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Journal Articles

Situating the phosphonated calixarene–cytochrome C association by molecular dynamics simulations

Alessio Bartocci, Elise Dumont
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 105101 (2024)
https://doi.org/10.1063/5.0198522
Published: March 2024
View article titled, Situating the phosphonated calixarene–cytochrome C association by molecular dynamics simulations
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Includes: Supplementary data
Journal Articles

Electron transfer in a crystalline cytochrome with four hemes

William W. Parson, Jingcheng Huang, Martin Kulke, Josh V. Vermaas, David M. Kramer
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 065101 (2024)
https://doi.org/10.1063/5.0186958
Published: February 2024
View article titled, Electron transfer in a crystalline cytochrome with four hemes
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Includes: Supplementary data
Journal Articles

Bacterial extracellular electron transfer components are spin selective

Christina M. Niman, Nir Sukenik, Tram Dang, Justus Nwachukwu, Miyuki A. Thirumurthy, Anne K. Jones, Ron Naaman, Kakali Santra, Tapan K. Das, Yossi Paltiel, Lech Tomasz Baczewski, Mohamed Y. El-Naggar
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 145101 (2023)
https://doi.org/10.1063/5.0154211
Published: October 2023
View article titled, Bacterial extracellular electron transfer components are spin selective
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Includes: Supplementary data
Journal Articles

A deep encoder–decoder framework for identifying distinct ligand binding pathways

Satyabrata Bandyopadhyay, Jagannath Mondal
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 194103 (2023)
https://doi.org/10.1063/5.0145197
Published: May 2023
View article titled, A deep encoder–decoder framework for identifying distinct ligand binding pathways
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Includes: Supplementary data
Journal Articles

Amino acid deprotonation rates from classical force fields

Themis Lazaridis, Aliasghar Sepehri
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 085101 (2022)
https://doi.org/10.1063/5.0101960
Published: August 2022
View article titled, Amino acid deprotonation rates from classical force fields
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Journal Articles

Information flow and allosteric communication in proteins

Aysima Hacisuleyman, Burak Erman
Journal: The Journal of Chemical Physics
J. Chem. Phys. 156, 185101 (2022)
https://doi.org/10.1063/5.0088522
Published: May 2022
View article titled, Information flow and allosteric communication in proteins
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Includes: Supplementary data
Journal Articles

High suitability of tryptophan residues as a spectroscopic thermometer for local temperature in proteins under nonequilibrium conditions

Satoshi Yamashita, Misao Mizuno, Yasuhisa Mizutani
Journal: The Journal of Chemical Physics
J. Chem. Phys. 156, 075101 (2022)
https://doi.org/10.1063/5.0079797
Published: February 2022
View article titled, High suitability of tryptophan residues as a spectroscopic thermometer for local temperature in proteins under nonequilibrium conditions
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Includes: Supplementary data
Journal Articles

Calculation of CYP450 protein–ligand binding and dissociation free energy paths

Kuan-Hsuan Su, Chin-Teng Wu, Shang-Wei Lin, Seiji Mori, Wei-Min Liu, Hsiao-Ching Yang
Journal: The Journal of Chemical Physics
J. Chem. Phys. 155, 025101 (2021)
https://doi.org/10.1063/5.0046169
Published: July 2021
View article titled, Calculation of CYP450 protein–ligand binding and dissociation free energy paths
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Includes: Supplementary data
Journal Articles

Lessons from combined experimental and theoretical examination of the FTIR and 2D-IR spectroelectrochemistry of the amide I region of cytochrome c

Youssef El Khoury, Guillaume Le Breton, Ana. V. Cunha, Thomas L. C. Jansen, Luuk J. G. W. van Wilderen, Jens Bredenbeck
Journal: The Journal of Chemical Physics
J. Chem. Phys. 154, 124201 (2021)
https://doi.org/10.1063/5.0039969
Published: March 2021
View article titled, Lessons from combined experimental and theoretical examination of the FTIR and 2D-IR spectroelectrochemistry of the amide I region of cytochrome <em>c</em>
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Includes: Supplementary data
Journal Articles

The importance of exact exchange—A methodological investigation of NO reduction in heme–copper oxidases

Margareta R. A. Blomberg
Journal: The Journal of Chemical Physics
J. Chem. Phys. 154, 055103 (2021)
https://doi.org/10.1063/5.0035634
Published: February 2021
View article titled, The importance of exact exchange—A methodological investigation of NO reduction in heme–copper oxidases
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Includes: Supplementary data
Journal Articles

Elucidating the effect of the ionic liquid type and alkyl chain length on the stability of ionic liquid–iron porphyrin complexes

Atiya Banerjee, Jindal K. Shah
Journal: The Journal of Chemical Physics
J. Chem. Phys. 153, 034306 (2020)
https://doi.org/10.1063/5.0007815
Published: July 2020
View article titled, Elucidating the effect of the ionic liquid type and alkyl chain length on the stability of ionic liquid–iron porphyrin complexes
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Includes: Supplementary data
Journal Articles

On urea and temperature dependences of m-values

Alah Amsdr, Negar Dehghan Noudeh, Lutan Liu, Tigran V. Chalikian
Journal: The Journal of Chemical Physics
J. Chem. Phys. 150, 215103 (2019)
https://doi.org/10.1063/1.5097936
Published: June 2019
View article titled, On urea and temperature dependences of m-values
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Includes: Supplementary data
Journal Articles

Theoretical analysis of the domain-swapped dimerization of cytochrome c: An MD and 3D-RISM approach

Norio Yoshida, Masahiro Higashi, Hideyoshi Motoki, Shun Hirota
Journal: The Journal of Chemical Physics
J. Chem. Phys. 148, 025102 (2018)
https://doi.org/10.1063/1.5009785
Published: January 2018
View article titled, Theoretical analysis of the domain-swapped dimerization of cytochrome <em>c</em>: An MD and 3D-RISM approach
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Journal Articles

Interaction-component analysis of the effects of urea and its alkylated derivatives on the structure of T4-lysozyme

Yu Yamamori, Nobuyuki Matubayasi
Journal: The Journal of Chemical Physics
J. Chem. Phys. 146, 225103 (2017)
https://doi.org/10.1063/1.4985222
Published: June 2017
View article titled, Interaction-component analysis of the effects of urea and its alkylated derivatives on the structure of T4-lysozyme
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Journal Articles

Effect of alcohol on the structure of cytochrome C: FCS and molecular dynamics simulations

Md. Asif Amin, Ritaban Halder, Catherine Ghosh, Biman Jana, Kankan Bhattacharyya
Journal: The Journal of Chemical Physics
J. Chem. Phys. 145, 235102 (2016)
https://doi.org/10.1063/1.4972065
Published: December 2016
View article titled, Effect of alcohol on the structure of cytochrome C: FCS and molecular dynamics simulations
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Includes: Supplementary data
Journal Articles

Interaction-component analysis of the hydration and urea effects on cytochrome c

Yu Yamamori, Ryosuke Ishizuka, Yasuhito Karino, Shun Sakuraba, Nobuyuki Matubayasi
Journal: The Journal of Chemical Physics
J. Chem. Phys. 144, 085102 (2016)
https://doi.org/10.1063/1.4941945
Published: February 2016
View article titled, Interaction-component analysis of the hydration and urea effects on cytochrome <em>c</em>
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Journal Articles

Network representation of conformational transitions between hidden intermediates of Rd-apocytochrome b562

Mojie Duan, Hanzhong Liu, Minghai Li, Shuanghong Huo
Journal: The Journal of Chemical Physics
J. Chem. Phys. 143, 135101 (2015)
https://doi.org/10.1063/1.4931921
Published: October 2015
View article titled, Network representation of conformational transitions between hidden intermediates of Rd-apocytochrome <em>b</em><sub>562</sub>
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Includes: Supplementary data
Journal Articles

Memetic algorithms for ligand expulsion from protein cavities

J. Rydzewski, W. Nowak
Journal: The Journal of Chemical Physics
J. Chem. Phys. 143, 124101 (2015)
https://doi.org/10.1063/1.4931181
Published: September 2015
View article titled, Memetic algorithms for ligand expulsion from protein cavities
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Journal Articles

Effect of kinetic energy on the doping efficiency of cesium cations into superfluid helium droplets

Lei Chen, Jie Zhang, William M. Freund, Wei Kong
Journal: The Journal of Chemical Physics
J. Chem. Phys. 143, 044310 (2015)
https://doi.org/10.1063/1.4927471
Published: July 2015
View article titled, Effect of kinetic energy on the doping efficiency of cesium cations into superfluid helium droplets
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Journal Articles

Ab initio dynamics of the cytochrome P450 hydroxylation reaction

Justin E. Elenewski, John C Hackett
Journal: The Journal of Chemical Physics
J. Chem. Phys. 142, 064307 (2015)
https://doi.org/10.1063/1.4907733
Published: February 2015
View article titled, <em>Ab initio</em> dynamics of the cytochrome P450 hydroxylation reaction
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Includes: Supplementary data