151
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Komenda J, Sobotka R, Nixon PJ. The biogenesis and maintenance of PSII: Recent advances and current challenges. THE PLANT CELL 2024; 36:3997-4013. [PMID: 38484127 PMCID: PMC11449106 DOI: 10.1093/plcell/koae082] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/27/2024] [Indexed: 10/05/2024]
Abstract
The growth of plants, algae, and cyanobacteria relies on the catalytic activity of the oxygen-evolving PSII complex, which uses solar energy to extract electrons from water to feed into the photosynthetic electron transport chain. PSII is proving to be an excellent system to study how large multi-subunit membrane-protein complexes are assembled in the thylakoid membrane and subsequently repaired in response to photooxidative damage. Here we summarize recent developments in understanding the biogenesis of PSII, with an emphasis on recent insights obtained from biochemical and structural analysis of cyanobacterial PSII assembly/repair intermediates. We also discuss how chlorophyll synthesis is synchronized with protein synthesis and suggest a possible role for PSI in PSII assembly. Special attention is paid to unresolved and controversial issues that could be addressed in future research.
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Affiliation(s)
- Josef Komenda
- Center Algatech, Institute of Microbiology of the Czech Academy of Sciences, 37901 Třeboň, Czech Republic
| | - Roman Sobotka
- Center Algatech, Institute of Microbiology of the Czech Academy of Sciences, 37901 Třeboň, Czech Republic
| | - Peter J Nixon
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, S. Kensington Campus, London SW7 2AZ, UK
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152
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Johnson KA, Garrett SC, Noble-Molnar C, Elgarhi HA, Woodside WT, Cooper C, Zhang X, Olson S, Catchpole RJ, Graveley BR, Terns MP. Selective degradation of phage RNAs by the Csm6 ribonuclease provides robust type III CRISPR immunity in Streptococcus thermophilus. Nucleic Acids Res 2024:gkae856. [PMID: 39360614 DOI: 10.1093/nar/gkae856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 09/14/2024] [Accepted: 09/19/2024] [Indexed: 10/04/2024] Open
Abstract
Type III CRISPR immune systems bind viral or plasmid RNA transcripts and activate Csm3/Cmr4 and Cas10 nucleases to uniquely cleave both invader RNA and DNA, respectively. Additionally, type III effector complexes generate cyclic oligoadenylate (cOA) signaling molecules to activate trans-acting, auxiliary Csm6/Csx1 ribonucleases, previously proposed to be non-specific in their in vivo RNA cleavage preference. Despite extensive in vitro studies, the nuclease requirements of type III systems in their native contexts remain poorly understood. Here we systematically investigated the in vivo roles for immunity of each of the three Streptococcus thermophilus (Sth) type III-A Cas nucleases and cOA signaling by challenging nuclease defective mutant strains with plasmid and phage infections. Our results reveal that RNA cleavage by Csm6 is both sufficient and essential for maintaining wild-type levels of immunity. Importantly, Csm6 RNase activity leads to immunity against even high levels of phage challenge without causing host cell dormancy or death. Transcriptomic analyses during phage infection indicated Csm6-mediated and crRNA-directed preferential cleavage of phage transcripts. Our findings highlight the critical role of Csm6 RNase activity in type III immunity and demonstrate specificity for invader RNA transcripts by Csm6 to ensure host cell survival upon phage infection.
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Affiliation(s)
- Katie A Johnson
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Sandra C Garrett
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | | | - Hanna A Elgarhi
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Walter T Woodside
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Clare Cooper
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Xinfu Zhang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Sara Olson
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Ryan J Catchpole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Michael P Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
- Department of Microbiology, University of Georgia, Athens, GA, USA
- Department of Genetics, University of Georgia, Athens, GA, USA
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153
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Coray R, Navarro P, Scaramuzza S, Stahlberg H, Castaño-Díez D. Automated fiducial-based alignment of cryo-electron tomography tilt series in Dynamo. Structure 2024; 32:1808-1819.e4. [PMID: 39079528 DOI: 10.1016/j.str.2024.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/06/2024] [Accepted: 07/03/2024] [Indexed: 10/06/2024]
Abstract
With the advent of modern technologies for cryo-electron tomography (cryo-ET), high-quality tilt series are more rapidly acquired than processed and analyzed. Thus, a robust and fast-automated alignment for batch processing in cryo-ET is needed. While different software packages have made available several approaches for automated marker-based alignment of tilt series, manual user intervention remains necessary for many datasets, thus preventing high-throughput tomography. We have developed a MATLAB-based framework integrated into the Dynamo software package for automatic detection of fiducial markers that generates a robust alignment model with minimal input parameters. This approach allows high-throughput, unsupervised volume reconstruction. This new module extends Dynamo with a large repertory of tools for tomographic alignment and reconstruction, as well as specific visualization browsers to rapidly assess the biological relevance of the dataset. Our approach has been successfully tested on a broad range of datasets that include diverse biological samples and cryo-ET modalities.
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Affiliation(s)
- Raffaele Coray
- Instituto Biofisika (Consejo Superior de Investigaciones Científicas, Universidad del País Vasco), University of Basque Country, 48940 Leioa, Spain
| | - Paula Navarro
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland; Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Stefano Scaramuzza
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland; Laboratory of Biological Electron Microscopy, Institute of Physics, School of Basic Science, EPFL, and Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Daniel Castaño-Díez
- Instituto Biofisika (Consejo Superior de Investigaciones Científicas, Universidad del País Vasco), University of Basque Country, 48940 Leioa, Spain; Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland.
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154
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Poudel B, Vanegas JM. Structural Rearrangement of the AT1 Receptor Modulated by Membrane Thickness and Tension. J Phys Chem B 2024; 128:9470-9481. [PMID: 39298653 DOI: 10.1021/acs.jpcb.4c03325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
Membrane-embedded mechanosensitive (MS) proteins, including ion channels and G-protein coupled receptors (GPCRs), are essential for the transduction of external mechanical stimuli into biological signals. The angiotensin II type 1 (AT1) receptor plays many important roles in cardiovascular regulation and is associated with diseases such as hypertension and congestive heart failure. The membrane-mediated activation of the AT1 receptor is not well understood, despite this being one of the most widely studied GPCRs within the context of biased agonism. Here, we use extensive molecular dynamics (MD) simulations to characterize the effect of the local membrane environment on the activation of the AT1 receptor. We show that membrane thickness plays an important role in the stability of active and inactive states of the receptor, as well as the dynamic interchange between states. Furthermore, our simulation results show that membrane tension is effective in driving large-scale structural changes in the inactive state such as the outward movement of transmembrane helix 6 to stabilize intermediate active-like conformations. We conclude by comparing our simulation observations with AlphaFold 2 predictions, as a proxy to experimental structures, to provide a framework for how membrane mediated stimuli can facilitate activation of the AT1 receptor through the β-arrestin signaling pathway.
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Affiliation(s)
- Bharat Poudel
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Juan M Vanegas
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
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155
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Yasuda T, Morita R, Shigeta Y, Harada R. BEMM-GEN: A Toolkit for Generating a Biomolecular Environment-Mimicking Model for Molecular Dynamics Simulation. J Chem Inf Model 2024. [PMID: 39361452 DOI: 10.1021/acs.jcim.4c01467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2024]
Abstract
Understanding the influence of the cellular environment on protein conformations is crucial for elucidating protein functions within living cells. In studies using molecular dynamics (MD) simulation, carbon nanotubes and hydrophobic cages have been widely used to emulate the cellular environment inside specific large biomolecules such as ribosome tunnels and chaperones. However, recent studies suggest that these uniform hydrophobic models may not adequately capture the environmental effects inside each biomolecule. Based on these facts, it is necessary to generate spherical and cylindrical models with varied chemical properties corresponding to the components within target biomolecules. We developed a biomolecular environment-mimicking model generator (BEMM-GEN) that generates spherical and cylindrical models with user-specified chemical properties and allows the integration of arbitrary protein conformations into the generated models. BEMM-GEN provides model and protein complex structures, along with the corresponding parameter files for MD simulation (AMBER and GROMACS), and users immediately run their MD simulation based on the generated input files. BEMM-GEN can be freely downloaded and installed via a Python package manager (pip install BEMM-gen). The source code files and a user manual for operation are provided on GitHub (https://github.com/y4suda/BEMM-GEN).
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Affiliation(s)
- Takunori Yasuda
- Doctoral Program in Biology, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Rikuri Morita
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
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156
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Singh B, Mondal A, Gaalswyk K, MacCallum JL, Perez A. MELD-Adapt: On-the-Fly Belief Updating in Integrative Molecular Dynamics. J Chem Theory Comput 2024. [PMID: 39356805 DOI: 10.1021/acs.jctc.4c00690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2024]
Abstract
Integrative structural biology synergizes experimental data with computational methods to elucidate the structures and interactions within biomolecules, a task that becomes critical in the absence of high-resolution structural data. A challenging step for integrating the data is knowing the expected accuracy or belief in the dataset. We previously showed that the Modeling Employing Limited Data (MELD) approach succeeds at predicting structures and finding the best interpretation of the data when the initial belief is equal to or slightly lower than the real value. However, the initial belief might be unknown to the user, as it depends on both the technique and the system of study. Here we introduce MELD-Adapt, designed to dynamically evaluate and infer the reliability of input data while at the same time finding the best interpretation of the data and the structures compatible with it. We demonstrate the utility of this method across different systems, particularly emphasizing its capability to correct initial assumptions and identify the correct fraction of data to produce reliable structural models. The approach is tested with two benchmark sets: the folding of 12 proteins with coarse physical insights and the binding of peptides with varying affinities to the extraterminal domain using chemical shift perturbation data. We find that subtle differences in data structure (e.g., locally clustered or globally distributed), starting belief, and force field preferences can have an impact on the predictions, limiting the possibility of a transferable protocol across all systems and data types. Nonetheless, we find a wide range of initial setup conditions that will lead to successful sampling and identification of native states, leading to a robust pipeline. Furthermore, disagreements about how much data is enforced and satisfied rapidly serve to identify incorrect setup conditions.
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Affiliation(s)
- Bhumika Singh
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida 32611-7011, United States
| | - Arup Mondal
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida 32611-7011, United States
| | - Kari Gaalswyk
- Department of Chemistry, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Justin L MacCallum
- Department of Chemistry, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Alberto Perez
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida 32611-7011, United States
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157
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Xu C, Käser T, Xia Y, Kumar N, Zenobi R. Probing Deuteration-Induced Phase Separation in Supported Lipid Monolayers using Hyperspectral TERS Imaging. J Phys Chem Lett 2024:10237-10243. [PMID: 39356968 DOI: 10.1021/acs.jpclett.4c01994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2024]
Abstract
In this study, we investigate the impact of deuteration on the formation of phase-separated domains in supported lipid monolayers using hyperspectral Tip-Enhanced Raman Spectroscopy (TERS) imaging. The intricate organization of biological membranes plays a crucial role in cellular functions. Various factors that influence domain formation have been identified in previous studies such as lipid tail length and cholesterol concentration. Deuterium labeling of lipids has proven useful for probing cellular structures and dynamics, but its impact on lipid phase separation remains underexplored. By examining 1:1 mixed monolayers of dipalmitoylphosphatidylcholine (DPPC) and deuterated DPPC on Au(111) surfaces, we reveal partial segregation of domains rich in deuterated and nondeuterated lipids. This study addresses a gap in knowledge by examining the impact of deuteration on lipid tail behavior, offering new insights into how even subtle structural modifications can influence phase behavior. Furthermore, it demonstrates that TERS can be a powerful, nondestructive, and label-free nanoanalytical tool for analyzing lipid membranes and advance the field of membrane biophysics.
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Affiliation(s)
- Chengcheng Xu
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Timon Käser
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Yuanzhi Xia
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Naresh Kumar
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
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158
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Ma S, Gao J, Tian Y, Wen L. Recent progress in chemoenzymatic synthesis of human glycans. Org Biomol Chem 2024; 22:7767-7785. [PMID: 39246045 DOI: 10.1039/d4ob01006j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2024]
Abstract
Glycan is an essential cell component that usually exists in either a free form or a glycoconjugated form. Glycosylation affects the regulatory function of glycoconjugates in health and disease development, indicating the key role of glycan in organisms. Because of the complexity and diversity of glycan structures, it is challenging to prepare structurally well-defined glycans, which hinders the investigation of biological functions at the molecular level. Chemoenzymatic synthesis is an attractive approach for preparing complex glycans, because it avoids tedious protecting group manipulations in chemical synthesis and ensures high regio- and stereo-selectivity of glucosides during glycan assembly. Herein, enzymes, such as glycosyltransferases (GTs) and glycosidases (GHs), and sugar donors involved in the chemoenzymatic synthesis of human glycans are initially discussed. Many state-of-the-art chemoenzymatic methodologies are subsequently displayed and summarized to illustrate the development of synthetic human glycans, for example, N- and O-linked glycans, human milk oligosaccharides, and glycosaminoglycans. Thus, we provide an overview of recent chemoenzymatic synthetic designs and applications for synthesizing complex human glycans, along with insights into the limitations and perspectives of the current methods.
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Affiliation(s)
- Shengzhou Ma
- Carbohydrate-Based Drug Research Center, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinhua Gao
- Carbohydrate-Based Drug Research Center, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Yinping Tian
- Carbohydrate-Based Drug Research Center, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Liuqing Wen
- Carbohydrate-Based Drug Research Center, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
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159
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Wlodarczyk J, Bhattacharyya R, Dore K, Ho GPH, Martin DDO, Mejias R, Hochrainer K. Altered Protein Palmitoylation as Disease Mechanism in Neurodegenerative Disorders. J Neurosci 2024; 44:e1225242024. [PMID: 39358031 DOI: 10.1523/jneurosci.1225-24.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 07/12/2024] [Accepted: 07/16/2024] [Indexed: 10/04/2024] Open
Abstract
Palmitoylation, a lipid-based posttranslational protein modification, plays a crucial role in regulating various aspects of neuronal function through altering protein membrane-targeting, stabilities, and protein-protein interaction profiles. Disruption of palmitoylation has recently garnered attention as disease mechanism in neurodegeneration. Many proteins implicated in neurodegenerative diseases and associated neuronal dysfunction, including but not limited to amyloid precursor protein, β-secretase (BACE1), postsynaptic density protein 95, Fyn, synaptotagmin-11, mutant huntingtin, and mutant superoxide dismutase 1, undergo palmitoylation, and recent evidence suggests that altered palmitoylation contributes to the pathological characteristics of these proteins and associated disruption of cellular processes. In addition, dysfunction of enzymes that catalyze palmitoylation and depalmitoylation has been connected to the development of neurological disorders. This review highlights some of the latest advances in our understanding of palmitoylation regulation in neurodegenerative diseases and explores potential therapeutic implications.
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Affiliation(s)
- Jakub Wlodarczyk
- Laboratory of Cell Biophysics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw 02-093, Poland
| | - Raja Bhattacharyya
- Genetics and Aging Research Unit, Department of Neurology, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - Kim Dore
- Department of Neurosciences, Center for Neural Circuits and Behavior, UCSD, La Jolla, California 92093
| | - Gary P H Ho
- Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Dale D O Martin
- Department of Biology, Faculty of Science, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Rebeca Mejias
- Department of Physiology, School of Biology, Universidad de Sevilla, Seville, 41012 Spain
- Instituto de Investigaciones Biomédicas de Sevilla, IBIS/Universidad de Sevilla/Hospital Universitario Virgen del Rocío/Junta de Andalucía/CSIC, Seville 41013, Spain
| | - Karin Hochrainer
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York 10065
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160
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Thakuria S, Paul S. Salt-bridge mediated conformational dynamics in the figure-of-eight knotted ketol acid reductoisomerase (KARI). Phys Chem Chem Phys 2024; 26:24963-24974. [PMID: 39297222 DOI: 10.1039/d4cp02677b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2024]
Abstract
The utility of knotted proteins in biological activities has been ambiguous since their discovery. From their evolutionary significance to their functionality in stabilizing the native protein structure, a unilateral conclusion hasn't been achieved yet. While most studies have been performed to understand the stabilizing effect of the knotted fold on the protein chain, more ideas are yet to emerge regarding the interactions in stabilizing the knot. Using classical molecular dynamics (MD) simulations, we have explored the dynamics of the figure-of-eight knotted domain present in ketol acid reductoisomerase (KARI). Our main focus was on the presence of a salt bridge network evident within the knotted region and its role in shaping the conformational dynamics of the knotted chain. Through the potential of mean forces (PMFs) calculation, we have also marked the specific salt bridges that are pivotal in stabilizing the knotted structure. The correlated motions have been further monitored with the help of principal component analysis (PCA) and dynamic cross-correlation maps (DCCM). Furthermore, mutation of the specific salt bridges led to a change in their conformational stability, vindicating their importance.
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Affiliation(s)
- Sanjib Thakuria
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam, 781039, India.
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam, 781039, India.
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161
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Lei L, Ikami K, Diaz Miranda EA, Ko S, Wilson F, Abbott H, Pandoy R, Jin S. The mouse Balbiani body regulates primary oocyte quiescence via RNA storage. Commun Biol 2024; 7:1247. [PMID: 39358443 DOI: 10.1038/s42003-024-06900-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 09/16/2024] [Indexed: 10/04/2024] Open
Abstract
In mammalian females, the transition from dormancy in primordial follicles to follicular development is critical for maintaining ovarian function and reproductive longevity. In mice, the quiescent primary oocyte of the primordial follicle contains a Balbiani body (B-body), an organelle aggregate comprised of a spherical structure of Golgi complexes. Here we show that the structure of the B-body is maintained by microtubules and actin. The B-body stores mRNA-capping enzyme and 597 mRNAs associated with mRNA-decapping enzyme 1 A (DCP1A). Gene ontology analysis results indicate that proteins encoded by these mRNAs function in enzyme binding, cellular component organization and packing of telomere ends. Pharmacological depolymerization of microtubules or actin led to B-body disassociation and nascent protein synthesis around the dissociated B-bodies within three hours. An increased number of activated developing follicles were observed in ovaries with prolonged culture and the in vivo mouse model. Our results indicate that the mouse B-body is involved in the activation of dormant primordial follicles likely via translation of the B-body-associated RNAs in primary oocytes.
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Affiliation(s)
- Lei Lei
- Department of Obstetrics, Gynecology and Women's Health, University of Missouri School of Medicine, Columbia, MO, 65211, USA.
- Division of Biological Sciences, College of Arts and Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Kanako Ikami
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Buck Institute for Research on Aging, Novato, California, 94949, USA
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, California, 95616, USA
| | - Edgar Andres Diaz Miranda
- Department of Obstetrics, Gynecology and Women's Health, University of Missouri School of Medicine, Columbia, MO, 65211, USA
| | - Sooah Ko
- Department of Obstetrics, Gynecology and Women's Health, University of Missouri School of Medicine, Columbia, MO, 65211, USA
| | - Faith Wilson
- Department of Obstetrics, Gynecology and Women's Health, University of Missouri School of Medicine, Columbia, MO, 65211, USA
- Division of Biological Sciences, College of Arts and Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Haley Abbott
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Ronald Pandoy
- Buck Institute for Research on Aging, Novato, California, 94949, USA
| | - Shiying Jin
- Department of Obstetrics, Gynecology and Women's Health, University of Missouri School of Medicine, Columbia, MO, 65211, USA
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162
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Michael ARM, Amaral BC, Ball KL, Eiriksson KH, Schriemer DC. Cell fixation improves performance of in situ crosslinking mass spectrometry while preserving cellular ultrastructure. Nat Commun 2024; 15:8537. [PMID: 39358380 DOI: 10.1038/s41467-024-52844-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 09/24/2024] [Indexed: 10/04/2024] Open
Abstract
Crosslinking mass spectrometry (XL-MS) has the potential to map the interactome of the cell with high resolution and depth of coverage. However, current in vivo XL-MS methods are hampered by crosslinkers that demonstrate low cell permeability and require long reaction times. Consequently, interactome sampling is not high and long incubation times can distort the cell, bringing into question the validity any protein interactions identified by the method. We address these issues with a fast formaldehyde-based fixation method applied prior to the introduction of secondary crosslinkers. Using human A549 cells and a range of reagents, we show that 4% formaldehyde fixation with membrane permeabilization preserves cellular ultrastructure and simultaneously improves reaction conditions for in situ XL-MS. Protein labeling yields can be increased even for nominally membrane-permeable reagents, and surprisingly, high-concentration formaldehyde does not compete with conventional amine-reactive crosslinking reagents. Prefixation with permeabilization uncouples cellular dynamics from crosslinker dynamics, enhancing control over crosslinking yield and permitting the use of any chemical crosslinker.
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Affiliation(s)
- Andrew R M Michael
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, T2N-4N1, Canada
| | - Bruno C Amaral
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, T2N-4N1, Canada
| | - Kallie L Ball
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, T2N-4N1, Canada
| | - Kristen H Eiriksson
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, T2N-4N1, Canada
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, T2N-4N1, Canada.
- Department of Chemistry, University of Calgary, Calgary, Alberta, T2N-4N1, Canada.
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163
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Kravchenko P, Tachibana K. Rise and SINE: roles of transcription factors and retrotransposons in zygotic genome activation. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00772-6. [PMID: 39358607 DOI: 10.1038/s41580-024-00772-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2024] [Indexed: 10/04/2024]
Abstract
In sexually reproducing organisms, life begins with the fusion of transcriptionally silent gametes, the oocyte and sperm. Although initiation of transcription in the embryo, known as zygotic genome activation (ZGA), is universally required for development, the transcription factors regulating this process are poorly conserved. In this Perspective, we discuss recent insights into the mechanisms of ZGA in totipotent mammalian embryos, namely ZGA regulation by several transcription factors, including by orphan nuclear receptors (OrphNRs) such as the pioneer transcription factor NR5A2, and by factors of the DUX, TPRX and OBOX families. We performed a meta-analysis and compiled a list of pan-ZGA genes, and found that most of these genes are indeed targets of the above transcription factors. Remarkably, more than a third of these ZGA genes appear to be regulated both by OrphNRs such as NR5A2 and by OBOX proteins, whose motifs co-occur in SINE B1 retrotransposable elements, which are enriched near ZGA genes. We propose that ZGA in mice is activated by recruitment of multiple transcription factors to SINE B1 elements that function as enhancers, and discuss a potential relevance of this mechanism to Alu retrotransposable elements in human ZGA.
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Affiliation(s)
- Pavel Kravchenko
- Department of Totipotency, Max Planck Institute of Biochemistry, Munich, Germany
| | - Kikuë Tachibana
- Department of Totipotency, Max Planck Institute of Biochemistry, Munich, Germany.
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Sun M, Song R, Fang Y, Xu J, Yang Z, Zhang H. DNA-Based Complexes and Composites: A Review of Fabrication Methods, Properties, and Applications. ACS APPLIED MATERIALS & INTERFACES 2024; 16:51899-51915. [PMID: 39314016 DOI: 10.1021/acsami.4c13357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Deoxyribonucleic acid (DNA), a macromolecule that stores genetic information in organisms, has recently been gradually developed into a building block for new materials due to its stable chemical structure and excellent biocompatibility. The efficient preparation and functional integration of various molecular complexes and composite materials based on nucleic acid skeletons have been successfully achieved. These versatile materials possess excellent physical and chemical properties inherent to certain inorganic or organic molecules but are endowed with specific physiological functions by nucleic acids, demonstrating unique advantages and potential applications in materials science, nanotechnology, and biomedical engineering in recent years. However, issues such as the production cost, biological stability, and potential immunogenicity of DNA have presented some unprecedented challenges to the application of these materials in the field. This review summarizes the cutting-edge manufacturing techniques and unique properties of DNA-based complexes and composites and discusses the trends, challenges, and opportunities for the future development of nucleic acid-based materials.
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Affiliation(s)
- Mengqiu Sun
- School of Physical Sciences, Great Bay University, Dongguan 523000, China
- Department of Materials Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Rui Song
- School of Physical Sciences, Great Bay University, Dongguan 523000, China
- Research & Development Institute of Northwestern Polytechnical University in Shenzhen, Shenzhen 518063, China
| | - Yangwu Fang
- School of Physical Sciences, Great Bay University, Dongguan 523000, China
| | - Jiuzhou Xu
- School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zhaoqi Yang
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Hao Zhang
- School of Physical Sciences, Great Bay University, Dongguan 523000, China
- Research & Development Institute of Northwestern Polytechnical University in Shenzhen, Shenzhen 518063, China
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165
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Tresset G, Li S, Gargowitsch L, Matthews L, Pérez J, Zandi R. Glass-like Relaxation Dynamics during the Disorder-to-Order Transition of Viral Nucleocapsids. J Phys Chem Lett 2024:10210-10218. [PMID: 39356145 DOI: 10.1021/acs.jpclett.4c02158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2024]
Abstract
Nucleocapsid self-assembly is an essential yet elusive step in virus replication. Using time-resolved small-angle X-ray scattering on a model icosahedral ssRNA virus, we reveal a previously unreported kinetic pathway. Initially, RNA-bound capsid subunits rapidly accumulate beyond the stoichiometry of native virions. This is followed by a disorder-to-order transition characterized by glass-like relaxation dynamics and the release of excess subunits. Our molecular dynamics simulations, employing a coarse-grained elastic model, confirm the physical feasibility of self-ordering accompanied by subunit release. The relaxation can be modeled by an exponential integral decay on the mean squared radius of gyration, with relaxation times varying within the second range depending on RNA type and subunit concentration. A nanogel model suggests that the initially disordered nucleoprotein complexes quickly reach an equilibrium size, while their mass fractal dimension continues to evolve. Understanding virus self-assembly is not only crucial for combating viral infections, but also for designing synthetic virus-inspired nanocages for drug delivery applications.
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Affiliation(s)
- Guillaume Tresset
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, 91405 Orsay, France
| | - Siyu Li
- Department of Physics and Astronomy, University of California, Riverside, California 92521, United States
| | - Laetitia Gargowitsch
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, 91405 Orsay, France
| | | | - Javier Pérez
- SOLEIL Synchrotron, 91192 Gif-sur-Yvette, France
| | - Roya Zandi
- Department of Physics and Astronomy, University of California, Riverside, California 92521, United States
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166
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Tang Y, Chen F, Fang G, Zhang H, Zhang Y, Zhu H, Zhang X, Han Y, Cao Z, Guo F, Wang W, Ye D, Ju J, Tan L, Li C, Zhao Y, Zhou Z, An L, Jiao S. A cofactor-induced repressive type of transcription factor condensation can be induced by synthetic peptides to suppress tumorigenesis. EMBO J 2024:10.1038/s44318-024-00257-4. [PMID: 39358623 DOI: 10.1038/s44318-024-00257-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 08/23/2024] [Accepted: 09/17/2024] [Indexed: 10/04/2024] Open
Abstract
Transcriptional factors (TFs) act as key determinants of cell death and survival by differentially modulating gene expression. Here, we identified many TFs, including TEAD4, that form condensates in stressed cells. In contrast to YAP-induced transcription-activating condensates of TEAD4, we found that co-factors such as VGLL4 and RFXANK alternatively induced repressive TEAD4 condensates to trigger cell death upon glucose starvation. Focusing on VGLL4, we demonstrated that heterotypic interactions between TEAD4 and VGLL4 favor the oligomerization and assembly of large TEAD4 condensates with a nonclassical inhibitory function, i.e., causing DNA/chromatin to be aggregated and entangled, which eventually impede gene expression. Based on these findings, we engineered a peptide derived from the TEAD4-binding motif of VGLL4 to selectively induce TEAD4 repressive condensation. This "glue" peptide displayed a strong antitumor effect in genetic and xenograft mouse models of gastric cancer via inhibition of TEAD4-related gene transcription. This new type of repressive TF phase separation exemplifies how cofactors can orchestrate opposite functions of a given TF, and offers potential new antitumor strategies via artificial induction of repressive condensation.
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Grants
- 2020YFA0803200 MOST | National Key Research and Development Program of China (NKPs)
- 2023YFC2505903 MOST | National Key Research and Development Program of China (NKPs)
- 32270747,92168116, 22077002, 82222052 MOST | National Natural Science Foundation of China (NSFC)
- 32200567, 31930026, 82150112 MOST | National Natural Science Foundation of China (NSFC)
- 32070710, 82372613 MOST | National Natural Science Foundation of China (NSFC)
- 82361168638, 32170706, 82002493 MOST | National Natural Science Foundation of China (NSFC)
- 22ZR1448100, 22QA1407200, 23ZR1448900 STCSM | Natural Science Foundation of Shanghai Municipality ()
- 22QA1407300, 23ZR1480400, 23YF1432900 STCSM | Natural Science Foundation of Shanghai Municipality ()
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Affiliation(s)
- Yang Tang
- Department of Medical Ultrasound, Department of Stomatology, Shanghai Tenth People's Hospital, Tongji University Cancer Center, Tongji University School of Medicine, Shanghai, 200072, China
| | - Fan Chen
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Gemin Fang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, China
| | - Hui Zhang
- Department of General Surgery, Hua'shan Hospital, Fudan University Shanghai Medical College, Shanghai, 200040, China
| | - Yanni Zhang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, China
| | - Hanying Zhu
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, China
| | - Xinru Zhang
- Department of Medical Ultrasound, Department of Stomatology, Shanghai Tenth People's Hospital, Tongji University Cancer Center, Tongji University School of Medicine, Shanghai, 200072, China
| | - Yi Han
- Department of Medical Ultrasound, Department of Stomatology, Shanghai Tenth People's Hospital, Tongji University Cancer Center, Tongji University School of Medicine, Shanghai, 200072, China
| | - Zhifa Cao
- Department of Medical Ultrasound, Department of Stomatology, Shanghai Tenth People's Hospital, Tongji University Cancer Center, Tongji University School of Medicine, Shanghai, 200072, China
| | - Fenghua Guo
- Department of General Surgery, Hua'shan Hospital, Fudan University Shanghai Medical College, Shanghai, 200040, China
| | - Wenjia Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Dan Ye
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Junyi Ju
- Department of Medical Ultrasound, Department of Stomatology, Shanghai Tenth People's Hospital, Tongji University Cancer Center, Tongji University School of Medicine, Shanghai, 200072, China
| | - Lijie Tan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Chuanchuan Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Yun Zhao
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Zhaocai Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China.
- Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.
| | - Liwei An
- Department of Medical Ultrasound, Department of Stomatology, Shanghai Tenth People's Hospital, Tongji University Cancer Center, Tongji University School of Medicine, Shanghai, 200072, China.
| | - Shi Jiao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China.
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Huang W, Wan Y, Su H, Zhang Z, Liu Y, Sadeeq M, Xian M, Feng X, Xiong P, Hou F. Recent Advances in Phenazine Natural Products: Biosynthesis and Metabolic Engineering. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:21364-21379. [PMID: 39300971 DOI: 10.1021/acs.jafc.4c05294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
Phenazine natural products are a class of nitrogen-containing heterocyclic compounds produced by microorganisms. The tricyclic ring molecules show various chemical structures and extensive pharmacological activities, such as antimicrobial, anticancer, antiparasitic, anti-inflammatory, and insecticidal activities, with low toxicity to the environment. Since phenazine-1-carboxylic acid has been developed as a registered biopesticide, the application of phenazine natural products will be promising in the field of agriculture pathogenic fungi control based on broad-spectrum antifungal activity, minimal toxicity to the environment, and improvement of crop production. Currently, there are still plenty of intriguing hidden biosynthetic pathways of phenazine natural products to be discovered, and the titer of naturally occurring phenazine natural products is insufficient for agricultural applications. In this review, we spotlight the progress regarding biosynthesis and metabolic engineering research of phenazine natural products in the past decade. The review provides useful insights concerning phenazine natural products production and more clues on new phenazine derivatives biosynthesis.
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Affiliation(s)
- Wei Huang
- Shandong Freda Biotech Co., Ltd, 250101 Jinan, China
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
| | - Yupeng Wan
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
| | - Huai Su
- Shandong Freda Biotech Co., Ltd, 250101 Jinan, China
| | - Zhe Zhang
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
| | - Yingjie Liu
- Shandong Freda Biotech Co., Ltd, 250101 Jinan, China
| | - Mohd Sadeeq
- Shandong University of Technology, School of Life Sciences and Medicine, 255000 Zibo, China
| | - Mo Xian
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
| | - Xinjun Feng
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
| | - Peng Xiong
- Shandong University of Technology, School of Life Sciences and Medicine, 255000 Zibo, China
| | - Feifei Hou
- Shandong University of Technology, School of Life Sciences and Medicine, 255000 Zibo, China
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168
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Hu S, Tian G, Bai Y, Qu A, He Q, Chen L, Xu P. Alternative splicing dynamically regulates common carp embryogenesis under thermal stress. BMC Genomics 2024; 25:918. [PMID: 39358679 DOI: 10.1186/s12864-024-10838-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 09/26/2024] [Indexed: 10/04/2024] Open
Abstract
BACKGROUND Thermal stress is a major environmental factor affecting fish development and survival. Common carp (Cyprinus carpio) are susceptible to heat stress in their embryonic and larval phases, but the thermal stress response of alternative splicing during common carp embryogenesis remains poorly understood. RESULTS Using RNA-seq data from eight developmental stages and four temperatures, we constructed a comprehensive profile of alternative splicing (AS) during the embryogenesis of common carp, and found that AS genes and events are widely distributed among all stages. A total of 5,835 developmental stage-specific AS (SAS) genes, 21,368 temperature-specific differentially expressed genes (TDEGs), and 2,652 temperature-specific differentially AS (TDAS) genes were identified. Hub TDAS genes in each developmental stage, such as taf2, hnrnpa1, and drg2, were identified through protein-protein interaction (PPI) network analysis. The early developmental stages may be more sensitive to temperature, with thermal stress leading to a massive increase in the number of expressed transcripts, TDEGs, and TDAS genes in the morula stage, followed by the gastrula stage. GO and KEGG analyses showed that from the morula stage to the neurula stage, TDAS genes were more involved in intracellular transport, protein modification, and localization processes, while from the optic vesicle stage to one day post-hatching, they participated more in biosynthetic processes. Further subgenomic analysis revealed that the number of AS genes and events in subgenome B was generally higher than that in subgenome A, and the homologous AS genes were significantly enriched in basic life activity pathways, such as mTOR signaling pathway, p53 signaling pathway, and MAPK signaling pathway. Additionally, lncRNAs can play a regulatory role in the response to thermal stress by targeting AS genes such as lmnl3, affecting biological processes such as apoptosis and axon guidance. CONCLUSIONS In short, thermal stress can affect alternative splicing regulation during common carp embryogenesis at multiple levels. Our work complemented some gaps in the study of alternative splicing at both levels of embryogenesis and thermal stress in C. carpio and contributed to the comprehension of environmental adaptation formation in polyploid fishes during embryogenesis.
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Affiliation(s)
- Shuimu Hu
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Guopeng Tian
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Yulin Bai
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Ang Qu
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Qian He
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Lin Chen
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
| | - Peng Xu
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
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169
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Lv X, Zhang Y, Sun K, Yang Q, Luo J, Tao L, Lu P. De novo design of mini-protein binders broadly neutralizing Clostridioides difficile toxin B variants. Nat Commun 2024; 15:8521. [PMID: 39358329 DOI: 10.1038/s41467-024-52582-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 09/12/2024] [Indexed: 10/04/2024] Open
Abstract
Clostridioides difficile toxin B (TcdB) is the key virulence factor accounting for C. difficile infection-associated symptoms. Effectively neutralizing different TcdB variants with a universal solution poses a significant challenge. Here we present the de novo design and characterization of pan-specific mini-protein binders against major TcdB subtypes. Our design successfully binds to the first receptor binding interface (RBI-1) of the varied TcdB subtypes, exhibiting affinities ranging from 20 pM to 10 nM. The cryo-electron microscopy (cryo-EM) structures of the mini protein binder in complex with TcdB1 and TcdB4 are consistent with the computational design models. The engineered and evolved variants of the mini-protein binder and chondroitin sulfate proteoglycan 4 (CSPG4), another natural receptor that binds to the second RBI (RBI-2) of TcdB, better neutralize major TcdB variants both in cells and in vivo, as demonstrated by the colon-loop assay using female mice. Our findings provide valuable starting points for the development of therapeutics targeting C. difficile infections (CDI).
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Affiliation(s)
- Xinchen Lv
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, 310024, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Yuanyuan Zhang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China
- Center for Infectious Disease Research, School of Medicine, Westlake University, Hangzhou, Zhejiang, 310024, China
- Center for General Practice Medicine, Department of Infectious Diseases, Zhejiang Provincial People's Hospital, Hangzhou Medical College Affiliated People's Hospital, Hangzhou, Zhejiang, 310014, China
| | - Ke Sun
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Qi Yang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China
- Center for Infectious Disease Research, School of Medicine, Westlake University, Hangzhou, Zhejiang, 310024, China
| | - Jianhua Luo
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, 310024, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China
- Center for Infectious Disease Research, School of Medicine, Westlake University, Hangzhou, Zhejiang, 310024, China
| | - Liang Tao
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, 310024, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, 310024, China.
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.
- Center for Infectious Disease Research, School of Medicine, Westlake University, Hangzhou, Zhejiang, 310024, China.
| | - Peilong Lu
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, 310024, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, 310024, China.
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China.
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170
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Kongjaroon S, Lawan N, Trisrivirat D, Chaiyen P. Enhancement of tryptophan 2-monooxygenase thermostability by semi-rational enzyme engineering: a strategic design to minimize experimental investigation. RSC Chem Biol 2024; 5:989-1001. [PMID: 39363964 PMCID: PMC11446241 DOI: 10.1039/d4cb00102h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Accepted: 07/22/2024] [Indexed: 10/05/2024] Open
Abstract
Tryptophan 2-monooxygenase (TMO) is an FAD-bound flavoenzyme which catalyzes the oxidative decarboxylation of l-tryptophan to produce indole-3-acetamide (IAM) and carbon dioxide. The reaction of TMO is the first step of indole-3-acetic acid (IAA) biosynthesis. Although TMO is of interest for mechanistic studies and synthetic biology applications, the enzyme has low thermostability and soluble expression yield. Herein, we employed a combined approach of rational design using computational tools with site-saturation mutagenesis to screen for TMO variants with significantly improved thermostability properties and soluble protein expression. The engineered TMO variants, TMO-PWS and TMO-PWSNR, possess melting temperatures (T m) of 65 °C, 17 °C higher than that of the wild-type enzyme (TMO-WT). At 50 °C, the stabilities (t 1/2) of TMO-PWS and TMO-PWSNR were 85-fold and 92.4-fold higher, while their soluble expression yields were 1.4-fold and 2.1-fold greater than TMO-WT, respectively. Remarkably, the kinetic parameters of these variants were similar to those of the wild-type enzymes, illustrating that they are promising candidates for future studies. Molecular dynamic simulations of the wild-type and thermostable TMO variants identified key interactions for enhancing these improvements in the biophysical properties of the TMO variants. The introduced mutations contributed to hydrogen bond formation and an increase in the regional hydrophobicity, thereby, strengthening the TMO structure.
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Affiliation(s)
- Sirus Kongjaroon
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
| | - Narin Lawan
- Department of Chemistry, Faculty of Science, Chiang Mai University Chiang Mai 50200 Thailand
| | - Duangthip Trisrivirat
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
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171
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Chen L, Huang L, Gu Y, Li C, Sun P, Xiang Y. Novel post-translational modifications of protein by metabolites with immune responses and immune-related molecules in cancer immunotherapy. Int J Biol Macromol 2024; 277:133883. [PMID: 39033895 DOI: 10.1016/j.ijbiomac.2024.133883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 06/30/2024] [Accepted: 07/13/2024] [Indexed: 07/23/2024]
Abstract
Tumour immunotherapy is an effective and essential treatment for cancer. However, the heterogeneity of tumours and the complex and changeable tumour immune microenvironment (TME) creates many uncertainties in the clinical application of immunotherapy, such as different responses to tumour immunotherapy and significant differences in individual efficacy. It makes anti-tumour immunotherapy face many challenges. Immunometabolism is a critical determinant of immune cell response to specific immune effector molecules, significantly affecting the effects of tumour immunotherapy. It is attributed mainly to the fact that metabolites can regulate the function of immune cells and immune-related molecules through the protein post-translational modifications (PTMs) pathway. This study systematically summarizes a variety of novel protein PTMs including acetylation, propionylation, butyrylation, succinylation, crotonylation, malonylation, glutarylation, 2-hydroxyisobutyrylation, β-hydroxybutyrylation, benzoylation, lactylation and isonicotinylation in the field of tumour immune regulation and immunotherapy. In particular, we elaborate on how different PTMs in the TME can affect the function of immune cells and lead to immune evasion in cancer. Lastly, we highlight the potential treatment with the combined application of target-inhibited protein modification and immune checkpoint inhibitors (ICIs) for improved immunotherapeutic outcomes.
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Affiliation(s)
- Lihua Chen
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, PR China; National Clinical Research Center for Obstetric & Gynecologic Diseases, PR China
| | - Lixiang Huang
- Laboratory of Gynecologic Oncology, Department of Gynecology, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou 350001, Fujian, PR China; Fujian Key Laboratory of Women and Children's Critical Diseases Research, Fuzhou 350001, Fujian, PR China
| | - Yu Gu
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, PR China; National Clinical Research Center for Obstetric & Gynecologic Diseases, PR China
| | - Chen Li
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, PR China; National Clinical Research Center for Obstetric & Gynecologic Diseases, PR China
| | - Pengming Sun
- Laboratory of Gynecologic Oncology, Department of Gynecology, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou 350001, Fujian, PR China; Fujian Key Laboratory of Women and Children's Critical Diseases Research, Fuzhou 350001, Fujian, PR China.
| | - Yang Xiang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, PR China; National Clinical Research Center for Obstetric & Gynecologic Diseases, PR China.
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172
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Cunningham CB, Shelby EA, McKinney EC, Simmons AM, Moore AJ, Moore PJ. An association between Dnmt1 and Wnt in the production of oocytes in the whitefly Bemisia tabaci. INSECT MOLECULAR BIOLOGY 2024; 33:467-480. [PMID: 38335444 DOI: 10.1111/imb.12893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/08/2024] [Indexed: 02/12/2024]
Abstract
The function of DNA methylation in insects and the DNA methyltransferase (Dnmt) genes that influence methylation remains uncertain. We used RNA interference to reduce the gene expression of Dnmt1 within the whitefly Bemisia tabaci (Hemiptera:Aleyrodidae; Gennadius), a hemipteran species that relies on Dnmt1 for proper gametogenesis. We then used RNA-seq to test an a priori hypothesis that meiosis-related genetic pathways would be perturbed. We generally did not find an overall effect on meiosis-related pathways. However, we found that genes in the Wnt pathway, genes associated with the entry into meiosis in vertebrates, were differentially expressed. Our results are consistent with Dnmt1 knockdown influencing specific pathways and not causing general transcriptional response. This is a finding that is also seen with other insect species. We also characterised the methylome of B. tabaci and assessed the influence of Dnmt1 knockdown on cytosine methylation. This species has methylome characteristics comparable to other hemipterans regarding overall level, enrichment within gene bodies, and a bimodal distribution of methylated/non-methylated genes. Very little differential methylation was observed, and difference in methylation were not associated with differences in gene expression. The effect on Wnt presents an interesting new candidate pathway for future studies.
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Affiliation(s)
| | - Emily A Shelby
- Department of Entomology, University of Georgia, Athens, Georgia, USA
| | | | - Alvin M Simmons
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, South Carolina, USA
| | - Allen J Moore
- Department of Entomology, University of Georgia, Athens, Georgia, USA
| | - Patricia J Moore
- Department of Entomology, University of Georgia, Athens, Georgia, USA
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173
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Çi Ftçi B, Teki N R. Prediction of viral families and hosts of single-stranded RNA viruses based on K-Mer coding from phylogenetic gene sequences. Comput Biol Chem 2024; 112:108114. [PMID: 38852362 DOI: 10.1016/j.compbiolchem.2024.108114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 05/06/2024] [Accepted: 05/25/2024] [Indexed: 06/11/2024]
Abstract
There are billions of virus species worldwide, and viruses, the smallest parasitic entities, pose a serious threat. Therefore, fighting associated disorders requires an understanding of the genetic structure of viruses. Considering the wide diversity and rapid evolution of viruses, there is a critical need to quickly and accurately classify viral species and their potential hosts to better understand transmission dynamics, facilitating the development of targeted therapies. Recognizing this, this study has investigated the classes of RNA viruses based on their genomic sequences using Machine Learning (ML) and Deep Learning (DL) models. The PhyVirus dataset, consisting of pathogenic Single-stranded RNA viruses of Baltimore group four (+ssRNA) and five (-ssRNA) with different hosts and species, was analyzed. The dataset containing viral gene sequences was analyzed using the K-Mer coding technique, which is based on base words of various lengths. The study used classical ML algorithms (Random Forest, Gradient Boosting and Extra Trees) and the Fully Connected Deep Neural Network, a Deep Learning algorithm, to predict viral families and hosts. Detailed analyses were performed on the classifier performance in scenarios with different train-test ratios and different word lengths (k-values) for K-Mer. The observed results show that Fully Connected Deep Neural Network has a high success rate of 99.60 % in predicting virus families. In predicting virus hosts, the Extra Trees classifier achieved the highest success rate of 81.53 %. This study is considered to be the first classification study in the literature on this dataset, which has a very large family and host diversity consisting of gene sequences of Single-stranded RNA viruses. Our detailed investigations on how varying word lengths based on K-Mer coding in gene sequences affect the classification into viral families and hosts make this study particularly valuable. This study shows that ML and DL methods have the potential to produce valuable results in phylogenetic studies. In addition, the results and high-performance values show that these methods can be successfully used in regenerative applications of gene sequences or in studies such as the elimination of losses in gene sequences.
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Affiliation(s)
- Bahar Çi Ftçi
- Batman University, Institute of Graduate Studies, Department of Electrical and Electronic Engineering, Turkey; Siirt University, Distance Education Application and Research Center, Turkey.
| | - Ramazan Teki N
- Batman University, Faculty of Engineering and Architecture, Department of Computer Engineering, Turkey.
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174
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Bilgin N, Tumber A, Dhingra S, Salah E, Al-Salmy A, Martín SP, Wang Y, Schofield CJ, Mecinović J. Substrate selectivity and inhibition of the human lysyl hydroxylase JMJD7. Protein Sci 2024; 33:e5162. [PMID: 39276004 PMCID: PMC11400632 DOI: 10.1002/pro.5162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 08/12/2024] [Accepted: 08/19/2024] [Indexed: 09/16/2024]
Abstract
Jumonji-C (JmjC) domain-containing protein 7 (JMJD7) is a human Fe(II) and 2-oxoglutarate dependent oxygenase that catalyzes stereospecific C3-hydroxylation of lysyl-residues in developmentally regulated GTP binding proteins 1 and 2 (DRG1/2). We report studies exploring a diverse set of lysine derivatives incorporated into the DRG1 peptides as potential human JMJD7 substrates and inhibitors. The results indicate that human JMJD7 has a relatively narrow substrate scope beyond lysine compared to some other JmjC hydroxylases and lysine-modifying enzymes. The geometrically constrained (E)-dehydrolysine is an efficient alternative to lysine for JMJD7-catalyzed C3-hydroxylation. γ-Thialysine and γ-azalysine undergo C3-hydroxylation, followed by degradation to formylglycine. JMJD7 also catalyzes the S-oxidation of DRG1-derived peptides possessing methionine and homomethionine residues in place of lysine. Inhibition assays show that DRG1 variants possessing cysteine/selenocysteine instead of the lysine residue efficiently inhibit JMJD7 via cross-linking. The overall results inform on the substrate selectivity and inhibition of human JMJD7, which will help enable the rational design of selective small-molecule and peptidomimetic inhibitors of JMJD7.
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Affiliation(s)
- Nurgül Bilgin
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Siddhant Dhingra
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Eidarus Salah
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Aziza Al-Salmy
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Sandra Pinzón Martín
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Yicheng Wang
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
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175
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Wu Z, Sun X, Su J, Zhang X, Hu J, Li C. Revealing the graded activation mechanism of neurotensin receptor 1. Int J Biol Macromol 2024; 278:134488. [PMID: 39111461 DOI: 10.1016/j.ijbiomac.2024.134488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 08/02/2024] [Accepted: 08/02/2024] [Indexed: 08/16/2024]
Abstract
Graded activation contributes to the precise regulation of GPCR activity, presenting new opportunities for drug design. In this work, a total of 10 μs enhanced-sampling simulations are performed to provide molecular insights into the binding dynamics differences of the neurotensin receptor 1 (NTSR1) to the full agonist SRI-9829, partial agonist RTI-3a and inverse agonist SR48692. The possible graded activation mechanism of NTSR1 is revealed by an integrated analysis utilizing the reweighted potential of mean force (PMF), deep learning (DL) and transfer entropy (TE). Specifically, the orthosteric pocket is observed to undergo expansion and contraction, with the G-protein-binding site experiencing interconversions among the inactive, intermediate and active-like states. Detailed structural comparisons capture subtle conformational differences arising from ligand binding in allosteric signaling, which can well explain the graded activation. Critical microswitches that contribute to graded activation are efficiently identified with the DL model. TE calculations enable the visualization of allosteric communication networks within the receptor, elucidating the driver-responder relationships associated with signal transduction. Fortunately, the dissociation of the full agonist from the orthosteric pocket is observed. The current findings systematically reveal the mechanism of NTSR1 graded activation, and also provide implications for structure-based drug design.
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Affiliation(s)
- Zhixiang Wu
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
| | - Xiaohan Sun
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
| | - Jingjie Su
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
| | - Xinyu Zhang
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
| | - Jianping Hu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China.
| | - Chunhua Li
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, China.
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176
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Roy S, Malik B, Chawla R, Bora S, Ghosh T, Santhosh R, Thakur R, Sarkar P. Biocompatible film based on protein/polysaccharides combination for food packaging applications: A comprehensive review. Int J Biol Macromol 2024; 278:134658. [PMID: 39128751 DOI: 10.1016/j.ijbiomac.2024.134658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 07/20/2024] [Accepted: 08/08/2024] [Indexed: 08/13/2024]
Abstract
Protein and polysaccharides are the mostly used biopolymers for developing packaging film and their combination-based composite produced better quality film compared to their single counterpart. The combination of protein and polysaccharides are superior owing to the better physical properties like water resistance, mechanical and barrier properties of the film. The protein/polysaccharide-based composite film showed promising result in active and smart food packaging regime. This work discussed the recent advances on the different types of protein/polysaccharide combinations used for making bio-based sustainable packaging film formulation and further utilized in food packaging applications. The fabrication and properties of various protein/polysaccharide combination are comprehensively discussed. This review also presents the use of the multifunctional composite film in meat, fish, fruits, vegetables, milk products, and bakery products, etc. Developing composite is a promising approach to improve physical properties and practical applicability of packaging film. The low water resistance properties, mechanical performance, and barrier properties limit the real-time use of biopolymer-based packaging film. The combination of protein/polysaccharide can be one of the promising solutions to the biopolymer-based packaging and thus recently many works has been published which is suitable to preserve the shelf life of food as well trace the food spoilage during food storage.
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Affiliation(s)
- Swarup Roy
- Department of Food Technology and Nutrition, School of Agriculture, Lovely Professional University, Phagwara, Punjab 144411, India.
| | - Bhawna Malik
- College of Dairy Science and Technology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana 141004, Punjab, India
| | - Rekha Chawla
- College of Dairy Science and Technology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana 141004, Punjab, India
| | - Susmita Bora
- Department of Food Engineering and Technology, School of Engineering, Tezpur University, Tezpur, Assam 784028, India
| | - Tabli Ghosh
- Department of Food Engineering and Technology, School of Engineering, Tezpur University, Tezpur, Assam 784028, India
| | - R Santhosh
- Department of Food Process Engineering, National Institute of Technology Rourkela, Odisha 769008, India
| | - Rahul Thakur
- Department of Food Process Engineering, National Institute of Technology Rourkela, Odisha 769008, India
| | - Preetam Sarkar
- Department of Food Process Engineering, National Institute of Technology Rourkela, Odisha 769008, India
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177
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Chandra Jena B, Flaherty DP, O'Brien VP, Watts VJ. Biochemical pharmacology of adenylyl cyclases in cancer. Biochem Pharmacol 2024; 228:116160. [PMID: 38522554 PMCID: PMC11410551 DOI: 10.1016/j.bcp.2024.116160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/11/2024] [Accepted: 03/21/2024] [Indexed: 03/26/2024]
Abstract
Globally, despite extensive research and pharmacological advancement, cancer remains one of the most common causes of mortality. Understanding the signaling pathways involved in cancer progression is essential for the discovery of new drug targets. The adenylyl cyclase (AC) superfamily comprises glycoproteins that regulate intracellular signaling and convert ATP into cyclic AMP, an important second messenger. The present review highlights the involvement of ACs in cancer progression and suppression, broken down for each specific mammalian AC isoform. The precise mechanisms by which ACs contribute to cancer cell proliferation and invasion are not well understood and are variable among cancer types; however, AC overactivation, along with that of downstream regulators, presents a potential target for novel anticancer therapies. The expression patterns of ACs in numerous cancers are discussed. In addition, we highlight inhibitors of AC-related signaling that are currently under investigation, with a focus on possible anti-cancer strategies. Recent discoveries with small molecules regarding more direct modulation AC activity are also discussed in detail. A more comprehensive understanding of different components in AC-related signaling could potentially lead to the development of novel therapeutic strategies for personalized oncology and might enhance the efficacy of chemoimmunotherapy in the treatment of various cancers.
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Affiliation(s)
- Bikash Chandra Jena
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, USA
| | - Daniel P Flaherty
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, USA
| | - Valerie P O'Brien
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, USA.
| | - Val J Watts
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, USA.
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178
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Fonda BD, Kato M, Li Y, Murray DT. Cryo-EM and solid state NMR together provide a more comprehensive structural investigation of protein fibrils. Protein Sci 2024; 33:e5168. [PMID: 39276003 PMCID: PMC11400629 DOI: 10.1002/pro.5168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 08/25/2024] [Accepted: 08/26/2024] [Indexed: 09/16/2024]
Abstract
The tropomyosin 1 isoform I/C C-terminal domain (Tm1-LC) fibril structure is studied jointly with cryogenic electron microscopy (cryo-EM) and solid state nuclear magnetic resonance (NMR). This study demonstrates the complementary nature of these two structural biology techniques. Chemical shift assignments from solid state NMR are used to determine the secondary structure at the level of individual amino acids, which is faithfully seen in cryo-EM reconstructions. Additionally, solid state NMR demonstrates that the region not observed in the reconstructed cryo-EM density is primarily in a highly mobile random coil conformation rather than adopting multiple rigid conformations. Overall, this study illustrates the benefit of investigations combining cryo-EM and solid state NMR to investigate protein fibril structure.
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Affiliation(s)
- Blake D. Fonda
- Department of ChemistryUniversity of CaliforniaDavisCaliforniaUSA
| | - Masato Kato
- Department of BiochemistryUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Yang Li
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Dylan T. Murray
- Department of Molecular and Cell BiologyUniversity of ConnecticutStorrsConnecticutUSA
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179
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Martínez-Lumbreras S, Morguet C, Sattler M. Dynamic interactions drive early spliceosome assembly. Curr Opin Struct Biol 2024; 88:102907. [PMID: 39168044 DOI: 10.1016/j.sbi.2024.102907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/21/2024] [Accepted: 07/23/2024] [Indexed: 08/23/2024]
Abstract
Splicing is a critical processing step during pre-mRNA maturation in eukaryotes. The correct selection of splice sites during the early steps of spliceosome assembly is highly important and crucial for the regulation of alternative splicing. Splice site recognition and alternative splicing depend on cis-regulatory sequence elements in the RNA and trans-acting splicing factors that recognize these elements and crosstalk with the canonical splicing machinery. Structural mechanisms involving early spliceosome complexes are governed by dynamic RNA structures, protein-RNA interactions and conformational flexibility of multidomain RNA binding proteins. Here, we highlight structural studies and integrative structural biology approaches, which provide complementary information from cryo-EM, NMR, small angle scattering, and X-ray crystallography to elucidate mechanisms in the regulation of early spliceosome assembly and quality control, highlighting the role of conformational dynamics.
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Affiliation(s)
- Santiago Martínez-Lumbreras
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Technical University of Munich, TUM School of Natural Sciences, Bavarian NMR Center and Department of Bioscience, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Clara Morguet
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Technical University of Munich, TUM School of Natural Sciences, Bavarian NMR Center and Department of Bioscience, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Michael Sattler
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Technical University of Munich, TUM School of Natural Sciences, Bavarian NMR Center and Department of Bioscience, Lichtenbergstrasse 4, 85747 Garching, Germany.
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180
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Martin FJO, Santiveri M, Hu H, Taylor NMI. Ion-driven rotary membrane motors: From structure to function. Curr Opin Struct Biol 2024; 88:102884. [PMID: 39053417 DOI: 10.1016/j.sbi.2024.102884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 05/16/2024] [Accepted: 06/21/2024] [Indexed: 07/27/2024]
Abstract
Ion-driven membrane motors, essential across all domains of life, convert a gradient of ions across a membrane into rotational energy, facilitating diverse biological processes including ATP synthesis, substrate transport, and bacterial locomotion. Herein, we highlight recent structural advances in the understanding of two classes of ion-driven membrane motors: rotary ATPases and 5:2 motors. The recent structure of the human F-type ATP synthase is emphasised along with the gained structural insight into clinically relevant mutations. Furthermore, we highlight the diverse roles of 5:2 motors and recent mechanistic understanding gained through the resolution of ions in the structure of a sodium-driven motor, combining insights into potential unifying mechanisms of ion selectivity and rotational torque generation in the context of their function as part of complex biological systems.
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Affiliation(s)
- Freddie J O Martin
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Mònica Santiveri
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Haidai Hu
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Nicholas M I Taylor
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
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181
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Eisermann J, Liang Y, Wright JJ, Clifford E, Wilton-Ely JDET, Kuimova MK, Roessler MM. The Effect of Reactive Oxygen Species on Respiratory Complex I Activity in Liposomes. Chemistry 2024; 30:e202402035. [PMID: 39058376 DOI: 10.1002/chem.202402035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 07/23/2024] [Accepted: 07/25/2024] [Indexed: 07/28/2024]
Abstract
Respiratory complex I (R-CI) is an essential enzyme in the mitochondrial electron transport chain but also a major source of reactive oxygen species (ROS), which are implicated in neurodegenerative diseases and ageing. While the mechanism of ROS production by R-CI is well-established, the feedback of ROS on R-CI activity is poorly understood. Here, we perform EPR spectroscopy on R-CI incorporated in artificial membrane vesicles to reveal that ROS (particularly hydroxyl radicals) reduce R-CI activity by making the membrane more polar and by increasing its hydrogen bonding capability. Moreover, the mechanism that we have uncovered reveals that the feedback of ROS on R-CI activity via the membrane is transient and not permanent; lipid peroxidation is negligible for the levels of ROS generated under these conditions. Our successful use of modular proteoliposome systems in conjunction with EPR spectroscopy and other biophysical techniques is a powerful approach for investigating ROS effects on other membrane proteins.
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Affiliation(s)
- Jana Eisermann
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, London, W12 0BZ, UK
- Department of Chemistry, University of Stuttgart, Institute of Physical Chemistry, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Yuxin Liang
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, London, W12 0BZ, UK
| | - John J Wright
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Building, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK
| | - Eleanor Clifford
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, London, W12 0BZ, UK
| | - James D E T Wilton-Ely
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, London, W12 0BZ, UK
| | - Marina K Kuimova
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, London, W12 0BZ, UK
| | - Maxie M Roessler
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, London, W12 0BZ, UK
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182
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Abrusán G, Zelezniak A. Cellular location shapes quaternary structure of enzymes. Nat Commun 2024; 15:8505. [PMID: 39353940 PMCID: PMC11445431 DOI: 10.1038/s41467-024-52662-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 09/18/2024] [Indexed: 10/03/2024] Open
Abstract
The main forces driving protein complex evolution are currently not well understood, especially in homomers, where quaternary structure might frequently evolve neutrally. Here we examine the factors determining oligomerisation by analysing the evolution of enzymes in circumstances where homomers rarely evolve. We show that 1) In extracellular environments, most enzymes with known structure are monomers, while in the cytoplasm homomers, indicating that the evolution of oligomers is cellular environment dependent; 2) The evolution of quaternary structure within protein orthogroups is more consistent with the predictions of constructive neutral evolution than an adaptive process: quaternary structure is gained easier than it is lost, and most extracellular monomers evolved from proteins that were monomers also in their ancestral state, without the loss of interfaces. Our results indicate that oligomerisation is context-dependent, and even when adaptive, in many cases it is probably not driven by the intrinsic properties of enzymes, like their biochemical function, but rather the properties of the environment where the enzyme is active. These factors might be macromolecular crowding and excluded volume effects facilitating the evolution of interfaces, and the maintenance of cellular homeostasis through shaping cytoplasm fluidity, protein degradation, or diffusion rates.
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Affiliation(s)
- György Abrusán
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, New Hunt's House, London, UK.
| | - Aleksej Zelezniak
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, New Hunt's House, London, UK
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Institute of Biotechnology, Life Sciences Centre, Vilnius University, Vilnius, Lithuania
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183
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Liu J, Lu F. Beyond simple tails: poly(A) tail-mediated RNA epigenetic regulation. Trends Biochem Sci 2024; 49:846-858. [PMID: 39004583 DOI: 10.1016/j.tibs.2024.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/19/2024] [Accepted: 06/19/2024] [Indexed: 07/16/2024]
Abstract
The poly(A) tail is an essential structural component of mRNA required for the latter's stability and translation. Recent technologies have enabled transcriptome-wide profiling of the length and composition of poly(A) tails, shedding light on their overlooked regulatory capacities. Notably, poly(A) tails contain not only adenine but also uracil, cytosine, and guanine residues. These findings strongly suggest that poly(A) tails could encode a wealth of regulatory information, similar to known reversible RNA chemical modifications. This review aims to succinctly summarize our current knowledge on the composition, dynamics, and regulatory functions of RNA poly(A) tails. Given their capacity to carry rich regulatory information beyond the genetic code, we propose the concept of 'poly(A) tail epigenetic information' as a new layer of RNA epigenetic regulation.
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Affiliation(s)
- Jingwen Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Falong Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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184
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Baskakova KO, Kuzmichev PK, Karbyshev MS. Advanced applications of Nanodiscs-based platforms for antibodies discovery. Biophys Chem 2024; 313:107290. [PMID: 39002246 DOI: 10.1016/j.bpc.2024.107290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 06/18/2024] [Accepted: 07/08/2024] [Indexed: 07/15/2024]
Abstract
Due to their fundamental biological importance, membrane proteins (MPs) are attractive targets for drug discovery, with cell surface receptors, transporters, ion channels, and membrane-bound enzymes being of particular interest. However, due to numerous challenges, these proteins present underutilized opportunities for discovering biotherapeutics. Antibodies hold the promise of exquisite specificity and adaptability, making them the ideal candidates for targeting complex membrane proteins. They can target specific conformations of a particular membrane protein and can be engineered into various formats. Generating specific and effective antibodies targeting these proteins is no easy task due to several factors. The antigen's design, antibody-generation strategies, lead optimization technologies, and antibody modalities can be modified to tackle these challenges. The rational employment of cutting-edge lipid nanoparticle systems for retrieving the membrane antigen has been successfully implemented to simplify the mechanism-based therapeutic antibody discovery approach. Despite the highlighted MP production challenges, this review unequivocally underscores the advantages of targeting complex membrane proteins with antibodies and designing membrane protein antigens. Selected examples of lipid nanoparticle success have been illustrated, emphasizing the potential of therapeutic antibody discovery in this regard. With further research and development, we can overcome these challenges and unlock the full potential of therapeutic antibodies directed to target complex MPs.
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Affiliation(s)
- Kristina O Baskakova
- Laboratory of Molecular Therapy of Cancer, Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russian Federation
| | - Pavel K Kuzmichev
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudniy, Russian Federation
| | - Mikhail S Karbyshev
- Laboratory of Molecular Therapy of Cancer, Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russian Federation; Department of Biochemistry and Molecular Biology, Pirogov Russian National Research Medical University, Moscow, Russian Federation.
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185
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Ahlawat S, Shukla BN, Singh V, Sharma Y, Choudhary P, Rao A. GLYCOCINS: The sugar peppered antimicrobials. Biotechnol Adv 2024; 75:108415. [PMID: 39033836 DOI: 10.1016/j.biotechadv.2024.108415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 06/19/2024] [Accepted: 07/16/2024] [Indexed: 07/23/2024]
Abstract
Glycosylated bacteriocins, known as glycocins, were first discovered in 2011. These bioactive peptides are produced by bacteria to gain survival advantages. They exhibit diverse types of glycans and demonstrate varied antimicrobial activity. Currently, there are 13 experimentally known glycocins, with over 250 identified in silico across different bacterial phyla. Notably, glycocins are recognized for their glycan-mediated antimicrobial activity, proving effective against drug-resistant and foodborne pathogens. Many glycocins contain rare S-linked glycans. Glycosyltransferases (GTs), responsible for transferring sugar to glycocins and involved in glycocin biosynthesis, often cluster together in the producer's genome. This clustering makes them valuable for custom glycoengineering with diverse substrate specificities. Heterologous expression of glycocins has paved the way for the establishment of microbial factories for glycopeptide and glycoconjugate production across various industries. In this review, we emphasize the primary roles of fully and partially characterized glycocins and their glycosylating enzymes. Additionally, we explore how specific glycan structures facilitate these functions in antibacterial activities. Furthermore, we discuss newer approaches and increasing efforts aimed at exploiting bacterial glycobiology for the development of food preservatives and as replacements or complements to traditional antibiotics, particularly in the face of antibiotic-resistant pathogenic bacteria.
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Affiliation(s)
- Shimona Ahlawat
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India; Academy of Scientific and Innovation Research (AcSIR), Ghaziabad 201002, India
| | | | - Vaidhvi Singh
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Yogita Sharma
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | | | - Alka Rao
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India; Academy of Scientific and Innovation Research (AcSIR), Ghaziabad 201002, India; Current address: Food Safety and Standards Authority of India (FSSAI), New Delhi 110002, India.
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186
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Lee H, Liao JD, Tsai HP, Wang H, Sitjar J. Focused ion beam-fabricated nanorod substrate for label-free surface-enhanced Raman spectroscopy and enabling dual virus detection. Talanta 2024; 278:126466. [PMID: 38944940 DOI: 10.1016/j.talanta.2024.126466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 05/27/2024] [Accepted: 06/22/2024] [Indexed: 07/02/2024]
Abstract
The COVID-19 pandemic presents global challenges, notably with co-infections in respiratory tract involving SARS-CoV-2 variants and influenza strains. Detecting multiple viruses simultaneously is crucial for accurate diagnosis, effective tracking infectious sources, and containment of the epidemic. This study uses a label-free surface-enhanced Raman spectroscopy (SERS) method using Au NPs/pZrO2 (250) and FIB-made Au NRs (100) to detect dual viruses, including SARS-CoV-2 Delta variant (D) and influenza A (A) or B (B) virus. Results demonstrate distinct peaks facilitating virus differentiation, especially between D and A or B, with clear disparities between substrates; specific peaks at 950 and 1337 cm-1 are pivotal for discerning viruses using Au NPs/pZrO2 (250), while those at 1050, 1394, and 1450 cm-1 and 1033, 1165, 1337, and 1378 cm-1 are key for validation using Au NRs (100). Differences in substrate surface morphology and spatial disposition of accommodating viruses significantly influence hotspot formation and Raman signal amplification efficiency, thereby affecting the ability to distinguish various viruses. Furthermore, both substrates offer insights, even in the presence of oxymetazoline hydrochloride (an interfering substance), with practical implications in viral diagnosis. The customized design and reproducibility underscore efficient Raman signal amplification, even in challenging environments, highlighting potential for widespread virus detection.
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Affiliation(s)
- Han Lee
- Laboratory of Engineered Materials for Biomedical Applications, Department of Materials Science and Engineering, National Cheng Kung University, 1 University Road, Tainan, 701, Taiwan.
| | - Jiunn-Der Liao
- Laboratory of Engineered Materials for Biomedical Applications, Department of Materials Science and Engineering, National Cheng Kung University, 1 University Road, Tainan, 701, Taiwan.
| | - Huey-Pin Tsai
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 704, Taiwan; Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Hao Wang
- Laboratory of Engineered Materials for Biomedical Applications, Department of Materials Science and Engineering, National Cheng Kung University, 1 University Road, Tainan, 701, Taiwan.
| | - Jaya Sitjar
- Laboratory of Engineered Materials for Biomedical Applications, Department of Materials Science and Engineering, National Cheng Kung University, 1 University Road, Tainan, 701, Taiwan.
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187
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Duangjan C, Arpawong TE, Spatola BN, Curran SP. Hepatic WDR23 proteostasis mediates insulin homeostasis by regulating insulin-degrading enzyme capacity. GeroScience 2024; 46:4461-4478. [PMID: 38767782 PMCID: PMC11336002 DOI: 10.1007/s11357-024-01196-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/08/2024] [Indexed: 05/22/2024] Open
Abstract
Maintaining insulin homeostasis is critical for cellular and organismal metabolism. In the liver, insulin is degraded by the activity of the insulin-degrading enzyme (IDE). Here, we establish a hepatic regulatory axis for IDE through WDR23-proteostasis. Wdr23KO mice have increased IDE expression, reduced circulating insulin, and defective insulin responses. Genetically engineered human cell models lacking WDR23 also increase IDE expression and display dysregulated phosphorylation of insulin signaling cascade proteins, IRS-1, AKT2, MAPK, FoxO, and mTOR, similar to cells treated with insulin, which can be mitigated by chemical inhibition of IDE. Mechanistically, the cytoprotective transcription factor NRF2, a direct target of WDR23-Cul4 proteostasis, mediates the enhanced transcriptional expression of IDE when WDR23 is ablated. Moreover, an analysis of human genetic variation in WDR23 across a large naturally aging human cohort in the US Health and Retirement Study reveals a significant association of WDR23 with altered hemoglobin A1C (HbA1c) levels in older adults, supporting the use of WDR23 as a new molecular determinant of metabolic health in humans.
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Affiliation(s)
- Chatrawee Duangjan
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Thalida Em Arpawong
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Brett N Spatola
- Dornsife College of Letters, Arts, and Science, University of Southern California, Los Angeles, CA, 90089, USA
| | - Sean P Curran
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA.
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188
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Gamage YI, Wadumesthri Y, Gutiérrez HR, Voronine DV, Pan J. The impact of transmembrane peptides on lipid bilayer structure and mechanics: A study of the transmembrane domain of the influenza A virus M2 protein. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184373. [PMID: 39047857 DOI: 10.1016/j.bbamem.2024.184373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/15/2024] [Accepted: 07/16/2024] [Indexed: 07/27/2024]
Abstract
Transmembrane peptides play important roles in many biological processes by interacting with lipid membranes. This study investigates how the transmembrane domain of the influenza A virus M2 protein, M2TM, affects the structure and mechanics of model lipid bilayers. Atomic force microscopy (AFM) imaging revealed small decreases in bilayer thickness with increasing peptide concentrations. AFM-based force spectroscopy experiments complemented by theoretical model analysis demonstrated significant decreases in bilayer's Young's modulus (E) and lateral area compressibility modulus (KA). This suggests that M2TM disrupts the cohesive interactions between neighboring lipid molecules, leading to a decrease in both the bilayer's resistance to indentation (E) and its ability to resist lateral compression/expansion (KA). The large decreases in bilayer elastic parameters (i.e., E and KA) contrast with small changes in bilayer thickness, implying that bilayer mechanics are not solely dictated by bilayer thickness in the presence of transmembrane peptides. The observed significant reduction in bilayer mechanical properties suggests a softening effect on the bilayer, potentially facilitating membrane curvature generation, a crucial step for M2-mediated viral budding. In parallel, our Raman spectroscopy revealed small but statistically significant changes in hydrocarbon chain vibrational dynamics, indicative of minor disordering in lipid chain conformation. Our findings provide useful insights into the complex interplay between transmembrane peptides and lipid bilayers, highlighting the significance of peptide-lipid interactions in modulating membrane structure, mechanics, and molecular dynamics.
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Affiliation(s)
| | - Yasinthara Wadumesthri
- Department of Physics, University of South Florida, Tampa, FL 33620, United States of America
| | | | - Dmitri V Voronine
- Department of Physics, University of South Florida, Tampa, FL 33620, United States of America
| | - Jianjun Pan
- Department of Physics, University of South Florida, Tampa, FL 33620, United States of America.
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189
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Breimann S, Kamp F, Steiner H, Frishman D. AAontology: An Ontology of Amino Acid Scales for Interpretable Machine Learning. J Mol Biol 2024; 436:168717. [PMID: 39053689 DOI: 10.1016/j.jmb.2024.168717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/15/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]
Abstract
Amino acid scales are crucial for protein prediction tasks, many of them being curated in the AAindex database. Despite various clustering attempts to organize them and to better understand their relationships, these approaches lack the fine-grained classification necessary for satisfactory interpretability in many protein prediction problems. To address this issue, we developed AAontology-a two-level classification for 586 amino acid scales (mainly from AAindex) together with an in-depth analysis of their relations-using bag-of-word-based classification, clustering, and manual refinement over multiple iterations. AAontology organizes physicochemical scales into 8 categories and 67 subcategories, enhancing the interpretability of scale-based machine learning methods in protein bioinformatics. Thereby it enables researchers to gain a deeper biological insight. We anticipate that AAontology will be a building block to link amino acid properties with protein function and dysfunctions as well as aid informed decision-making in mutation analysis or protein drug design.
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Affiliation(s)
- Stephan Breimann
- Department of Bioinformatics, School of Life Sciences, Technical University of Munich, Freising, Germany; Ludwig-Maximilians-University Munich, Biomedical Center, Division of Metabolic Biochemistry, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Frits Kamp
- Ludwig-Maximilians-University Munich, Biomedical Center, Division of Metabolic Biochemistry, Munich, Germany
| | - Harald Steiner
- Ludwig-Maximilians-University Munich, Biomedical Center, Division of Metabolic Biochemistry, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Dmitrij Frishman
- Department of Bioinformatics, School of Life Sciences, Technical University of Munich, Freising, Germany.
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190
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Wu Y, Chen Y, Corner TP, Nakashima Y, Salah E, Li Z, Zhang L, Yang L, Tumber A, Sun Z, Wen Y, Zhong A, Yang F, Li X, Zhang Z, Schofield CJ, Zhang X. A Small-Molecule Inhibitor of Factor Inhibiting HIF Binding to a Tyrosine-Flip Pocket for the Treatment of Obesity. Angew Chem Int Ed Engl 2024; 63:e202410438. [PMID: 38923188 DOI: 10.1002/anie.202410438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 06/24/2024] [Accepted: 06/26/2024] [Indexed: 06/28/2024]
Abstract
In animals, limiting oxygen upregulates the hypoxia-inducible factor (HIF) and promotes a metabolic shift towards glycolysis. Factor inhibiting HIF (FIH) is an asparaginyl hydroxylase that regulates HIF function by reducing its interaction with histone acetyl transferases. HIF levels are negatively regulated by the HIF prolyl hydroxylases (PHDs) which, like FIH, are 2-oxoglutarate (2OG) oxygenases. Genetic loss of FIH promotes both glycolysis and aerobic metabolism. FIH has multiple non-HIF substrates making it challenging to connect its biochemistry with physiology. A structure-mechanism guided approach identified a highly potent in vivo active FIH inhibitor, ZG-2291, the binding of which promotes a conformational flip of a catalytically important tyrosine, enabling the selective inhibition of FIH over other Jumonji C subfamily 2OG oxygenases. Consistent with genetic studies, ZG-2291 promotes thermogenesis and ameliorates symptoms of obesity and metabolic dysfunction in ob/ob mice. The results reveal ZG-2291 as a useful probe for the physiological functions of FIH and identify FIH inhibition as a promising strategy for obesity treatment.
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Affiliation(s)
- Yue Wu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, and Department of Chemistry, China Pharmaceutical University, Nanjing, 211198, China
| | - Yafen Chen
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, and Department of Chemistry, China Pharmaceutical University, Nanjing, 211198, China
| | - Thomas P Corner
- Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Yu Nakashima
- Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
- Present address: Institute of Natural Medicine, University of Toyama, 2630-Sugitani, 930-0194, Toyama, Japan
| | - Eidarus Salah
- Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Zhihong Li
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, and Department of Chemistry, China Pharmaceutical University, Nanjing, 211198, China
| | - Linjian Zhang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, and Department of Chemistry, China Pharmaceutical University, Nanjing, 211198, China
| | - Le Yang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, and Department of Chemistry, China Pharmaceutical University, Nanjing, 211198, China
| | - Anthony Tumber
- Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Zhuoli Sun
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, and Department of Chemistry, China Pharmaceutical University, Nanjing, 211198, China
| | - Yukang Wen
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, and Department of Chemistry, China Pharmaceutical University, Nanjing, 211198, China
| | - Ailin Zhong
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, and Department of Chemistry, China Pharmaceutical University, Nanjing, 211198, China
| | - Fulai Yang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, and Department of Chemistry, China Pharmaceutical University, Nanjing, 211198, China
| | - Xiang Li
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, and Department of Chemistry, China Pharmaceutical University, Nanjing, 211198, China
| | - Zhihong Zhang
- Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Christopher J Schofield
- Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Xiaojin Zhang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, and Department of Chemistry, China Pharmaceutical University, Nanjing, 211198, China
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191
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Xu K, Saaoud F, Shao Y, Lu Y, Yang Q, Jiang X, Wang H, Yang X. A new paradigm in intracellular immunology: Mitochondria emerging as leading immune organelles. Redox Biol 2024; 76:103331. [PMID: 39216270 PMCID: PMC11402145 DOI: 10.1016/j.redox.2024.103331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 08/23/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024] Open
Abstract
Mitochondria, traditionally recognized as cellular 'powerhouses' due to their pivotal role in energy production, have emerged as multifunctional organelles at the intersection of bioenergetics, metabolic signaling, and immunity. However, the understanding of their exact contributions to immunity and inflammation is still developing. This review first introduces the innovative concept of intracellular immunity, emphasizing how mitochondria serve as critical immune signaling hubs. They are instrumental in recognizing and responding to pathogen and danger signals, and in modulating immune responses. We also propose mitochondria as the leading immune organelles, drawing parallels with the broader immune system in their functions of antigen presentation, immune regulation, and immune response. Our comprehensive review explores mitochondrial immune signaling pathways, their therapeutic potential in managing inflammation and chronic diseases, and discusses cutting-edge methodologies for mitochondrial research. Targeting a broad readership of both experts in mitochondrial functions and newcomers to the field, this review sets forth new directions that could transform our understanding of intracellular immunity and the integrated immune functions of intracellular organelles.
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Affiliation(s)
- Keman Xu
- Lemole Center for Integrated Lymphatics and Vascular Research, USA
| | - Fatma Saaoud
- Lemole Center for Integrated Lymphatics and Vascular Research, USA
| | - Ying Shao
- Lemole Center for Integrated Lymphatics and Vascular Research, USA
| | - Yifan Lu
- Lemole Center for Integrated Lymphatics and Vascular Research, USA
| | | | - Xiaohua Jiang
- Lemole Center for Integrated Lymphatics and Vascular Research, USA; Metabolic Disease Research and Thrombosis Research Center, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Hong Wang
- Metabolic Disease Research and Thrombosis Research Center, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Xiaofeng Yang
- Lemole Center for Integrated Lymphatics and Vascular Research, USA; Metabolic Disease Research and Thrombosis Research Center, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA.
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192
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Carminati M, Vecchia L, Stoos L, Thomä NH. Pioneer factors: Emerging rules of engagement for transcription factors on chromatinized DNA. Curr Opin Struct Biol 2024; 88:102875. [PMID: 38991237 DOI: 10.1016/j.sbi.2024.102875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/12/2024] [Accepted: 06/12/2024] [Indexed: 07/13/2024]
Abstract
Pioneering transcription factors (TFs) can drive cell fate changes by binding their DNA motifs in a repressive chromatin environment. Recent structures illustrate emerging rules for nucleosome engagement: TFs distort the nucleosomal DNA to gain access or employ alternative DNA-binding modes with smaller footprints, they preferentially access solvent-exposed motifs near the entry/exit sites, and frequently interact with histones. The extent of TF-histone interactions, in turn, depends on the motif location on the nucleosome, the type of DNA-binding fold, and adjacent domains present. TF-histone interactions can phase TF motifs relative to nucleosomes, and we discuss how these complex and surprisingly diverse interactions between nucleosomes and TFs contribute to function.
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Affiliation(s)
- Manuel Carminati
- Swiss Institute for Experimental Cancer Research (ISREC), EPFL, Lausanne 1015, Switzerland
| | - Luca Vecchia
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel 4058, Switzerland
| | - Lisa Stoos
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel 4058, Switzerland
| | - Nicolas H Thomä
- Swiss Institute for Experimental Cancer Research (ISREC), EPFL, Lausanne 1015, Switzerland; Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel 4058, Switzerland.
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193
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Naim M, Mohammat MF, Mohd Ariff PNA, Uzir MH. Biocatalytic approach for the synthesis of chiral alcohols for the development of pharmaceutical intermediates and other industrial applications: A review. Enzyme Microb Technol 2024; 180:110483. [PMID: 39033578 DOI: 10.1016/j.enzmictec.2024.110483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/27/2024] [Accepted: 07/14/2024] [Indexed: 07/23/2024]
Abstract
Biocatalysis has emerged as a strong tool for the synthesis of active pharmaceutical ingredients (APIs). In the early twentieth century, whole cell biocatalysis was used to develop the first industrial biocatalytic processes, and the precise work of enzymes was unknown. Biocatalysis has evolved over the years into an essential tool for modern, cost-effective, and sustainable pharmaceutical manufacturing. Meanwhile, advances in directed evolution enable the rapid production of process-stable enzymes with broad substrate scope and high selectivity. Large-scale synthetic pathways incorporating biocatalytic critical steps towards >130 APIs of authorized pharmaceuticals and drug prospects are compared in terms of steps, reaction conditions, and scale with the corresponding chemical procedures. This review is designed on the functional group developed during the reaction forming alcohol functional groups. Some important biocatalyst sources, techniques, and challenges are described. A few APIs and their utilization in pharmaceutical drugs are explained here in this review. Biocatalysis has provided shorter, more efficient, and more sustainable alternative pathways toward existing small molecule APIs. Furthermore, non-pharmaceutical applications of biocatalysts are also mentioned and discussed. Finally, this review includes the future outlook and challenges of biocatalysis. In conclusion, Further research and development of promising enzymes are required before they can be used in industry.
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Affiliation(s)
- Mohd Naim
- School of Chemical Engineering, Engineering Campus, Universiti Sains Malaysia, Nibong Tebal, Pulau Pinang 14300, Malaysia.
| | - Mohd Fazli Mohammat
- Centre for Chemical Synthesis & Polymer Technology, Institute of Science (IoS), Kompleks Inspirasi, Universiti Teknologi MARA, Shah Alam, Selangor Darul Ehsan 40450, Malaysia.
| | - Putri Nur Arina Mohd Ariff
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso, Showa-ku, Nagoya 466-8555, Japan.
| | - Mohamad Hekarl Uzir
- School of Chemical Engineering, Engineering Campus, Universiti Sains Malaysia, Nibong Tebal, Pulau Pinang 14300, Malaysia.
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194
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Kang Y, Yeap YJ, Yang J, Ma S, Lim KL, Zhang Q, Lu L, Zhang C. Role of lipid droplets in neurodegenerative diseases: From pathogenesis to therapeutics. Neurosci Biobehav Rev 2024; 165:105867. [PMID: 39208878 DOI: 10.1016/j.neubiorev.2024.105867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 08/19/2024] [Accepted: 08/25/2024] [Indexed: 09/04/2024]
Abstract
Neurodegenerative diseases (NDDs) are a series of disorders characterized by the progressive loss of specific neurons, leading to cognitive and locomotor impairment. NDDs affect millions of patients worldwide but lack effective treatments. Dysregulation of lipids, particularly the accumulation of lipid droplets (LDs), is strongly implicated in the pathogenesis of NDDs. How LDs contribute to the occurrence and development of NDDs, and their potential as therapeutic targets remain to be addressed. In present review, we first introduce the processes of LDs formation, transportation and degradation. We then highlight how the accumulation of LDs contributes to the pathogenesis of NDDs in a cell type-specific manner. Moreover, we discuss currently available methods for detecting LDs and elaborate on LDs-based therapeutic strategies for NDDs. Lastly, we identify gaps that need to be filled to better leverage LD-based theranostics in NDDs and other diseases. We hope this review could shed light on the role of LDs in NDDs and facilitate the development of novel therapeutic strategies for NDDs.
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Affiliation(s)
- Yubing Kang
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan 030000, China
| | - Yee Jie Yeap
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
| | - Jing Yang
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan 030000, China
| | - Sufang Ma
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan 030000, China
| | - Kah Leong Lim
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
| | - Qin Zhang
- Yuncheng Central Hospital, Yuncheng 044020, China.
| | - Li Lu
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan 030000, China; Shanxi Engineering Research Center for Precisive Diagnosis and Treatment of Neurodegenerative Diseases, Jinzhong 030600, China.
| | - Chengwu Zhang
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan 030000, China; Shanxi Engineering Research Center for Precisive Diagnosis and Treatment of Neurodegenerative Diseases, Jinzhong 030600, China.
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195
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Sun J, Liu J, Liu M, Bi X, Huang C. New perspective for pathomechanism and clinical applications of animal toxins: Programmed cell death. Toxicon 2024; 249:108071. [PMID: 39134227 DOI: 10.1016/j.toxicon.2024.108071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 08/03/2024] [Accepted: 08/09/2024] [Indexed: 08/15/2024]
Abstract
Various animal toxins pose a significant threat to human safety, necessitating urgent attention to their treatment and research. The clinical potential of programmed cell death (PCD) is widely regarded as a target for envenomation, given its crucial role in regulating physiological and pathophysiological processes. Current research on animal toxins examines their specific components in pathomechanisms and injuries, as well as their clinical applications. This review explores the relationship between various toxins and several types of PCD, such as apoptosis, necroptosis, autophagy, ferroptosis, and pyroptosis, to provide a reference for future understanding of the pathophysiology of toxins and the development of their potential clinical value.
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Affiliation(s)
- Jiaqi Sun
- Queen Mary School, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Jiahao Liu
- School of Basic Medicine Sciences, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Meiling Liu
- School of Basic Medicine Sciences, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Xiaowen Bi
- School of Basic Medicine Sciences, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China.
| | - Chunhong Huang
- School of Basic Medicine Sciences, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China.
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196
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Shamanaev A, Litvak M, Ivanov I, Srivastava P, Sun MF, Dickeson SK, Kumar S, He TZ, Gailani D. Factor XII Structure-Function Relationships. Semin Thromb Hemost 2024; 50:937-952. [PMID: 37276883 PMCID: PMC10696136 DOI: 10.1055/s-0043-1769509] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Factor XII (FXII), the zymogen of the protease FXIIa, contributes to pathologic processes such as bradykinin-dependent angioedema and thrombosis through its capacity to convert the homologs prekallikrein and factor XI to the proteases plasma kallikrein and factor XIa. FXII activation and FXIIa activity are enhanced when the protein binds to a surface. Here, we review recent work on the structure and enzymology of FXII with an emphasis on how they relate to pathology. FXII is a homolog of pro-hepatocyte growth factor activator (pro-HGFA). We prepared a panel of FXII molecules in which individual domains were replaced with corresponding pro-HGFA domains and tested them in FXII activation and activity assays. When in fluid phase (not surface bound), FXII and prekallikrein undergo reciprocal activation. The FXII heavy chain restricts reciprocal activation, setting limits on the rate of this process. Pro-HGFA replacements for the FXII fibronectin type 2 or kringle domains markedly accelerate reciprocal activation, indicating disruption of the normal regulatory function of the heavy chain. Surface binding also enhances FXII activation and activity. This effect is lost if the FXII first epidermal growth factor (EGF1) domain is replaced with pro-HGFA EGF1. These results suggest that FXII circulates in blood in a "closed" form that is resistant to activation. Intramolecular interactions involving the fibronectin type 2 and kringle domains maintain the closed form. FXII binding to a surface through the EGF1 domain disrupts these interactions, resulting in an open conformation that facilitates FXII activation. These observations have implications for understanding FXII contributions to diseases such as hereditary angioedema and surface-triggered thrombosis, and for developing treatments for thrombo-inflammatory disorders.
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Affiliation(s)
- Aleksandr Shamanaev
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Maxim Litvak
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Ivan Ivanov
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Priyanka Srivastava
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Mao-Fu Sun
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - S. Kent Dickeson
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Sunil Kumar
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Tracey Z. He
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - David Gailani
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
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197
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Stanley P. Genetics of glycosylation in mammalian development and disease. Nat Rev Genet 2024; 25:715-729. [PMID: 38724711 DOI: 10.1038/s41576-024-00725-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2024] [Indexed: 09/19/2024]
Abstract
Glycosylation of proteins and lipids in mammals is essential for embryogenesis and the development of all tissues. Analyses of glycosylation mutants in cultured mammalian cells and model organisms have been key to defining glycosylation pathways and the biological functions of glycans. More recently, applications of genome sequencing have revealed the breadth of rare congenital disorders of glycosylation in humans and the influence of genetics on the synthesis of glycans relevant to infectious diseases, cancer progression and diseases of the immune system. This improved understanding of glycan synthesis and functions is paving the way for advances in the diagnosis and treatment of glycosylation-related diseases, including the development of glycoprotein therapeutics through glycosylation engineering.
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Affiliation(s)
- Pamela Stanley
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA.
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198
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Harla I, Pawluś W, Zarębski M, Dobrucki JW. Induction of DNA single- and double-strand breaks by excited intra- or extracellular green fluorescent protein. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2024; 259:113001. [PMID: 39180910 DOI: 10.1016/j.jphotobiol.2024.113001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 07/28/2024] [Accepted: 07/31/2024] [Indexed: 08/27/2024]
Abstract
Green fluorescent protein (GFP) has opened vast new avenues in studies of live cells and is generally perceived as a benign, nontoxic and harmless fluorescent tag. We demonstrat that excited GFP is capable of inducing substantial DNA damage in cells expressing fusion proteins. In the presence of GFP, even low doses of blue light (12 μJ) induce single strand breaks (SSBs). When the fluorescence of GFP located in the cell nucleus or in the cytoplasm is excited by a much higher dose (17 mJ), DNA double-strand breaks (DSBs) are also induced. Such breaks are induced even when GFP is placed and illuminated in culture medium outside of living cells. We demonstrate that DNA damage is induced by singlet oxygen, which is generated by excited GFP. Although short exposures of live cells to exciting light typically used in fluorescence microscopy induce SSBs but carry little risk of inducing DNA double-strand breaks, larger doses, which may be used in FRAP, FLIM, FCS and super-resolution fluorescence microscopy studies, are capable of inducing not only numerous SSBs but also DSBs.
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Affiliation(s)
- Izabela Harla
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, Kraków, Poland
| | - Weronika Pawluś
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Mirosław Zarębski
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Jurek W Dobrucki
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland.
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199
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Sugiyama T. Finding new roles of classic biomolecular condensates in the nucleus: Lessons from fission yeast. CELL INSIGHT 2024; 3:100194. [PMID: 39228923 PMCID: PMC11369484 DOI: 10.1016/j.cellin.2024.100194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 07/29/2024] [Indexed: 09/05/2024]
Abstract
Decades have passed since the initial discovery of membrane-less nuclear compartments, commonly called nuclear bodies or nuclear condensates. These compartments have drawn attention to their unique characteristics and functions, especially after introducing "liquid-liquid phase separation" to this research field. While the majority of the studies on nuclear condensates have been conducted in multicellular organisms, recent genetic, biochemical, and cell biological analyses using the fission yeast Schizosaccharomyces pombe have yielded valuable insights into biomolecular condensates. This review article focuses on two 'classic' nuclear condensates and discusses how research using fission yeast has unveiled previously unknown functions of these known nuclear bodies.
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Affiliation(s)
- Tomoyasu Sugiyama
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
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200
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Milon TI, Wang Y, Fontenot RL, Khajouie P, Villinger F, Raghavan V, Xu W. Development of a novel representation of drug 3D structures and enhancement of the TSR-based method for probing drug and target interactions. Comput Biol Chem 2024; 112:108117. [PMID: 38852360 PMCID: PMC11390338 DOI: 10.1016/j.compbiolchem.2024.108117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/13/2024] [Accepted: 05/31/2024] [Indexed: 06/11/2024]
Abstract
Understanding the mechanisms underlying interactions between drugs and target proteins is critical for drug discovery. In our earlier studies, we introduced the Triangular Spatial Relationship (TSR)-based algorithm, which enables the representation of a protein's 3D structure as a vector of integers (TSR keys). These TSR keys correspond to substructures of the 3D structure of a protein and are computed based on the triangles constructed by all possible triples of Cα atoms within the protein. In this study, we report on a new TSR-based algorithm for probing drug and target interactions. Specifically, we have extended the previous algorithm in three novel directions: TSR keys for representing the 3D structure of a drug or a ligand, cross TSR keys between drugs and their targets and intra-residual TSR keys for phosphorylated amino acids. The outcomes illustrate the key contributions as follows: (i) The TSR-based method, which uses the TSR keys as features, is unique in its capability to interpret hierarchical relationships of drugs as well as drug - target complexes using common and specific TSR keys. (ii) The method can distinguish not only the binding sites from the rest of the protein structures, but also the binding sites of primary targets from those of off-targets. (iii) The method has the potential to correlate the 3D structures of drugs with their functions. (iv) Representation of 3D structures by TSR keys has its unique advantage in terms of ease of making searching for similar substructures across structure datasets easier. In summary, this study presents a novel computational methodology, with significant advantages, for providing insights into the mechanism underlying drug and target interactions.
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Affiliation(s)
- Tarikul I Milon
- Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA
| | - Yuhong Wang
- National Center for Advancing Translational Sciences, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Ryan L Fontenot
- Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA
| | - Poorya Khajouie
- Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA; The Center for Advanced Computer Studies, University of Louisiana at Lafayette, LA 70504, USA
| | - Francois Villinger
- Department of Biology, University of Louisiana at Lafayette, New Iberia, LA 70560, USA
| | - Vijay Raghavan
- The Center for Advanced Computer Studies, University of Louisiana at Lafayette, LA 70504, USA
| | - Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA.
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