Article
Chemistry, Physical
Vitali Tugarinov, Alberto Ceccon, G. Marius Clore
Summary: The dynamics of methyl-bearing side chains in proteins were investigated through C-13 relaxation measurements, revealing correlations and anticorrelations between parameters, which can be partially decorrelated through the analysis of different C-13 magnetization modes.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Multidisciplinary Sciences
Yanjiao Wang, Ge Han, Xiuying Jiang, Tairan Yuwen, Yi Xue
Summary: NH groups in proteins or nucleic acids are challenging for chemical shift prediction. A lookup table linking base pair triplets to experimental chemical shifts can predict imino chemical shifts of RNAs accurately, even for non-canonical motifs. Combining this prediction with NMR relaxation dispersion experiments helps verify the presence of excited states in RNA motifs.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Kai Xue, Evgeny Nimerovsky, Kumar A. Tekwani Movellan, Stefan Becker, Loren B. Andreas
Summary: A new proton-detection method has been developed to measure protein torsion angles by recoupling NH and CH dipolar couplings, applicable to protonated or partly deuterated samples. The efficiency and precision of the method were demonstrated with microcrystalline chicken α-spectrin SH3 protein and the influenza A matrix 2 (M2) membrane protein. Pseudo-4D data for M2 revealed a turn between transmembrane and amphipathic helices.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Multidisciplinary
Zhen Yu, Dale F. Kreitler, Yin Ting T. Chiu, Ruiwen Xu, Austin T. Bruchs, Craig A. Bingman, Samuel H. Gellman
Summary: Peptide engineering has successfully delivered drugs for various human diseases. While side chain alteration is a common strategy, the modification of peptide backbone has received less attention. This study demonstrates that rational and coordinated side chain modification and backbone extension can engineer new and favorable contacts between target proteins and synthetic peptide ligands. These findings support the synergy between backbone and side chain modification in ligands of the parathyroid hormone receptor-1, motivating the adoption of coordinated modifications to enhance peptide ligand engagement with target proteins.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Emma E. Cawood, G. Marius Clore, Theodoros K. Karamanos
Summary: The T193A mutation in DNAJB6 reduces self-oligomerization and anti-aggregation activity while increasing the rate of formation of a partially folded state. This highlights the importance of chaperone dynamics in regulating protein aggregation and suggests potential therapeutic avenues targeting specific substrates.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Multidisciplinary Sciences
Stuart J. Elliott, O. Maduka Ogba, Lynda J. Brown, Daniel J. O'Leary
Summary: This article focuses on investigating how the breaking of rotameric symmetry in N-CH2D-2-methylpiperidine and other suitable CH2D-piperidine derivatives leads to a chemical shift difference, which can be tuned by factors such as temperature, acidity, and 2-substituted molecular groups. The study utilized a combination of experimental and computational approaches to explore this phenomenon.
Article
Multidisciplinary Sciences
Deniz Akpinaroglu, Jeffrey A. Ruffolo, Sai Pooja Mahajan, Jeffrey J. Gray
Summary: Antibody engineering is widely used in medicine and accurate modeling of antibody structures is crucial for effective engineering and design. We developed DeepSCAb, a deep learning method that predicts both backbone and side-chain conformations of antibodies, improving the accuracy of antibody structure prediction. This method is particularly useful for antibodies without known backbone structures.
Article
Biophysics
Shihui Fan, Jie Zhuang, Chenyun Guo, Donghai Lin, Xinli Liao
Summary: The study reported the NMR resonance assignments for MtPC, predicting its secondary structure. This represents a first step towards researching the structure and function of MtPC.
BIOMOLECULAR NMR ASSIGNMENTS
(2021)
Article
Chemistry, Medicinal
Jaswinder Singh, Kuldip Paliwal, Jaspreet Singh, Yaoqi Zhou
Summary: The dilated convolutional neural network method SPOT-RNA-1D predicts RNA backbone torsion and pseudotorsion angles with smaller mean absolute errors compared to random and helix prediction methods. It accurately recovers overall patterns of angle distributions but faces difficulty in predicting angles further away from bases involved in tertiary interactions. SPOT-RNA-1D yields more accurate dihedral angles than the best models in RNA-puzzles experiments, showing potential as model quality indicators and restraints for RNA structure prediction.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Chemistry, Physical
Vitali Tugarinov, Yusuke Okuno, Francesco Torricella, Theodoros K. Karamanos, G. Marius Clore
Summary: Degenerate spin systems are challenging for CPMG relaxation dispersion NMR experiments. A simple alternative method called the steady-state CPMG scheme is proposed, which utilizes acute-angle 1H radiofrequency pulses to establish a steady-state for effective rates of magnetization decay. The method is applied to two protein systems with different exchange regimes.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Multidisciplinary Sciences
Anthony C. Bishop, Glorise Torres-Montalvo, Sravya Kotaru, Kyle Mimun, A. Joshua Wand
Summary: The authors propose BARASA, an approach for assigning backbone triple resonance spectra of proteins. The algorithm uses Bayesian statistical analysis and inter-spin connectivities from triple resonance spectroscopy to identify the optimal resonance assignments. BARASA outperforms current algorithms, especially in cases of sparse data, and can be evaluated in real-time during data acquisition.
NATURE COMMUNICATIONS
(2023)
Article
Biophysics
Christoph Wiedemann, Kingsley Benjamin Obika, Sandra Liebscher, Jan Jirschitzka, Oliver Ohlenschlager, Frank Bordusa
Summary: The Human Genome Project revealed that the human DNA contains 20,000 to 25,000 protein coding genes, with a large number of these proteins remaining functionally uncharacterized. Structural characterization of these unknown proteins may help identify their cellular tasks. By using bioinformatics and nuclear magnetic resonance spectroscopy, researchers were able to determine that the 108 amino acid human uncharacterized protein CXorf51A is an intrinsically disordered protein.
BIOMOLECULAR NMR ASSIGNMENTS
(2021)
Article
Biochemistry & Molecular Biology
Varun V. Sakhrani, Rittik K. Ghosh, Eduardo Hilario, Kevin L. Weiss, Leighton Coates, Leonard J. Mueller
Summary: The backbone chemical shift assignments of Toho-1 beta-lactamase were determined using NMR experiments, allowing for site-specific characterization. The study revealed high rigidity on short timescales and active site flexibility on longer timescales, which is consistent with achieving high catalytic efficiency and broad substrate specificity. These findings suggest that induced active site dynamics in the enzyme play a crucial role in accommodating variously sized substrates and sampling the optimal conformation for catalysis.
JOURNAL OF BIOMOLECULAR NMR
(2021)
Article
Chemistry, Physical
Souvik Dey, Matthew MacAinsh, Huan-Xiang Zhou
Summary: For intrinsically disordered proteins (IDPs), the dynamics of the backbone play a key role in encoding their function. The dynamics are regulated by local interactions, secondary structures, and glycines. These sequence-dependent changes in backbone dynamics allow IDPs to respond to binding partners in a versatile manner.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Jianquan Zhang, Fujin Bai, Indunil Angunawela, Xiaoyun Xu, Siwei Luo, Chao Li, Gaoda Chai, Han Yu, Yuzhong Chen, Huawei Hu, Zaifei Ma, Harald Ade, He Yan
Summary: Side-chain modifications of NFAs play a crucial role in enhancing the performance of OSCs. By introducing bulkier alkyl chains branched at specific positions, it is possible to alter molecular packing, improve open-circuit voltage, and achieve better device performance. The side-chain branching design of NFAs shows great potential in optimizing molecular properties and promoting photovoltaic performance.
ADVANCED ENERGY MATERIALS
(2021)
Article
Biochemistry & Molecular Biology
Da-Wei Li, Cheng Wang, Rafael Bruschweiler
JOURNAL OF BIOMOLECULAR NMR
(2017)
Review
Chemistry, Multidisciplinary
Dawei Li, Alexandar L. Hansen, Lei Bruschweiler-Li, Rafael Bruschweiler
CHEMISTRY-A EUROPEAN JOURNAL
(2018)
Article
Chemistry, Multidisciplinary
Mouzhe Xie, Da-Wei Li, Jiaqi Yuan, Alexandar L. Hansen, Rafael Bruschweiler
CHEMISTRY-A EUROPEAN JOURNAL
(2018)
Article
Chemistry, Multidisciplinary
Gregory Jameson, Alexandar L. Hansen, Dawei Li, Lei Bruschweiler-Li, Rafael Bruschweiler
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2019)
Article
Chemistry, Analytical
Cheng Wang, Bo Zhang, Istvan Timari, Arpad Somogyi, Da-Wei Li, Haley E. Adcox, John S. Gunn, Lei Bruschweiler-Li, Rafael Bruschweiler
ANALYTICAL CHEMISTRY
(2019)
Article
Chemistry, Physical
Lei Yu, Da-Wei Li, Rafael Brueschweiler
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2020)
Article
Biochemical Research Methods
Cheng Wang, Istvan Timari, Bo Zhang, Da-Wei Li, Abigail Leggett, Amal O. Amer, Lei Bruschweiler-Li, Rachel E. Kopec, Rafael Brueschweiler
JOURNAL OF PROTEOME RESEARCH
(2020)
Article
Chemistry, Multidisciplinary
Da-Wei Li, Mouzhe Xie, Rafael Bruschweiler
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2020)
Article
Chemistry, Physical
Lei Yu, Da-Wei Li, Rafael Bruschweiler
Summary: This study compared the performance of four recent molecular dynamics force fields on simulating intrinsically disordered proteins, revealing substantial differences between these force fields at the individual residue level. The study highlighted limitations of current force fields and showed that incorporating coil library information, as demonstrated by ff99SBnmr2, can significantly improve performance and sampling realism.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Analytical
Alexandar L. Hansen, Erriks Kupce, Da-Wei Li, Lei Bruschweiler-Li, Cheng Wang, Rafael Brueschweiler
Summary: This study presents sensitivity-improved versions of two-dimensional NMR experiments optimized for small biological molecules encountered in metabolomics, allowing for rapid acquisition techniques and incorporation into supersequences for compact acquisition of multiple 2D NMR data sets. These new pulse sequences offer an attractive approach for efficient measurement of multiple 2D NMR spectra in a single experiment, enhancing identification and quantitation of metabolites in metabolomics samples. The advantages of 2D NMR have been extended to metabolomics studies with larger sample cohorts.
ANALYTICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Da-Wei Li, Alexandar L. Hansen, Chunhua Yuan, Lei Bruschweiler-Li, Rafael Bruschweiler
Summary: The study introduces a deep learning-based method for analyzing NMR spectra, which is challenging even for experts. DEEP Picker plays an important role in the analysis of complex biochemical samples, providing valuable information.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Analytical
Da-Wei Li, Abigail Leggett, Lei Bruschweiler-Li, Rafael Brueschweiler
Summary: COLMARq is a new public web server for the analysis of cohorts of samples using 2D HSQC spectra. It enables quantitative metabolomics analysis, including biomarker identification, of complex biological mixtures such as bacterial cultures of Pseudomonas aeruginosa in both its biofilm and planktonic states.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Yina Gu, Da-Wei Li, Rafael Bruschweiler
Article
Chemistry, Multidisciplinary
Alexandar L. Hansen, Dawei Li, Cheng Wang, Rafael Bruschweiler
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2017)
Article
Chemistry, Physical
Felix Hoffmann, Da-Wei Li, Daniel Sebastiani, Rafael Brueschweiler
JOURNAL OF PHYSICAL CHEMISTRY A
(2017)