Article
Biochemistry & Molecular Biology
Mary C. Clay, Tamjeed Saleh, Samuel Kamatham, Paolo Rossi, Charalampos G. Kalodimos
Summary: Methyl-TROSY spectroscopy has expanded the application of solution-state NMR to study supra-molecular machineries. Accurate methyl chemical shift assignment remains a challenge. This work presents the current technology for methyl labeling, data collection, data analysis, and automated methyl assignment approaches, along with Python extensions and a standalone network analysis program for the task.
Article
Chemistry, Multidisciplinary
Victoria Aladin, Arun K. Sreemantula, Thomas Biedenbaender, Alexander Marchanka, Bjoern Corzilius
Summary: An approach is presented to enhance NMR spectroscopic signals by site-specific enhancement of the protein-RNA binding site within a ribonucleoprotein (RNP) using dynamic nuclear polarization (DNP). This approach utilizes biochemical techniques for sparse isotope labeling and exploits the molecular dynamics of C-13-labeled methyl groups exclusively present in the protein, resulting in improved sensitivity and specificity for solid-state NMR structure determination of large biomolecules.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Multidisciplinary Sciences
Santrupti Nerli, Viviane S. De Paula, Andrew C. McShan, Nikolaos G. Sgourakis
Summary: The authors introduce MAUS, a method for assigning methyl groups using raw NOE data. They demonstrate its effectiveness by using eight proteins in the 10-45kDa size range as test cases and show that MAUS yields 100% accurate assignments at high completeness levels.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Fa-An Chao, Srisathiyanarayanan Dharmaiah, Troy Taylor, Simon Messing, William Gillette, Dominic Esposito, Dwight Nissley, Frank McCormick, R. Andrew Byrd, Dhirendra K. Simanshu, Gabriel Cornilescu
Summary: This article investigates the influence of conformational dynamics of RAS proteins on their interactions with downstream effectors and explains and predicts the altered binding affinities of different mutants.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biotechnology & Applied Microbiology
Lorena Fernandez-Cabezon, Berta Rosich Bosch, Ekaterina Kozaeva, Nicolas Gurdo, Pablo Ivan Nikel
Summary: In this study, we successfully engineered the soil bacterium Pseudomonas putida to produce high titer of anthranilate by regulating the gene expression of the shikimate pathway using a polymerase inhibitor. This method avoids the need for expensive additives used in traditional strategies.
METABOLIC ENGINEERING
(2022)
Article
Biochemistry & Molecular Biology
Piotr Paluch, Rafal Augustyniak, Mai-Liis Org, Kalju Vanatalu, Ats Kaldma, Ago Samoson, Jan Stanek
Summary: In nuclear magnetic resonance spectroscopy of proteins, methyl protons are important in studying dynamics, allosteric effects, and protein-protein interactions. This study addresses the challenge of assigning chemical shifts to methyl protons by using solid-state H-1-detected methods, fast magic-angle spinning, partial deuteration, and high-magnetic fields. The performance of different RF schemes for transferring coherence between methyl and backbone resonances is evaluated, and optimal parameters are determined through simulations. The concept of linearizing C-13 side chains by appropriate isotope labeling and resolution enhancement provided by 4D spectroscopy are also demonstrated.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
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
Biochemistry & Molecular Biology
Qiong Tong, Huan Tan, Jianping Li, Huayong Xie, Yongxiang Zhao, Yanke Chen, Jun Yang
Summary: The study proposes a new approach utilizing reverse labeling combined with alternate C-13-C-12 labeling to simplify the spectral analysis and extraction of distance restraints for membrane proteins. The quantitative analysis of the impact of reverse labeling on other residue labeling highlights its feasibility and effectiveness.
JOURNAL OF BIOMOLECULAR NMR
(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
Chemistry, Multidisciplinary
Veronika Slachtova, Simona Bellova, Agustina La-Venia, Juraj Galeta, Martin Dracinsky, Karel Chalupsky, Alexandra Dvorakova, Helena Mertlikova-Kaiserova, Peter Rukovansky, Rastislav Dzijak, Milan Vrabel
Summary: The development of reagents selective in complex biological media is a significant challenge. We demonstrate that N1-alkylation of 1,2,4-triazines produces more reactive triazinium salts when reacting with strained alkynes compared to the parent 1,2,4-triazines. These salts facilitate efficient modification of peptides and proteins through a powerful bioorthogonal ligation. The positively charged N1-alkyl triazinium salts possess favorable cell permeability and outperform analogous 1,2,4,5-tetrazines for intracellular fluorescent labeling applications. These new ionic heterodienes exhibit high reactivity, stability, synthetic accessibility, and improved water solubility, making them valuable additions to the repertoire of modern bioorthogonal reagents.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Review
Biochemistry & Molecular Biology
Haoyi Ge, Huixia Wang, Benxun Pan, Dandan Feng, Canyong Guo, Lingyun Yang, Dongsheng Liu, Kurt Wuethrich
Summary: GPCRs are a membrane protein family present in higher organisms, including humans, and play a key role in cellular responses and physiological functions. Understanding the structure and dynamics of GPCRs is crucial for drug design and involves the modulation of extrinsic ligands and intracellular binding partners.
Article
Biochemistry & Molecular Biology
Elif Karaman, Alp Ertunga Eyupoglu, Lena Mahmoudi Azar, Serdar Uysal
Summary: Nanobodies, the smallest fragments of naturally produced camelid antibodies, have potential applications in imaging, diagnostics, and biotechnology. In this study, a practical and scalable platform for large-scale production of functional VHH antibodies using pyrG auxotrophic A. oryzae was established. The affinity of anti-RNase A VHH expressed in pyrG auxotrophic A. oryzae was significantly higher than in Escherichia coli, demonstrating the effectiveness of this biotechnological platform.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Jian Li, Zihao Rei Gao, Qing-Fang Lin, Chenxu Liu, Fangxin Gao, Cong Lin, Siyao Zhang, Hua Deng, Alvaro Mayoral, Wei Fan, Song Luo, Xiaobo Chen, Hong He, Miguel A. Camblor, Fei-Jian Chen, Jihong Yu
Summary: ZEO-3 is a highly stable pure silica zeolite with a multidimensional, interconnected system of extra-large pores open through windows made by 16 and 14 silicate tetrahedra. It has a higher specific surface area compared to other zeolites and metal-organic frameworks, and exhibits excellent performance for volatile organic compound abatement and recovery.
Article
Chemistry, Physical
Frederic A. Perras, Dragos F. Flesariu, Scott A. Southern, Constantinos Nicolaides, J. David Bazak, Nancy M. Washton, Theodossis Trypiniotis, Christos P. Constantinides, Panayiotis A. Koutentis
Summary: The Overhauser effect, which requires the modulation of electron-nuclear hyperfine interactions, dominates dynamic nuclear polarization (DNP) in liquids and metals. This effect can also occur in insulating solids through rapid structural modulations linked to a modulation in hyperfine coupling. In this study, the addition of a methyl group to Blatter's radical was found to trigger Overhauser DNP. The rotation of the methyl group leads to a modulation of the hyperfine coupling to its protons, facilitating electron-nuclear cross-relaxation. The findings suggest the possibility of designing tailor-made Overhauser DNP polarizing agents for high-field MAS-DNP.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Mathematics, Applied
Tomas Roubicek
Summary: This study investigates the isothermal quasistatic hardening-free plasticity problem at large strains. The model is reformulated in terms of rates and the plastic distortion is completely eliminated. The existence and regularity of weak solutions are proved using a regularization combined with Galerkin approximation. The study also considers rate-dependent plasticity and includes the Jeffreys' viscoelastic rheology and Kelvin-Voigt rheology.
JOURNAL OF NONLINEAR SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Youlin Xia, Tairan Yuwen, Aizhuo Liu, Charalampos G. Kalodimos
Summary: NMR has the capability to offer integrated insight into both the structure and intrinsic dynamics of biomolecules, with CEST experiments allowing quantitative investigation of chemical exchange phenomena. However, using the simple CW method can lead to H-2 decoupling sidebands in the CEST experiments, affecting the detection of minor dips of excited states. By developing methods using pseudo-continuous waves for H-2 decoupling, the sidebands can be successfully removed, as validated on Bruker spectrometers at different field strengths.
JOURNAL OF BIOMOLECULAR NMR
(2021)
Article
Chemistry, Organic
Brandon M. Young, Paolo Rossi, P. Jake Slavish, Yixin Cui, Munia Sowaileh, Jitendra Das, Charalampos G. Kalodimos, Zoran Rankovic
Summary: Isotopically labeled amino acids are commonly used for studying protein structure and dynamics by NMR. This study presents a facile gram-scale synthesis of compounds 1b and 2b under standard laboratory conditions from a common intermediate. The improved signal intensity with lower amounts of labeled precursor makes 1b and 2b potential alternatives to current labeling approaches.
Article
Biochemistry & Molecular Biology
Tao Xie, Tamjeed Saleh, Paolo Rossi, Darcie Miller, Charalampos G. Kalodimos
Summary: Imatinib binds to an allosteric pocket on Abl, promoting kinase activity and providing a mechanism for drug resistance in Abl variants with imatinib-resistant mutations in the catalytic site. Combining imatinib with allosteric inhibitors maximizes their inhibitory effect on Bcr-Abl.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Biao Yuan, Athina G. Portaliou, Rinky Parakra, Jochem H. Smit, Jiri Wald, Yichen Li, Bindu Srinivasu, Maria S. Loos, Harveer Singh Dhupar, Dirk Fahrenkamp, Charalampos G. Kalodimos, Franck Duong van Hoa, Thorben Cordes, Spyridoula Karamanou, Thomas C. Marlovits, Anastassios Economou
Summary: Type III protein secretion is common in Gram-negative pathogens, with SctV forming peripheral oligomeric clusters in EPEC and serving as a key receptor for different chaperone/exported protein pairs. The dynamic motions of SctV protomers, modulated by chaperones and ATPase, may allosterically affect the secretion process.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Andrey V. Reshetnyak, Paolo Rossi, Alexander G. Myasnikov, Munia Sowaileh, Jyotidarsini Mohanty, Amanda Nourse, Darcie J. Miller, Irit Lax, Joseph Schlessinger, Charalampos G. Kalodimos
Summary: ALK is a receptor tyrosine kinase that regulates important functions in the central nervous system, and mutations in this gene may lead to neuroblastoma. Research has revealed a mechanism of RTK activation that allows dimerization by different ligands, with the complex architecture of the receptor-ligand complex playing a key role in this process.
Article
Biochemistry & Molecular Biology
Mary C. Clay, Tamjeed Saleh, Samuel Kamatham, Paolo Rossi, Charalampos G. Kalodimos
Summary: Methyl-TROSY spectroscopy has expanded the application of solution-state NMR to study supra-molecular machineries. Accurate methyl chemical shift assignment remains a challenge. This work presents the current technology for methyl labeling, data collection, data analysis, and automated methyl assignment approaches, along with Python extensions and a standalone network analysis program for the task.
Article
Biology
Motonori Matsusaki, Rina Okada, Yuya Tanikawa, Shingo Kanemura, Dai Ito, Yuxi Lin, Mai Watabe, Hiroshi Yamaguchi, Tomohide Saio, Young-Ho Lee, Kenji Inaba, Masaki Okumura
Summary: The physiological functions of proteins are determined by their unique three-dimensional structures, with conserved disulfide-catalysts and chaperone networks playing a crucial role in correct protein folding and prevention of aggregation. Disruption of these networks is implicated in pathology. Complex formation among PDIs accelerates protein folding and prevents aggregation.
Article
Biology
Haojie Zhu, Motonori Matsusaki, Taiga Sugawara, Koichiro Ishimori, Tomohide Saio
Summary: Metal ions like Zn2+ play crucial roles in the activity regulation of Thermus thermophilus trigger factor (TtTF), a zinc-dependent molecular chaperone. Through in vitro biophysical experiments, it was discovered that Zn2+ binds to TtTF with a 1:1 ratio, induces partial structural changes, and promotes oligomerization of TtTF.
Article
Biochemistry & Molecular Biology
Soichiro Kawagoe, Munehiro Kumashiro, Takuya Mabuchi, Hiroyuki Kumeta, Koichiro Ishimori, Tomohide Saio
Summary: In this study, the heat-induced conformational transition mechanism of Hsf1 leading to oligomerization was investigated using solution biophysical methods. The results showed that Hsf1 exists as a monomer in the resting state and is activated by oligomerization upon heat shock. The conformational change to an open state allows Hsf1 to interact with multiple cellular components, thereby regulating stress response.
Article
Chemistry, Physical
Yoan Monneau, Cyrielle Arrault, Coraline Duroux, Marie Martin, Fabien Chirot, Luke Mac Aleese, Marion Girod, Clothilde Comby-Zerbino, Agnes Hagege, Olivier Walker, Maggy Hologne
Summary: Silver has been used as an antimicrobial agent, but some Gram-negative bacteria have developed resistance, leading to deaths in burn units. The protein SilE plays a crucial role in bacterial silver resistance. Through various techniques, it has been found that SilE consists of four helical segments and has four strong silver binding sites. These findings enhance our understanding of the mechanism of SilE in the silver efflux pump complex and aid in the development of inhibitors to combat bacterial silver resistance.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Yi-Shiang Wang, Chun-Hsiang Huang, Gunn-Guang Liou, Hsueh-Wen Hsueh, Chi-Ting Liang, Hsi-Ching Tseng, Shing-Jong Huang, Chi-Chao Chao, Sung-Tsang Hsieh, Shiou-Ru Tzeng
Summary: Transthyretin (TTR)-related amyloidosis (ATTR) is characterized by the deposition of fibrillar materials containing TTR variants. Substitution of polar Ser for small hydrophobic side chain Ala at residue 97 of TTR influences the packing density of the FG-loop, leading to conformational instability, increased monomeric species, and enhanced amyloidogenicity of apo-A97S.
Article
Clinical Neurology
Sung -Pin Fan, Yih-Chih Kuo, Ni-Chung Lee, Yin-Hsiu Chien, Wuh-Liang Hwu, Yu-Hsuan Huang, Han- Lin, Tai -Chung Tseng, Tung -Hung Su, Shiou-Ru Tzeng, Chien -Ting Hsu, Huey -Ling Chen, Chin-Hsien Lin, Yen-Hsuan Ni
Summary: In this retrospective analysis, the clinical characteristics and long-term outcomes of a large cohort of WD patients were determined. Differences were observed between the neuro-psychiatric group and the hepatic group in terms of presentation, neuroimaging, genetic information, and prognosis. The findings suggest that the clinical characteristics and prognosis of WD are influenced by ethnic differences.
JOURNAL OF MOVEMENT DISORDERS
(2023)
Article
Clinical Neurology
Shin-Joe Yeh, Ti-Yen Yeh, Yi-Shiang Wang, Chi-Chao Chao, Shiou-Ru Tzeng, Tsz-Yi Tang, Jung-Hsien Hsieh, Yu-Yu Kan, Wei-Kang Yang, Sung-Tsang Hsieh
Summary: Microangiopathy with thromboinflammation is characteristic of advanced-stage ATTRv nerves, which provides an add-on mechanism and therapeutic target for nerve degeneration.
ANNALS OF CLINICAL AND TRANSLATIONAL NEUROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Masato Miyake, Mitsuaki Sobajima, Kiyoe Kurahashi, Akira Shigenaga, Masaya Denda, Akira Otaka, Tomohide Saio, Naoki Sakane, Hidetaka Kosako, Seiichi Oyadomari
Summary: A small molecule called KM04794 has been identified to alleviate protein aggregation and cell death caused by ER stress, and enhance insulin levels, thereby improving the function of pancreatic insulin-secreting cells.
CELL CHEMICAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Soichiro Kawagoe, Koichiro Ishimori, Tomohide Saio
Summary: Despite recent developments, the process of protein folding, especially the folding of multidomain proteins, remains poorly understood. Molecular chaperones play a crucial role in assisting the folding of multidomain proteins, but the detailed mechanisms are still unclear. This review summarizes the biophysical and structural studies on the mechanism of molecular chaperone-mediated multidomain protein folding, as well as the recognition and alteration of client protein folding properties by molecular chaperones.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)