Article
Chemistry, Multidisciplinary
Taylor N. Lewis, Claire Tonnele, William G. Shuler, Zachary A. Kasun, Hiroki Sato, Adam J. Berges, Jacob R. Rodriguez, Michael J. Krische, David Casanova, Christopher J. Bardeen
Summary: In this study, a newly developed triple-stranded cage architecture is used to analyze the optical and electronic properties as well as the conformational freedom of benzene-capped and triazine-capped 5,5'(2,2-bithiophene)-containing arylene cages. The properties of the chromophore assemblies can be tuned by selecting different linking groups, providing a new approach for controlling the properties of discrete chromophore assemblies.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Multidisciplinary Sciences
D. Mayer, F. Lever, D. Picconi, J. Metje, S. Alisauskas, F. Calegari, S. Duesterer, C. Ehlert, R. Feifel, M. Niebuhr, B. Manschwetus, M. Kuhlmann, T. Mazza, M. S. Robinson, R. J. Squibb, A. Trabattoni, M. Wallner, P. Saalfrank, T. J. A. Wolf, M. Guehr
Summary: Tracking the charge flow in photoexcited molecules using time-resolved X-ray photoelectron spectroscopy allows for real-time observation of changes in charge density and reveals the dynamics of electron motion. This provides important insights into photophysical and photochemical processes and is a valuable tool for studying molecular dynamics.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Physical
Bronte J. Charette, Shelby R. King, Jiaqi Chen, Annika R. Holm, Justin T. Malme, Robert D. Cook, Richard D. Schaller, Nicholas E. Jackson, Lisa Olshansky
Summary: The conversion of solar energy into chemical fuel is a crucial goal for the 21st century and has the potential to generate terawatts of power worldwide. However, the discrepancy between the time scales of photodriven charge separation and chemical reactions poses a bottleneck for solar-to-fuels technology. To address this, researchers are developing coordination complexes that undergo conformational rearrangements to accelerate charge separation and slow down charge recombination. This study presents a new series of copper coordination complexes with a twisted intramolecular charge transfer fluorophore, demonstrating improved photophysics and providing insights for future optimizations. Evaluation: 8/10.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Multidisciplinary
Ziyue Yang, Maghesree Chakraborty, Andrew D. White
Summary: The study utilizes graph neural networks (GNNs) for NMR chemical shift prediction, accurately capturing important chemical shift phenomena such as hydrogen bonding-induced downfield shift and shifts of organic molecules. These GNN models do not require feature engineering, only data training, yet are as accurate as previous empirical protein NMR models.
Article
Biochemistry & Molecular Biology
Valeria Jaramillo-Martinez, Matthew J. Dominguez, Gemma M. Bell, Megan E. Souness, Anna H. Carhart, M. Adriana Cuibus, Elahe Masoumzadeh, Benjamin J. Lantz, Aaron J. Adkins, Michael P. Latham, K. Aurelia Ball, Elliott J. Stollar
Summary: Charged residues on protein surfaces play important roles in protein stability and interactions. Proteins with highly charged binding regions have weak stability due to electrostatic repulsion, but these regions are useful for binding to oppositely charged targets. Increasing salt concentration stabilizes the protein folds by mimicking electrostatic interactions during target binding. The yeast SH3 domain was studied to understand the contributions of electrostatic and hydrophobic interactions in folding. The addition of salt primarily affects the folding rate, indicating that hydrophobic collapse and electrostatic repulsion occur in the transition state.
Article
Chemistry, Multidisciplinary
Nan Gao, Zhenqi Liu, Haochen Zhang, Chun Liu, Dongqin Yu, Jinsong Ren, Xiaogang Qu
Summary: Post-translational modification (PTM) can alter protein conformation and function. In this study, a new approach using chemical PTM modification to inhibit amyloid aggregation was presented. Polyoxometalates (POMs) were used as inhibitors and the superiority of the chemical PTM method was demonstrated through various techniques.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Radiology, Nuclear Medicine & Medical Imaging
Yoshiharu Ohno, Masao Yui, Kaori Yamamoto, Daisuke Takenaka, Hisanobu Koyama, Hiroyuki Nagata, Takahiro Ueda, Hirotaka Ikeda, Yoshiyuki Ozawa, Hiroshi Toyama, Takeshi Yoshikawa
Summary: This study compared the predictive capability of APTw/CEST imaging, DWI, and FDG-PET/CT for the therapeutic effect of chemoradiotherapy on stage III NSCLC patients, and found that APTw/CEST imaging performed similarly to DWI and FDG-PET/CT.
JOURNAL OF MAGNETIC RESONANCE IMAGING
(2023)
Article
Biochemistry & Molecular Biology
Cullen Demakis, Matthew C. Childers, Valerie Daggett
Summary: This study uses high temperature unfolding simulations to explore the folding and unfolding pathways of the SH3 domain. Results show that SH3 domain proteins with different sequences can unfold through two main pathways, while certain structural characteristics remain conserved regardless of sequence. Disparate sequences can provide similar interactions that influence folding and lead to similar structures.
Article
Chemistry, Physical
Vladimir Palivec, Radek Pohl, Jakub Kaminsky, Hector Martinez-Seara
Summary: Determining the structure of saccharides in their native environment is crucial for understanding their function. In this study, we propose two cost-effective protocols for simulating sugar chemical shifts and recommend their use. These protocols not only help interpret experimental spectra, but can also independently predict structure.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Man Shi, Xinsheng Jin, Zheng Wan, Xiao He
Summary: The AF-QM/MM approach was applied to accurately calculate the C-13 and H-1 NMR chemical shifts in molecular crystals, showing that the results are close to convergence under certain conditions. Different density functionals and basis sets have varying impacts on the predictions, with the choice affecting the accuracy of the results. By selecting suitable combinations, the accuracy of the predictions can be improved.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Medicinal
Kexin Zhang, Kyrillos Abdallah, Pujan Ajmera, Kyle Finos, Andrew Looka, Joseph Mekhael, Aaron T. Frank
Summary: CS-Annotate is a tool that annotates structural features in RNA using assigned NMR chemical shifts, utilizing a multitask deep learning model to classify solvent exposure, base-stacking and -pairing status, and conformation of individual RNA residues from their chemical shift fingerprint. The classifier was trained and tested, demonstrating its application to a model RNA system, and can be accessed through the SMALTR Science Gateway.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Biochemical Research Methods
Ajith Kumar, Kulkarni Madhurima, Athi N. Naganathan, Pramodh Vallurupalli, Ashok Sekhar
Summary: Over 40% of eukaryotic proteomes and 15% of bacterial proteomes are predicted to be intrinsically disordered based on their amino acid sequence. NMR spectroscopy has made significant contributions to our understanding of intrinsically disordered proteins (IDPs) due to its ability to characterize heterogeneity at atomic resolution. A new 1H alpha CEST pulse sequence has been developed to overcome resonance overlap problem in the 1H alpha-13C alpha plane of IDPs. This sequence has been applied to determine the excited state 1H alpha chemical shifts of the intrinsically disordered DNA binding domain of the bacterial cytidine repressor.
Article
Engineering, Environmental
Jiajun Han, Jesse Fu, Jianxian Sun, David Ross Hall, Diwen Yang, Donovan Blatz, Keith Houck, Carla Ng, Jon Doering, Carlie LaLone, Hui Peng
Summary: The study developed a quantitative interspecies thermal shift assay (QITSA) for investigating chemical-protein interactions across species, using liver fatty acid binding protein (L-FABP) as a case study. Results showed that PFOS exhibited the highest binding affinity to human L-FABP, with variations observed in binding affinities among different species. The experimental strategy implemented in this study may have implications for assessing the toxicity of other chemical contaminants in the future.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Zhenguang Zhao, Reem Mousa, Norman Metanis
Summary: SELENOF is an endoplasmic reticulum selenoprotein that may be responsible for reducing non-native disulfide bonds in misfolded glycoproteins.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Alice Triveri, Carlos Sanchez-Martin, Luca Torielli, Stefano A. Serapian, Filippo Marchetti, Giovanni D'Acerno, Valentina Pirota, Matteo Castelli, Elisabetta Moroni, Mariarosaria Ferraro, Paolo Quadrelli, Andrea Rasola, Giorgio Colombo
Summary: In this study, the allosteric inhibition of the mitochondrial chaperone TRAP1 by a small molecule ligand is examined. The findings are used to design novel derivatives with interesting biological properties. The implications of this approach in understanding molecular regulation and designing allosteric small molecule modulators are discussed.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Tairan Yuwen, Ashok Sekhar, Lewis E. Kay
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2017)
Article
Biochemistry & Molecular Biology
Rui Huang, Jacob P. Brady, Ashok Sekhar, Tairan Yuwen, Lewis E. Kay
JOURNAL OF BIOMOLECULAR NMR
(2017)
Article
Biochemistry & Molecular Biology
Pramodh Vallurupalli, Ashok Sekhar, Tairan Yuwen, Lewis E. Kay
JOURNAL OF BIOMOLECULAR NMR
(2017)
Article
Chemistry, Physical
Nandakumar Rajasekaran, Ashok Sekhar, Athi N. Naganathan
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2017)
Article
Multidisciplinary Sciences
Jacob P. Brady, Patrick J. Farber, Ashok Sekhar, Yi-Hsuan Lin, Rui Huang, Alaji Bah, Timothy J. Nott, Hue Sun Chan, Andrew J. Baldwin, Julie D. Forman-Kay, Lewis E. Kay
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2017)
Article
Multidisciplinary Sciences
Robert M. Culik, Ashok Sekhar, Jayashree Nagesh, Harmeen Deol, Jessica A. O. Rumfeldt, Elizabeth M. Meiering, Lewis E. Kay
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2018)
Article
Biology
Ashok Sekhar, Algirdas Velyvis, Guy Zoltsman, Rina Rosenzweig, Guillaume Bouvignies, Lewis E. Kay
Article
Chemistry, Multidisciplinary
Tairan Yuwen, Ashok Sekhar, Andrew J. Baldwin, Pramodh Vallurupalli, Lewis E. Kay
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2018)
Review
Biophysics
Ashok Sekhar, Lewis E. Kay
ANNUAL REVIEW OF BIOPHYSICS, VOL 48
(2019)
Article
Biochemistry & Molecular Biology
Sneha Munshi, Sandhyaa Subramanian, Samyuktha Ramesh, Hemashree Golla, Divakar Kalivarathan, Madhurima Kulkarni, Luis A. Campos, Ashok Sekhar, Athi N. Naganathan
Article
Biochemistry & Molecular Biology
Ajith Kumar, Vaishali Narayanan, Ashok Sekhar
Article
Biochemical Research Methods
Ahallya Jaladeep, Claris Niya Varghese, Ashok Sekhar
Summary: The method leverages intrinsic modulations observed in offset-dependent NMR nutation profiles of small molecules to measure RF field amplitudes accurately and precisely. It can determine B-1 values ranging from 1 to 2000 Hz, as well as the inhomogeneity in B-1 distributions. The approach can be used in conjunction with a suitable external small molecule standard for large biomolecules where modulations are obscured by high transverse relaxation rate constants.
JOURNAL OF MAGNETIC RESONANCE
(2021)
Article
Biochemistry & Molecular Biology
Vaishali Narayanan, Kishore Babu Bobbili, Nukathoti Sivaji, Nisha G. Jayaprakash, Kaza Suguna, Avadhesha Surolia, Ashok Sekhar
Summary: This study provides insights into the structure and carbohydrate recognition of the lectin Horcolin, which shows promising antiviral potential by binding to the envelope glycoprotein of HIV-1. The findings reveal that Horcolin is non-mitogenic and has two carbohydrate-binding sites with different binding affinities. The study also suggests the presence of allosteric communication between the two binding sites.
Article
Chemistry, Physical
Divya Rajendran, Shrutarshi Mitra, Hiroyuki Oikawa, Kulkarni Madhurima, Ashok Sekhar, Satoshi Takahashi, Athi N. Naganathan
Summary: We investigated the conformational properties of the intrinsically disordered DNA-binding domain of CytR in the presence of polymeric crowder polyethylene glycol (PEG). Our findings demonstrate that the disordered CytR adopts a well-folded conformation in its native ensemble, while the unfolded ensemble collapses and folds with increasing crowder density, regardless of the size of the crowder. We estimate a 10% reduction in the accessible conformational space of a residue in the unfolded state at 300 mg/mL PEG8000. The experimentally constructed PEG-temperature phase diagram shows that entropic effects stabilize disordered CytR by 10 kJ mol-1, promoting the equilibrium towards folded conformations under physiological conditions. Our work highlights the flexible conformational landscape of CytR, reveals the presence of a folded conformation in the disordered ensemble, and proposes a scaling relation for quantifying excluded volume effects on protein stability.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Biochemistry & Molecular Biology
Enrico Rennella, Ashok Sekhar, Lewis E. Kay
