WorldCat Identities

Ichiye, Toshiko

Overview
Works: 11 works in 22 publications in 1 language and 1,598 library holdings
Genres: Academic theses 
Roles: Author, Contributor, Other
Classifications: QP535.F4, 612.3924
Publication Timeline
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Most widely held works by Toshiko Ichiye
Iron-sulfur clusters in chemistry and biology by Tracey A Rouault( )

5 editions published in 2014 in English and held by 1,069 WorldCat member libraries worldwide

This volume on iron-sulfur clusters includes chapters that cover the history of the discovery of iron-sulfur clusters in the 1960s to discoveries of their role in the enzyme, aconitase (1980s), and numerous other proteins. It explains basic chemistry principles, how microbes, plants, and animals synthesize these complex prosthetic groups, and why it is important to understand the chemistry and biogenesis of FeS proteins
Characterization, Properties and Applications : Volume 1: Characterization, Properties and Applications by Francesco Bonomi( )

2 editions published in 2017 in English and held by 460 WorldCat member libraries worldwide

Iron-sulfur clusters in chemistry and biology by Tracey A Rouault( )

3 editions published in 2017 in English and held by 41 WorldCat member libraries worldwide

This volume on iron-sulfur proteins includes chapters that describe the initial discovery of iron-sulfur proteins in the 1960s to elucidation of the roles of iron sulfur clusters as prosthetic groups of enzymes, such as the citric acid cycle enzyme, aconitase, and numerous other proteins, ranging from nitrogenase to DNA repair proteins. The capacity of iron sulfur clusters to accept and delocalize single electrons is explained by basic chemical principles, which illustrate why iron sulfur proteins are uniquely suitable for electron transport and other activities. Techniques used for detection and stabilization of iron-sulfur clusters, including EPR and Mossbauer spectroscopies, are discussed because they are important for characterizing unrecognized and elusive iron sulfur proteins. Recent insights into how nitrogenase works have arisen from multiple advances, described here, including studies of high-resolution crystal structures
Electron transfer proteins by Toshiko Ichiye( Book )

4 editions published between 2010 and 2015 in English and Undetermined and held by 11 WorldCat member libraries worldwide

Theoretical studies of iron-sulfur electron transfer proteins by Elizabeth Astill Dolan( )

1 edition published in 2003 in English and held by 5 WorldCat member libraries worldwide

In this work, we focus on a single class of electron transfer proteins, namely, the iron-sulfur proteins, which appear in a wide range of biological reactions. Classical molecular mechanical computational methods are used to analyze the structure and energetics of two types of iron-sulfur electron transfer proteins, namely, rubredoxins and ferredoxins. Here, two levels of interaction between the protein matrix and the reduction potential are explored. First, the protein matrix can create large differences in reduction potential (on the order of 1 V) due to the inhomogeneous protein partially surrounding the redox site. Second, specific residues can be used to fine-tune the reduction potential (on the order of 100 mV). Three different questions about the role of protein structure in influencing electron transfer are studied here. First, how does the entire protein matrix structure influence electron transfer reactions? Second, how do specific amino acids affect the reduction potential of the redox site? Finally, what are the thermodynamic properties of an electron transfer reaction, and how does the protein matrix contribute to these properties?
Environmental effects on the structure and function of rubredoxin by Can Erol Ergenekan( )

1 edition published in 2003 in English and held by 5 WorldCat member libraries worldwide

Molecular mechanics techniques such as energy minimization and molecular dynamics can be used in combination with crystal structure and sequence analysis to explore how mutations in the protein and changes in the environment of the protein affect structure, and ultimately function. These studies are vital because changes to the protein structure are too complex to be predicted by simple physiochemical relationships. Here rubredoxin is used as a model system to explore how changes in the protein sequence and environment affect the protein structure. The first two studies examine how mutations near the redox site alter the polar environment around the redox site and thereby modulate the reduction potential. In Chapter 2, the relationship of side chain size of valine versus alanine at residue 44 to reduction potential is investigated with the other non-polar residues glycine, isoleucine, and leucine. This change from valine to alanine was previously shown to be responsible for a 50 mV shift in the reduction potential of rubredoxin because of a backbone shift. However, the size and backbone position relationship does not extend past alanine and valine, with the other mutations affecting the reduction potential through other structural determinants. In Chapter 3, the sequence determinants of the 250 mV increase in reduction potential of the rubredoxin-like domain of rubrerythrin over that of rubredoxin are studied. It is predicted that the addition of two polar side chains near the redox center would increase the electrostatic potential at the redox site and thus the reduction potential by more than 250 mV; however, the two side chains also decrease the solvent accessibility compared to wt, which would cancel part of the increase. In Chapter 4, the effect of protein environment on protein structure is explored by using molecular dynamics simulations of rubredoxin in the crystal state at a cryo-temperature, the crystal state at room temperature, and the solution state at room temperature. It appears that the extreme cryo-temperatures sometimes used for solving crystal structures of proteins will affect the structure more than the crystal lattice of the crystalline state
The internal dynamics of proteins by Toshiko Ichiye( )

2 editions published in 1985 in English and held by 3 WorldCat member libraries worldwide

Electron Transfer and Assembly in Fe-S Proteins by Bradley S Perrin Jr.( )

1 edition published in 2011 in English and held by 1 WorldCat member library worldwide

The iron-sulfur (Fe-S) proteins are a major class of metalloproteins, with metal sites consisting of varying numbers of iron and sulfur atoms. Most Fe-S proteins are electron transfer proteins involved in processes such as respiration, photosynthesis, and nitrogen fixation. The reduction potentials of these proteins determine the driving forces for their electron transfer. For a given redox site, reduction potentials of non-homologous proteins can span a range of ~1 V, while those of homologous proteins can span a range of ~400 V. Here, a method for calculating the reduction potentials of metalloproteins is presented in which the redox site or inner sphere contribution is calculated by density functional theory (DFT) and the protein or outer sphere contribution is calculated by Poisson-Boltzmann (PB) continuum electrostatics. Reduction potentials calculated using the DFT+PB method are in excellent agreement with the experimental values for several Fe-S proteins. Moreover, the calculations show that for the outer sphere, the protein fold makes the largest contribution while the sequence tunes it. Furthermore, they show that the fold contribution is determined mainly by the burial of the redox site within the protein and the polarization of the protein environment around the redox site. Based on this, an electret-dielectric spheres (EDS) model is developed in terms of R<sub>p</sub>, a measure of the redox site burial and <italic> & phi;</italic><sub>p</sub>, the electrostatic potential at the redox site. The DFT+PB method is also used to identify sequence determinants of reduction potentials, which can be tested by site-specific mutagenesis experiments
Reduction Potential Properties of Electron Transfer Proteins by Kelly Nora Tran( )

1 edition published in 2018 in English and held by 1 WorldCat member library worldwide

Here, a method for calculating the reduction potentials of metalloproteins is presented in which the redox site or inner sphere contribution is calculated by density functional theory (DFT) and the protein and solvent environment or outer sphere contribution is calculated by Poisson-Boltzmann (PB) continuum electrostatics. Reduction potentials calculated using the DFT+PB method are in good agreement with the experimental values for and the nine Fe-S clusters in respiratory complex I. Moreover, the method used here is a useful computational tool to study other questions about complex I. In addition, the method is being extended to the blue copper proteins
Characterization by Toshiko Ichiye( Book )

1 edition published in 2017 in English and held by 1 WorldCat member library worldwide

Enzymes Under Pressure by Qi Huang( )

1 edition published in 2018 in English and held by 1 WorldCat member library worldwide

Finally, the simulations of homologous AK from extremophiles show that the nanosec-plus timescale MSF of the CORE domain are similar to the results for DHFR. In particular, the MSF are almost constant at the TG and PG of the parent organisms, indicating they are corresponding states
 
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WorldCat IdentitiesRelated Identities
Iron-sulfur clusters in chemistry and biology
Covers
Characterization, Properties and Applications : Volume 1: Characterization, Properties and ApplicationsIron-sulfur clusters in chemistry and biology
Languages
English (21)