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Journal Articles

ProteinReDiff: Complex-based ligand-binding proteins redesign by equivariant diffusion-based generative models

Viet Thanh Duy Nguyen, Nhan D. Nguyen, Truong Son Hy

Struct. Dyn. 11, 064102 (2024)

https://doi.org/10.1063/4.0000271

Published: November 2024

View article titled, ProteinReDiff: Complex-based ligand-binding proteins redesign by equivariant diffusion-based generative models

Journal Articles

High-throughput thermal denaturation of tryptophanyl-tRNA synthetase combinatorial mutants reveals high-order energetic coupling determinants of conformational stability

Violetta Weinreb, Gabriel Weinreb, Charles W. Carter, Jr.

Struct. Dyn. 10, 044304 (2023)

https://doi.org/10.1063/4.0000182

Published: August 2023

View article titled, High-throughput thermal denaturation of tryptophanyl-tRNA synthetase combinatorial mutants reveals high-order energetic coupling determinants of conformational stability

Includes: Supplementary data

Journal Articles

Microcalorimetry reveals multi-state thermal denaturation of G. stearothermophilus tryptophanyl-tRNA synthetase

Srinivas Niranj Chandrasekaran, Jhuma Das, Nikolay V. Dokholyan, Charles W. Carter, Jr.

Struct. Dyn. 10, 044301 (2023)

https://doi.org/10.1063/4.0000181

Published: July 2023

View article titled, Microcalorimetry reveals multi-state thermal denaturation of G. stearothermophilus tryptophanyl-tRNA synthetase

Journal Articles

Charge-induced chemical dynamics in glycine probed with time-resolved Auger electron spectroscopy

Struct. Dyn. 9, 064301 (2022)

https://doi.org/10.1063/4.0000165

Published: November 2022

View article titled, Charge-induced chemical dynamics in glycine probed with time-resolved Auger electron spectroscopy

Journal Articles

Comparative studies of IR spectra of deprotonated serine with classical and thermostated ring polymer molecular dynamics simulations

V. S. Sandeep Inakollu, Haibo Yu

Struct. Dyn. 8, 054101 (2021)

https://doi.org/10.1063/4.0000124

Published: September 2021

View article titled, Comparative studies of IR spectra of deprotonated serine with classical and thermostated ring polymer molecular dynamics simulations

Journal Articles

Development of membrane-insertable lipid scrambling peptides: A time-resolved small-angle neutron scattering study

Hiroyuki Nakao, Yusuke Kimura, Ami Sakai, Keisuke Ikeda, Minoru Nakano

Struct. Dyn. 8, 024301 (2021)

https://doi.org/10.1063/4.0000045

Published: March 2021

View article titled, Development of membrane-insertable lipid scrambling peptides: A time-resolved small-angle neutron scattering study

Includes: Supplementary data

Journal Articles

Secondary structure effects on internal proton transfer in poly-peptides

M. Bouakil, F. Chirot, M. Girod, P. Dugourd, L. MacAleese

Struct. Dyn. 7, 024302 (2020)

https://doi.org/10.1063/4.0000003

Published: March 2020

View article titled, Secondary structure effects on internal proton transfer in poly-peptides

Includes: Supplementary data

Journal Articles

Fragment screening for a protein-protein interaction inhibitor to WDR5

Matthew L. Dennis, Benjamin J. Morrow, Olan Dolezal, Anthony N. Cuzzupe, Alexandra E. Stupple, Janet Newman, John Bentley, Meghan Hattarki, Stewart D. Nuttall, Richard C. Foitzik, Ian P. Street, Paul A. Stupple, Brendon J. Monahan, Thomas. S. Peat

Struct. Dyn. 6, 064701 (2019)

https://doi.org/10.1063/1.5122849

Published: November 2019

View article titled, Fragment screening for a protein-protein interaction inhibitor to WDR5

Includes: Supplementary data

Journal Articles

High-resolution crystal structures of a myxobacterial phytochrome at cryo and room temperatures

Struct. Dyn. 6, 054701 (2019)

https://doi.org/10.1063/1.5120527

Published: September 2019

View article titled, High-resolution crystal structures of a myxobacterial phytochrome at cryo and room temperatures

Includes: Supplementary data

Journal Articles

Structural and dynamical description of the enzymatic reaction of a phosphohexomutase

Kyle M. Stiers, Abigail C. Graham, Jian-She Zhu, David L. Jakeman, Jay C. Nix, Lesa J. Beamer

Struct. Dyn. 6, 024703 (2019)

https://doi.org/10.1063/1.5092803

Published: April 2019

View article titled, Structural and dynamical description of the enzymatic reaction of a phosphohexomutase

Includes: Supplementary data

Journal Articles

Conformation-specific detection of calmodulin binding using the unnatural amino acid p-azido-phenylalanine (AzF) as an IR-sensor

Anne Creon, Inokentijs Josts, Stephan Niebling, Nils Huse, Henning Tidow

Struct. Dyn. 5, 064701 (2018)

https://doi.org/10.1063/1.5053466

Published: November 2018

View article titled, Conformation-specific detection of calmodulin binding using the unnatural amino acid p-azido-phenylalanine (AzF) as an IR-sensor

Includes: Supplementary data

Journal Articles

Dynamic multiple-scattering treatment of X-ray absorption: Parameterization of a new molecular dynamics force field for myoglobin

Giovanni Chillemi, Massimiliano Anselmi, Nico Sanna, Cristiano Padrin, Lodovico Balducci, Marco Cammarata, Elisabetta Pace, Majed Chergui, Maurizio Benfatto

Struct. Dyn. 5, 054101 (2018)

https://doi.org/10.1063/1.5031806

Published: September 2018

View article titled, Dynamic multiple-scattering treatment of X-ray absorption: Parameterization of a new molecular dynamics force field for myoglobin

Includes: Supplementary data

Journal Articles

Implications of short time scale dynamics on long time processes

Krystel El Hage, Sebastian Brickel, Sylvain Hermelin, Geoffrey Gaulier, Cédric Schmidt, Luigi Bonacina, Siri C. van Keulen, Swarnendu Bhattacharyya, Majed Chergui, Peter Hamm, Ursula Rothlisberger, Jean-Pierre Wolf, Markus Meuwly

Struct. Dyn. 4, 061507 (2017)

https://doi.org/10.1063/1.4996448

Published: December 2017

View article titled, Implications of short time scale dynamics on long time processes

Journal Articles

Partial-occupancy binders identified by the Pan-Dataset Density Analysis method offer new chemical opportunities and reveal cryptic binding sites

Nicholas M. Pearce, Anthony R. Bradley, Tobias Krojer, Brian D. Marsden, Charlotte M. Deane, Frank von Delft

Struct. Dyn. 4, 032104 (2017)

https://doi.org/10.1063/1.4974176

Published: February 2017

View article titled, Partial-occupancy binders identified by the Pan-Dataset Density Analysis method offer new chemical opportunities and reveal cryptic binding sites

Includes: Supplementary data

Journal Articles

Augmenting the anisotropic network model with torsional potentials improves PATH performance, enabling detailed comparison with experimental rate data

Srinivas Niranj Chandrasekaran, Charles W. Carter, Jr.

Struct. Dyn. 4, 032103 (2017)

https://doi.org/10.1063/1.4976142

Published: February 2017

View article titled, Augmenting the anisotropic network model with torsional potentials improves PATH performance, enabling detailed comparison with experimental rate data

Journal Articles

Combining multi-mutant and modular thermodynamic cycles to measure energetic coupling networks in enzyme catalysis

Charles W. Carter, Jr., Srinivas Niranj Chandrasekaran, Violetta Weinreb, Li Li, Tishan Williams

Struct. Dyn. 4, 032101 (2017)

https://doi.org/10.1063/1.4974218

Published: January 2017

View article titled, Combining multi-mutant and modular thermodynamic cycles to measure energetic coupling networks in enzyme catalysis

Journal Articles

Structural enzymology using X-ray free electron lasers

Struct. Dyn. 4, 044003 (2017)

https://doi.org/10.1063/1.4972069

Published: December 2016

View article titled, Structural enzymology using X-ray free electron lasers

Includes: Supplementary data

Journal Articles

A comparison of the innate flexibilities of six chains in F₁-ATPase with identical secondary and tertiary folds; 3 active enzymes and 3 structural proteins

Monique M. Tirion

Struct. Dyn. 4, 044001 (2017)

https://doi.org/10.1063/1.4967226

Published: November 2016

View article titled, A comparison of the innate flexibilities of six chains in F1-ATPase with identical secondary and tertiary folds; 3 active enzymes and 3 structural proteins

Journal Articles

Comment on “Structural dynamics of cisplatin binding to histidine in a protein” [Struct. Dyn. 1 , 034701 (2014)]

S. W. M. Tanley, J. R. Helliwell

Struct. Dyn. 3, 037101 (2016)

https://doi.org/10.1063/1.4948613

Published: May 2016

View article titled, Comment on “Structural dynamics of cisplatin binding to histidine in a protein” [Struct. Dyn. 1 , 034701 (2014)]

Journal Articles

Structural dynamics of a methionine γ-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking with pyridoxal phosphate

Hongnan Cao, Kemin Tan, Fengbin Wang, Lance Bigelow, Ragothaman M. Yennamalli, Robert Jedrzejczak, Gyorgy Babnigg, Craig A. Bingman, Andrzej Joachimiak, Madan K. Kharel, Shanteri Singh, Jon S. Thorson, George N. Phillips, Jr.

Struct. Dyn. 3, 034702 (2016)

https://doi.org/10.1063/1.4948539

Published: April 2016

View article titled, Structural dynamics of a methionine γ-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking with pyridoxal phosphate

Includes: Supplementary data

NARROW

Topics

ProteinReDiff: Complex-based ligand-binding proteins redesign by equivariant diffusion-based generative models

High-throughput thermal denaturation of tryptophanyl-tRNA synthetase combinatorial mutants reveals high-order energetic coupling determinants of conformational stability

Microcalorimetry reveals multi-state thermal denaturation of G. stearothermophilus tryptophanyl-tRNA synthetase

Charge-induced chemical dynamics in glycine probed with time-resolved Auger electron spectroscopy

Comparative studies of IR spectra of deprotonated serine with classical and thermostated ring polymer molecular dynamics simulations

Development of membrane-insertable lipid scrambling peptides: A time-resolved small-angle neutron scattering study

Secondary structure effects on internal proton transfer in poly-peptides

Fragment screening for a protein-protein interaction inhibitor to WDR5

High-resolution crystal structures of a myxobacterial phytochrome at cryo and room temperatures

Structural and dynamical description of the enzymatic reaction of a phosphohexomutase

Conformation-specific detection of calmodulin binding using the unnatural amino acid p-azido-phenylalanine (AzF) as an IR-sensor

Dynamic multiple-scattering treatment of X-ray absorption: Parameterization of a new molecular dynamics force field for myoglobin

Implications of short time scale dynamics on long time processes

Partial-occupancy binders identified by the Pan-Dataset Density Analysis method offer new chemical opportunities and reveal cryptic binding sites

Augmenting the anisotropic network model with torsional potentials improves PATH performance, enabling detailed comparison with experimental rate data

Combining multi-mutant and modular thermodynamic cycles to measure energetic coupling networks in enzyme catalysis

Structural enzymology using X-ray free electron lasers

A comparison of the innate flexibilities of six chains in F₁-ATPase with identical secondary and tertiary folds; 3 active enzymes and 3 structural proteins

Comment on “Structural dynamics of cisplatin binding to histidine in a protein” [Struct. Dyn. 1 , 034701 (2014)]

Structural dynamics of a methionine γ-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking with pyridoxal phosphate

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