Hiroshi Kihara - Academia.edu (original) (raw)

Papers by Hiroshi Kihara

Meeting abstracts of the Physical Society of Japan, Mar 9, 2001

Journal of Applied Crystallography, Jan 17, 2004

FEBS Letters, Nov 2, 2001

Journal of Molecular Biology, 1998

Journal of Molecular Biology, Aug 1, 2002

1 Department of Physics, Kansai Medical University, 18-89 Uyama-Higashi Hirakata, Osaka 573-1136,... more 1 Department of Physics, Kansai Medical University, 18-89 Uyama-Higashi Hirakata, Osaka 573-1136, Japan 2 Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 14 2575 Sand Hill Rd, MS69, Menlo Park, CA, 94025 USA 3 Department of Biochemistry, Yong Loo Lin School of Medicine and Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 119260, Singapore 4 SR center, Ritsumeikan University, 1-1-1 Noji-Higashi Kusatsu, Shiga, 525-8577, Japan

Alexander Timchenko , Igor Serdyuk, Boris Negrutskii, Alexandra Novosylna , Evgeny Prituzhalov ,K... more Alexander Timchenko , Igor Serdyuk, Boris Negrutskii, Alexandra Novosylna , Evgeny Prituzhalov ,Kazumoto Kimura, Hiroshi Kihara 1 Institute of Protein Research, Pushchino, Russia, 142290; 2 Institute of Molecular Biology & Genetics NAS, Kiev, Ukraine, 03143; 3 Tula State University, Russia, 300600; Center for Medical Informatics, Dokkyo Medical Univ.Hospital, Mibu, Tochigi 321-0293, Japan 5 Department of Physics ,Kansai Medical University, Hirakata Osaka 573-1136, Japan

Result Structures are shown in Fig. 1. TF-crystal is from PDB 1w26. MC-crystal and NM-crystal are... more Result Structures are shown in Fig. 1. TF-crystal is from PDB 1w26. MC-crystal and NM-crystal are calculated by omitting domains from TF-crystal. The structure of TF in solution showed very similar to the crystal structure in shape and size. The structure of C419 in solution is similar to that of TF but slightly different from that of TF. The structure of C360 in solution is clearly different from that of TF. It is composed of two domains with a link part, which is coincident with the results of p(r) function having two peaks [1]. The apparent crystal structure of NM is special. As C-domain, located in the middle of the TF structure, is truncated, the NM crystal forms a “linear” structure. In contrast, NM in solution takes a compact structure. Thus, NM does not take the “linear” structure. The structure of MC (N-terminal is truncated) in solution remains almost the same structure with the crystal, which suggests the N-terminal does not affect the stability of M and C parts of the pr...

Results Scattering patterns for S1 and its fragment plotted in the Guinier coordinates showed the... more Results Scattering patterns for S1 and its fragment plotted in the Guinier coordinates showed the nonlinear behaviour with the initial ordinate indicating the association of protein molecules in free state and in the presence of GDP. The analysis of protein conformation in these associates from the scattering patterns plotted in the Kratky coordinates showed in both cases the bell-shaped plot corresponding to compact particles. At the same time the arrangement of monomers inside of associates differs for both proteins in free state and in the presence of GDP. In Fig.1, the plot for the evaluation of crosssection of particles is presented for protein S1. One can see the elongated conformation of associates in free state (Rc=30A) and some branched conformation upon interaction with GDP. For 49 kDa fragment of S1 one can see in Fig.2 that the addition of GDP stimulates the growth of elongated particles (Rc=13A) Thus, GDP strongly influences on the conformation of protein associates and...

Shushma DUBEY, Nirupama GUPTA, Masaji SHINJO, Jinsong, LI, Masaki KOJIMA, Yoshitaka MATSUMURA , H... more Shushma DUBEY, Nirupama GUPTA, Masaji SHINJO, Jinsong, LI, Masaki KOJIMA, Yoshitaka MATSUMURA , Hiroshi KIHARA*, Haripalsingh M. SONAWAT* 1 Dept. of Chem. Sci., Tata Institute of Fundamental Research, Mumbai – 400 005, India 2 Dept. of Phys., Kansai Medical University, Hirakata 573-1136, Japan 3 School of Life Sci., Tokyo Univ. of Pharm. & Life Sci., Hachioji, Tokyo 192-0392, Japan 4 Faculty of Engineering and Design, Kyoto Institute of Technol., Kyoto 606-8585, Japan.

Introduction Previously, we have reported thermodynamic and kinetic studies of src SH3 domain and... more Introduction Previously, we have reported thermodynamic and kinetic studies of src SH3 domain and its mutant, A45G, by various probes including X-ray solution scattering [1, 2]. We have started the study on another SH3 domain, PI3K SH3 domain. This protein is also mainly composed of -sheets as src SH3 domain [3]. In the present study, we performed guanidine-hydrochloride (GuHCl) titration of PI3K SH3 domain in the presence of 45% ethylene glycol at pH 6 at 4 C.

Introduction Protein polypeptide chain in strong denaturant solutions have the conformation of ra... more Introduction Protein polypeptide chain in strong denaturant solutions have the conformation of random coil approaching in ideal case to Gaussian coil conformation. In ideal solvent the dimension of coil is proportional to M. In good solvents the power is between 0.5-0.8. Study of unfolded proteins is the first step to elucidate a protein selforganisation and shed light on the conformation of partially folded proteins. Much information on protein conformation can be extracted from SAXS patterns. For Gaussian coil the scattering factor P(q) is given by formulae: P(x)=2*(x-1+exp(-x))/x, where x=(q*Rg) with Rgradius of gyration and qmodule of scattering vector[1]. Unfortunately, the Guinier region for Rg evaluation of Gaussian coil is very small (x<0.3) causing the difficulties with precise its measurement due to intermolecular interference influence on the SAXS pattern. But the region for Rg evaluation can be increased up to x<12 with about 0.5% accuracy according to approximatio...

Introduction Actual topic at present is the analysis of formation of amyloid fibrils which often ... more Introduction Actual topic at present is the analysis of formation of amyloid fibrils which often cause numerous diseases. This problem is closely related to the protein folding/ misfolding [1]. At the last time the application of artificial protein hybrid constructions (target proteinpolypeptide linker-carrier protein) for biochemical assays is widespread one. Very often the aim of such construction is to enhance the protein solubility and decrease its association. However, mutual influence of parts in the fused protein may significantly change their properties. Thus, the artificial protein albebetin (ABB) and its derivatives containing biologically active fragments of natural proteins form fibrils at physiological pH [2]. Recently it has been shown that the fused ABB-thioredoxin protein (ABB-TR) also forms amyloid-like aggregates. Here we study by SAXS this process in detail for ABB-TR and its H65F, H30F mutants.

Introduction We have studied trigger factor (TF), and its mutants. TF is a 3-domain protein, name... more Introduction We have studied trigger factor (TF), and its mutants. TF is a 3-domain protein, namely composed of Nterminal domain, middle part domain and C-terminal domain. To investigate conformational analysis, We prepared wild type TF and its truncated mutants, called C419, C360, NM and MC. They mean: 13 and 72 residues from C-terminal are truncated, whole C-domain is truncated, and whole N-domain is truncated, respectively. The number of amino acids for TF, C419, C360, NM and MC are 432, 419, 360, 251 and 287, respectively.

Meeting abstracts of the Physical Society of Japan, Mar 9, 2001

Journal of Applied Crystallography, Jan 17, 2004

FEBS Letters, Nov 2, 2001

Journal of Molecular Biology, 1998

Journal of Molecular Biology, Aug 1, 2002

1 Department of Physics, Kansai Medical University, 18-89 Uyama-Higashi Hirakata, Osaka 573-1136,... more 1 Department of Physics, Kansai Medical University, 18-89 Uyama-Higashi Hirakata, Osaka 573-1136, Japan 2 Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 14 2575 Sand Hill Rd, MS69, Menlo Park, CA, 94025 USA 3 Department of Biochemistry, Yong Loo Lin School of Medicine and Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 119260, Singapore 4 SR center, Ritsumeikan University, 1-1-1 Noji-Higashi Kusatsu, Shiga, 525-8577, Japan

Alexander Timchenko , Igor Serdyuk, Boris Negrutskii, Alexandra Novosylna , Evgeny Prituzhalov ,K... more Alexander Timchenko , Igor Serdyuk, Boris Negrutskii, Alexandra Novosylna , Evgeny Prituzhalov ,Kazumoto Kimura, Hiroshi Kihara 1 Institute of Protein Research, Pushchino, Russia, 142290; 2 Institute of Molecular Biology & Genetics NAS, Kiev, Ukraine, 03143; 3 Tula State University, Russia, 300600; Center for Medical Informatics, Dokkyo Medical Univ.Hospital, Mibu, Tochigi 321-0293, Japan 5 Department of Physics ,Kansai Medical University, Hirakata Osaka 573-1136, Japan

Result Structures are shown in Fig. 1. TF-crystal is from PDB 1w26. MC-crystal and NM-crystal are... more Result Structures are shown in Fig. 1. TF-crystal is from PDB 1w26. MC-crystal and NM-crystal are calculated by omitting domains from TF-crystal. The structure of TF in solution showed very similar to the crystal structure in shape and size. The structure of C419 in solution is similar to that of TF but slightly different from that of TF. The structure of C360 in solution is clearly different from that of TF. It is composed of two domains with a link part, which is coincident with the results of p(r) function having two peaks [1]. The apparent crystal structure of NM is special. As C-domain, located in the middle of the TF structure, is truncated, the NM crystal forms a “linear” structure. In contrast, NM in solution takes a compact structure. Thus, NM does not take the “linear” structure. The structure of MC (N-terminal is truncated) in solution remains almost the same structure with the crystal, which suggests the N-terminal does not affect the stability of M and C parts of the pr...

Results Scattering patterns for S1 and its fragment plotted in the Guinier coordinates showed the... more Results Scattering patterns for S1 and its fragment plotted in the Guinier coordinates showed the nonlinear behaviour with the initial ordinate indicating the association of protein molecules in free state and in the presence of GDP. The analysis of protein conformation in these associates from the scattering patterns plotted in the Kratky coordinates showed in both cases the bell-shaped plot corresponding to compact particles. At the same time the arrangement of monomers inside of associates differs for both proteins in free state and in the presence of GDP. In Fig.1, the plot for the evaluation of crosssection of particles is presented for protein S1. One can see the elongated conformation of associates in free state (Rc=30A) and some branched conformation upon interaction with GDP. For 49 kDa fragment of S1 one can see in Fig.2 that the addition of GDP stimulates the growth of elongated particles (Rc=13A) Thus, GDP strongly influences on the conformation of protein associates and...

Shushma DUBEY, Nirupama GUPTA, Masaji SHINJO, Jinsong, LI, Masaki KOJIMA, Yoshitaka MATSUMURA , H... more Shushma DUBEY, Nirupama GUPTA, Masaji SHINJO, Jinsong, LI, Masaki KOJIMA, Yoshitaka MATSUMURA , Hiroshi KIHARA*, Haripalsingh M. SONAWAT* 1 Dept. of Chem. Sci., Tata Institute of Fundamental Research, Mumbai – 400 005, India 2 Dept. of Phys., Kansai Medical University, Hirakata 573-1136, Japan 3 School of Life Sci., Tokyo Univ. of Pharm. & Life Sci., Hachioji, Tokyo 192-0392, Japan 4 Faculty of Engineering and Design, Kyoto Institute of Technol., Kyoto 606-8585, Japan.

Introduction Previously, we have reported thermodynamic and kinetic studies of src SH3 domain and... more Introduction Previously, we have reported thermodynamic and kinetic studies of src SH3 domain and its mutant, A45G, by various probes including X-ray solution scattering [1, 2]. We have started the study on another SH3 domain, PI3K SH3 domain. This protein is also mainly composed of -sheets as src SH3 domain [3]. In the present study, we performed guanidine-hydrochloride (GuHCl) titration of PI3K SH3 domain in the presence of 45% ethylene glycol at pH 6 at 4 C.

Introduction Protein polypeptide chain in strong denaturant solutions have the conformation of ra... more Introduction Protein polypeptide chain in strong denaturant solutions have the conformation of random coil approaching in ideal case to Gaussian coil conformation. In ideal solvent the dimension of coil is proportional to M. In good solvents the power is between 0.5-0.8. Study of unfolded proteins is the first step to elucidate a protein selforganisation and shed light on the conformation of partially folded proteins. Much information on protein conformation can be extracted from SAXS patterns. For Gaussian coil the scattering factor P(q) is given by formulae: P(x)=2*(x-1+exp(-x))/x, where x=(q*Rg) with Rgradius of gyration and qmodule of scattering vector[1]. Unfortunately, the Guinier region for Rg evaluation of Gaussian coil is very small (x<0.3) causing the difficulties with precise its measurement due to intermolecular interference influence on the SAXS pattern. But the region for Rg evaluation can be increased up to x<12 with about 0.5% accuracy according to approximatio...

Introduction Actual topic at present is the analysis of formation of amyloid fibrils which often ... more Introduction Actual topic at present is the analysis of formation of amyloid fibrils which often cause numerous diseases. This problem is closely related to the protein folding/ misfolding [1]. At the last time the application of artificial protein hybrid constructions (target proteinpolypeptide linker-carrier protein) for biochemical assays is widespread one. Very often the aim of such construction is to enhance the protein solubility and decrease its association. However, mutual influence of parts in the fused protein may significantly change their properties. Thus, the artificial protein albebetin (ABB) and its derivatives containing biologically active fragments of natural proteins form fibrils at physiological pH [2]. Recently it has been shown that the fused ABB-thioredoxin protein (ABB-TR) also forms amyloid-like aggregates. Here we study by SAXS this process in detail for ABB-TR and its H65F, H30F mutants.

Introduction We have studied trigger factor (TF), and its mutants. TF is a 3-domain protein, name... more Introduction We have studied trigger factor (TF), and its mutants. TF is a 3-domain protein, namely composed of Nterminal domain, middle part domain and C-terminal domain. To investigate conformational analysis, We prepared wild type TF and its truncated mutants, called C419, C360, NM and MC. They mean: 13 and 72 residues from C-terminal are truncated, whole C-domain is truncated, and whole N-domain is truncated, respectively. The number of amino acids for TF, C419, C360, NM and MC are 432, 419, 360, 251 and 287, respectively.