Deep Knot Structure for Construction of Active Site and Cofactor Binding Site of tRNA Modification Enzyme

AbstractThe tRNA(Gm18) methyltransferase (TrmH) catalyzes the 2′-O methylation of guanosine 18 (Gua18) of tRNA. We solved the crystal structure of Thermus thermophilus TrmH complexed with S-adenosyl-L-methionine at 1.85 Å resolution. The catalytic domain contains a deep trefoil knot, which mutational analyses revealed to be crucial for the formation of the catalytic site and the cofactor binding pocket. The tRNA dihydrouridine(D)-arm can be docked onto the dimeric TrmH, so that the tRNA D-stem is clamped by the N- and C-terminal helices from one subunit while the Gua18 is modified by the other subunit. Arg41 from the other subunit enters the catalytic site and forms a hydrogen bond with a bound sulfate ion, an RNA main chain phosphate analog, thus activating its nucleophilic state. Based on Gua18 modeling onto the active site, we propose that once Gua18 binds, the phosphate group activates Arg41, which then deprotonates the 2′-OH group for methylation

Long Rayleigh length confocal microscope: A fast evaluation tool for obtaining quantum properties of color centers

Color centers in wide band-gap semiconductors, which have superior quantum properties even at room temperature and atmospheric pressure, have been actively applied to quantum sensing devices. Characterization of the quantum properties of the color centers in the semiconductor materials and ensuring that these properties are uniform over a wide area are key issues for developing quantum sensing devices based on color center. In this article, we will describe the principle and performance of a newly developed confocal microscope system with a long Rayleigh length (LRCFM). This system can characterize a wider area faster than the confocal microscope systems commonly used for color center evaluation

Microscopic Temperature Control Reveals Cooperative Regulation of Actin–Myosin Interaction by Drebrin E

胎児の神経を形作る仕組みは精密な温度センサー --母体の体温維持が神経の成熟に重要であることを示唆--. 京都大学プレスリリース. 2021-11-10.Drebrin E is a regulatory protein of intracellular force produced by actomyosin complexes, that is, myosin molecular motors interacting with actin filaments. The expression level of drebrin E in nerve cells decreases as the animal grows, suggesting its pivotal but unclarified role in neuronal development. Here, by applying the microscopic heat pulse method to actomyosin motility assay, the regulatory mechanism is examined from the room temperature up to 37 °C without a thermal denaturing of proteins. We show that the inhibition of actomyosin motility by drebrin E is eliminated immediately and reversibly during heating and depends on drebrin E concentration. The direct observation of quantum dot-labeled drebrin E implies its stable binding to actin filaments during the heat-induced sliding. Our results suggest that drebrin E allosterically modifies the actin filament structure to regulate cooperatively the actomyosin activity at the maintained in vivo body temperature

Magnetic-field-dependent stimulated emission from nitrogen-vacancy centers in diamond

Negatively charged nitrogen-vacancy (NV) centers in diamond are promising magnetic field quantum sensors. Laser threshold magnetometry theory predicts improved NV center ensemble sensitivity via increased signal strength and magnetic field contrast. Here, we experimentally demonstrate laser threshold magnetometry. We use a macroscopic high-finesse laser cavity containing a highly NV-doped and low absorbing diamond gain medium that is pumped at 532 nm and resonantly seeded at 710 nm. This enables a 64% signal power amplification by stimulated emission. We test the magnetic field dependency of the amplification and thus demonstrate magnetic field-dependent stimulated emission from an NV center ensemble. This emission shows an ultrahigh contrast of 33% and a maximum output power in the milliwatt regime. The coherent readout of NV centers pave the way for novel cavity and laser applications of quantum defects and diamond NV magnetic field sensors with substantially improved sensitivity for the health, research, and mining sectors

Fabrication of a quantum sensor to reveal a topic in thermal physiology

これまで発表者が行ってきた筋肉と温度の関係についての研究の紹介を通して生体内の温度を測ることの面白さ、重要さを導入することで、温度を高感度に計測出来る量子センサー開発の重要性を説明する。量子センサーの一つとしてダイヤモンドNVセンターが挙げられるが、センサーの高感度化にはNVセンターを効率よく高濃度に形成することが求められる。そこで本発表では電子線照射を通したNVセンター形成メカニズムについて我々が行ってきた研究の一つを発表する。電子線照射は室温で実施し、照射を進める過程で熱処理を行い、その都度P1センター（格子中窒素不純物）の消費の様子や形成されたNVセンターの電荷状態、総量と照射量の関係を調べた。その結果、高効率でのNVセンター形成が確認出来た一方でP1センターがNVセンター以外の欠陥に消費されている可能性が示唆された。The 4th International Forum on Quantum Metrology and Sensin

Opto-thermal technologies for microscopic analysis of cellular temperature-sensing systems

Could enzymatic activities and their cooperative functions act as cellular temperature-sensing systems? This review introduces recent opto-thermal technologies for microscopic analyses of various types of cellular temperature-sensing system. Optical microheating technologies have been developed for local and rapid temperature manipulations at the cellular level. Advanced luminescent thermometers visualize the dynamics of cellular local temperature in space and time during microheating. An optical heater and thermometer can be combined into one smart nanomaterial that demonstrates hybrid function.These technologies have revealed a variety of cellular responses to spatial and temporal changes in temperature. Spatial temperature gradients cause asymmetric deformations during mitosis and neurite outgrowth. Rapid changes in temperature causes imbalance of intracellular Ca2+ homeostasis and membrane potential. Among those responses, heat-induced muscle contractions are highlighted. It is also demonstrated that the short-term heating hyperactivates molecular motors to exceed their maximal activities at optimal temperatures. We discuss future prospects for opto-thermal manipulation of cellular functions and contributions to obtain a deeper understanding of the mechanisms of cellular temperature-sensing systems

Opto-thermal technologies for microscopic analysis of cellular temperature-sensing systems

Could enzymatic activities and their cooperative functions act as cellular temperature-sensing systems? This review introduces recent opto-thermal technologies for microscopic analyses of various types of cellular temperature-sensing system. Optical microheating technologies have been developed for local and rapid temperature manipulations at the cellular level. Advanced luminescent thermometers visualize the dynamics of cellular local temperature in space and time during microheating. An optical heater and thermometer can be combined into one smart nanomaterial that demonstrates hybrid function.These technologies have revealed a variety of cellular responses to spatial and temporal changes in temperature. Spatial temperature gradients cause asymmetric deformations during mitosis and neurite outgrowth. Rapid changes in temperature causes imbalance of intracellular Ca2+ homeostasis and membrane potential. Among those responses, heat-induced muscle contractions are highlighted. It is also demonstrated that the short-term heating hyperactivates molecular motors to exceed their maximal activities at optimal temperatures. We discuss future prospects for opto-thermal manipulation of cellular functions and contributions to obtain a deeper understanding of the mechanisms of cellular temperature-sensing systems

Opto-thermal technologies for microscopic analysis of cellular temperature-sensing systems

Could enzymatic activities and their cooperative functions act as cellular temperature-sensing systems? This review introduces recent opto-thermal technologies for microscopic analyses of various types of cellular temperature-sensing system. Optical microheating technologies have been developed for local and rapid temperature manipulations at the cellular level. Advanced luminescent thermometers visualize the dynamics of cellular local temperature in space and time during microheating. An optical heater and thermometer can be combined into one smart nanomaterial that demonstrates hybrid function.These technologies have revealed a variety of cellular responses to spatial and temporal changes in temperature. Spatial temperature gradients cause asymmetric deformations during mitosis and neurite outgrowth. Rapid changes in temperature causes imbalance of intracellular Ca2+ homeostasis and membrane potential. Among those responses, heat-induced muscle contractions are highlighted. It is also demonstrated that the short-term heating hyperactivates molecular motors to exceed their maximal activities at optimal temperatures. We discuss future prospects for opto-thermal manipulation of cellular functions and contributions to obtain a deeper understanding of the mechanisms of cellular temperature-sensing systems