Search results for: Kazuyuki Akasaka

Items from 1 to 20 out of 62 results

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Direct high-pressure NMR observation of dipicolinic acid leaking from bacterial spore: A crucial step for thermal inactivation

Kazuyuki Akasaka, Akihiro Maeno, Akira Yamazaki

Biophysical Chemistry > 2017 > 231 > C > 10-14

A bacterial spore protects itself with an unusually high concentration (~10% in dry weight of spore) of dipicolinic acid (DPA), the release of which is considered the crucial step for inactivating it under mild pressure and temperature conditions. However, the process of how the spore releases DPA in response to pressure remains obscure. Here we apply ¹H high-resolution high-pressure NMR spectroscopy,...

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Sequential backbone resonance assignments of the E. coli dihydrofolate reductase Gly67Val mutant: folate complex

Sunilkumar Puthenpurackal Narayanan, Akihiro Maeno, Yuji Wada, Shin-ichi Tate, more

Biomolecular NMR Assignments > 2016 > 10 > 1 > 125-129

Occasionally, a mutation in an exposed loop region causes a significant change in protein function and/or stability. A single mutation Gly67Val of E. coli dihydrofolate reductase (DHFR) in the exposed CD loop is such an example. We have carried out the chemical shift assignments for H^N, N^H, C^α and C^β atoms of the Gly67Val mutant of E. coli DHFR complexed with folate at pH 7.0, 35 °C, and then evaluated...

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Functional conformer of c‐Myb DNA‐binding domain revealed by variable temperature studies

Satomi Inaba, Akihiro Maeno, Kazumasa Sakurai, Sunilkumar Puthenpurackal Narayanan, more

The FEBS Journal > 282 > 23 > 4497 - 4514

The conformational fluctuation in the minimum DNA‐binding domain of c‐Myb, repeats 2 and 3 (R2R3), was studied under closely physiological conditions. A global unfolding transition, involving both the main chain and the side chains, was found to take place at the approximate temperature range 30–70 °C, with a transition temperature of approximately 50 °C. In addition, the observation of simultaneous...

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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

Tyrosine/tyrosinate fluorescence at 700MPa: A pressure unfolding study of chicken ovomucoid at pH12

Akihiro Maeno, Hiroshi Matsuo, Kazuyuki Akasaka

Biophysical Chemistry > 2013 > 183 > Complete > 57-63

The utility of tyrosine/tyrosinate fluorescence for pressure-unfolding studies of Trp-lacking proteins has been explored for the first time, with chicken ovomucoid (OVM) as target. A newly developed fluorescence spectrometer working in the range 0.1–700MPa is employed for this purpose. At 25°C at pH12, all six Tyr residues give tyrosine emission at 306nm, implying that all five Tyr residues are well...

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...

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High-pressure macromolecular crystallography and NMR: status, achievements and prospects

Roger Fourme, Eric Girard, Kazuyuki Akasaka

Current Opinion in Structural Biology > 2012 > 22 > 5 > 636-642

Biomacromolecules are thermodynamic entities that exist in general as an equilibrium mixture of the basic folded state and various higher-energy substates including all functionally relevant ones. Under physiological conditions, however, the higher-energy substates are usually undetectable on spectroscopy, as their equilibrium populations are extremely low. Hydrostatic pressure gives a general solution...

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Pressure dependence of activity and stability of dihydrofolate reductases of the deep-sea bacterium Moritella profunda and Escherichia coli

Eiji Ohmae, Chiho Murakami, Shin-ichi Tate, Kunihiko Gekko, more

BBA - Proteins and Proteomics > 2012 > 1824 > 3 > 511-519

To understand the pressure-adaptation mechanism of deep-sea enzymes, we studied the effects of pressure on the enzyme activity and structural stability of dihydrofolate reductase (DHFR) of the deep-sea bacterium Moritella profunda (mpDHFR) in comparison with those of Escherichia coli (ecDHFR). mpDHFR exhibited optimal enzyme activity at 50MPa whereas ecDHFR was monotonically inactivated by pressure,...

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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

Extensively Hydrated but Folded: A Novel State of Globular Proteins Stabilized at High Pressure and Low Temperature

Sunilkumar Puthenpurackal Narayanan, Akihiro Maeno, Hiroshi Matsuo, Masayuki Oda, more

Biophysical Journal > 2012 > 102 > 2 > L8-L10

We studied conformational fluctuations of the transcription factor c-Myb R2 subdomain (52 residues with three Trp) at high pressure and low temperature (5°C) using two different spectroscopic methods, Trp fluorescence and ¹H NMR, on its chemically stable mutant C130I (pseudo-wild-type (WT^S)), which has a large internal cavity. As pressure was increased from 3 to 300 MPa, the Trp fluorescence λ_max...

article

Pressure-Accelerated Dissociation of Amyloid Fibrils in Wild-Type Hen Lysozyme

Buddha R. Shah, Akihiro Maeno, Hiroshi Matsuo, Hideki Tachibana, more

Biophysical Journal > 2012 > 102 > 1 > 121-126

The dynamics of amyloid fibrils, including their formation and dissociation, could be of vital importance in life. We studied the kinetics of dissociation of the amyloid fibrils from wild-type hen lysozyme at 25°C in vitro as a function of pressure using Trp fluorescence as a probe. Upon 100-fold dilution of 8 mg ml⁻¹ fibril solution in 80 mM NaCl, pH 2.2, no immediate change occurred in Trp fluorescence,...

article

Mössbauer effect of Ni-doped strontium ferrite

Naoki Miyajima, Kazuyuki Akasaka, Takeshi Waki, Yoshikazu Tabata, more

Hyperfine Interactions > 2012 > 206 > 1-3 > 115-118

We applied ⁵⁷Fe Mössbauer spectroscopy to determine occupation sites of Ni atoms in the hexagonal M-type strontium ferrite. From spectral analyses of Sr_1 − xLa_xFe_{11.6 − x}Ni_xO₁₉ with x ≤ 0.35 at room temperature, we propose that Ni atoms occupy preferentially octahedral Fe (12k, 4f ₂ and 2a) sites.

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Cavity hydration as a gateway to unfolding: An NMR study of hen lysozyme at high pressure and low temperature

Yuji O. Kamatari, Lorna J. Smith, Christopher M. Dobson, Kazuyuki Akasaka

Biophysical Chemistry > 2011 > 156 > 1 > 24-30

We have used low temperatures (down to −20°C) and high pressures (up to 2000bar) to populate low-lying excited state conformers of hen lysozyme, and have analyzed their structures site-specifically using ¹⁵ N/ ¹ H two-dimensional HSQC NMR spectroscopy. The resonances of a number of residues were found to be selectively broadened, as the temperature was lowered at a pressure of 2000bar...

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 dependence of the apparent specific volume of bovine serum albumin: Insight into the difference between isothermal and adiabatic compressibilities

Kunihiko Gekko, Mariko Araga, Tadashi Kamiyama, Eiji Ohmae, more

Biophysical Chemistry > 2009 > 144 > 1-2 > 67-71

There are some theoretical arguments related to interpreting the adiabatic compressibility (β _s ) of a protein determined from the sound velocity and the difference between β _s and isothermal compressibility (β _T ). To address these problems experimentally, we constructed a high-pressure oscillating densitometer and used it to measure the apparent specific volume of bovine...

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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

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Search results for: Kazuyuki Akasaka

Direct high-pressure NMR observation of dipicolinic acid leaking from bacterial spore: A crucial step for thermal inactivation

Sequential backbone resonance assignments of the E. coli dihydrofolate reductase Gly67Val mutant: folate complex

Functional conformer of c‐Myb DNA‐binding domain revealed by variable temperature studies

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

Tyrosine/tyrosinate fluorescence at 700MPa: A pressure unfolding study of chicken ovomucoid at pH12

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

Exploring the folding energy landscape with pressure

High-pressure macromolecular crystallography and NMR: status, achievements and prospects

Pressure dependence of activity and stability of dihydrofolate reductases of the deep-sea bacterium Moritella profunda and Escherichia coli

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

Extensively Hydrated but Folded: A Novel State of Globular Proteins Stabilized at High Pressure and Low Temperature

Pressure-Accelerated Dissociation of Amyloid Fibrils in Wild-Type Hen Lysozyme

Mössbauer effect of Ni-doped strontium ferrite

Cavity hydration as a gateway to unfolding: An NMR study of hen lysozyme at high pressure and low temperature

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 dependence of the apparent specific volume of bovine serum albumin: Insight into the difference between isothermal and adiabatic compressibilities

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 ^†

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