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Journal Articles

Seven cysteine-deficient mutants depict interplay between thermal and chemical stabilities of individual cysteine residues in MAP kinase JNK1

Nakaniwa, Tetsuko*; Kuroki, Ryota; Kinoshita, Takayoshi*

Nihon Kessho Gakkai-Shi, 55(3), p.197 - 202, 2013/06

To characterize the role of cysteine residues on the structure, function and stability of JNK1, we prepared and evaluated the wild-type JNK1 and seven cysteine-deficient JNK1 proteins. The solvent exposed cysteine residues did not influence biological function and mutating these residues raised the thermal stability because of newly formed hydrogen bonds and of higher hydration as speculated by the mutant structures. The surface cysteine involved in the molecular surface hydrophobic pocket did not affect biological function; although a moderate thermal destabilization was observed. Cysteines in the loosely-assembled hydrophobic environment moderately contributed to thermal stability and the mutations of these cysteines had negligible effect on enzyme activity. The other cysteines are involved in the tightly-filled hydrophobic core and mutation of these residues conferred the adverse effects on the thermal stability and enzyme activity.

Journal Articles

Seven cysteine-deficient mutants depict the interplay between thermal and chemical stabilities of individual cysteine residues in mitogen-activated protein kinase c-Jun N-terminal kinase 1

Nakaniwa, Tetsuko*; Fukata, Harumi*; Inoue, Tatsuya*; Goda, Masaki*; Nakai, Ryoko*; Kirii, Yasuyuki*; Adachi, Motoyasu; Tamada, Taro; Segawa, Shinichi*; Kuroki, Ryota; et al.

Biochemistry, 51(42), p.8410 - 8421, 2012/10

 Times Cited Count:17 Percentile:43.17(Biochemistry & Molecular Biology)

Protein kinase is a vital drug target for the treatment of a wide range of diseases. To investigate the effect of cysteine mutation on the function, stability and structure of kinase, free cysteines of c-Jun N-terminal kinase 1 (JNK1) were systematically removed by mutation. Two cysteine-destructed mutants in which three (M3) and seven (M7) cysteine residues are removed, yielded about 5 and 2 times than wild type JNK-1 (M0). SDS PAGE analysis showed that the aggregation was less in the case of M3 and M7. Thermal unfolding experiment of M0, M3 and M7 using by differential scanning calorimetry proceeded at least three state unfolding. Crystal structure of the M3 mutant was determined to 2.6 ${AA}$ resolution, which was identical to that of the wild-type. Consequently, due to the highest yield, its improved stability against aggregation and its structural similarity to the wild type, the M3 mutant is suitable for the use of further characterization of its function and structure.

Journal Articles

Elucidation of advanced function by combined high-resolution neutron and X-ray analysis

Tamada, Taro; Kinoshita, Takayoshi*; Tada, Toshiji*; Kuroki, Ryota

Nihon Kessho Gakkai-Shi, 52(2), p.133 - 138, 2010/04

To help resolve long-standing questions regarding the catalytic activity of the serine proteases the structure of porcine pancreatic elastase has been analyzed by high-resolution neutron (1.65 ${AA}$ resolution) and X-ray (0.94 ${AA}$ resolution) crystallography. In order to mimic the tetrahedral transition intermediate, a peptidic inhibitor was used. The neutron and X-ray data show that the hydrogen bond between His57 and Asp102 is not consistent with a low-barrier hydrogen which is predicted to have the hydrogen midway between the donor and acceptor atom. The neutron analysis also shows that the oxygen of the oxopropyl group of the inhibitor is present as an oxygen anion rather than a hydroxyl group, supporting the role of the "oxyanion hole" in stabilizing the tetrahedral intermediate in catalysis.

Journal Articles

Combined high-resolution neutron and X-ray analysis of inhibited elastase confirms the active-site oxyanion hole but rules against a low-barrier hydrogen bond

Tamada, Taro; Kinoshita, Takayoshi*; Kurihara, Kazuo; Adachi, Motoyasu; Ohara, Takashi; Imai, Keisuke*; Kuroki, Ryota; Tada, Toshiji*

Journal of the American Chemical Society, 131(31), p.11033 - 11040, 2009/07

 Times Cited Count:56 Percentile:79.06(Chemistry, Multidisciplinary)

To help resolve long-standing questions regarding the catalytic activity of the serine proteases the structure of porcine pancreatic elastase has been analyzed by high-resolution neutron and X-ray crystallography. In order to mimic the tetrahedral transition intermediate a peptidic inhibitor was used. A single large crystal was used to collect room-temperature neutron data to 1.65 ${AA}$ resolution and X-ray data to 1.20 ${AA}$ resolution. Another crystal provided a low-temperature X-ray data set to 0.94 ${AA}$ resolution. The neutron data are to higher resolution than previously reported for a serine protease and the X-ray data are comparable with other studies. The neutron and X-ray data show that the hydrogen bond between His57 and Asp102 (chymotrypsin numbering) is 2.60 ${AA}$ in length and that the hydrogen-bonding hydrogen is 0.80-0.96 ${AA}$ from the histidine nitrogen. This is not consistent with a low-barrier hydrogen which is predicted to have the hydrogen midway between the donor and acceptor atom. The observed interaction between His57 and Asp102 is essentially a short but conventional hydrogen bond, sometimes described as a short ionic hydrogen bond. The neutron analysis also shows that the oxygen of the oxopropyl group of the inhibitor is present as an oxygen anion rather than a hydroxyl group, supporting the role of the "oxyanion hole" in stabilizing the tetrahedral intermediate in catalysis.

Journal Articles

Crystallization of porcine pancreatic elastase and a preliminary neutron diffraction experiment

Kinoshita, Takayoshi*; Tamada, Taro; Imai, Keisuke*; Kurihara, Kazuo; Ohara, Takashi; Kuroki, Ryota

Acta Crystallographica Section F, 63(4), p.315 - 317, 2007/04

 Times Cited Count:8 Percentile:66.61(Biochemical Research Methods)

Porcine pancreatic elastase (PPE) resembles the attractive drug target leukocyte elastase, which has been implicated in a number of inflammatory disorders. In order to investigate the structural characteristics of the covalent inhibitor bound to PPE, including hydrogen and hydration of water, a single crystal of PPE for neutron diffraction study was grown in D$$_{2}$$O containing 0.2 M sodium sulfate (pD=5.0) using the sitting-drop vapor diffusion method. The crystal was grown to a size of 1.6 mm$$^{3}$$ by repeated macro-seeding. The neutron diffraction data were collected at room temperature using a BIX-3 diffractometer at the JRR-3 research reactor of the Japan Atomic Energy Agency (JAEA). The data set was integrated and scaled to 2.3${AA}$ resolution with space group P212121 and cell dimensions of a=51.2${AA}$, b=57.8${AA}$ and c=75.6${AA}$.

Oral presentation

Ultrahigh-resolution X-ray and neutron structural analysis of the complex of elastase with lead compound to drug

Tamada, Taro; Kinoshita, Takayoshi*; Kuroki, Ryota; Tada, Toshiji*

no journal, , 

no abstracts in English

Oral presentation

Neutron structural analysis of the complex of elastase with lead compound to drug

Tamada, Taro; Kinoshita, Takayoshi*; Tada, Toshiji*; Kurihara, Kazuo; Ohara, Takashi; Kuroki, Ryota

no journal, , 

no abstracts in English

Oral presentation

Neutron structural analysis of the complex of elastase with lead compound to drug

Tamada, Taro; Kinoshita, Takayoshi*; Ohara, Takashi; Kurihara, Kazuo; Tada, Toshiji*; Kuroki, Ryota

no journal, , 

no abstracts in English

Oral presentation

Neutron structure analysis of the complex of porcine pancreatic elastase with its inhibitor

Tamada, Taro; Kinoshita, Takayoshi*; Ohara, Takashi; Kurihara, Kazuo; Tada, Toshiji*; Kuroki, Ryota

no journal, , 

no abstracts in English

Oral presentation

Tertiary structure of porcine pancreatic elastase in complex with a potent inhibitor determined by neutron crystallography

Tamada, Taro; Kinoshita, Takayoshi*; Ohara, Takashi; Kurihara, Kazuo; Imai, Keisuke*; Kuroki, Ryota; Tada, Toshiji*

no journal, , 

Porcine pancreatic elastase (PPE) is a serine protease classified in the chymotrypsin family. We determined two crystal structures of PPE in complex with peptidic inhibitor FR130180, which mimics the tetrahedral transition intermediate. One is the structure determined using 1.65 ${AA}$ resolution neutron diffraction in the combination with 1.20 ${AA}$ resolution X-ray diffraction data obtained using the same crystal. The other is the sub-angstrom X-ray structure determined to 0.94 ${AA}$ resolution. The structural features obtained from neutron diffraction and X-ray diffraction were compared to understand the detailed scheme of interaction between PPE and its inhibitor. From the observation of hydrogen atom located between the active site His57 and Asp102 by neutron and high resolution X-ray diffraction experiment, it is revealed that the interaction is not a low barrier hydrogen bond, but a short ionic hydrogen bond. Moreover, using neutron diffraction data we show that the hydroxyl group of inhibitor FR13080 bound within the "oxy-anion hole" exhibits an oxy-anion-like tetrahedral intermediate.

Oral presentation

Structure of porcine pancreatic elastase in complex with peptidic inhibitor determined by high resolution neutron and X-ray crystallography

Tamada, Taro; Kinoshita, Takayoshi*; Kurihara, Kazuo; Adachi, Motoyasu; Ohara, Takashi; Tada, Toshiji*; Kuroki, Ryota

no journal, , 

To help resolve long-standing questions regarding the catalytic activity of the serine proteases the structure of porcine pancreatic elastase has been analyzed by high-resolution neutron and X-ray crystallography. In order to mimic the tetrahedral transition intermediate a peptidic inhibitor was used. A single large crystal was used to collect room-temperature neutron data to 1.65 ${AA}$ resolution and X-ray data to 1.20 ${AA}$ resolution. Another crystal provided a low-temperature X-ray data set to 0.94 ${AA}$ resolution. The neutron data are to higher resolution than previously reported for a serine protease and the X-ray data are comparable with other studies. The neutron and X-ray data show that the hydrogen bond between His57 and Asp102 is 2.60 ${AA}$ in length and that the hydrogen-bonding hydrogen is 0.80-0.96 ${AA}$ from the histidine nitrogen. This is not consistent with a low-barrier hydrogen which is predicted to have the hydrogen midway between the donor and acceptor atom. The observed interaction between His57 and Asp102 is essentially a short but conventional hydrogen bond, sometimes described as a short ionic hydrogen bond. The neutron analysis also shows that the oxygen of the oxopropyl group of the inhibitor is present as an oxygen anion rather than a hydroxyl group, supporting the role of the "oxyanion hole" in stabilizing the tetrahedral intermediate in catalysis.

Oral presentation

Improvement of crystal packing of human MAP kinase JNK1 by point mutation for neutron crystallography

Nakaniwa, Tetsuko*; Fukata, Harumi*; Inoue, Tatsuya*; Kinoshita, Takayoshi*; Adachi, Motoyasu; Tamada, Taro; Kuroki, Ryota; Tada, Toshiji*

no journal, , 

JNK1 is a MAP kinase responsible for response of stress. JNK1 has 4 and 3 cysteine residues in embedded region and at molecular surface, respectively. Those cysteine residues would cause inactivation and aggregation of the molecule. Based of the analysis of packing in crystal of isozyme of JNK1, we found more salt bridge and hydrogen bonding interactions on the interface. In this study, we focus on the two cysteine residues and introduced modification into M3 mutant previously reported.

Oral presentation

High-resolution neutron structural analyses of porcine pancreatic elastase

Tamada, Taro; Kinoshita, Takayoshi*; Yamada, Mitsugu; Kurihara, Kazuo; Ohara, Takashi; Adachi, Motoyasu; Tada, Toshiji*; Kuroki, Ryota

no journal, , 

no abstracts in English

Oral presentation

High-resolution neutron structure analyses of porcine pancreatic elastase

Tamada, Taro; Kinoshita, Takayoshi*; Kurihara, Kazuo; Tada, Toshiji*; Kuroki, Ryota

no journal, , 

Elastase is a serine protease classified in the chymotrypsin family, and is attractive target for studies of structure based drug design (SBDD). The structural information including hydrogen positions and hydration will help us to further elucidate the catalytic mechanism of serine protease. To obtain such structural information, we performed the neutron structure analyses of porcine pancreatic elastase (PPE) with and without its inhibitor using diffraction data obtained at a BIX-3 diffractometer in the research reactor JRR-3. The PPE structure in complex with/without peptidic inhibitor, which was used to mimic the tetrahedral intermediate state, was determined to 1.65/1.90 ${AA}$ resolution, respectively. This structural information allows us to understand the role of resting state upon the catalytic reaction. Furthermore, the structural change of the active site residues including hydration structure obtained from the comparison between structures with and without inhibitor may help designing potent inhibitors by SBDD.

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