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Miyakawa, Kazuya; Kashiwaya, Koki*; Komura, Yuto*; Nakata, Kotaro*
Geochemical Journal, 57(5), p.155 - 175, 2023/00
Times Cited Count：0 Percentile：0.01(Geochemistry & Geophysics)In the thick marine sediments, groundwater altered from seawater during the burial diagenesis may exist. Such altered ancient seawater will be called fossil seawater. In such a field, groundwater flow is considered extremely slow because it is not affected by the seepage of meteoric water even after the uplift. During diagenesis, dehydration from silicates causes changes such as a decrease in the salinity of the porewater. However, dehydration reactions alone cannot quantitatively explain water chemistry changes. In this study, we developed an analytical model that considers the dehydration reaction from silicates during the burial process and the upward migration of porewater due to compaction and examined the possible evolution of porewater chemistry. The results showed that the water chemistry, which was strongly influenced by the dehydration reaction from opal-A to quartz and from smectite, was similar to the observations from boring surveys. The results suggest that the fossil seawater formed during the diagenesis may have been preserved since the uplift and strongly supports the slow groundwater flow in the area where the fossil seawater exists.
resolutionChatake, Toshiyuki*; Kurihara, Kazuo; Tanaka, Ichiro*; Tsyba, I.*; Bau, R.*; Jenney, F. E. Jr.*; Adams, M. W. W.*; Niimura, Nobuo
Acta Crystallographica Section D, 60(8), p.1364 - 1373, 2004/08
Times Cited Count：34 Percentile：88.87(Biochemical Research Methods)A neutron diffraction study has been carried out at 1.6 resolution on a mutant rubredoxin from 
using the BIX-3 single-crystal diffractometer at the JRR-3 reactor of JAERI. In order to study the unusual thermostability of rubredoxin from 
, the hydrogen-bonding patterns were compared between the native and a 'triple-mutant' variant where three residues were changed so that they are identical to those in a mesophilic rubredoxin. In the present study, some minor changes were found between the wild-type and mutant proteins in the hydrogen-bonding patterns of the Trp3/Tyr3 region. The H/D-exchange ratios in the protein were also studied. The results suggest that the backbone amide bonds near the four Cys residues of the FeS
redox center are most resistant to H/D exchange. In addition, the 1.6 resolution of the present neutron structure determination has revealed a more detailed picture than previously available of some portions of the water structure, including ordered and disordered O-D bonds.
by BIX-3, a single-crystal diffractometer for biomacromoleculesKurihara, Kazuo; Tanaka, Ichiro*; Chatake, Toshiyuki*; Adams, M. W. W.*; Jenney, F. E. Jr.*; Moiseeva, N.*; Bau, R.*; Niimura, Nobuo
Proceedings of the National Academy of Sciences of the United States of America, 101(31), p.11215 - 11220, 2004/08
Times Cited Count：48 Percentile：61.07(Multidisciplinary Sciences)The structure of a rubredoxin (Rd) from , an organism that grows optimally at 100 
C, was determined using the neutron single-crystal diffractometer for biological macromolecules (BIX-3) at the JRR-3 reactor of JAERI. Data were collected at room temperature up to a resolution of 1.5 , and the completeness of the data set was 81.9 %. The model contains 306 H atoms and 50 D atoms. A total of 37 hydration water molecules were identified. The model has been refined to final agreement factors of 
= 18.6 % and 
= 21.7 %. Several orientations of the O-D bonds of side chains, whose assignments from X-ray data were previously ambiguous, were clearly visible in the neutron structure. While most backbone N-H bonds had undergone some degree of H/D exchange throughout the molecule, five H atom positions still had distinctly negative (H) peaks. The neutron Fourier maps clearly showed the details of an extensive set of H bonds involving the ND
terminus that may contribute to the unusual thermostability of this molecule.
Niimura, Nobuo; Kurihara, Kazuo; Tanaka, Ichiro
Kagaku, 59(2), p.46 - 47, 2004/02
no abstracts in English
Kurihara, Kazuo; Tanaka, Ichiro; Adams, M. W. W.*; Jenney, F. E. Jr.*; Moiseeva, N.*; Bau, R.*; Niimura, Nobuo
Journal of the Physical Society of Japan, Vol.70, Supplement A, p.400 - 402, 2001/05
With the new single-crystal diffractometer BIX-3 at the JRR-3M reactor of JAERI, a single-crystal neutron diffraction analysis of the structure of the small protein rubredoxin from the hyperthermophile Pyrococcus furiosus is currently under way. Data were collected at room temperature up to a resolution of 1.5 
intervals in 
and exposure times ranging from 60 to 77 minutes per frame. The completeness factor of the 1.5-
. Included in the refinement are 301 hydrogen atoms and 40 deuterium atoms, and 29 water molecules were also identified. In the present model, the current value for R and R
are 24.0 
and 26.3 , respectively.
Miyakawa, Kazuya; Kashiwaya, Koki*; Komura, Yuto*; Nakata, Kotaro*
no journal, ,
no abstracts in English
