Article
Chemistry, Physical
Jaya Lakshmi Tyagi, Goutami Naidu, Meenakshi Sharma, Krishna Mohan Poluri
Summary: Conformational transitions of proteins, regulated by pH-dependent conformational switching, play a crucial role in determining the structure, stability, and activity of proteins. Histidine residues in T7 endolysin are involved in pH-induced conformational transitions, with His48, His69, and His18 playing key roles in regulating the structural stability, amidase activity, and pH-dependent conformational switching of T7L. This study provides experimental evidence on the regulatory role of histidine molecular switches in the structure-activity paradigm of bacteriophage amidases.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Chemistry, Multidisciplinary
Alexander A. Shcherbakov, Merissa Brousseau, Katherine A. Henzler-Wildman, Mei Hong
Summary: EmrE is a bacterial transporter protein that effluxes cationic polyaromatic substrates against the concentration gradient by coupling to proton transport. The structure and dynamics of EmrE provide insights into the mechanism of transport by this family of proteins.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Sompriya Chatterjee, Abbas Salimi, Jin Yong Lee
Summary: The study investigates the conformational characteristics of the huPrP (125-160) monomer under the histidine tautomerism effect using extensive REMD simulations. The hypothesis of histidine tautomerization is proposed as a new mechanism for prion accumulation, potentially aiding in the understanding of prion disease pathobiology and inhibitor design.
ACS CHEMICAL NEUROSCIENCE
(2021)
Article
Engineering, Environmental
Cai'e Zhang, Yaya Zhang, Liwen Wang, Hongbo Wu, Baohua Wu, Zheng Tang, Wei Ma, Zhenghui Luo, Cuihong Li, Zhishan Bo, Chuluo Yang
Summary: In this study, three novel small molecular acceptors (SMAs) were designed and synthesized. The addition of intramolecular noncovalent interaction led to the formation of planar molecular backbone in these acceptors. Among them, the acceptor with four side chains exhibited the highest solubility and formed more suitable nanomorphology when blended with PBDB-T, resulting in an outstanding power conversion efficiency (PCE) of 14.25% in organic solar cells. Our findings suggest that the combination of sidechain engineering and intramolecular conformation lock holds great promise in designing high-performance SMAs for solar cells.
CHEMICAL ENGINEERING JOURNAL
(2022)
Article
Chemistry, Physical
Xiaofeng Li, Kuan Yang, Ziqin Li, Jing Guo, Jifu Zheng, Shenghai Li, Suobo Zhang, Tauqir A. Sherazi
Summary: Controlling the length of the polymer side chain is an effective method for building high-performance anion exchange membranes, with alkaline stability and hydroxide ion conductivity improving as the side chain length increases. The peak power density of PFBA-6C-QA reaches 278 mW cm(-2) at 60 degrees C, with no degradation observed during immersion in 2 M NaOH at 80 degrees C for 30 days.
INTERNATIONAL JOURNAL OF HYDROGEN ENERGY
(2022)
Article
Polymer Science
Zhejing Zhang, Na Yu, Haoran Sun, Ruihong Liu, Yixin Xu, Jingshuai Yang
Summary: We designed and prepared a series of anion exchange membranes (AEMs) based on poly(ether ketone cardo) (PEKC) to achieve high chemical stability and ionic conductivity. Among them, the PEKC-AP-Pip membrane shows the highest OH- conductivity, excellent mechanical strength, and good alkaline stability, making it a promising candidate for alkaline energy devices.
EUROPEAN POLYMER JOURNAL
(2023)
Article
Electrochemistry
Weiqin Tang, Yunfei Yang, Xinli Liu, Jianhao Dong, Huanhuan Li, Jingshuai Yang
Summary: The newly synthesized PBI-BPTMA membrane shows excellent performance in ion exchange capacity, hydrophilicity, and conductivity, especially demonstrating superior performance and stability in vanadium redox flow batteries.
ELECTROCHIMICA ACTA
(2021)
Article
Chemistry, Physical
Fanghui Wang, Hanfei Zhang, Jing Sang, Yahui Cui, Hong Zhu
Summary: To solve the problems of SEBS being difficult to dissolve and poor mechanical properties, SEBS-C16D60-DMHP-X anion exchange membranes (AEMs) with different cationic graft ratios were prepared. The introduction of hydrophobic long chains onto the SEBS skeleton improved its solubility and ion conductivity. The AEMs exhibited enhanced mechanical properties and controlled swelling ratio, as well as improved alkaline resistance.
ACS APPLIED ENERGY MATERIALS
(2023)
Article
Biochemistry & Molecular Biology
Matthias Dreydoppel, Roman J. Lichtenecker, Mikael Akke, Ulrich Weininger
Summary: Aromatic side chains play an important role in protein dynamics and can be studied using relaxation dispersion experiments. The newly introduced H-1 R-1 rho relaxation dispersion experiment allows for faster exchange processes compared to existing methods, with the use of site-specific isotope labeling schemes to avoid anomalous relaxation dispersion profiles. This approach has been validated in measuring ring-flip kinetics in the protein GB1, providing useful information on exchange rates and serving as a complement to C-13-based methods.
JOURNAL OF BIOMOLECULAR NMR
(2021)
Article
Chemistry, Organic
Rachael Dickman, Serena A. Mitchell, Angelo M. Figueiredo, D. Flemming Hansen, Alethea B. Tabor
JOURNAL OF ORGANIC CHEMISTRY
(2019)
Article
Chemistry, Multidisciplinary
Rachael Dickman, Emma Danelius, Serena A. Mitchell, D. Flemming Hansen, Mate Erdelyi, Alethea B. Tabor
CHEMISTRY-A EUROPEAN JOURNAL
(2019)
Article
Chemistry, Medicinal
Simon O. R. Greenwood, A. W. Edith Chan, D. Flemming Hansen, Charles M. Marson
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
(2020)
Article
Cell Biology
Yun Song, Lisbeth Dagil, Louise Fairall, Naomi Robertson, Mingxuan Wu, T. J. Ragan, Christos G. Savva, Almutasem Saleh, Nobuhiro Morone, Micha B. A. Kunze, Andrew G. Jamieson, Philip A. Cole, D. Flemming Hansen, John W. R. Schwabe
Article
Chemistry, Physical
Gogulan Karunanithy, Jochen Reinstein, D. Flemming Hansen
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2020)
Article
Multidisciplinary Sciences
Nicolas D. Werbeck, Vaibhav Kumar Shukla, Micha B. A. Kunze, Havva Yalinca, Ruth B. Pritchard, Lucas Siemons, Somnath Mondal, Simon O. R. Greenwood, John Kirkpatrick, Charles M. Marson, D. Flemming Hansen
NATURE COMMUNICATIONS
(2020)
Article
Biochemistry & Molecular Biology
Gogulan Karunanithy, D. Flemming Hansen
Summary: The article introduces a deep neural network architecture called FID-Net, inspired by WaveNet, for analyzing time domain NMR data and demonstrates its effectiveness in reconstructing NUS biomolecular NMR spectra.
JOURNAL OF BIOMOLECULAR NMR
(2021)
Article
Chemistry, Multidisciplinary
Gogulan Karunanithy, Harold W. Mackenzie, D. Flemming Hansen
Summary: The study introduces a method of virtual decoupling using deep neural networks, which enhances the resolution of nuclear magnetic resonance experiments and reduces the phase cycles required for experiments. This approach successfully decouples various protein NMR spectra, offering a flexible and effective solution where traditional methods may fail.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Correction
Biochemistry & Molecular Biology
Tim A. Mollner, Patrick G. Isenegger, Brian Josephson, Charles Buchanan, Lukas Lercher, Daniel Oehlrich, D. Flemming Hansen, Shabaz Mohammed, Andrew J. Baldwin, Veronique Gouverneur, Benjamin G. Davis
NATURE CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Tim A. Mollner, Patrick G. Isenegger, Brian Josephson, Charles Buchanan, Lukas Lercher, Daniel Oehlrich, D. Flemming Hansen, Shabaz Mohammed, Andrew J. Baldwin, Veronique Gouverneur, Benjamin G. Davis
Summary: Post-translational formation of boronoalanine in proteins through C beta-B gamma bond allows for mild, direct, and site-selective access, enabling tunable interactions and de novo function.
NATURE CHEMICAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Gogulan Karunanithy, Tairan Yuwen, Lewis E. Kay, D. Flemming Hansen
Summary: This article introduces a DNN for the analysis of CEST data, which can accurately predict the chemical shifts of nuclei in exchanging species involving two or three sites, along with the associated uncertainty. The developed DNN method allows for autonomous analysis of complex NMR data.
JOURNAL OF BIOMOLECULAR NMR
(2022)
Article
Biochemistry & Molecular Biology
Nicolas Bolik-Coulon, D. Flemming Hansen, Lewis E. Kay
Summary: For the past decade, chemical exchange saturation transfer (CEST) experiments have been successfully used to study exchange processes in biomolecules involving sparsely populated, transiently formed conformers. This study shows that the commonly used lengthy sampling schemes may not be optimal and proposes a reduced frequency sampling approach that does not require a priori knowledge of exchange parameters.
JOURNAL OF BIOMOLECULAR NMR
(2022)
Article
Multidisciplinary Sciences
Vaibhav Kumar Shukla, Lucas Siemons, D. Flemming Hansen
Summary: Enzymes sample various conformations, and the dynamic sampling of conformations determines both enzymatic activity and inhibitor potency. Precise structures alone often cannot explain the effect of mutations on enzymatic activity and drug potency.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Biochemistry & Molecular Biology
Vaibhav Kumar Shukla, Gabriella T. Heller, D. Flemming Hansen
Summary: Biomolecular nuclear magnetic resonance (NMR) spectroscopy and artificial intelligence (AI) have a strong synergy. AI can improve the acquisition and analysis of NMR spectra, enhancing accuracy and reliability. Deep learning also enables the development of new types of NMR experiments, expanding the scope and potential of biomolecular NMR spectroscopy. The combination of AI and NMR has the potential to revolutionize structural biology and drug discovery.
Article
Chemistry, Multidisciplinary
Vaibhav Kumar Shukla, Lucas Siemons, Francesco L. Gervasio, D. Flemming Hansen
Summary: This study demonstrates a strong correlation between the conformation of aromatic side chains near the active site and the opening and closing of functional loops of HDAC8. Mutations I19S-HDAC8 and S39E-HDAC8 were found to affect product release and substrate binding, providing insights into the mechanism of substantial downregulation caused by allosteric mutations.