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Baba, Takumi*; Ueno, Go*; Oe, Chika*; Saji, Shuku*; Yamamoto, Sachiko*; Yamamoto, Masaki*; Nakagawa, Hiroshi; Okazaki, Nobuo*; Ouchida, Mamoru*; Kawasaki-Ohmori, Iori*; et al.
Biochimica et Biophysica Acta; General Subjects, 1869(12), p.130860_1 - 130860_7, 2025/12
Times Cited Count：0 Percentile：0.00(Biochemistry & Molecular Biology)Neuronal degeneration and chronic kidney disease have been observed in Trx-F54L mutant rats; however, the details of why the Trx mutation causes these phenomena remain unknown. This study investigates molecular changes caused by the F54L mutation and explores the factors contributing to the Adem rat phenotype. Results showed that the F54L mutant was less active than WT Txn1 on insulin substrates, but no significant difference in redox potential was observed. On the other hand, F54L is more sensitive to degeneration in the body temperature range than the wild type. Furthermore, the crystal structure showed that F54 formed hydrophobic interactions with the surrounding hydrophobic amino acids. Moreover, the MD simulation results show increased fluctuations around the F54L mutation, as well as a tendency for the distance between residues C32 and C35 at the catalytic center to widen. The molecular dynamics of the F54L mutation may affect the substrate reduction activity, thermal stability, and kinetic stability.
Nakagawa, Hiroshi; Kataoka, Mikio*
Biochimica et Biophysica Acta; General Subjects, 1864(4), p.129536_1 - 129536_6, 2020/04
Times Cited Count：7 Percentile：28.24(Biochemistry & Molecular Biology)The rigidity and flexibility of a protein is reflected in its structural dynamics. Studies on protein dynamics often focus on flexibility and softness; this review focuses on protein structural rigidity. The extent of rigidity can be assessed experimentally with incoherent neutron scattering; a method that is complementary to molecular dynamics simulation. This experimental technique can provide information about protein dynamics in timescales of pico- to nanoseconds and at spatial scales of nanometers; these dynamics can help quantify the rigidity of a protein by indices such as force constant, Boson peak, dynamical transition, and dynamical heterogeneity. These indicators also reflect the rigidity of a protein's secondary and tertiary structures. In addition, the indices reveal how rigidity is influenced by different environmental parameters, such as hydration, temperature, pressure, and protein-protein interactions. Hydration affects both rigidity and softness more than other environmental factors. Interestingly, hydration affects harmonic and anharmonic motions in opposite ways. This difference is probably due to the protein's dynamic coupling with water molecules via hydrogen bonding.
Seto, Hideki; Ito, Shinichi; Yokoo, Tetsuya*; Endo, Hitoshi*; Nakajima, Kenji; Shibata, Kaoru; Kajimoto, Ryoichi; Kawamura, Seiko; Nakamura, Mitsutaka; Kawakita, Yukinobu; et al.
Biochimica et Biophysica Acta; General Subjects, 1861(1), p.3651 - 3660, 2017/01
Times Cited Count：42 Percentile：81.58(Biochemistry & Molecular Biology)J-PARC, Japan Proton Accelerator Research Complex provides short pulse proton beam at a repetition rate 25 Hz and the maximum power is expected to be 1 MW. Materials and Life Science Experimental Facility (MLF) has 23 neutron beam ports and 21 instruments have already been operated or under construction / commissioning. There are 6 inelastic / quasi-elastic neutron scattering spectrometers and the complementary use of these spectrometers will open new insight for life science.
