Search results for: Ryo Kitahara

Items from 1 to 20 out of 26 results

article

Dynamic aspects of pressure and temperature‐stabilized intermediates of outer surface protein A

Takuro Wakamoto, Soichiro Kitazawa, Tomoshi Kameda, Ryo Kitahara

Proteins: Structure, Function, and Bioinformatics > 88 > 11 > 1423 - 1433

Structural characterization of alternatively folded and partially disordered protein conformations remains challenging. Outer surface protein A (OspA) is a pivotal protein in Borrelia infection, which is the etiological agent of Lyme disease. OspA exists in equilibrium with intermediate conformations, in which the central and the C‐terminal regions of the protein have lower stabilities than the N‐terminal...

article

Paramagnetic relaxation enhancement‐assisted structural characterization of a partially disordered conformation of ubiquitin

Takuro Wakamoto, Teppei Ikeya, Soichiro Kitazawa, Nicola J. Baxter, more

Protein Science > 28 > 11 > 1993 - 2003

Nuclear magnetic resonance (NMR) is a powerful tool to study three‐dimensional structures as well as protein conformational fluctuations in solution, but it is compromised by increases in peak widths and missing signals. We previously reported that ubiquitin has two folded conformations, N₁ and N₂ and plus another folded conformation, I, in which some amide group signals of residues 33–41 almost disappeared...

article

Nuclear magnetic resonance‐based determination of dioxygen binding sites in protein cavities

Ryo Kitahara, Shun Sakuraba, Tomoshi Kameda, Sanshiro Okuda, more

Protein Science > 27 > 3 > 769 - 779

The location and ligand accessibility of internal cavities in cysteine‐free wild‐type T4 lysozyme was investigated using O₂ gas‐pressure NMR spectroscopy and molecular dynamics (MD) simulation. Upon increasing the concentration of dissolved O₂ in solvent to 8.9 mM, O₂‐induced paramagnetic relaxation enhancements (PREs) to the backbone amide and side chain methyl protons were observed, specifically...

article

Analysis of O2-binding Sites in Proteins Using Gas-Pressure NMR Spectroscopy: Outer Surface Protein A

Takahiro Kawamura, Takuro Wakamoto, Soichiro Kitazawa, Shun Sakuraba, more

Biophysical Journal > 2017 > 112 > 9 > 1820-1828

Internal cavities in proteins produce conformational fluctuations and enable the binding of small ligands. Here, we report a NMR analysis of O₂-binding sites by O₂-induced paramagnetic relaxation enhancements (PREs) on amide groups of proteins in solution. Outer surface protein A contains a nonglobular single-layer β-sheet that connects the N- and C-terminal globular domains. Several cavities have...

article

Aberrant increase of NMR signal in hydrogen exchange experiments. Observation and explanation

Mengjun Xue, Ryo Kitahara, Yuichi Yoshimura, Frans A.A. Mulder

Biochemical and Biophysical Research Communications > 2016 > 478 > 3 > 1185-1188

Hydrogen exchange (HX) NMR spectroscopy is widely used for monitoring structure, stability and dynamics of proteins at the level of individual residues. The stochastic replacement of protons by deuterons typically leads to an exponential decrease of the NMR signals. However, an unusual signal increase was observed in HX of several amides for T4 lysozyme L99A. This effect can be attributed to peak...

article

Cavity as a Source of Conformational Fluctuation and High-Energy State: High-Pressure NMR Study of a Cavity-Enlarged Mutant of T4Lysozyme

Akihiro Maeno, Daniel Sindhikara, Fumio Hirata, Renee Otten, more

Biophysical Journal > 2015 > 108 > 1 > 133-145

Although the structure, function, conformational dynamics, and controlled thermodynamics of proteins are manifested by their corresponding amino acid sequences, the natural rules for molecular design and their corresponding interplay remain obscure. In this study, we focused on the role of internal cavities of proteins in conformational dynamics. We investigated the pressure-induced responses from...

article

Solvent environments significantly affect the enzymatic function of Escherichia coli dihydrofolate reductase: Comparison of wild-type protein and active-site mutant D27E

Eiji Ohmae, Yurina Miyashita, Shin-ichi Tate, Kunihiko Gekko, more

BBA - Proteins and Proteomics > 2013 > 1834 > 12 > 2782-2794

To investigate the contribution of solvent environments to the enzymatic function of Escherichia coli dihydrofolate reductase (DHFR), the salt-, pH-, and pressure-dependence of the enzymatic function of the wild-type protein were compared with those of the active-site mutant D27E in relation to their structure and stability. The salt concentration-dependence of enzymatic activity indicated that inorganic...

article

Pressure-induced chemical shifts as probes for conformational fluctuations in proteins

Ryo Kitahara, Kazumi Hata, Hua Li, Mike P. Williamson, more

Progress in Nuclear Magnetic Resonance Spectroscopy > 2013 > 71 > Complete > 35-58

article

Exploring the folding energy landscape with pressure

Kazuyuki Akasaka, Ryo Kitahara, Yuji O. Kamatari

Archives of Biochemistry and Biophysics > 2013 > 531 > 1-2 > 110-115

The unique role of pressure in protein folding studies is emphasized. Variable-pressure NMR experiments carried out under equilibrium conditions give unique opportunities to explore the energy landscape for protein folding. Intermediate conformers that may appear transiently in the kinetic folding experiments may be stably trapped under pressure, allowing examination of their conformations in site-specific...

article

A Delicate Interplay of Structure, Dynamics, and Thermodynamics for Function: A High Pressure NMR Study of Outer Surface Protein A

Ryo Kitahara, Alana K. Simorellis, Kazumi Hata, Akihiro Maeno, more

Biophysical Journal > 2012 > 102 > 4 > 916-926

Outer surface protein A (OspA) is a crucial protein in the infection of Borrelia burgdorferi causing Lyme disease. We studied conformational fluctuations of OspA with high-pressure ¹⁵N/¹H two-dimensional NMR along with high-pressure fluorescence spectroscopy. We found evidence within folded, native OspA for rapid local fluctuations of the polypeptide backbone in the nonglobular single layer β-sheet...

article

Design Strategy for High Free-Energy States of Proteins Based on High-Pressure NMR Study: Alternatively Folded Conformation of Ubiquitin

Ryo Kitahara, Soichiro Kitazawa, Maho Yagi-Utsumi, Akemi Ido, more

Biophysical Journal > 2012 > 102 > 3 Supplement 1 > 25a

chapter

Overview of ISDB-Tmm services and technologies

Akira Yamada, Hosei Matsuoka, Tomoyuki Ohya, Ryo Kitahara, more

2011 IEEE International Symposium on Broadband Multimedia Systems and Broadcasting (BMSB) > 1 - 5

2011 IEEE International Symposium on Broadband Multimedia Systems and Broadcasting (BMSB)

A multimedia broadcasting service for mobile receivers based on the ISDB-Tmm standards using spectrum from 207.5MHz to 222MHz after the shutdown of analog TV service will be launched in spring 2012 in Japan. The ISDB-Tmm is a broadcast technology based on ISDB-T, which is used for digital terrestrial TV services and has superior transmission characteristics in mobile environments. The ISDB-Tmm has...

article

Structural plasticity of staphylococcal nuclease probed by perturbation with pressure and pH

Ryo Kitahara, Kazumi Hata, Akihiro Maeno, Kazuyuki Akasaka, more

Proteins: Structure, Function, and Bioinformatics > 79 > 4 > 1293 - 1305

The ionization of internal groups in proteins can trigger conformational change. Despite this being the structural basis of most biological energy transduction, these processes are poorly understood. Small angle X‐ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy experiments at ambient and high hydrostatic pressure were used to examine how the presence and ionization of Lys‐66,...

article

Solution structure of LC5, the CCR5‐ derived peptide for HIV‐1 inhibition

Kazuhide Miyamoto, Kayo Togiya, Ryo Kitahara, Kazuyuki Akasaka, more

Journal of Peptide Science > 16 > 4 > 165 - 170

The synthetic peptide fragment (LC5: LRCRNEKKRHRAVRLIFTI) inhibits human immunodeficiency virus type 1 (HIV‐1) infection of MT‐4 cells. In this study, the solution structure of LC5 in SDS micelles was elucidated by using the standard ¹H two‐dimensional NMR spectroscopic method along with circular dichroism and fluorescence quenching. The peptide adopts a helical structure in the C‐terminal region...

article

Pressure-Dependent Structure Changes in Barnase on Ligand Binding Reveal Intermediate Rate Fluctuations

David J. Wilton, Ryo Kitahara, Kazuyuki Akasaka, Maya J. Pandya, more

Biophysical Journal > 2009 > 97 > 5 > 1482-1490

In this work we measured ¹H NMR chemical shifts for the ribonuclease barnase at pressures from 3 MPa to 200 MPa, both free and bound to d(CGAC). Shift changes with pressure were used as restraints to determine the change in structure with pressure. Free barnase is compressed by ∼0.7%. The largest changes are on the ligand-binding face close to Lys-27, which is the recognition site for the cleaved...

article

Pressure-dependent ¹³C chemical shifts in proteins: origins and applications

David J. Wilton, Ryo Kitahara, Kazuyuki Akasaka, Mike P. Williamson

Journal of Biomolecular NMR > 2009 > 44 > 1 > 25-33

Pressure-dependent ¹³C chemical shifts have been measured for aliphatic carbons in barnase and Protein G. Up to 200 MPa (2 kbar), most shift changes are linear, demonstrating pressure-independent compressibilities. CH₃, CH₂ and CH carbon shifts change on average by +0.23, −0.09 and −0.18 ppm, respectively, due to a combination of bond shortening and changes in bond angles, the latter matching one...

article

Basic Folded and Low-Populated Locally Disordered Conformers of SUMO-2 Characterized by NMR Spectroscopy at Varying Pressures ^†

Ryo Kitahara, Chenhua Zhao, Kohei Saito, Seizo Koshiba, more

Biochemistry > 2008 > 47 > 1 > 30 - 39

article

Local Conformational Transition of Hydrogenobacter thermophilus Cytochrome c ₅₅₂ Relevant to Its Redox Potential ^† ^, ^‡

Shin-ichi J. Takayama, Yo-ta Takahashi, Shin-ichi Mikami, Kiyofumi Irie, more

Biochemistry > 2007 > 46 > 32 > 9215 - 9224

article

Evolutionally Conserved Intermediates Between Ubiquitin and NEDD8

Ryo Kitahara, Yoshiki Yamaguchi, Eri Sakata, Takeshi Kasuya, more

Journal of Molecular Biology > 2006 > 363 > 2 > 395-404

The investigation of common structural motifs provides additional information on why proteins conserve similar topologies yet may have non-conserved amino acid sequences. Proteins containing the ubiquitin superfold have similar topologies, although the sequence conservation is rather poor. Here, we present novel similarities and differences between the proteins ubiquitin and NEDD8. They have 57% identical...

article

NMR Snapshots of a Fluctuating Protein Structure: Ubiquitin at 30bar–3kbar

Ryo Kitahara, Shigeyuki Yokoyama, Kazuyuki Akasaka

Journal of Molecular Biology > 2005 > 347 > 2 > 277-285

Conformational fluctuation plays a key role in protein function, but we know little about the associated structural changes. Here we present a general method for elucidating, at the atomic level, a large-scale shape change of a protein molecule in solution undergoing conformational fluctuation. The method utilizes the intimate relationship between conformation and partial molar volume and determines...

Publication date

Set your own date range

Publication type

article (25)
book (1)

Keywords

PRESSURE (5)
NMR (3)
ACTIVATION VOLUME (2)
HIGH PRESSURE (2)
HIGH PRESSURE NMR (2)
PARAMAGNETIC RELAXATION ENHANCEMENT (2)
PROTEIN FOLDING (2)
RAPID EYE MOVEMENTS (2)
UBIQUITIN (2)
13C CHEMICAL SHIFT (1)
Γ-GAUCHE EFFECT (1)
ACTIVE-SITE MUTATION (1)
AGGREGATION (1)
AL-FEC (1)
CAVITY AND HYDRATION (1)
CCR5 (1)
CIRCULAR DICHROISM (1)
COLD DENATURATION (1)
COMPRESSION (1)
CONFORMATIONAL DYNAMICS (1)
CONFORMATIONAL FLUCTUATION (1)
CONFORMATIONAL FLUCTUATIONS (1)
DIHYDROFOLATE REDUCTASE (1)
DIPOLE-DIPOLE INTERACTION (1)
ELECTROENCEPHALOGRAM (1)
ELECTROOCULOGRAM (1)
ENERGY LANDSCAPE (1)
ENZYME FUNCTION (1)
EQUILIBRIUM INTERMEDIATES (1)
FLUORESCENCE (1)
FLUORESCENCE QUENCHING (1)
GAS‐PRESSURE NMR (1)
GENETIC ALGORITHM (1)
HELICAL DENATURED STATE (1)
HIGH ENERGY CONFORMER (1)
HIGH FREQUENCY ELECTROENCEPHALOGRAMS (1)
HIGH-PRESSURE NMR (1)
HIV‐1 (1)
HIV‐1 INHIBITOR (1)
HYDROGEN/DEUTERIUM EXCHANGE (1)
INTERMEDIATE STATES (1)
INTERMEDIATES (1)
ISDB-TMM (1)
KINETIC INTERMEDIATES (1)
LDPC STAIRCASE (1)
LOW-LYING EXCITED STATES (1)
MOBILE TV (1)
MOLECULAR DYNAMICS SIMULATION (1)
MOLTEN GLOBULE (1)
NEDD8 (1)
NMR SNAPSHOTS (1)
NMR SPECTROSCOPY (1)
NMR STRUCTURE IN MICELLES (1)
NON-LINEAR PRESSURE SHIFTS (1)
NON-NATIVE STATES (1)
NUCLEAR MAGNETIC RESONANCE (1)
OSPA (1)
OXYGEN (1)
PARTIAL MOLAR VOLUME (1)
PRESSURE DENATURATION (1)
PRESSURE-INDUCED CHEMICAL SHIFTS (1)
PROTECTION FACTORS (1)
PROTEIN ELECTROSTATICS (1)
RANDOM COILED PEPTIDE (1)
RAPID EYE MOVEMENTS ANTICIPATORY PHASIC POTENTIALS (1)
REM SLEEP (1)
REM-RELATED PHASIC EVENTS (1)
SAXS (1)
SERVICE DEPLOYMENTS (1)
SIGNAL PROCESSING (1)
SLEEP-STAGE SCORING (1)
SLOW CONFORMATIONAL FLUCTUATION (1)
SOLVENT EFFECT (1)
T4 LYSOZYME (1)
T4 LYSOZYME L99A (1)
[ABR] CD; CIRCULAR DICHROISM (1)
[ABR] CSM; CENTER OF FLUORESCENCE SPECTRAL MASS (1)
[ABR] DHF; DIHYDROFOLATE (1)
[ABR] DHFR; DIHYDROFOLATE REDUCTASE (1)
[ABR] HSQC; HETERONUCLEAR SINGLE QUANTUM CORRELATION (1)
[ABR] MES; 2-(N-MORPHOLINO)ETHANESULFONIC ACID (1)
[ABR] MTE; 50MM MES, 25MM TRIS 25MM ETHANOLAMINE (BUFFER) (1)
[ABR] MTEN; MTE CONTAINING 100MM SODIUM CHLORIDE (BUFFER) (1)
[ABR] NMR; NUCLEAR MAGNETIC RESONANCE (1)
[ABR] PEG; POLYETHYLENE GLYCOL (1)
[ABR] PI; PHOSPHATE (1)
[ABR] THF; TETRAHYDROFOLATE (1)
[ABR] TMA; TETRAMETHYLAMMONIUM (1)
more

Data set

Elsevier (14)
Wiley (5)
ACS (3)
Springer (3)
ieee (1)

Journal

Biophysical Journal (5)
Journal of Molecular Biology (4)
Biochemistry (3)
Protein Science (2)
Proteins: Structure, Function, and Bioinformatics (2)
Sleep and Biological Rhythms (2)
Archives of Biochemistry and Biophysics (1)
BBA - Proteins and Proteomics (1)
Biochemical and Biophysical Research Communications (1)
Journal of Biomolecular NMR (1)
Journal of Peptide Science (1)
Methods (1)
Progress in Nuclear Magnetic Resonance Spectroscopy (1)
more

INFONA - science communication portal

Search results for: Ryo Kitahara

Dynamic aspects of pressure and temperature‐stabilized intermediates of outer surface protein A

Paramagnetic relaxation enhancement‐assisted structural characterization of a partially disordered conformation of ubiquitin

Nuclear magnetic resonance‐based determination of dioxygen binding sites in protein cavities

Analysis of O2-binding Sites in Proteins Using Gas-Pressure NMR Spectroscopy: Outer Surface Protein A

Aberrant increase of NMR signal in hydrogen exchange experiments. Observation and explanation

Cavity as a Source of Conformational Fluctuation and High-Energy State: High-Pressure NMR Study of a Cavity-Enlarged Mutant of T4Lysozyme

Solvent environments significantly affect the enzymatic function of Escherichia coli dihydrofolate reductase: Comparison of wild-type protein and active-site mutant D27E

Pressure-induced chemical shifts as probes for conformational fluctuations in proteins

Exploring the folding energy landscape with pressure

A Delicate Interplay of Structure, Dynamics, and Thermodynamics for Function: A High Pressure NMR Study of Outer Surface Protein A

Design Strategy for High Free-Energy States of Proteins Based on High-Pressure NMR Study: Alternatively Folded Conformation of Ubiquitin

Overview of ISDB-Tmm services and technologies

Structural plasticity of staphylococcal nuclease probed by perturbation with pressure and pH

Solution structure of LC5, the CCR5‐ derived peptide for HIV‐1 inhibition

Pressure-Dependent Structure Changes in Barnase on Ligand Binding Reveal Intermediate Rate Fluctuations

Pressure-dependent ¹³C chemical shifts in proteins: origins and applications

Basic Folded and Low-Populated Locally Disordered Conformers of SUMO-2 Characterized by NMR Spectroscopy at Varying Pressures ^†

Local Conformational Transition of Hydrogenobacter thermophilus Cytochrome c ₅₅₂ Relevant to Its Redox Potential ^† ^, ^‡

Evolutionally Conserved Intermediates Between Ubiquitin and NEDD8

NMR Snapshots of a Fluctuating Protein Structure: Ubiquitin at 30bar–3kbar

Filter options

Publication date

Publication type

Keywords

Data set

Journal

INFONA - science communication portal

Search results for: Ryo Kitahara

Add recipient

Sending message cancelled

Are you sure you want to cancel sending this message?

Send message

Filter options

Publication date

Date range setting

Set the date range to filter the displayed results. You can set a starting date, ending date or both. You can enter the dates manually or choose them from the calendar.

Publication type

Keywords

Data set

Journal

Reporting an error / abuse

Sending the report failed

Accessibility options