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Imai, H.

Publications and source records attributed to Imai, H..

At least 19 recordsLinked to original sources

Antibody-mediated VWF targeting reconstitutes ADAMTS13 metalloproteinase activity and prevents thrombocytopenia in mice

ADAMTS13 (a multidomain metalloproteinase) cleaves von Willebrand factor (VWF), thereby preventing the accumulation of ultra-large VWF multimers that promote platelet-rich thrombus formation. Severe ADAMTS13 deficiency causes thrombotic thrombocytopenic purpura (TTP). In immune-mediated TTP (iTTP), anti-ADAMTS13 autoantibodies inhibit ADAMTS13 activity, often by targeting non-catalytic domains that mediate substrate recognition. We developed ADAMTS13 mimetics by fusing the ADAMTS13 metalloproteinase domain to anti-human VWF A2 domain antibodies, aiming to replace native substrate-recognition domains with antibody-mediated substrate targeting while removing major autoantibody-targeted ADAMTS13 domains. The resulting mimetics bound to the recombinant VWF A2 domain and showed proteolytic activity toward both the recombinant VWF A2 domain and FRETS-VWF73 substrate. Kinetic analysis showed that the mimetics had not only lower kcat values than ADAMTS13 but also lower Km values, thereby maintaining overall catalytic efficiency. Importantly, ADAMTS13 mimetics retained VWF A2-cleaving activity in the presence of a spacer domain-directed anti-ADAMTS13 autoantibody both in vitro and in vivo. In an iTTP mouse model, ADAMTS13 mimetics prevented recombinant VWF-induced thrombocytopenia, whereas the parental anti-VWF A2 domain antibody did not. Platelet-preserving activity was also observed in ADAMTS13-deficient mice. In further analyses, some mimetics showed reduced binding to a conformationally restricted VWF A2 domain, resulting in reduced cleavage activity. Antibody binding correlated with platelet recovery in the iTTP mouse model, suggesting that epitope accessibility and antibody-mediated positioning contribute to in vivo activity. These findings demonstrate that antibody-mediated substrate targeting can reconstitute the VWF-cleaving activity of the ADAMTS13 metalloproteinase domain and suggest that ADAMTS13 mimetics represent a potential therapeutic approach for iTTP.

biochemistry↗

Characterization of the trimeric TOM complex by HS-AFM single-molecule analysis

The translocase of the outer mitochondrial membrane (TOM) complex is the main entry gate for mitochondrial proteins. Approximately 99 % of mitochondrial proteins are synthesized as precursor proteins (preproteins) in the cytosol and subsequently translocated into mitochondria through the TOM complex. The TOM complex exists in a dynamic equilibrium among multiple assembly states through spatial rearrangements of its subunits. The recent cryo-electron microscopy (cryo-EM) studies revealed near-atomic structures of the TOM core dimer, whereas previous biochemical studies indicated the TOM complex functions as a trimer in intact mitochondria. However, the relationship between the core dimer and the functional trimer remains unclear. In the present study, we analyzed the dynamics of the TOM complex using high-speed atomic force microscopy (HS-AFM) to investigate the assembly states and conformation transitions of the TOM complexes. We demonstrated that purified yeast TOM complexes predominantly adopt a trimeric organization but dynamically dissociate into dimeric and monomeric states during HS-AFM observation. The trimeric particles observed by HS-AFM exhibited spherical molecular shapes consistent with a trimeric structural model proposed from previous crosslinking analyses. In contrast, the dissociated dimeric particles closely resembled the dimensions of the TOM core-dimer structures determined by cryo-EM. Furthermore, HS-AFM analyses provided insight into the spatial arrangement of the Tom20 receptor, consistent with previous models of the trimeric TOM complex. These observations enabled characterization of the trimeric TOM complex in vitro and provide a foundation for future structural and functional analyses of TOM complex assembly. Significance statementThe translocase of the mitochondrial outer membrane (TOM) complex is the universal entry gate for almost all mitochondrial proteins, yet its native organization has remained elusive. By combining high-speed atomic force microscopy with cryo-electron microscopy, we provide evidence that the yeast TOM complex predominantly adopts a trimeric assembly with three protein-conducting channels, rather than the dimeric architecture proposed by previous structural studies. Furthermore, single-molecule imaging directly visualized interactions with mitochondrial precursor proteins and receptor-specific antibodies, enabling the experimental identification of receptor subunits within the trimeric TOM complex. Together, these findings uncover previously unrecognized structural and dynamic features of the TOM complex and provide a framework for understanding the molecular mechanism of mitochondrial protein import.

biochemistry↗

An atlas of microtubule lattice parameters regulated through ligand binding to the microtubule stabilizing sites.

Microtubules (MTs) are dynamic cytoskeletal polymers whose lattice architecture regulates force generation, nucleotide hydrolysis, and recognition by motor proteins and microtubule-associated proteins (MAPs). Microtubule-stabilizing agents (MSAs), including taxanes and laulimalide/peloruside-site ligands, suppress depolymerization by binding to defined lattice sites, yet stabilization is not structurally neutral. How ligand chemistry reshapes lattice organization and function remains unresolved. Here, we address three mechanistic questions. First, do distinct ligand classes induce defined lattice states? Using X-ray fiber diffraction, we show that MSAs selectively stabilize two preferred longitudinal conformations, a compact state ([~]4.06 nm monomer rise) and an expanded state ([~]4.17 nm), while modulating lateral organization reflected in shifts in mean MT radius. These axial spacings cluster around discrete values across chemotypes, indicating stabilization of pre-existing conformational minima rather than continuous distortion. Second, are these states interconvertible upon changes in ligand occupancy? Time-resolved diffraction reveals that longitudinal transitions occur within seconds of ligand addition even at substoichiometric occupancy; whereas, lateral equilibration proceeds slower, consistent with redistribution within heterogeneous protofilament organizations. Third, do such structural states alter nucleotide hydrolysis and motor/MAP behavior? Expanded lattices are associated with reduced apparent GTP hydrolysis rates under steady-state assembly conditions and altered kinesin motility, whereas compact lattices preferentially promote tau binding and distinct motor interaction profiles. Together, these findings establish longitudinal lattice conformation as a regulatory parameter and position microtubule-stabilizing agents as chemical tools that bias a dynamic structural landscape with predictable catalytic and transport consequences. Significance statementMicrotubules generate force and support intracellular transport through lattice geometries selectively recognized by motor proteins and microtubule-associated proteins. Microtubule-stabilizing drugs such as taxanes and epothilones are widely used in chemotherapy but can cause neurotoxicity, likely because stabilization alters lattice architecture rather than simply preventing depolymerization. Here, we show that stabilizing ligands bias microtubules between two preferred longitudinal conformations, compact and expanded, that can switch within seconds of binding, while lateral organization adjusts slower. These structural states differentially regulate GTP hydrolysis and recognition by tau and kinesin, linking lattice geometry to catalytic and transport functions. By establishing lattice conformation as a tunable regulatory parameter, this work provides a framework for interpreting drug effects and designing structure-selective stabilizers with improved therapeutic profiles.

biophysics↗

Tegmental atrophy in isolated REM sleep behaviour disorder: Ex vivo-informed in vivo imaging

Isolated rapid eye movement (REM) sleep behaviour disorder (iRBD) is an early-stage synucleinopathy characterized by brainstem pathology. In rodents, the pontine tegmentum contains an REM sleep centre, the sublaterodorsal nucleus (SLD), which expresses corticotropin-releasing hormone binding protein (CRHBP). While the involvement of brainstem pathophysiology is thus implicated in iRBD, its solid evidence remains scarce in humans due to the difficulty in identifying small brainstem nuclei with conventional MRI technology alone. Here, we aimed to detect tegmental atrophy in iRBD with voxel-based morphometry (VBM) analysis combined with a novel human brainstem atlas. Structural MRIs from 98 patients with iRBD and 114 controls were analysed to investigate grey matter volume (GMV) using VBM. Our unique approach involved detailed assessments of the VBM results, guided by a high-resolution MRI-based atlas of the human brainstem. This brainstem atlas was founded on ex vivo MRI of 10 postmortem human specimens. We validated it with CRHBP immunostaining, which aided in identifying putative REM sleep-regulating nuclei in humans. We applied this brainstem atlas to identify atrophy in specific brainstem regions in iRBD and correlate their volumes with clinical measures, including autonomic functions. VBM revealed a focal cluster of grey matter atrophy in the dorsal pontine tegmentum of iRBD patients, including the laterodorsal tegmental nucleus, ventral part (LDTgV) and the pedunculopontine tegmental nucleus (PTg). Our atlas-based analysis confirmed the LDTgV as the site of most conspicuous atrophy, revealing a significant volume reduction in iRBD patients compared to controls with a moderate effect size (Cohens d = 0.46, Bonferroni-corrected p = 0.019). Furthermore, greater atrophy in the LDTgV and the PTg was associated with more severe autonomic dysfunction as measured by Scales for Outcomes in Parkinsons Disease-Autonomic dysfunction (SCOPA-AUT) scores (partial r = -0.237, p = 0.019 and partial r = -0.236, p = 0.019, respectively). Histological analysis confirmed that the LDTgV is selectively enriched with CRHBP-positive neurons, a putative marker for REM sleep-on neurons. We provided novel evidence for the involvement of LDTgV, the putative human homolog of the murine SLD, in iRBD. The present findings advance our understanding of the neuroanatomical basis of iRBD and will contribute to the development of early biomarkers for -synucleinopathies.

neuroscience↗

Post-fertilization transcription initiation in an ancestral LTR retrotransposon drives lineage-specific genomic imprinting of ZDBF2

The imprinted ZDBF2 gene is controlled by oocyte-derived DNA methylation, but its epigenetic regulation is quite different from that of other canonically imprinted genes that are dependent on DNA methylation deposited in the gametes. At the ZDBF2 locus, maternal DNA methylation in the imprinted differentially methylated region (DMR) does not persist after implantation. Instead, a transient transcript expressed in the early embryo exclusively from the unmethylated paternal allele of the DMR, known as GPR1-AS in humans and Liz in mice, contributes to establishing secondary DMRs that maintain paternal expression of ZDBF2 in the somatic lineage. While the imprinting of ZDBF2 is evident in humans and mice, whether this process is conserved in other mammals has not been addressed. Here, we show that the first exon of human GPR1-AS overlaps with that of a long terminal repeat (LTR) belonging to the MER21C subfamily of retrotransposons. Although this LTR family appears and is amplified in Boroeutherians, the magnorder of placental mammals that includes the Euarchontoglires and Laurasiatheria superorders, the MER21C insertion into the GPR1-AS orthologous region occurred specifically in the common ancestor of Euarchontoglires, a clade that includes extant primates, rodents, and rabbits. The first exon of mouse Liz does not overlap with an annotated LTR in standard repeat annotation; however, promoter activity assay and multiple sequence alignment suggests that it retains a functionally conserved relationship with the MER21C-overlapping first exon of GPR1-AS. Furthermore, directional RNA sequencing of placental tissues from rabbits and nonhuman primates also revealed GPR1-AS orthologs, with their first exon embedded within the same ancestral LTR. In contrast, allele-specific expression profiling of cow and tammar wallaby, mammals outside the Euarchontoglires group, revealed expression from both alleles in all tissues analyzed. Taken together, these observations suggest that imprinting of ZDBF2 in Euarchontoglires had its genesis in the insertion of a MER21C element in their common ancestor. Our previous studies showed that LTRs reactivated in oocytes contribute to lineage-specific imprinting during mammalian evolution. The data presented here suggest that post-fertilization activation of an ancestral LTR-derived sequence can also contribute to the lineage-specific establishment of imprinted genes.

genomics↗

Lymphatic vessel development in human embryos

Lymphatic vessel development has been a subject of research for about 120 years. Studies employing mice and zebrafish models have elucidated that lymphatic endothelial cells (LECs) predominantly differentiate from venous endothelial cells via the expression of transcription factor Prospero homeobox protein 1 (Prox1), a master regulator of lymphatic vessel development. On the other hand, it has been found that LECs can also be generated from undifferentiated mesodermal or hemogenic endothelial cells, suggesting potential diversity in their origins depending on the organ or anatomical location. However, knowledge of human lymphatic vessel development remains limited. Here, we examined early lymphatic development in humans by analyzing 31 embryos and three 9-week old fetuses. We found that human embryos produce Prox1-expressing LECs in and around the cardinal veins, which converged to form initial lymph sacs. Furthermore, we also examined lymphatic vessel development in the heart, lungs, lower jaw, mesentery, intestines and kidneys. Lymphatic vessels appeared to develop at different rates in each organ and to display temporal differences in marker expression. These observation showed the possibility that there could exist different patterns of lymphatic vessel development across organs, which may reflect different cellular origins or developmental signaling in each organ. Our research clarifies the early development of human lymphatic vessels, contributing to a better understanding of the evolution and phylogenetic relationships of lymphatic systems, and enriching our knowledge of the role of lymphatics in various human diseases. Significance StatementLymphatic vessel development has been a focus of research for over a century. Recent studies across a variety of species have demonstrated that lymphatic endothelial cells originate from embryonic veins, and undifferentiated mesodermal cells. However, whether these findings are applicable to human has yet to be determined. In this study, we explored lymphatic vessel development in humans. Our analysis demonstrated that lymphatic endothelial cells in human embryos initially derived from embryonic veins. Notably, we found that lymphatic vessels in different organs displayed distinct developmental and marker expression patterns, suggesting a diversity in lymphatic vessel development across organs. Our research revealed the human lymphatic vessel development, contributing to the understanding of phylogenetics of lymphatic vessels and lymph-related diseases.

developmental biology↗

CD4+ T-cell immunity of SARS-CoV-2 patients determine pneumonia development

Most humans infected with SARS-CoV-2 will recover without developing pneumonia. A few SARS-CoV-2 infected patients, however, develop pneumonia, and occasionally develop cytokine storms. In such cases, it is assumed that there is an inadequate immune response to eliminate viral infected cells and an excessive inappropriate immune response causing organ damage, but little is known about this mechanism. In this study, we used single cell RNA sequencing and mass cytometry to analyze peripheral blood T cells from patients hospitalized with proven COVID-19 infection in order to clarify the differences in host immune status among COVID-19 pneumonia cases, non-pneumonia cases, and healthy controls. The results showed that a specific CD4+ T cell cluster with chemokine receptor expression patterns, CXCR3+CCR4-CCR6+ (Th1/17), was less abundant in COVID-19 pneumonia patients. Interestingly, these CD4+ T-cell clusters were identical to those we have reported to correlate with antitumor immunity and predict programmed cell death (PD)-1 blockade treatment response in lung cancer. The Th1/17 cell percentages had biomarker performance in diagnosing pneumonia cases. In addition, CTLA-4 expression of type17 helper T cells (Th17) and regulatory T cells (Treg) was found to be significantly lower. This indicates that functional suppression of Th17 was less effective and Treg function was impaired in pneumonia cases. These results suggest that imbalance of CD4+ T-cell immunity generates excessive immunity that does not lead to viral eradication. This might be a potential therapeutic target mechanism to prevent severe viral infections. ImportanceIn this observational study, 49 consecutive patients with SARS-CoV-2 infection confirmed by PCR testing and admitted to Saitama Medical University Hospital and Saitama Medical University International Medical Centre between December 4, 2020 and January 17, 2022 were included. Of these 49 patients, 29 were diagnosed with COVID-19 pneumonia by computed tomography (CT) scan (Table 1). The unique CD4+ T-cell immunity with less abundant Th1/17 CD4+ T-cell cluster and low expression of CTLA-4 in Th17 and Treg was consistently found in SARS-CoV-2 pneumonia patients on admission and 1-week of admission. The imbalance of CD4+ T-cell immunity may contribute to develop pneumonia in SARS-CoV-2 virus infected patients by delaying viral clearance and resulting in an excessive immune response. O_TBL View this table: org.highwire.dtl.DTLVardef@1aac015org.highwire.dtl.DTLVardef@128c14dorg.highwire.dtl.DTLVardef@aacabaorg.highwire.dtl.DTLVardef@e39c8eorg.highwire.dtl.DTLVardef@13b439a_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 1C_FLOATNO O_TABLECAPTIONPatient demographics C_TABLECAPTION C_TBL

immunology↗

Simultaneous measurement of nascent transcriptome and translatome using 4-thiouridine metabolic RNA labeling and translating ribosome affinity purification

Regulation of gene expression in response to various biological processes, including extracellular stimulation and environmental adaptation requires de novo RNA synthesis and translation. Analysis of the coordinated and circular regulation of dynamic RNA synthesis and translation is required to determine functional protein production. However, reliable methods for the simultaneous measurement of nascent RNA synthesis and translation at the gene level are limited. Here, we developed a novel method for the simultaneous assessment of nascent RNA synthesis and translation by combining 4-thiouridine (4sU) metabolic RNA labeling and translating ribosome affinity purification (TRAP) using a monoclonal antibody against evolutionarily conserved ribosomal P-stalk proteins. The P-stalk-mediated TRAP (P-TRAP) technique recovered endogenous translating ribosomes, allowing easy translatome analysis of various eukaryotes. We validated this method in mammalian cells by demonstrating that acute unfolded protein response (UPR) in the endoplasmic reticulum (ER) induces dynamic reprograming of nascent RNA synthesis and translation. Our method can serve as a simple and powerful tool for analyzing the coordinated regulation of transcription and translation of individual genes in various eukaryotes.

molecular biology↗

Txn1 mutation causes epilepsy associated with vacuolar degeneration in the midbrain

Thioredoxin (TXN), encoded by Txn1, acts as a critical antioxidant in the defense against oxidative stress by regulating the dithiol/disulfide balance of interacting proteins. The role of TXN in the central nervous system (CNS) is largely unknown. A phenotype-driven study of N-ethyl-N-nitrosourea-mutated rats with running seizures at around five-week of age revealed the relevance of Txn1 mutations to CNS disorders. Genetic mapping identified Txn1-F54L in epileptic rats. The insulin-reducing activity of Txn1-F54L rats was approximately one-third that of the wild-type. Vacuolar degeneration in the midbrain, mainly in the thalamus and the inferior colliculus, was observed in the Txn1-F54L rats. The lesions displayed neuronal and oligodendrocyte cell death. Neurons in Txn1-F54L rats showed morphological changes in the mitochondria. Vacuolar degeneration began at three weeks of age, and spontaneous repair began at seven weeks; a dramatic change from cell death to repair occurred in the midbrain during a restricted period. In conclusion, Txn1 is essential for the development of the midbrain in juvenile rats.

neuroscience↗

High permeability of the CSF flow in the juvenile mouse brain by brain-wide DCE-MRI

The vasculature system with a lymphatic function in the brain is manifested as meningeal lymphatic vessels and the glymphatic system, which drain waste products from cerebrospinal fluid (CSF) and produce interstitial fluid. Invasion of stimulated immune cells or inflammatory cytokines during the maturation is regarded as a sign of the disruption of brain functions through excessive immune stresses. However, it is unclear when the lymphatic system is functionally completed and in which parts of the organ the brain immunity is privileged (i.e., the blood-brain barrier is fully established). Here, we visualized the whole-head signal of gadolinium (Gd) contrast agents in mouse brains to investigate the CSF flow from the signals of Gd-contrast agents using magnetic resonance imaging (MRI) in the course of developmental stages. We found higher Gd-signals in the olfactory bulbs, prefrontal cortex, parietal surface regions of the neocortex along with dorsal meningeal lymphatic vessels, ventral midbrain, and a part of cerebellum, as well as in the basal brain regions, at the immature stage of postnatal (P) 4 weeks, compared to the P8-12 weeks. Our results suggest that the barrier of the vasculature system in mouse brains is still permeable until P1-month and small molecules can leak into the parenchyma.

neuroscience↗

The Brachypodium distachyon cold-acclimated plasma membrane proteome is primed for stress resistance

In order to survive sub-zero temperatures, some plants undergo cold acclimation where low, non-freezing temperatures and/or shortened day lengths allow cold hardening and survival during subsequent freeze events. Central to this response is the plasma membrane, where low-temperature is perceived and cellular homeostasis must be preserved by maintaining membrane integrity. Here, we present the first plasma membrane proteome of cold-acclimated Brachypodium distachyon, a model species for the study of monocot crops. A time course experiment investigated cold acclimation-induced changes in the proteome following two-phase partitioning plasma membrane enrichment and label-free quantification by nano-liquid chromatography mass spectrophotometry. Two days of cold acclimation were sufficient for membrane protection as well as an initial increase in sugar levels, and coincided with a significant change in the abundance of 154 proteins. Prolonged cold acclimation resulted in further increases in soluble sugars and abundance changes in more than 680 proteins, suggesting both a necessary early response to low-temperature treatment, as well as a sustained cold acclimation response elicited over several days. A meta-analysis revealed that the identified plasma membrane proteins have known roles in low-temperature tolerance, metabolism, transport, and pathogen defense as well as drought, osmotic stress and salt resistance suggesting crosstalk between stress responses, such that cold acclimation may prime plants for other abiotic and biotic stresses. The plasma membrane proteins identified here present keys to an understanding of cold tolerance in monocot crops and the hope of addressing economic losses associated with modern climate-mediated increases in frost events.

plant biology↗

The growth hormone gene has evolved independently in African Pygmy Mouse Mus minutoides

Mus minutoides (the African pygmy mouse) is one of the smallest mammals. We determined the nucleotide sequence of the growth hormone (Gh) gene and the sequence of the putative coding region in M. minutoides, where is predicted to be distinct in the functional and transcriptional regulatory regions between M. minutoides and Mus musculus (the House mouse). To investigate the evolutionary characteristics of Gh in M. minutoides, we constructed a phylogenetic tree based on the putative amino acid sequences of Gh in M. musculus and mammals by neighbor-joining method, suggesting that Gh diverged relatively earlier than other Mus genus and may have evolved independently in M. minutoides. Furthermore, analysis of Gh gene expression levels showed a tendency to be higher in M. minutoides than in M. musculus. Our results suggest that Gh may have evolved independently in M. minutoides and may have different functions and signaling in Mus genus.

genetics↗

Histological analysis of implantation embryos in large Japanese field mouse (Apodemus speciosus) and estimation of developmental stage.

The large Japanese field mice (Apodemus speciosus) are small rodent specie endemic to Japan. The genetic characteristics of A. speciosus is different chromosome numbers within one species. Furthermore, A. speciosus is used for research in radiation and genetics. In this present study, a pregnant A. speciosus was obtained, and histochemical analysis of the implanted embryos was performed and compared with developmental stages of the mouse. Although there were some differences, the structures of the implanted embryos including the primitive streak and placenta of A. speciosus were similar to that of the mouse. Our study will be important report in the construction of a developmental atlas of A. speciosus.

developmental biology↗

Genetic characteristics of Apodemus speciosus at Akiyoshidai Quasi-National Park in Yamaguchi Prefecture

The large Japanese field mouse (Apodemus speciosus) is a small rodent endemic to Japan. The mice have a genetic characteristic in which the number of chromosomes differs between those from western Japan and those from eastern Japan. A. spesiosus, found throughout Japan, is used as a model animal for geogenetics and monitoring of radiation effects of wildlife. In this present study, to elucidate the genetic characteristics of the mice Akiyoshidai Quasi-National Park in Yamaguchi Prefecture, we investigated mitochondrial DNA and chromosome numbers. As a result, A. speciosus from Yamaguchi Prefecture were classified into the Honshu-Shikoku-Kyushu group and had a western Japan-type chromosome set of 2n=46; however, some Yamaguchi Prefecture mice formed a genetic cluster in Yamaguchi Prefecture, suggesting that continuous monitoring is needed to reveal the dynamics of genetic diversity.

genetics↗

Direct visualization of translational GTPase factor-pool formed around the archaeal ribosomal P-stalk by high-speed atomic force microscopy

The ribosomal stalk protein plays an essential role in the recruitment of translational GTPase factors EF1A and EF2 to the ribosome and their GTP hydrolysis for efficient translation elongation. However, due to the flexible nature of the ribosomal stalk, its structural dynamics and mechanism of action remain unclear. Here, we applied high-speed atomic force microscopy (HS-AFM) to directly visualize the action of the archaeal ribosomal stalk (P-stalk). HS-AFM movies clearly demonstrated the wobbling motion of the P-stalk on the large ribosomal subunit, where the stalk base adopted two conformational states, a predicted canonical state, and a newly identified flipped state. Intriguingly, archaeal aEF1A and aEF2 molecules spontaneously assembled around the ribosomal P-stalk up to the maximum number of available binding sites. These results provide the first visual evidence for the factor-pooling mechanism and reveal that the ribosomal P-stalk promotes translation elongation by increasing the local concentration of translational GTPase factors.Competing Interest StatementThe authors have declared no competing interest.View Full Text

biophysics↗

Light-induced difference FTIR spectroscopy of primate blue-sensitive visual pigment at 163 K

Structural studies of color visual pigments lag far behind those of rhodopsin for scotopic vision. Using difference FTIR spectroscopy at 77 K, we report the first structural data of three primate color visual pigments, monkey red (MR), green (MG), and blue (MB), where the batho-intermediate (Batho) exhibits photoequilibrium with the unphotolyzed state. This photochromic property is highly advantageous for limited samples since the signal-to-noise ratio is improved, but may not be applicable to late intermediates, because of large structural changes to proteins. Here we report the photochromic property of MB at 163 K, where the BL intermediate, formed by the relaxation of Batho, is in photoequilibrium with the initial MB state. A comparison of the difference FTIR spectra at 77 and 163 K provided information on what happens in the process of transition from Batho to BL in MB. The coupled C11=C12 HOOP vibration in the planer structure in MB is decoupled by distortion in Batho after retinal photoisomerization, but returns to the coupled C11=C12 HOOP vibration in the all-trans chromophore in BL. This suggests that BL harbors a planer all-trans configuration of retinal. The Batho formation accompanies helical structural perturbation, which is relaxed in BL. The H-D unexchangeable X-H stretch weakens the hydrogen bond in Batho, but strengthens it in BL. Protein-bound water molecules that form an extended water cluster near the retinal chromophore change hydrogen bonds differently for Batho and BL, being stronger in the latter than in the initial state. In addition to structural dynamics, the present FTIR spectra at 163 K show no signals of protonated carboxylic acids as well as 77 K, suggesting that E181 is deprotonated in MB, Batho and BL.

biophysics↗

Unique retinal binding pocket of primate blue-sensitive visual pigment

The visual pigments of humans contain 11-cis retinal as the chromophore of light perception, and its photoisomerization to the all-trans form initiates visual excitation in our eyes. It is well known that three isomeric states of retinal (11-cis, all-trans, and 9-cis) are in photoequilibrium at very low temperatures such as 77 K. Here we report the lack of formation of the 9-cis form in monkey blue (MB) at 77 K, as revealed by light-induced difference FTIR spectroscopy. This indicates that the chromophore binding pocket of MB does not accommodate the 9-cis form, even though it accommodates the all-trans form by twisting the chromophore. Mutation of the blue-specific tyrosine at position 265 into tryptophan, which is highly conserved in other animal rhodopsins, led to formation of the 9-cis form in MB, suggesting that Y265 is one of the determinants of the unique photochemistry in blue pigments. We also found that 9-cis retinal does not bind to MB opsin, implying that the chromophore binding pocket does not accommodate the 9-cis form at physiological temperature. The unique property of MB is discussed based on the present results.

biochemistry↗

GTP-dependent formation of straight oligomers leads to nucleation of microtubules

Microtubule (MT) nucleation is essential for cellular activities, but its mechanism is not known because of the difficulty involved in capturing rare stochastic events in the early stage of polymerization. In cells, MTs are nucleated at tubulin concentrations significantly lower than those required for spontaneous nucleation in vitro. The high efficiency of nucleation is due to the synergistic effects of various cellular factors, but the underlying mechanism has not been clarified yet. Here, combining negative stain electron microscopy and kinetic analysis, we demonstrate that the formation of single-stranded straight oligomers with critical size is essential for nucleation in vitro. While the single-stranded oligomers of GTP-tubulin that form prior to MT nucleation show variable curvatures including a few straight oligomers, only curved oligomers are observed among the GDP-bound counterparts. The Y222F mutation in {beta}-tubulin increases the proportion of straight oligomers and drastically accelerates MT nucleation. Our results support a model in which GTP binding causes a small shift in the distribution of oligomer curvature, generating a minor population of straight oligomers compatible with lateral association and further growth to MTs. Our study suggests that cellular factors involved in nucleation promote it via stabilization of straight oligomers.

biophysics↗