Article
Chemistry, Multidisciplinary
Anais M. E. Cassaignau, Tomasz Wlodarski, Sammy H. S. Chan, Lauren F. Woodburn, Ivana V. Bukvin, Julian O. Streit, Lisa D. Cabrita, Christopher A. Waudby, John Christodoulou
Summary: The study characterizes interactions between the ribosome surface and unfolded nascent chains, with the strongest interactions found in the C-terminal segment essential for folding. Quantitative agreement is demonstrated between these interactions and the energetics of co-translational folding. Competition between folding and binding provides a simple, dynamic mechanism for the modulation of co-translational folding by the ribosome.
Article
Biochemistry & Molecular Biology
Xabier Agirrezabala, Ekaterina Samatova, Meline Macher, Marija Liutkute, Manisankar Maiti, David Gil-Carton, Jiri Novacek, Mikel Valle, Marina Rodnina
Summary: Cellular proteins begin to fold as they emerge from the ribosome. The folding process is influenced by both the amino acid sequence and the interactions with the ribosome. Research shows that folding of a beta-barrel protein starts with the formation of a dynamic alpha-helix inside the ribosome, and the N-terminal part of the nascent chain refolds to a beta-hairpin structure before its release from the ribosome.
Article
Biochemistry & Molecular Biology
Richard D. Whitehead, Carolyn M. Teschke, Andrei T. Alexandrescu
Summary: Hydrodynamic radii calculated from diffusion coefficients can be used to compare folded and unfolded proteins. Native globular proteins showed an increase in hydrodynamic radii with molecular size, while unfolded proteins had similar scaling factors and persistence lengths under different conditions. Proteins with asymmetric sequence-distribution of charged residues showed atypically low hydrodynamic radii in certain solvents, potentially due to the formation of electrostatic hairpins.
Article
Biochemistry & Molecular Biology
Yaping Liu, Aldrex Munsayac, Ian Hall, Sarah C. Keane
Summary: The oncomiR-1, also known as the miR-17 similar to 92a polycistron, is overexpressed in multiple cancers and has oncogenic properties. The NPSL2 stem loop element is found to regulate the processing of pri-miR-92a, which is a constituent of oncomiR-1. The solution structure of NPSL2, which is the first high-resolution structure of an oncomiR-1 element, was determined using solution NMR spectroscopy. This study provides insights into the secondary and tertiary structure of an important RNA hairpin involved in miR biogenesis.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Endocrinology & Metabolism
Yanwu Yang, Michael D. Glidden, Balamurugan Dhayalan, Alexander N. Zaykov, Yen-Shan Chen, Nalinda P. Wickramasinghe, Richard D. DiMarchi, Michael A. Weiss
Summary: This article investigates the toxic misfolding of diabetes-associated proteins in beta-cells, and proposes a peptide model for classifying related mutations. The study found that the mutant variants exhibit successive structural perturbations, which are correlated with the phenotypic differences in diabetes.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Biochemistry & Molecular Biology
George D. Rose
Summary: The article introduces a mechanism in protein folding that emphasizes conformational entropy as the main organizer, suggesting that hydrogen bond satisfaction is thermodynamically necessary. It points out that the satisfaction or dissatisfaction of hydrogen bonds has a significant impact on the stability of proteins.
Review
Biochemistry & Molecular Biology
Nandakumar Rajasekaran, Christian M. Kaiser
Summary: The majority of proteins are composed of multiple domains connected in a single polypeptide, and understanding how these long sequences fold into functional structures without forming toxic misfolds or aggregates is still a challenge. Recent progress has revealed critical features of multi-domain protein folding and how molecular interactions shape folding and misfolding pathways.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Laura R. Blackholly, Nicola J. Harris, Heather E. Findlay, Paula J. Booth
Summary: The majority of alpha helical membrane proteins fold co-translationally during their synthesis on the ribosome. Cell-free translation of membrane proteins is emerging as a useful tool to address folding during translation by a ribosome. The bacterial leucine transporter, LeuT can be synthesised and inserted into lipid membranes using a variety of in vitro transcription translation systems. LeuT is considered a paradigm for neurotransmitter transporters and possesses a knotted structure that is characteristic of this transporter family.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biology
Janire Urrutia, Alejandra Aguado, Carolina Gomis-Perez, Arantza Muguruza-Montero, Oscar R. Ballesteros, Jiaren Zhang, Eider Nunez, Covadonga Malo, Hee Jung Chung, Aritz Leonardo, Aitor Bergara, Alvaro Villarroel
Summary: The W344R mutation in the Kv7.2 channel, associated with epilepsy, reduces channel function but does not affect interaction with Calmodulin in vitro. Molecular dynamic computations show minimal impact of the mutation on complex structure. In vivo, the mutation hinders proper folding during translation, leading to generation of non-functional ion channels that fail to reach correct neuronal compartments.
Article
Cell Biology
Anton A. Komar
Summary: Protein folding in the cell is largely co-translational, occurring during protein synthesis on the ribosome. It has been found that co-translational folding is characteristic of almost all types of proteins in the cell, including single and multidomain, single and multisubunit, cytosolic, secretory, and membrane proteins. However, many details of co-translational folding are still not fully understood. Recent research has shown that folding of a beta-barrel protein begins with the formation of an alpha-helix inside the ribosome, which then rearranges into a beta-hairpin structure as the peptide grows and reaches the wider region of the ribosomal exit tunnel.
Review
Biochemistry & Molecular Biology
Tom Joshua Eisenack, Debora Broch Trentini
Summary: Proteins are versatile molecular machines that control and execute cellular processes. They go through a multilayered synthesis process with many opportunities for error, and must navigate a complex folding-energy landscape. Newly synthesized proteins are at increased risk of misfolding and toxic aggregation, but cells employ molecular chaperones and quality control factors to maintain proteostasis.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Chemistry, Physical
Enping Lin, Zhemin Bai, Yifei Yuan, Zhiwei Chen, Yu Yang, Yuqing Huang, Zhong Chen
Summary: Multidimensional NMR spectroscopy is a powerful tool for structure elucidation and dynamic analysis of complex samples, particularly biological macromolecules. However, the reconstruction of Laplace-related NMR, which involves relaxation or diffusion detection, presents challenges due to its ill-posed property. Existing reconstruction methods for Laplace-related NMR sparse sampling suffer from poor resolution and possible artifacts, highlighting the need for more effective optimization algorithms.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Hannah Welte, Pia Sinn, Michael Kovermann
Summary: This study investigates the binding affinity between proteins and nucleic acids using fluorine labeling technology, and proposes a reliable experimental approach to determine the affinity between single stranded DNA molecules and target proteins in complex biological environments. By applying high-resolution F-19 NMR spectroscopy, this research advances the identification of intermolecular interactions in native surroundings, offering a potent platform for future studies in cell applications.
Article
Biochemistry & Molecular Biology
Aleksandra M. Kusova, Ilnaz T. Rakipov, Yuriy F. Zuev
Summary: The intracellular environment involves the interaction of proteins, sugars, and nucleic acids in a restricted medium. The excluded volume effect in the cytoplasm accounts for 40% of the available volume for macromolecules. This study examines the diffusion of proteins in crowded solutions and demonstrates the deviation from conventional Brownian motion under conditions of altered medium viscosity and rigid obstacles.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Heidi Zetzsche, Laura Raschke, Boris Fuertig
Summary: In this study, the activation mechanism of RhlB by RNase E was investigated using NMR spectroscopy and an RNA centered approach. The results showed that RNase E binding increases the affinity of RhlB towards certain RNA substrates, leading to increased ATP turnover rates. The study also revealed a unique activation mode of RhlB among DEAD-Box helicases, as it can induce partial duplex opening of RNA even in the absence of ATP.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Linh Nguyen, Kelli A. McCord, Duong T. Bui, Kim M. Bouwman, Elena N. Kitova, Mohamed Elaish, Dhanraj Kumawat, Gour C. Daskhan, Ilhan Tomris, Ling Han, Pradeep Chopra, Tzu-Jing Yang, Steven D. Willows, Andrew L. Mason, Lara K. Mahal, Todd L. Lowary, Lori J. West, Shang-Te Danny Hsu, Tom Hobman, Stephen M. Tompkins, Geert-Jan Boons, Robert P. de Vries, Matthew S. Macauley, John S. Klassen
Summary: Evidence suggests that host glycans, specifically glycolipids containing sialic acid, play a role in facilitating the entry of SARS-CoV-2 virus into host cells by binding to the receptor-binding domain (RBD) of the spike protein. Depletion of cell surface sialic acid levels through various methods decreases RBD binding and infection of the virus, indicating the importance of sialylated glycans in viral entry.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Cell Biology
Tzu-Jing Yang, Tian-Neng Li, Rih-Sheng Huang, Max Yu-Chen Pan, Shu-Yu Lin, Steven Lin, Kuen-Phon Wu, Lily Hui-Ching Wang, Shang-Te Danny Hsu
Summary: The subcellular localization of BAP1 is crucial for its tumor suppressor activity. This study reveals that transportin-1 (TNPO1) plays a key role in the nuclear import of BAP1 by binding to its unique nuclear localization signal (PY-NLS) motif. TNPO1 also dissociates the dimeric structure of BAP1 and prevents its monoubiquitination to counteract the cytosolic retention by UBE2O.
JOURNAL OF CELL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sarita Puri, Szu-Ni Chen, Yi-Hsiang Chiu, Piotr Draczkowski, Kuang-Ting Ko, Tzu-Jing Yang, Yong-Sheng Wang, Susumu Uchiyama, Shang-Te Danny Hsu
Summary: This study investigates the effects of non-catalytic mutations within BAP1-UCH on the structure and function of the protein. The findings reveal that these mutations can lead to protein instability and increased aggregation propensity, providing insights into the molecular basis of their involvement in oncogenesis.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Limnology
Chih-Chang Chen, Irene B. Rodriguez, Yuh-ling Lee Chen, Jonathan P. Zehr, Yun-Ru Chen, Shang-Te Danny Hsu, Shun-Chung Yang, Tung-Yuan Ho
Summary: Under high solar radiation conditions, nickel superoxide dismutase (NiSOD) protects the nitrogen fixation process of Trichodesmium from oxidative stress, allowing it to provide a significant amount of bioavailable nitrogen in challenging ocean environments.
LIMNOLOGY AND OCEANOGRAPHY LETTERS
(2022)
Article
Multidisciplinary Sciences
Cheng-Yu Huang, Piotr Draczkowski, Yong-Sheng Wang, Chia-Yu Chang, Yu-Chun Chien, Yun-Han Cheng, Yi-Min Wu, Chun-Hsiung Wang, Yuan-Chih Chang, Yen-Chen Chang, Tzu-Jing Yang, Yu-Xi Tsai, Kay-Hooi Khoo, Hui-Wen Chang, Shang-Te Danny Hsu
Summary: In this study, the structural polymorphism of a pig coronavirus spike protein within intact viral particles and how glycosylation modulates the conformational changes pertinent to host recognition were revealed using cryo-electron tomography, cryo-electron microscopy, and mass spectrometry. This research is important for understanding the interaction between the virus and the host, developing vaccines, and antigenic analysis.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Chu-Wei Kuo, Ning-En Chang, Pei-Yu Yu, Tzu-Jing Yang, Shang-Te Danny Hsu, Kay-Hooi Khoo
Summary: To fully identify all N-glycosylation sites on the SARS-CoV2 spike protein, multiple proteases are needed in addition to trypsin. The commonly used Byonic software for peptide identification often introduces errors due to similar mass differences. By manually interpreting MS2 spectra, this study identifies common errors, especially those caused by chymotrypsin. By using a stringent acceptance threshold and considering results from the pGlyco3 search engine, erroneous assignment can be controlled within 15% in Byonic. A representative N-glycosylation pattern can be constructed by quantifying the overlapping subset of confidently identified N-glycopeptides. Applying two complimentary glycoproteomic software tools, this study confirms significant differences in glycosylation at certain sites between the unstable Omicron spike protein and the stable trimeric form of the parental D614G variant.
Article
Chemistry, Multidisciplinary
Yu-Chun Chien, Yong-Sheng Wang, Deepa Sridharan, Chu-Wei Kuo, Chih-Ta Chien, Takayuki Uchihashi, Koichi Kato, Takashi Angata, Tzu-Ching Meng, Shang-Te Danny Hsu, Kay-Hooi Khoo
Summary: The intracellular phosphatase domain of PTPRA plays a crucial role in regulating cell adhesion through c-Src kinase activation. The site-specific glycosylation pattern of the heavily glycosylated ectodomain of PTPRA has been determined, revealing the presence of O-glycan at the N-glycosylation sites. The structural features of the ectodomain, combined with the glycosylation information, support the dynamic structural model of the densely glycosylated PTPRA ectodomain.
Article
Biochemistry & Molecular Biology
Sarita Puri, Cheng-Yu Liu, I-Chen Hu, Chih-Hsuan Lai, Shang-Te Danny Hsu, Ping-Chiang Lyu
Summary: In this study, the conformational and stability changes of the CP74 protein were investigated by substituting tryptophan residues with phenylalanine. The results showed minimal perturbations to the native structures in the tryptophan variants and the conservation of the domain-swapped ternary structure. However, asymmetry was observed in the a-helix 5 of the W72F variant. Thermal and chemical stability analyses indicated the important role of W100 in the folding of CP74, followed by W19 and W72. NMR spectroscopy and mass spectrometry revealed the accumulation of a native-like intermediate state where the hinge region contributed to maintaining the domain-swapped ternary structure of CP74.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Biotechnology & Applied Microbiology
Cheng-Pu Sun, Chi-Wen Chiu, Ping-Yi Wu, Szu- Tsung, I-Jung Lee, Chih-Wei Hu, Min-Feng Hsu, Tzu-Jiun Kuo, Yu-Hua Lan, Li-Yao Chen, Hui-Yee Ng, Meng-Jhe Chung, Hsin-Ni Liao, Sheng-Che Tseng, Chia-Hui Lo, Yung-Jiun Chen, Chun-Che Liao, Chih-Shin Chang, Jian-Jong Liang, Piotr Draczkowski, Sarita Puri, Yuan-Chih Chang, Jing-Siou Huang, Cheng-Cheung Chen, Jyh-Hwa Kau, Yen-Hui Chen, Wen-Chun Liu, Han-Chun Wu, Shang-Te Danny, I-Hsuan Wang, Mi-Hua Tao
Summary: The study isolated and humanized a monoclonal anti-human angiotensin-converting enzyme 2 (hACE2) antibody, ch2H2, which effectively blocked the binding of viral receptor-binding domain (RBD) to hACE2. In vitro and in vivo experiments demonstrated that the ch2H2 antibody exhibited potent inhibitory activity against multiple SARS-CoV-2 variants, including the Omicron variant. The adeno-associated virus (AAV)-mediated delivery of the antibody also showed promising results in reducing viral load and mitigating pulmonary pathological changes.
Article
Biochemical Research Methods
Hsi-Wen Kao, Wei-Lin Lu, Meng-Ru Ho, Yu-Fong Lin, Yun-Jung Hsieh, Tzu-Ping Ko, Shang-Te Danny Hsu, Kuen-Phon Wu
Summary: We used ProteinMPNN, a deep learning tool, to redesign ubiquitin (Ub) as a specific and functionally stimulating/enhancing binder of the Rsp5 E3 ligase. We generated 20 extensively mutated Ub variants (UbVs) named R1 to R20, which displayed well-folded structures and high thermal stabilities. These UbVs can form stable complexes with Rsp5, as predicted by AlphaFold2. Three of the UbVs showed low micromolar affinity to Rsp5, with R4 and R12 effectively enhancing Rsp5 activity six folds. AlphaFold2 predicts that R4 and R12 bind to Rsp5's exosite in the same manner as the Rsp5-Ub template, thereby allosterically activating Rsp5-Ub thioester formation. Thus, we present a virtual solution for rapidly and cost-effectively designing functional modulators of Ub-related enzymes.
ACS SYNTHETIC BIOLOGY
(2023)
Meeting Abstract
Biochemistry & Molecular Biology
Shang-Te Danny Hsu, Tzu-Jing Yang, Pei-Yu Yu, Yu-Xi Tsai, Ning-En Chang, Kay-Hooi Khoo, Cyril Hanus, Mateusz Sikora
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Shang-Te Danny Hsu
Summary: The topologically knotted proteins have entangled structural elements that play a crucial role in their folding, stability, and biological functions.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Sarita Puri, Shang-Te Danny Hsu
Summary: Understanding the folding mechanisms of knotted proteins is challenging, but experimental and computational studies have provided insights. This study focuses on using multiple measurement methods to understand the effects of different structural probes on the folding mechanisms of knotted proteins.
INTEGRATED METHODS IN PROTEIN BIOCHEMISTRY, PT A
(2022)
Article
Cell Biology
I-Jung Lee, Cheng-Pu Sun, Ping-Yi Wu, Yu-Hua Lan, I-Hsuan Wang, Wen-Chun Liu, Joyce Pei-Yi Yuan, Yu-Wei Chang, Sheng-Che Tseng, Szu- Tsung, Yu-Chi Chou, Monika Kumari, Yin-Shiou Lin, Hui-Feng Chen, Tsung-Yen Chen, Chih-Chao Lin, Chi-Wen Chiu, Chung-Hsuan Hsieh, Cheng-Ying Chuang, Chao-Min Cheng, Hsiu-Ting Lin, Wan-Yu Chen, Fu-Fei Hsu, Ming-Hsiang Hong, Chun-Che Liao, Chih-Shin Chang, Jian-Jong Liang, Hsiu-Hua Ma, Ming-Tsai Chiang, Hsin-Ni Liao, Hui-Ying Ko, Liang-Yu Chen, Yi-An Ko, Pei-Yu Yu, Tzu-Jing Yang, Po-Cheng Chiang, Shang-Te Hsu, Yi-Ling Lin, Chong-Chou Lee, Han-Chung Wu, Mi-Hua Tao
Summary: This study reports an mRNA-based vaccine using an engineered hybrid receptor binding domain that can generate neutralizing antibodies and T cell responses against various SARS-CoV-2 variants. The results demonstrate that including different antigenic mutations from different variants is a feasible approach to develop vaccines with broad protection.
JOURNAL OF BIOMEDICAL SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Chu-Wei Kuo, Tzu-Jing Yang, Yu-Chun Chien, Pei-Yu Yu, Shang-Te Danny Hsu, Kay-Hooi Khoo
Summary: The extensive glycosylation of the spike protein of SARS-CoV-2 not only protects it from host immune responses, but also affects its conformation dynamics and receptor binding. As new variants emerge, it is unclear how mutations in the spike protein would affect its glycosylation pattern. Mass spectrometry analysis showed that the Alpha variant has significant changes in the processing state of N-glycans at a specific site, indicating altered spatial accessibility that may impact its transmissibility.