift of the CD band is attributed to the excitonic coupling between retinal chromophores. Further analysis reveals that the weak excitonic coupling plays a crucial role in the shape of the CD spectrum. The present approach provides a basis for understanding the origin of the KR2 CD spectrum and is useful for analyzing the mechanism of chromophore-chromophore interactions in biological systems.

A novel biofunctionalizing peptide for metallic alloy.

OBJECTIVES: Improving biocompatibility of metallic alloy biomaterials has been of great interest to prevent implant associated-diseases, such as stent thrombosis. Herein a simple and efficient procedure was designed to biofunctionalize a biomaterial surface by isolating a SUS316L stainless steel binding peptide. RESULTS: After three rounds of phage panning procedure, 12 mer peptide (SBP-A; VQHNTKYSVVIR) was identified as SUS316L-binding peptide. The SBP-A peptide formed a stable bond to a SUS316L modified surface and was not toxic to HUVECs. The SBP-A was then used for anti-ICAM antibody modification on SUS316L to construct a vascular endothelial cell-selective surface. The constructed surface dominantly immobilized vascular endothelial cells to smooth muscle cells, demonstrating that the SBP-A enabled simple immobilization of biomolecules without disturbing their active biological function. CONCLUSIONS: The SUS316L surface was successfully biofunctionalized using the novel isolated peptide SBP-A, showing its potential as an ideal interface molecule for stent modification. This is the first report of material binding peptide-based optimal surface functionalization to promote endothelialisation. This simple and efficient biofunctionalization procedure is expected to contribute to the development of biocompatible materials.

3,4-Dibromo-7-Azaindole Modulates Arabidopsis Circadian Clock by Inhibiting Casein Kinase 1 Activity.

The circadian clock is a timekeeping system for regulation of numerous biological daily rhythms. One characteristic of the circadian clock is that period length remains relatively constant in spite of environmental fluctuations, such as temperature change. Here, using the curated collection of in-house small molecule chemical library (ITbM chemical library), we show that small molecule 3,4-dibromo-7-azaindole (B-AZ) lengthened the circadian period of Arabidopsis thaliana (Arabidopsis). B-AZ has not previously been reported to have any biological and biochemical activities. Target identification can elucidate the mode of action of small molecules, but we were unable to make a molecular probe of B-AZ for target identification. Instead, we performed other analysis, gene expression profiling that potentially reveals mode of action of molecules. Short-term treatment of B-AZ decreased the expression of four dawn- and morning-phased clock-associated genes, CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1), LATE ELONGATED HYPOCOTYL (LHY), PSEUDO-RESPONSE REGULATOR 9 (PRR9) and PRR7. Consistently, amounts of PRR5 and TIMING OF CAB EXPRESSION 1 (TOC1) proteins, transcriptional repressors of CCA1, LHY, PRR9 and PRR7 were increased upon B-AZ treatment. B-AZ inhibited Casein Kinase 1 family (CK1) that phosphorylates PRR5 and TOC1 for targeted degradation. A docking study and molecular dynamics simulation suggested that B-AZ interacts with the ATP-binding pocket of human CK1 delta, whose amino acid sequences are highly similar to those of Arabidopsis CK1. B-AZ-induced period-lengthening effect was attenuated in prr5 toc1 mutants. Collectively, this study provides a novel and simple structure CK1 inhibitor that modulates circadian clock via accumulation of PRR5 and TOC1.

Protein-ligand docking using fitness learning-based artificial bee colony with proximity stimuli.

Protein-ligand docking is an optimization problem, which aims to identify the binding pose of a ligand with the lowest energy in the active site of a target protein. In this study, we employed a novel optimization algorithm called fitness learning-based artificial bee colony with proximity stimuli (FlABCps) for docking. Simulation results revealed that FlABCps improved the success rate of docking, compared to four state-of-the-art algorithms. The present results also showed superior docking performance of FlABCps, in particular for dealing with highly flexible ligands and proteins with a wide and shallow binding pocket.

Electronic coupling calculations with transition charges, dipoles, and quadrupoles derived from electrostatic potential fitting.

A transition charge, dipole, and quadrupole from electrostatic potential (TrESP-CDQ) method for electronic coupling calculations is proposed. The TrESP method is based on the classical description of electronic Coulomb interaction between transition densities for individual molecules. In the original TrESP method, only the transition charge interactions were considered as the electronic coupling. In the present study, the TrESP method is extended to include the contributions from the transition dipoles and quadrupoles as well as the transition charges. Hence, the self-consistent transition density is employed in the ESP fitting procedure. To check the accuracy of the present approach, several test calculations are performed to a helium dimer, a methane dimer, and an ethylene dimer. As a result, the TrESP-CDQ method gives a much improved description of the electronic coupling, compared with the original TrESP method. The calculated results also show that the self-consistent treatment to the transition densities contributes significantly to the accuracy of the electronic coupling calculations. Based on the successful description of the electronic coupling, the contributions to the electronic coupling are also analyzed. This analysis clearly shows a negligible contribution of the transition charge interaction to the electronic coupling. Hence, the distribution of the transition density is found to strongly influence the magnitudes of the transition charges, dipoles, and quadrupoles. The present approach is useful for analyzing and understanding the mechanism of excitation-energy transfer.

Extended theoretical modeling of reverse intersystem crossing for thermally activated delayed fluorescence materials.

Thermally activated delayed fluorescence (TADF) materials and multi-resonant (MR) variants are promising organic emitters that can achieve an internal electroluminescence quantum efficiency of ~100%. The reverse intersystem crossing (RISC) is key for harnessing triplet energies for fluorescence. Theoretical modeling is thus crucial to estimate its rate constant (kRISC) for material development. Here, we present a comprehensive assessment of the theory for simulating the RISC of MR-TADF molecules within a perturbative excited-state dynamics framework. Our extended rate formula reveals the importance of the concerted effects of nonadiabatic spin-vibronic coupling and vibrationally induced spin-orbital couplings in reliably determining kRISC of MR-TADF molecules. The excited singlet-triplet energy gap is another factor influencing kRISC. We present a scheme for gap estimation using experimental Arrhenius plots of kRISC. Erroneous behavior caused by approximations in Marcus theory is elucidated by testing 121 MR-TADF molecules. Our extended modeling offers in-depth descriptions of kRISC.

Current Concepts of Cervical Spine Alignment, Sagittal Deformity, and Cervical Spine Surgery.

There are not many reports on cervical spine alignment, and only a few analyze ideal surgical approaches and optimal amounts of correction needed for the various types of deformity. We comprehensively reviewed the present literature on cervical spinal deformities (with or without myelopathy) and their surgical management to provide a framework for surgical planning. A general assessment of the parameters actually in use and correlations between cervical and thoracolumbar spine alignment are provided. We also analyzed posterior, anterior, and combined cervical surgical approaches and indications for the associated techniques of laminoplasty, laminectomy and fusion, and anterior cervical discectomy and fusion. Finally, on the basis of the NDI, SF-36, VAS, and mJOA questionnaires, we fully evaluated the outcomes and measures of postoperative health-related quality of life. We found the need for additional prospective studies to further enhance our understanding of the importance of cervical alignment when assessing and treating cervical deformities with or without myelopathy. Future studies need to focus on correlations between cervical alignment parameters, disability scores, and myelopathy outcomes. Through this comprehensive literature review, we offer guidance on practical and important points of surgical technique, cervical alignment, and goals surgeons can meet to improve symptoms in all patients.

Molecular Mechanisms behind Circular Dichroism Spectral Variations between Channelrhodopsin and Heliorhodopsin Dimers.

Channelrhodopsin (ChR) and heliorhodopsin (HeR) are microbial rhodopsins with similar structures but different circular dichroism (CD) spectra: ChR shows biphasic negative and positive bands, whereas HeR shows a single positive band. We explored the physicochemical factors underlying these differences through computational methods. Using the exciton model based on first-principles computations, we obtained the CD spectra of ChR and HeR. The obtained spectra indicate that the protein dimer structures and the quantum mechanical treatment of the retinal chromophore and its interacting amino acids are crucial for accurately reproducing the experimental spectra. Further calculations revealed that the sign of the excitonic coupling was opposite between the ChR and HeR dimers, which was attributed to the contrasting second term of the orientation factor between the two retinal chromophores. These findings demonstrate that slight variations in the intermolecular orientation of the two chromophores can result in significant differences in the CD spectral shape.

Transcranial Magnetic Stimulation in the Diagnosis of Compressive Myelopathy at the Thoracolumbar Junction.

PURPOSE: The disc level in the thoracolumbar junction at which measurement of the central motor conduction time in the lower limbs (CMCT-LL) is useful for a diagnosis remains unclear. Therefore, this study investigated the spinal vertebral level at which compressive myelopathy due to ossification of the ligamentum flavum in the thoracolumbar junction is detectable using CMCT-LL. METHODS: We preoperatively measured CMCT-LL in 57 patients (42 men, 15 women; aged 35-85 years) with a single ossification of the ligamentum flavum from the T10-11 to T12-L1 disc levels and in 53 healthy controls. Motor evoked potentials after transcranial magnetic stimulation, compound muscle action potentials, and F waves were recorded from the abductor hallucis. Central motor conduction time in the lower limbs was calculated as follows: Motor evoked potential latency - (compound muscle action potential latency + F latency - 1)/2 (ms). Central motor conduction time in the lower limbs was compared between patients and controls. RESULTS: Compressive lesions were located at the T10 to 11 level in 27 patients, the T11 to 12 level in 28, and the T12-L1 level in 2. Central motor conduction time values in the lower limbs at the T10 to 11 level (19.9 ± 4.7 ms) and T11 to 12 level (18.1 ± 3.4 ms) were significantly longer than control values (11.8 ± 1.1 ms; P < 0.01). Central motor conduction time in the lower limbs was not calculated at the T12-L1 level because motor evoked potentials were not recorded in any patient. CONCLUSIONS: We confirmed that CMCT-LL was significantly longer in patients with ossification of the ligamentum flavum at the T10 to 11 and T11 to 12 levels because the S2 segment of the spinal cord is caudal at the T12 vertebral body level. Therefore, CMCT-LL is useful for diagnosing thoracolumbar junction disorders proximal to the T12 vertebral body level.

Resting-state functional magnetic resonance imaging indices are related to electrophysiological dysfunction in degenerative cervical myelopathy.

The age-related degenerative pathologies of the cervical spinal column that comprise degenerative cervical myelopathy (DCM) cause myelopathy due spinal cord compression. Functional neurological assessment of DCM can potentially reveal the severity and pathological mechanism of DCM. However, functional assessment by conventional MRI remains difficult. This study used resting-state functional MRI (rs-fMRI) to investigate the relationship between functional connectivity (FC) strength and neurophysiological indices and examined the feasibility of functional assessment by FC for DCM. Preoperatively, 34 patients with DCM underwent rs-fMRI scans. Preoperative central motor conduction time (CMCT) reflecting motor functional disability and intraoperative somatosensory evoked potentials (SEP) reflecting sensory functional disability were recorded as electrophysiological indices of severity of the cervical spinal cord impairment. We performed seed-to-voxel FC analysis and correlation analyses between FC strength and the two electrophysiological indices. We found that FC strength between the primary motor cortex and the precuneus correlated significantly positively with CMCT, and that between the lateral part of the sensorimotor cortex and the lateral occipital cortex also showed a significantly positive correlation with SEP amplitudes. These results suggest that we can evaluate neurological and electrophysiological severity in patients with DCM by analyzing FC strengths between certain brain regions.

A theoretical study of crystallochromy: spectral tuning of solid-state tetracenes.

The crystallochromy of the red and yellow solids of tetracenes was theoretically investigated using the transition-density-fragment interaction combined with transfer integral method [K. J. Fujimoto, J. Chem. Phys. 137, 034101 (2012)]. The calculated absorption and fluorescence energies were in good agreement with the experimental values for both solids. The spectral tuning mechanism was analyzed in terms of three contributions: side-chain conformational effect, electrostatic solid-state effect, and multimerization effect. This analysis provided an insight into the mechanism of the large spectral shift between the two solids. The multimerization effect was found to be primarily important for the large red-shift of the red solid. Further analysis also revealed the strong dependence of the excited state character on the molecular displacement. Such dependence was found to have a significant influence on the magnitudes of the absorption energy and oscillator strength. These results indicated that the present approach is useful for analyzing and understanding the mechanism of crystallochromy.

Laminoplasty is relevant for degenerative cervical spondylolisthesis when there is little risk of postoperative excessive kyphosis during neck flexion.

BACKGROUND: Elderly patients with degenerative cervical myelopathy frequently have severe symptoms due to spondylolisthesis. The effectiveness of laminoplasty for degenerative cervical spondylolisthesis (DCS) is an important question. OBJECTIVE: The aim of this study is to elucidate factors associated with the outcome of laminoplasty for DCS. METHOD: Eighty-nine patients with cervical spondylotic myelopathy (CSM) who underwent laminoplasty without instrumented posterior fusion were enrolled. Positive spondylolisthesis was defined as more than 2 mm during neck flexion or extension, from this, 46 DCS cases and 43 non-DCS cases were classified. Radiological parameters, including cervical alignment, balance, range of motion, and slippage along with the Japanese Orthopedic Association (JOA) score, were obtained before and 1 year after surgery. Factors associated with good surgical outcomes for DCS were analyzed using multivariate logistic analysis. RESULTS: There were no significant differences in background and preoperative JOA score, but the DCS group recovery rate was significantly less (42% vs 53%). Multivariate logistic analysis revealed only the postoperative C2-7 angle during neck flexion was associated with a favorable outcome for DCS (P = 0.0039, Odds ratio: 1.49, 95% CI: 1.14-1.94). Multivariate regression analysis positively correlated the preoperative C2-7 angle in neutral and during flexion with the postoperative C2-7 angle during flexion. CONCLUSION: The major factor related to poor outcome was the magnitude of postoperative kyphotic C2-7 angle during neck flexion. Slippage was not directly related to outcome and postoperative cervical alignment. Caution is recommended for surgeons performing laminoplasty on patients with risk factors for postoperative excessive kyphotic C2-7 angle during flexion.