Works by Ichiye, Toshiko

Results: 25

Molecular dynamics simulations of rubredoxin from Clostridium pasteurianum: Changes in structure and electrostatic potential duringredox reactions.

Published in:

Proteins, 1995, v. 22, n. 2, p. 154, doi. 10.1002/prot.340220208

By:

Yelle, Robert B.;
Park, Noh-Sum;
Ichiye, Toshiko

Publication type:

Article

Influence of protein flexibility on the redox potential of rubredoxin: Energy minimization studies.

Published in:

Proteins, 1993, v. 17, n. 2, p. 152, doi. 10.1002/prot.340170205

By:

Shenoy, Vaishali S.;
Ichiye, Toshiko

Publication type:

Article

Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations.

Published in:

Proteins, 1991, v. 11, n. 3, p. 205, doi. 10.1002/prot.340110305

By:

Ichiye, Toshiko;
Karplus, Martin

Publication type:

Article

Anisotropy and anharmonicity of atomic fluctuations in proteins: Analysis of a molecular dynamics simulation.

Published in:

Proteins, 1987, v. 2, n. 3, p. 236, doi. 10.1002/prot.340020308

By:

Ichiye, Toshiko;
Karplus, Martin

Publication type:

Article

Web-Based Computational Chemistry Education with CHARMMing III: Reduction Potentials of Electron Transfer Proteins.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003739

By:

Perrin Jr, B. Scott;
Miller, Benjamin T.;
Schalk, Vinushka;
Woodcock, H. Lee;
Brooks, Bernard R.;
Ichiye, Toshiko

Publication type:

Article

Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003719

By:

Miller, Benjamin T.;
Singh, Rishi P.;
Schalk, Vinushka;
Pevzner, Yuri;
Sun, Jingjun;
Miller, Carrie S.;
Boresch, Stefan;
Ichiye, Toshiko;
Brooks, Bernard R.;
Woodcock III, H. Lee

Publication type:

Article

Density functional theory calculations of redox properties of iron-sulphur protein analogues.

Published in:

Molecular Simulation, 2011, v. 37, n. 7, p. 572, doi. 10.1080/08927022.2011.582111

By:

Niu, Shuqiang;
Ichiye, Toshiko

Publication type:

Article

Planarity of acetamides, thioacetamides, and selenoacetamides: Crystal structure of N, N-dimethylselenoacetamide.

Published in:

Heteroatom Chemistry, 2002, v. 13, n. 4, p. 380, doi. 10.1002/hc.10056

By:

Niu, Shuqiang;
Li, Guang Ming;
Zingaro, Ralph A.;
Reibenspies, Joseph H.;
Ichiye, Toshiko

Publication type:

Article

Probing the structural effects on the intrinsic electronic and redox properties of [2Fe–2S]+ clusters, a broken-symmetry density functional theory study.

Published in:

Theoretical Chemistry Accounts: Theory, Computation, & Modeling, 2007, v. 117, n. 2, p. 275, doi. 10.1007/s00214-006-0136-y

By:

Shuqiang Niu;
Ichiye, Toshiko

Publication type:

Article

Pressure Adaptations in Deep-Sea Moritella Dihydrofolate Reductases: Compressibility versus Stability.

Published in:

Biology (2079-7737), 2021, v. 10, n. 11, p. 1211, doi. 10.3390/biology10111211

By:

Penhallurick, Ryan W.;
Ichiye, Toshiko

Publication type:

Article

Reduction potential calculations of the Fe–S clusters in Thermus thermophilus respiratory complex I.

Published in:

Journal of Computational Chemistry, 2019, v. 40, n. 12, p. 1248, doi. 10.1002/jcc.25785

By:

Tran, Kelly N.;
Niu, Shuqiang;
Ichiye, Toshiko

Publication type:

Article

Extreme biophysics: Enzymes under pressure.

Published in:

Journal of Computational Chemistry, 2017, v. 38, n. 15, p. 1174, doi. 10.1002/jcc.24737

By:

Huang, Qi;
Rodgers, Jocelyn M.;
Hemley, Russell J.;
Ichiye, Toshiko

Publication type:

Article

Effects of Pressure and Temperature on the Atomic Fluctuations of Dihydrofolate Reductase from a Psychropiezophile and a Mesophile.

Published in:

International Journal of Molecular Sciences, 2019, v. 20, n. 6, p. 1452, doi. 10.3390/ijms20061452

By:

Huang, Qi;
Rodgers, Jocelyn M.;
Ichiye, Toshiko;
Hemley, Russell J.

Publication type:

Article

Identifying sequence determinants of reduction potentials of metalloproteins.

Published in:

Journal of Biological Inorganic Chemistry (JBIC), 2013, v. 18, n. 6, p. 599, doi. 10.1007/s00775-013-1004-6

By:

Perrin, Bradley;
Ichiye, Toshiko

Publication type:

Article

Characterizing the effects of the protein environment on the reduction potentials of metalloproteins.

Published in:

Journal of Biological Inorganic Chemistry (JBIC), 2013, v. 18, n. 1, p. 103, doi. 10.1007/s00775-012-0955-3

By:

Perrin, Bradley;
Ichiye, Toshiko

Publication type:

Article

The unique hydrogen bonded water in the reduced form of Clostridium pasteurianum rubredoxin and its possible role in electron transfer.

Published in:

Journal of Biological Inorganic Chemistry (JBIC), 2004, v. 9, n. 4, p. 423, doi. 10.1007/s00775-004-0542-3

By:

Il Yeong Park;
Buhyun Youn;
Jill L. Harley;
Marly K. Eidsness;
Eugene Smith;
Toshiko Ichiye;
ChulHee Kang

Publication type:

Article

Adaptations for Pressure and Temperature in Dihydrofolate Reductases.

Published in:

Microorganisms, 2021, v. 9, n. 8, p. 1706, doi. 10.3390/microorganisms9081706

By:

Penhallurick, Ryan W.;
Durnal, Maya D.;
Harold, Alliyah;
Ichiye, Toshiko

Publication type:

Article

Calculating standard reduction potentials of [4Fe-4S] proteins.

Published in:

Journal of Computational Chemistry, 2013, v. 34, n. 7, p. 576, doi. 10.1002/jcc.23169

By:

Perrin, Bradley Scott;
Niu, Shuqiang;
Ichiye, Toshiko

Publication type:

Article

Fold versus sequence effects on the driving force for protein-mediated electron transfer.

Published in:

Proteins, 2010, v. 78, n. 13, p. 2798, doi. 10.1002/prot.22794

By:

Perrin, Bradley Scott;
Ichiye, Toshiko

Publication type:

Article

The role of backbone stability near Ala44 in the high reduction potential class of rubredoxins.

Published in:

Proteins, 2006, v. 62, n. 3, p. 708, doi. 10.1002/prot.20806

By:

Tan, Ming-Liang;
Kang, ChulHee;
Ichiye, Toshiko

Publication type:

Article

Effects of environment on the structure of Pyrococcus furiosus rubredoxin: A molecular dynamics study.

Published in:

Proteins, 2005, v. 61, n. 4, p. 823, doi. 10.1002/prot.20685

By:

Ergenekan, Can E.;
Tan, Ming-Liang;
Ichiye, Toshiko

Publication type:

Article

Crystallographic studies of V44 mutants of Clostridium pasteurianum rubredoxin: Effects of side-chain size on reduction potential.

Published in:

Proteins, 2004, v. 57, n. 3, p. 618, doi. 10.1002/prot.20243

By:

Park, Il Yeong;
Eidsness, Marly K.;
Lin, I-Jin;
Gebel, Erika B.;
Youn, Buhyun;
Harley, Jill L.;
Machonkin, Timothy E.;
Frederick, Ronnie O.;
Markley, John L.;
Smith, Eugene T.;
Ichiye, Toshiko;
Kang, ChulHee

Publication type:

Article

Adaptations for pressure and temperature effects on loop motion in Escherichia coli and Moritella profunda dihydrofolate reductase.

Published in:

High Pressure Research, 2019, v. 39, n. 2, p. 225, doi. 10.1080/08957959.2019.1584799

By:

Huang, Qi;
Rodgers, Jocelyn M.;
Hemley, Russell J.;
Ichiye, Toshiko

Publication type:

Article

Protein dynamics and the all-ferrous [Fe4S4] cluster in the nitrogenase iron protein.

Published in:

Protein Science: A Publication of the Protein Society, 2016, v. 25, n. 1, p. 12, doi. 10.1002/pro.2772

By:

Tan, Ming‐Liang;
Perrin, B. Scott;
Niu, Shuqiang;
Huang, Qi;
Ichiye, Toshiko

Publication type:

Article

Leucine 41 is a gate for water entry in the reduction of Clostridium pasteurianum rubredoxin.

Published in:

Protein Science: A Publication of the Protein Society, 2001, v. 10, n. 3, p. 613, doi. 10.1110/gad.34501

By:

Min, Tongpil;
Ergenekan, Can E.;
Eidsness, Marly K.;
Ichiye, Toshiko;
Kang, Chulhee

Publication type:

Article

Works by Ichiye, Toshiko

Molecular dynamics simulations of rubredoxin from Clostridium pasteurianum: Changes in structure and electrostatic potential duringredox reactions.

Influence of protein flexibility on the redox potential of rubredoxin: Energy minimization studies.

Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations.

Anisotropy and anharmonicity of atomic fluctuations in proteins: Analysis of a molecular dynamics simulation.

Web-Based Computational Chemistry Education with CHARMMing III: Reduction Potentials of Electron Transfer Proteins.

Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial.

Density functional theory calculations of redox properties of iron-sulphur protein analogues.

Planarity of acetamides, thioacetamides, and selenoacetamides: Crystal structure of N, N-dimethylselenoacetamide.

Probing the structural effects on the intrinsic electronic and redox properties of [2Fe–2S]<sup>+</sup> clusters, a broken-symmetry density functional theory study.

Pressure Adaptations in Deep-Sea Moritella Dihydrofolate Reductases: Compressibility versus Stability.

Reduction potential calculations of the Fe–S clusters in Thermus thermophilus respiratory complex I.

Extreme biophysics: Enzymes under pressure.

Effects of Pressure and Temperature on the Atomic Fluctuations of Dihydrofolate Reductase from a Psychropiezophile and a Mesophile.

Identifying sequence determinants of reduction potentials of metalloproteins.

Characterizing the effects of the protein environment on the reduction potentials of metalloproteins.

The unique hydrogen bonded water in the reduced form of Clostridium pasteurianum rubredoxin and its possible role in electron transfer.

Adaptations for Pressure and Temperature in Dihydrofolate Reductases.

Calculating standard reduction potentials of [4Fe-4S] proteins.

Fold versus sequence effects on the driving force for protein-mediated electron transfer.

The role of backbone stability near Ala<sub>44</sub> in the high reduction potential class of rubredoxins.

Effects of environment on the structure of Pyrococcus furiosus rubredoxin: A molecular dynamics study.

Crystallographic studies of V44 mutants of Clostridium pasteurianum rubredoxin: Effects of side-chain size on reduction potential.

Adaptations for pressure and temperature effects on loop motion in Escherichia coli and Moritella profunda dihydrofolate reductase.

Protein dynamics and the all-ferrous [Fe<sub>4</sub>S<sub>4</sub>] cluster in the nitrogenase iron protein.

Leucine 41 is a gate for water entry in the reduction of Clostridium pasteurianum rubredoxin.