Controlling the Substrate Specificity of an Enzyme through Structural Flexibility by Varying the Salt-Bridge Density

Many enzymes, particularly in one single family, with highly conserved structures and folds exhibit rather distinct substrate specificities. The underlying mechanism remains elusive, the resolution of which is of great importance for biochemistry, biophysics, and bioengineering. Here, we performed a neutron scattering experiment and molecular dynamics (MD) simulations on two structurally similar CYP450 proteins; CYP101 primarily catalyzes one type of ligands, then CYP2C9 can catalyze a large range of substrates. We demonstrated that it is the high density of salt bridges in CYP101 that reduces its structural flexibility, which controls the ligand access channel and the fluctuation of the catalytic pocket, thus restricting its selection on substrates. Moreover, we performed MD simulations on 146 different kinds of CYP450 proteins, spanning distinct biological categories including Fungi, Archaea, Bacteria, Protista, Animalia, and Plantae, and found the above mechanism generally valid. We demonstrated that, by fine changes of chemistry (salt-bridge density), the CYP450 superfamily can vary the structural flexibility of its member proteins among different biological categories, and thus differentiate their substrate specificities to meet the specific biological needs. As this mechanism is well-controllable and easy to be implemented, we expect it to be generally applicable in future enzymatic engineering to develop proteins of desired substrate specificities.

Stoichiometric Tuning of Lattice Flexibility and Na Diffusion in NaAlSiO4: Quasielastic Neutron Scattering Experiment and Ab-initio Molecular Dynamics Simulations

We have performed quasielastic neutron scattering (QENS) experiments up to 1243 K and ab-initio molecular dynamics (AIMD) simulations to investigate the Na diffusion in various phases of NaAlSiO4 (NASO), namely,...

Manufacturing and Testing of an In Situ Stretching Sample Environment Equipment for Neutron Scattering Experiments

Neutron scattering technology is one of the most promising ways to observe microstructures of different materials. As a powerful microstructure characterization technology, neutron scattering is widely used in many disciplines. With the help of sample environment equipment, the microstructure detection for materials in various application scenarios can be further realized. In order to detect the microstructure changes of materials under different tensile conditions, an in situ stretching sample environment equipment for neutron scattering experiments was designed and manufactured. Stretching force holding test, sample breaking test, and vacuum maintaining test were carried out. In those tests, a tensile force holding test with no less than 5 hours, a breaking test with a screw bolt as the sample, and a vacuum leakage rate test with no less than 5 hours were obtained, respectively. Through analyzing values obtained, it is shown that the developed prototype of the sample environment equipment is able to meet the experiment requirements. The present prototype provides a reference for further development of sample environment equipment for different application scenarios in neutron scattering experiment.

Measurement of temperature-dependent thermal neutron spectrum in CaH2 moderator material for space reactor

In order to accurately design a CaH2 moderated small high-temperature reactor, it is necessary to experimentally confirm the temperature-dependent thermal neutron spectrum in the CaH2 moderator material. To obtain the temperature-dependent thermal neutron spectrum in the CaH2, we have carried out the neutron scattering experiment using the TOF method at the Kyoto University Institute for Integrated Radiation and Nuclear Science - Linear Accelerator (KURNS-LINAC). In present experiment, we raised the temperature of the CaH2 from a room temperature 294 k to 392 K and 565 K, and obtained the change of the thermal neutron TOF spectrum for the increase of temperature. The obtained thermal neutron TOF spectra in the CaH2 are compared with the calculated results using the Monte-Carlo simulation code MCNP-6.2.

Characteristics and Structure of Hopeite-Mineral (Type A3(PO4)2.4H2O)

The aim of the study was to gain more information about the structural changes during the dewatering reactions of the above compounds. The paper is focus on the low-temperature absorption of hopeite clay mineral, afterward the phases are examined for the dependence of temperature at different pressures. Hopeite shows signs of a phase transformation. Their use for the dental cement industry as a lubricant for cold-rolling mills is to be emphasized, such as coating with phosphate mineral or carbonaceous crystal. This is shown by the appearance of the new reflexes. The observed changes take place below the dewatering known from the literature. The phase change was investigated using a neutron scattering experiment. A temperature-pressure phase diagram of the dewatering could be set up in the range of 275 K to 380 K and 10-3 mBar to 103 mBar with the temperature-dependent powder diffractometer at different pressures and the temperature-dependent neutron scattering experiment. In this work, it has been proved that the dewatering of the hopeite is dependent on pressure and that the dewatering process of the hopeite is a reversible process.