1
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Huang CY, Wang RC, Hsu TS, Hung TN, Shen MY, Chang CH, Wu HC. Developing an E. coli-Based Cell-Free Protein Synthesis System for Artificial Spidroin Production and Characterization. ACS Synth Biol 2025; 14:1829-1842. [PMID: 40256795 PMCID: PMC12090345 DOI: 10.1021/acssynbio.5c00241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2025] [Accepted: 04/14/2025] [Indexed: 04/22/2025]
Abstract
Spider silk spidroins, nature's advanced polymers, have long hampered efficient in vitro production due to their considerable size, repetitive sequences, and aggregation-prone nature. This study harnesses the power of a cell-free protein synthesis (CFPS) system, presenting the first successful in vitro production and detailed characterization of recombinant spider silk major ampullate spidroins (MaSps) utilizing a reformulated and optimizedEscherichia coli based CFPS system. Through systematic optimization, including cell strain engineering via knockout generation, energy sources, crowding agents, and amino acid supplementation, we effectively addressed the specific challenges associated with recombinant spidroin biosynthesis, resulting in high yields of 0.61 mg/mL for MaSp1 (69 kDa) and 0.52 mg/mL for MaSp2 (73 kDa). The synthesized spidroins self-assembled into micelles, facilitating efficient purification compared to in vivo methods, and were further processed into prototype silk fiber products. The functional characterization demonstrated that the purified spidroins maintain essential natural properties, such as phase separation and fiber formation triggered by pH and ions. This tailored CFPS platform also facilitates versatile cosynthesis and serves as an accessible platform for studying the supramolecular coassembly and dynamic interactions among spidroins. This CFPS platform offers a viable alternative to conventional in vivo methods, facilitating innovative approaches for silk protein engineering and biomaterial development in a high-throughput, efficient manner.
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Affiliation(s)
- Chang-Yen Huang
- Department of Biochemical
Science and Technology, National Taiwan
University, No. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
(ROC)
| | - Ruei-Chi Wang
- Department of Biochemical
Science and Technology, National Taiwan
University, No. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
(ROC)
| | - Tzy-Shyuan Hsu
- Department of Biochemical
Science and Technology, National Taiwan
University, No. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
(ROC)
| | - Tzu-Ning Hung
- Department of Biochemical
Science and Technology, National Taiwan
University, No. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
(ROC)
| | - Ming-Yan Shen
- Department of Biochemical
Science and Technology, National Taiwan
University, No. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
(ROC)
| | - Chung-Heng Chang
- Department of Biochemical
Science and Technology, National Taiwan
University, No. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
(ROC)
| | - Hsuan-Chen Wu
- Department of Biochemical
Science and Technology, National Taiwan
University, No. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
(ROC)
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2
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Yi S, Kim E, Yang S, Kim G, Bae D, Son S, Jeong B, Ji JS, Lee HH, Hahn J, Cha S, Yoon YJ, Lee NK. Direct Quantification of Protein-Protein Interactions in Living Bacterial Cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025; 12:e2414777. [PMID: 40125621 PMCID: PMC12097012 DOI: 10.1002/advs.202414777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2024] [Revised: 02/26/2025] [Indexed: 03/25/2025]
Abstract
Quantitative measurement of protein-protein interactions (PPIs) within living cells is vital for understanding their cellular functions at the molecular level and for applications in synthetic biology, protein engineering, and drug discovery. Although several techniques have been developed to measure PPI strength in vitro, direct measurement of PPI strength within living bacterial cells remains challenging. Here, a method for quantitatively measuring PPIs by determining the dissociation constant (Kd) in living E. coli using fluorescence resonance energy transfer (FRET), a technique termed KD-FRET, is reported. It is found that the direct excitation of the acceptor fluorophore among spectral crosstalks primarily results in non-interacting pairs exhibiting an apparent Kd, leading to false-positive signals. KD-FRET proves highly effective in quantifying various PPI Kd values, including both heterologous and homologous pairs. Moreover, KD-FRET enables the quantification of Kd for interaction pairs that are unmeasurable in vitro owing to their instability under standard buffer conditions. KD-FRET is successfully applied in the development of a novel synthetic biology tool to enhance naringenin production in E. coli and lycopene production in S. cerevisiae by precisely engineering metabolic pathway. These results demonstrate the potential of KD-FRET as a powerful tool for studying PPIs in their native cellular environments.
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Affiliation(s)
- Soojung Yi
- Department of ChemistrySeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Republic of Korea
| | - Eunji Kim
- Natural Products Research InstituteCollege of PharmacySeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Republic of Korea
| | - Sora Yang
- Department of ChemistrySeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Republic of Korea
| | - Gyeongmin Kim
- Department of Chemical and Biological EngineeringInstitute of Chemical ProcessesSeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Republic of Korea
| | - Da‐Woon Bae
- Department of Chemistry and NanoscienceEwha Womans University52 Ewhayeodae‐gil, Seodaemun‐guSeoul03760Republic of Korea
| | - Se‐Young Son
- Department of Chemistry and NanoscienceEwha Womans University52 Ewhayeodae‐gil, Seodaemun‐guSeoul03760Republic of Korea
| | - Bo‐Gyeong Jeong
- Department of Chemistry and NanoscienceEwha Womans University52 Ewhayeodae‐gil, Seodaemun‐guSeoul03760Republic of Korea
| | - Jeong Seok Ji
- Department of ChemistrySeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Republic of Korea
| | - Hyung Ho Lee
- Department of ChemistrySeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Republic of Korea
| | - Ji‐Sook Hahn
- Department of Chemical and Biological EngineeringInstitute of Chemical ProcessesSeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Republic of Korea
| | - Sun‐Shin Cha
- Department of Chemistry and NanoscienceEwha Womans University52 Ewhayeodae‐gil, Seodaemun‐guSeoul03760Republic of Korea
| | - Yeo Joon Yoon
- Natural Products Research InstituteCollege of PharmacySeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Republic of Korea
| | - Nam Ki Lee
- Department of ChemistrySeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Republic of Korea
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3
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Dong J, Cao H, Yang Z, Zhang Z, Yang Z, Jiang L, Wei J. Boosting Reaction Kinetics with Viscous Nanowire Dispersions. J Am Chem Soc 2025; 147:14614-14624. [PMID: 40259879 DOI: 10.1021/jacs.5c02034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2025]
Abstract
Higher viscosity typically slows chemical reactions by restricting molecular movement, while stirring accelerates reactions by enhancing reactant diffusion and collisions. However, in this study, we reveal that reaction rates in nanowire dispersions─with microscopic viscosity ∼300 times that of decane, can be enhanced by over an order of magnitude. Counterintuitively, stirring slows the reaction with higher stirring rates causing even greater deceleration. This phenomenon is observed in both photo- and thermally activated cyclic reactions. Molecular dynamics simulations and confocal laser scanning microscopy suggest that aliphatic chains grafted onto nanowires interact with anisotropic molecules, increasing their local concentrations near the nanowires. Notably, azobenzene photoisomerization is completely inhibited in the nanowire dispersion, despite completing within 30 s in the absence of nanowires. We propose that the aliphatic chains align reactive molecules directionally, while the confined space prevents bulky cis-isomer formation. These findings show that nanowires not only harvest and orient reactive molecules but also exclude bulky products, significantly enhancing the reaction kinetics in confined systems.
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Affiliation(s)
- Jurong Dong
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, P. R. China
| | - Hongkun Cao
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, South China University of Technology, Guangzhou 510640, China
| | - Zhiwei Yang
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, P. R. China
| | - Zongze Zhang
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, P. R. China
| | - Zhijie Yang
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, P. R. China
| | - Lingxiang Jiang
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, South China University of Technology, Guangzhou 510640, China
| | - Jingjing Wei
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, P. R. China
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4
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König B, Pezzotti S, Schwaab G, Havenith M. Tuning biological processes via co-solutes: from single proteins to protein condensates - the case of α-elastin condensation. Chem Sci 2025; 16:5897-5906. [PMID: 40060092 PMCID: PMC11883817 DOI: 10.1039/d4sc07335e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2024] [Accepted: 02/22/2025] [Indexed: 04/04/2025] Open
Abstract
Protein condensates as membrane-less compartments play a pivotal role in cellular processes. The stabilization of protein condensation can be tuned using cosolutes which directly impact biological function. In this study, we report the result of a rigorous study of the influence of cosolutes changes on hydration entropy and enthalpy upon condensate formation, by means of THz-calorimetry. Our results unveil quantitative insights into the fine tuning of the free energy imbalance, via hydrophobic/entropic and hydrophilic/enthalpic hydration which can result in cosolute-mediated stabilization or destabilization of protein condensates. These results shed new light on the regulatory potential of co-solutes within cells, to tune Liquid-Liquid Phase Separation (LLPS). Furthermore, we demonstrate the transferability of the underlying molecular concepts of cosolute addition to two fundamental biological processes: protein folding and denaturation. This study provides a blueprint for controlled modulating LLPS via cosolute additions, with promising implications in both biological and medical applications.
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Affiliation(s)
- B König
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum Bochum 44780 Germany
| | - S Pezzotti
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum Bochum 44780 Germany
| | - G Schwaab
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum Bochum 44780 Germany
| | - M Havenith
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum Bochum 44780 Germany
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5
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Tokunou Y, Yamazaki T, Fujikawa T, Okamoto A. Decoding in-cell respiratory enzyme dynamics by label-free in situ electrochemistry. Proc Natl Acad Sci U S A 2025; 122:e2418926122. [PMID: 40117313 PMCID: PMC11962448 DOI: 10.1073/pnas.2418926122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2024] [Accepted: 02/07/2025] [Indexed: 03/23/2025] Open
Abstract
Deciphering metabolic enzyme catalysis in living cells remains a formidable challenge due to the limitations of in vivo assays, which focus on enzymes isolated from respiration. This study introduces an innovative whole-cell electrochemical assay to reveal the Michaelis-Menten landscape of respiratory enzymes amid complex molecular interactions. We controlled the microbial current generation's rate-limiting step, extracting in vivo kinetic parameters (Km, Ki, and kcat) for the periplasmic nitrite (NrfA) and fumarate (FccA) reductases. Notably, while NrfA kinetics mirrored those of its purified form, FccA exhibited unique kinetic behavior. Further exploration using a mutant strain lacking CymA, a periplasmic hub protein, revealed its crucial role in modulating FccA's kinetics, challenging the prevailing view that molecular crowding is the main cause of discrepancies between in vivo and in vitro enzyme kinetics. This platform offers a groundbreaking approach to studying cellular respiratory enzymatic kinetics, paving the way for future research in bioenergetics and medicine.
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Affiliation(s)
- Yoshihide Tokunou
- Department of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki305-8572, Japan
- Research Center for Macromolecules and Biomaterials, National Institute for Materials Science, Tsukuba, Ibaraki305-0047, Japan
| | - Tomohiko Yamazaki
- Research Center for Macromolecules and Biomaterials, National Institute for Materials Science, Tsukuba, Ibaraki305-0047, Japan
- School of Life Science, Hokkaido University, Sapporo, Hokkaido060-0808, Japan
| | - Takashi Fujikawa
- Research Center for Macromolecules and Biomaterials, National Institute for Materials Science, Tsukuba, Ibaraki305-0047, Japan
| | - Akihiro Okamoto
- Department of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki305-8572, Japan
- Research Center for Macromolecules and Biomaterials, National Institute for Materials Science, Tsukuba, Ibaraki305-0047, Japan
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, Tsukuba, Ibaraki305-0044, Japan
- School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido060-8628, Japan
- Research Center for Autonomous Systems Materialogy, Institute of Integrated Research, Institute of Science Tokyo (Science Tokyo), Yokohama, Kanagawa226-8503, Japan
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6
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Kaur J, Jain R, Roychowdhury S, Roy R, Chattopadhyay K, Roy I. Influence of Magnesium Ions and Crowding Agents on Structure and Stability of RNA Aptamers. Biochemistry 2025; 64:1233-1243. [PMID: 39791862 DOI: 10.1021/acs.biochem.4c00468] [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: 01/12/2025]
Abstract
Aptamers bind to their targets with exceptional affinity and specificity. However, their intracellular application is hampered by the lack of knowledge about the effect of the cellular milieu on the RNA structure/stability. In this study, cellular crowding was mimicked using polyethylene glycol (PEG), and the crucial role of Mg2+ ions in stabilizing the structure of an RNA aptamer was investigated. Increasing the concentration of Mg2+ or PEG increased the thermal stability of the aptamer. The crowding effect lowered the requirement of the Mg2+ ion to form the binding-competent conformer of the aptamer. This suggests that crowding and other factors may compensate for a lower concentration of Mg2+ for proper folding of aptamers inside cells. Selective 2'-hydroxyl acylation and primer extension (SHAPE) probing permitted residue-level analysis of the aptamer. Mg2+ and/or PEG were shown to be involved in increasing the rigidity or flexibility of different regions of the aptamer. Fluorescence correlation spectroscopy showed a significantly low hydrodynamic radius (RH) in the presence of molecular crowders and Mg2+ ions. We believe that the decreased water activity due to crowding may be responsible for reduced RH. Our results show that in a crowded environment, the RNA aptamer was exposed to conformers that were not available to it in simple buffer solutions or solely in the presence of lower concentrations of Mg2+.
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Affiliation(s)
- Jaskirat Kaur
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar 160062, Punjab, India
| | - Rajeev Jain
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700 032, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre, (CSIR-HRDC) Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad 201002, Uttar Pradesh, India
| | - Sumangal Roychowdhury
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700 032, India
| | - Rajanya Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar 160062, Punjab, India
| | - Krishnananda Chattopadhyay
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700 032, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre, (CSIR-HRDC) Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad 201002, Uttar Pradesh, India
| | - Ipsita Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar 160062, Punjab, India
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7
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Shabnam, Bhat R. Flavones Suppress Aggregation and Amyloid Fibril Formation of Human Lysozyme under Macromolecular Crowding Conditions. Biochemistry 2024; 63:3194-3212. [PMID: 39385522 DOI: 10.1021/acs.biochem.4c00362] [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: 10/12/2024]
Abstract
The crowded milieu of a biological cell significantly impacts protein aggregation and interactions. Understanding the effects of macromolecular crowding on the aggregation and fibrillation of amyloidogenic proteins is crucial for the treatment of many amyloid-related disorders. Most in vitro studies of protein amyloid formation and its inhibition by small molecules are conducted in dilute buffers, which do not mimic the complexity of the cellular environment. In this study, we used PEGs to simulate macromolecular crowding and examined the inhibitory effects of flavones DHF, baicalein, and luteolin on human lysozyme (HuL) aggregation at pH 2. Naturally occurring flavones have been effective inhibitors of amyloid formation in some proteins. Our findings indicate that while flavones inhibit HuL aggregation and fibrillation in dilute buffer solutions, complete inhibition is observed with a combination of flavones and PEGs, as shown by ThT fluorescence, light scattering, TEM, and AFM studies. The species formed in the presence of PEG 8000 and flavones were less hydrophobic, less toxic, and α-helix-rich compared to control samples, which were hydrophobic and β-sheet-rich, as demonstrated by ANS hydrophobicity, MTT assay, and CD spectroscopy. Fluorescence titration studies of flavones with HuL showed a significant increase in binding constant values under crowding conditions. These findings highlight the importance of macromolecular crowding in modulating protein aggregation and amyloid inhibition. Further studies using disease-causing mutants of HuL and other amyloidogenic proteins are needed to explore the role of macromolecular crowding in small-molecule-mediated modulation and inhibition of protein aggregation and amyloid formation.
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Affiliation(s)
- Shabnam
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 100067, India
| | - Rajiv Bhat
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 100067, India
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8
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Rivas G, Minton AP. Surfaces as frameworks for intracellular organization. Trends Biochem Sci 2024; 49:942-954. [PMID: 39375067 DOI: 10.1016/j.tibs.2024.07.007] [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: 03/25/2024] [Revised: 07/23/2024] [Accepted: 07/31/2024] [Indexed: 10/09/2024]
Abstract
A large fraction of soluble protein within the interior of living cells may reversibly associate with structural elements, including proteinaceous fibers and phospholipid membranes. In this opinion, we present theoretical and experimental evidence that many of these associations are due to nonspecific attraction between the protein and the surface of the fiber or membrane, and that such associations may lead to substantial changes in the association state of the adsorbed proteins, the biological function of the adsorbed proteins, and the distribution of these proteins between the many microenvironments existing within the cell.
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Affiliation(s)
- Germán Rivas
- CIB Margarita Salas - Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.
| | - Allen P Minton
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
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9
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Dhillon N, Kamakaka RT. Transcriptional silencing in Saccharomyces cerevisiae: known unknowns. Epigenetics Chromatin 2024; 17:28. [PMID: 39272151 PMCID: PMC11401328 DOI: 10.1186/s13072-024-00553-7] [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: 07/02/2024] [Accepted: 09/02/2024] [Indexed: 09/15/2024] Open
Abstract
Transcriptional silencing in Saccharomyces cerevisiae is a persistent and highly stable form of gene repression. It involves DNA silencers and repressor proteins that bind nucleosomes. The silenced state is influenced by numerous factors including the concentration of repressors, nature of activators, architecture of regulatory elements, modifying enzymes and the dynamics of chromatin.Silencers function to increase the residence time of repressor Sir proteins at silenced domains while clustering of silenced domains enables increased concentrations of repressors and helps facilitate long-range interactions. The presence of an accessible NDR at the regulatory regions of silenced genes, the cycling of chromatin configurations at regulatory sites, the mobility of Sir proteins, and the non-uniform distribution of the Sir proteins across the silenced domain, all result in silenced chromatin that only stably silences weak promoters and enhancers via changes in transcription burst duration and frequency.These data collectively suggest that silencing is probabilistic and the robustness of silencing is achieved through sub-optimization of many different nodes of action such that a stable expression state is generated and maintained even though individual constituents are in constant flux.
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Affiliation(s)
- Namrita Dhillon
- Department of Biomolecular Engineering, University of California, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Rohinton T Kamakaka
- Department of MCD Biology, University of California, 1156 High Street, Santa Cruz, CA, 95064, USA.
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10
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Burke MJ, Batista VS, Davis CM. Similarity Metrics for Subcellular Analysis of FRET Microscopy Videos. J Phys Chem B 2024; 128:8344-8354. [PMID: 39186078 DOI: 10.1021/acs.jpcb.4c02859] [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: 08/27/2024]
Abstract
Understanding the heterogeneity of molecular environments within cells is an outstanding challenge of great fundamental and technological interest. Cells are organized into specialized compartments, each with distinct functions. These compartments exhibit dynamic heterogeneity under high-resolution microscopy, which reflects fluctuations in molecular populations, concentrations, and spatial distributions. To enhance our comprehension of the spatial relationships among molecules within cells, it is crucial to analyze images of high-resolution microscopy by clustering individual pixels according to their visible spatial properties and their temporal evolution. Here, we evaluate the effectiveness of similarity metrics based on their ability to facilitate fast and accurate data analysis in time and space. We discuss the capability of these metrics to differentiate subcellular localization, kinetics, and structures of protein-RNA interactions in Forster resonance energy transfer (FRET) microscopy videos, illustrated by a practical example from recent literature. Our results suggest that using the correlation similarity metric to cluster pixels of high-resolution microscopy data should improve the analysis of high-dimensional microscopy data in a wide range of applications.
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Affiliation(s)
- Michael J Burke
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Caitlin M Davis
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
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11
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Yasuda T, Morita R, Shigeta Y, Harada R. Ribosome Tunnel Environment Drives the Formation of α-Helix during Cotranslational Folding. J Chem Inf Model 2024; 64:6610-6622. [PMID: 39150098 PMCID: PMC11351022 DOI: 10.1021/acs.jcim.4c00901] [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: 05/24/2024] [Revised: 07/09/2024] [Accepted: 08/06/2024] [Indexed: 08/17/2024]
Abstract
Protein conformations in cells are not solely determined by amino acid sequences; they also depend on cellular environments. For instance, the ribosome tunnel induces its specific α-helix formation during cotranslational folding. Owing to the link between these temporally α-helix and biological functions, the mechanism of α-helix formation inside the ribosome tunnel has been previously explored. Consequently, the conformational restrictions of the tunnel were considered one of the driving forces of α-helix formation. Conversely, the ribosomal tunnel environment, including its chemical properties, appears to influence the α-helix formation. However, a comprehensive analysis of the ribosome tunnel environment's impact on the α-helix formation has not been conducted yet due to challenges in experimentally controlling it. Therefore, as a new computational approach, we proposed a ribosome environment-mimicking model (REMM) based on the radius and components of the experimentally determined ribosome tunnel structures. Using REMM, we assessed the impact of the ribosome tunnel environment on α-helix formation. Herein, we employed carbon nanotubes (CNT) as a reference model alongside REMM because CNT reproduce conformational restrictions rather than the ribosome tunnel environment. Quantitatively, the ability to reproduce the α-helix of nascent peptides in the experimental structure was compared between the CNT and REMM using enhanced all-atom molecular dynamics simulations. Consequently, the REMM more accurately reproduced the α-helix of the nascent peptides than the CNT, highlighting the significance of the ribosome tunnel environment in α-helix formation. Additionally, we analyzed the properties of the peptide inside each model to reveal the mechanism of ribosome tunnel-specific α-helix formation. Consequently, we revealed that the chemical diversities of the tunnel are essential for the formation of backbone-to-backbone hydrogen bonds in the peptides. In conclusion, the ribosome tunnel environment, with the diverse chemical properties, drives its specific α-helix formation. By proposing REMM, we newly provide the technical basis for investigating the protein conformations in various cellular environments.
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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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12
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Mukherjee P, Mazumder A. Macromolecular crowding has opposite effects on two critical sub-steps of transcription initiation. FEBS Lett 2024; 598:1022-1033. [PMID: 38479985 PMCID: PMC7615953 DOI: 10.1002/1873-3468.14851] [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: 12/23/2023] [Revised: 02/12/2024] [Accepted: 02/19/2024] [Indexed: 04/12/2024]
Abstract
Transcription initiation, the first step in gene expression, has been studied extensively in dilute buffer, a condition which fails to consider the crowded environment in live cells. Recent reports indicate the kinetics of promoter escape is altered in crowded conditions for a consensus bacterial promoter. Here, we use a real-time fluorescence enhancement assay to study the kinetics of unwound bubble formation and promoter escape for three separate promoters. We find that the effect of crowding on transcription initiation is complex, with lower rates of unwound bubble formation, higher rates of promoter escape, and large variations depending on promoter identity. Based on our results, we suggest that altered conditions of crowding inside a live cell can trigger global changes.
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Affiliation(s)
- Pratip Mukherjee
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre, Ghaziabad, India
| | - Abhishek Mazumder
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
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13
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Ghassemi Z, Leach JB. Impact of Confinement within a Hydrogel Mesh on Protein Thermodynamic Stability and Aggregation Kinetics. Mol Pharm 2024; 21:1137-1148. [PMID: 38277273 DOI: 10.1021/acs.molpharmaceut.3c00677] [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] [Indexed: 01/28/2024]
Abstract
Though protein stability and aggregation have been well characterized in dilute solutions, the influence of a confining environment that exists (e.g., in intercellular and tissue spaces and therapeutic formulations) on the protein structure is largely unknown. Herein, the effects of confinement on stability and aggregation were explored for proteins of different sizes, stability, and hydrophobicity when encapsulated in hydrophilic poly(ethylene glycol) hydrogels. Denaturation curves show linear correlations between confinement size (mesh size) and thermodynamic stability, i.e., unfolding free energy and surface area accessible for solvation (represented by m-value). Two clusters of protein types are identifiable from these correlations; the clusters are defined by differences in protein stability, surface area, and aggregation propensity. Proteins with higher stability, larger surface area, and lower aggregation propensity (e.g., lysozyme and myoglobin) are less affected by the confinement imposed by mesh size than proteins with lower stability, smaller surface area, and higher aggregation propensity (e.g., growth hormone and aldehyde dehydrogenase). According to aggregation kinetics measured by thioflavin T fluorescence, confinement in smaller mesh sizes resulted in slower aggregation rates than that in larger mesh sizes. Compared to that in buffer solution, the confinement of a hydrophobic protein (e.g., human insulin) in the hydrogels accelerates protein aggregation. Conversely, the confinement of a hydrophilic protein (e.g., human amylin) in the hydrogels decelerates or prevents aggregation, with the rates of aggregation inversely proportional to mesh size. These findings provide new insights into protein conformational stability in confined microenvironments relevant to various cellular, tissue, and therapeutics scenarios.
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Affiliation(s)
- Zahra Ghassemi
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County, ECS 314, 1000 Hilltop Circle, Baltimore, Maryland 21250, United States
| | - Jennie B Leach
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County, ECS 314, 1000 Hilltop Circle, Baltimore, Maryland 21250, United States
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14
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Cantero M, Rodríguez-Espinosa MJ, Strobl K, Ibáñez P, Díez-Martínez A, Martín-González N, Jiménez-Zaragoza M, Ortega-Esteban A, de Pablo PJ. Atomic Force Microscopy of Viruses: Stability, Disassembly, and Genome Release. Methods Mol Biol 2024; 2694:317-338. [PMID: 37824011 DOI: 10.1007/978-1-0716-3377-9_15] [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] [Indexed: 10/13/2023]
Abstract
In atomic force microscopy (AFM), the probe is a nanometric tip located at the end of a microcantilever which palpates the specimen under study as a blind person manages a walking stick. In this way, AFM allows obtaining nanometric resolution images of individual protein shells, such as viruses, in liquid milieu. Beyond imaging, AFM also enables not only the manipulation of single protein cages but also the evaluation of each physicochemical property which is able of inducing any measurable mechanical perturbation to the microcantilever that holds the tip. In this chapter, we start revising some recipes for adsorbing protein shells on surfaces and how the geometrical dilation of tips can affect to the AFM topographies. This work also deals with the abilities of AFM to monitor TGEV coronavirus under changing conditions of the liquid environment. Subsequently, we describe several AFM approaches to study cargo release, aging, and multilayered viruses with single indentation and fatigue assays. Finally, we comment on a combined AFM/fluorescence application to study the influence of crowding on GFP packed within individual P22 bacteriophage capsids.
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Affiliation(s)
- Miguel Cantero
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain
| | - María Jesús Rodríguez-Espinosa
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Klara Strobl
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain
| | - Pablo Ibáñez
- Department of Theoretical Physics of Condensed Matter, Universidad Autónoma de Madrid, Madrid, Spain
| | - Alejandro Díez-Martínez
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Manuel Jiménez-Zaragoza
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain
| | - Alvaro Ortega-Esteban
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain
| | - Pedro José de Pablo
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain.
- Solid Condensed Matter Institute IFIMAC, Universidad Autónoma de Madrid, Madrid, Spain.
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15
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Baverstock K. The Gene: An appraisal. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 186:e73-e88. [PMID: 38044248 DOI: 10.1016/j.pbiomolbio.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The gene can be described as the foundational concept of modern biology. As such, it has spilled over into daily discourse, yet it is acknowledged among biologists to be ill-defined. Here, following a short history of the gene, I analyse critically its role in inheritance, evolution, development, and morphogenesis. Wilhelm Johannsen's genotype-conception, formulated in 1910, has been adopted as the foundation stone of genetics, giving the gene a higher degree of prominence than is justified by the evidence. An analysis of the results of the Long-Term Evolution Experiment (LTEE) with E. coli bacteria, grown over 60,000 generations, does not support spontaneous gene mutation as the source of variance for natural selection. From this it follows that the gene is not Mendel's unit of inheritance: that must be Johannsen's transmission-conception at the gamete phenotype level, a form of inheritance that Johannsen did not consider. Alternatively, I contend that biology viewed on the bases of thermodynamics, complex system dynamics, and self-organisation, provides a new framework for the foundations of biology. In this framework, the gene plays a passive role as a vital information store: it is the phenotype that plays the active role in inheritance, evolution, development, and morphogenesis.
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Affiliation(s)
- Keith Baverstock
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio Campus, Kuopio, Finland.
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16
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Atia L, Fredberg JJ. A life off the beaten track in biomechanics: Imperfect elasticity, cytoskeletal glassiness, and epithelial unjamming. BIOPHYSICS REVIEWS 2023; 4:041304. [PMID: 38156333 PMCID: PMC10751956 DOI: 10.1063/5.0179719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/17/2023] [Indexed: 12/30/2023]
Abstract
Textbook descriptions of elasticity, viscosity, and viscoelasticity fail to account for certain mechanical behaviors that typify soft living matter. Here, we consider three examples. First, strong empirical evidence suggests that within lung parenchymal tissues, the frictional stresses expressed at the microscale are fundamentally not of viscous origin. Second, the cytoskeleton (CSK) of the airway smooth muscle cell, as well as that of all eukaryotic cells, is more solid-like than fluid-like, yet its elastic modulus is softer than the softest of soft rubbers by a factor of 104-105. Moreover, the eukaryotic CSK expresses power law rheology, innate malleability, and fluidization when sheared. For these reasons, taken together, the CSK of the living eukaryotic cell is reminiscent of the class of materials called soft glasses, thus likening it to inert materials such as clays, pastes slurries, emulsions, and foams. Third, the cellular collective comprising a confluent epithelial layer can become solid-like and jammed, fluid-like and unjammed, or something in between. Esoteric though each may seem, these discoveries are consequential insofar as they impact our understanding of bronchospasm and wound healing as well as cancer cell invasion and embryonic development. Moreover, there are reasons to suspect that certain of these phenomena first arose in the early protist as a result of evolutionary pressures exerted by the primordial microenvironment. We have hypothesized, further, that each then became passed down virtually unchanged to the present day as a conserved core process. These topics are addressed here not only because they are interesting but also because they track the journey of one laboratory along a path less traveled by.
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Affiliation(s)
- Lior Atia
- Ben Gurion University of the Negev, Beer Sheva, Israel
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17
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Socas LBP, Ambroggio EE. Linking surface tension to water polarization with a new hypothesis: The Ling-Damodaran Isotherm. Colloids Surf B Biointerfaces 2023; 230:113515. [PMID: 37634284 DOI: 10.1016/j.colsurfb.2023.113515] [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: 07/04/2023] [Revised: 08/08/2023] [Accepted: 08/11/2023] [Indexed: 08/29/2023]
Abstract
Studying aqueous solutions of complex (bio)polymers is essential from both theoretical and practical perspectives. To understand the principles that govern the properties of these solutions is pivotal for the study of biological processes, considering that the most distinguished components of the cells are polymers (proteins, nucleic acids). These macromolecular aqueous systems, known as colloids, has raise the interest of scientists in recent years. It is known that several physicochemical properties deviate from ideal behaviour in this kind of solutions and that the physical state of water is different compared to its pure state. Particularly, the surface tension of such mixtures often shows a peculiar profile at semi-dilute and concentrated conditions. Here, we joined the colloidal concept of water polarization (proposed in the Association-Induction Hypothesis) with Damodaran's formalism for surface tension to theoretically derive a compelling mathematical model that explains the behaviour of polymer solutions. We measured the surface tension and osmolarity of different polyethylene oxide solutions and we used the ACDAN fluorescence probe to assess the water dipolar relaxation (polarization) in these mixtures. As a proof of concept, we also studied the influence of these polymer solutions on lipid interfaces. Our isotherm model explains the experimental observations with a unifying view that correlates with other measured properties, such as osmolarity and water dipolar relaxation. This provides a link between interfacial and bulk physicochemical properties of polymer solutions, also giving a new framework for studying the interaction of colloidal systems with lipid membranes interfaces.
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Affiliation(s)
- L B P Socas
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Biológica-Ranwel Caputto, Haya de la Torre y Medina Allende s/n, Córdoba X5000HUA, Argentina; CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Haya de la Torre y Medina Allende s/n, Córdoba X5000HUA, Argentina.
| | - E E Ambroggio
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Biológica-Ranwel Caputto, Haya de la Torre y Medina Allende s/n, Córdoba X5000HUA, Argentina; CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Haya de la Torre y Medina Allende s/n, Córdoba X5000HUA, Argentina.
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18
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Maiuolo J, Costanzo P, Masullo M, D’Errico A, Nasso R, Bonacci S, Mollace V, Oliverio M, Arcone R. Hydroxytyrosol-Donepezil Hybrids Play a Protective Role in an In Vitro Induced Alzheimer's Disease Model and in Neuronal Differentiated Human SH-SY5Y Neuroblastoma Cells. Int J Mol Sci 2023; 24:13461. [PMID: 37686262 PMCID: PMC10488223 DOI: 10.3390/ijms241713461] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative pathology among progressive dementias, and it is characterized by the accumulation in the brain of extracellular aggregates of beta-amyloid proteins and neurofibrillary intracellular tangles consisting of τ-hyperphosphorylated proteins. Under normal conditions, beta-amyloid peptides exert important trophic and antioxidant roles, while their massive presence leads to a cascade of events culminating in the onset of AD. The fibrils of beta-amyloid proteins are formed by the process of fibrillogenesis that, starting from individual monomers of beta-amyloid, can generate polymers of this protein, constituting the hypothesis of the "amyloid cascade". To date, due to the lack of pharmacological treatment for AD without toxic side effects, chemical research is directed towards the realization of hybrid compounds that can act as an adjuvant in the treatment of this neurodegenerative pathology. The hybrid compounds used in this work include moieties of a hydroxytyrosol, a nitrohydroxytyrosol, a tyrosol, and a homovanillyl alcohol bound to the N-benzylpiperidine moiety of donepezil, the main drug used in AD. Previous experiments have shown different properties of these hybrids, including low toxicity and antioxidant and chelating activities. The purpose of this work was to test the effects of hybrid compounds mixed with Aβ1-40 to induce fibrillogenesis and mimic AD pathogenesis. This condition has been studied both in test tubes and by an in vitro model of neuronal differentiated human SH-SY5Y neuroblastoma cells. The results obtained from test tube experiments showed that some hybrids inhibit the activity of the enzymes AChE, BuChE, and BACE-1. Cell experiments suggested that hybrids could inhibit fibrillogenesis, negatively modulating caspase-3. They were also shown to exert antioxidant effects, and the acetylated hybrids were found to be more functional and efficient than nonacetylated forms.
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Affiliation(s)
- Jessica Maiuolo
- Department of Health Science, Institute of Research for Food Safety & Health (IRC-FSH), University Magna Græcia of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Paola Costanzo
- Department of Chemistry and Chemical Technologies, University of Calabria, Via P. Bucci, Cubo 12C, 87036 Rende, Italy
| | - Mariorosario Masullo
- Department of Movement Science and Well-Being, University “Parthenope” of Naples, Via Medina, 40, 80133 Napoli, Italy; (M.M.); (R.A.)
| | - Antonio D’Errico
- Department of Movement Science and Well-Being, University “Parthenope” of Naples, Via Medina, 40, 80133 Napoli, Italy; (M.M.); (R.A.)
| | - Rosarita Nasso
- Department of Movement Science and Well-Being, University “Parthenope” of Naples, Via Medina, 40, 80133 Napoli, Italy; (M.M.); (R.A.)
| | - Sonia Bonacci
- Department of Health Sciences, University Magna Græcia of Catanzaro, Viale Europa, 88100 Catanzaro, Italy (M.O.)
| | - Vincenzo Mollace
- Department of Health Science, Institute of Research for Food Safety & Health (IRC-FSH), University Magna Græcia of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Manuela Oliverio
- Department of Health Sciences, University Magna Græcia of Catanzaro, Viale Europa, 88100 Catanzaro, Italy (M.O.)
| | - Rosaria Arcone
- Department of Movement Science and Well-Being, University “Parthenope” of Naples, Via Medina, 40, 80133 Napoli, Italy; (M.M.); (R.A.)
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19
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Burkhart JG, Wu G, Song X, Raimondi F, McWeeney S, Wong MH, Deng Y. Biology-inspired graph neural network encodes reactome and reveals biochemical reactions of disease. PATTERNS (NEW YORK, N.Y.) 2023; 4:100758. [PMID: 37521042 PMCID: PMC10382942 DOI: 10.1016/j.patter.2023.100758] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/20/2022] [Accepted: 05/01/2023] [Indexed: 08/01/2023]
Abstract
Functional heterogeneity of healthy human tissues complicates interpretation of molecular studies, impeding precision therapeutic target identification and treatment. Considering this, we generated a graph neural network with Reactome-based architecture and trained it using 9,115 samples from Genotype-Tissue Expression (GTEx). Our graph neural network (GNN) achieves adjusted Rand index (ARI) = 0.7909, while a Resnet18 control model achieves ARI = 0.7781, on 370 held-out healthy human tissue samples from The Cancer Genome Atlas (TCGA), despite the Resnet18 using over 600 times the parameters. Our GNN also succeeds in separating 83 healthy skin samples from 95 lesional psoriasis samples, revealing that upregulation of 26S- and NUB1-mediated degradation of NEDD8, UBD, and their conjugates is central to the largest perturbed reaction network component in psoriasis. We show that our results are not discoverable using traditional differential expression and hypergeometric pathway enrichment analyses yet are supported by separate human multi-omics and small-molecule mouse studies, suggesting future molecular disease studies may benefit from similar GNN analytical approaches.
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Affiliation(s)
- Joshua G. Burkhart
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI 96813, USA
| | - Guanming Wu
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Xubo Song
- Department of Computer Science and Electrical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | | | - Shannon McWeeney
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Melissa H. Wong
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR 97201, USA
| | - Youping Deng
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI 96813, USA
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20
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Choi H, Covert MW. Whole-cell modeling of E. coli confirms that in vitro tRNA aminoacylation measurements are insufficient to support cell growth and predicts a positive feedback mechanism regulating arginine biosynthesis. Nucleic Acids Res 2023; 51:5911-5930. [PMID: 37224536 PMCID: PMC10325894 DOI: 10.1093/nar/gkad435] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 05/26/2023] Open
Abstract
In Escherichia coli, inconsistencies between in vitro tRNA aminoacylation measurements and in vivo protein synthesis demands were postulated almost 40 years ago, but have proven difficult to confirm. Whole-cell modeling can test whether a cell behaves in a physiologically correct manner when parameterized with in vitro measurements by providing a holistic representation of cellular processes in vivo. Here, a mechanistic model of tRNA aminoacylation, codon-based polypeptide elongation, and N-terminal methionine cleavage was incorporated into a developing whole-cell model of E. coli. Subsequent analysis confirmed the insufficiency of aminoacyl-tRNA synthetase kinetic measurements for cellular proteome maintenance, and estimated aminoacyl-tRNA synthetase kcats that were on average 7.6-fold higher. Simulating cell growth with perturbed kcats demonstrated the global impact of these in vitro measurements on cellular phenotypes. For example, an insufficient kcat for HisRS caused protein synthesis to be less robust to the natural variability in aminoacyl-tRNA synthetase expression in single cells. More surprisingly, insufficient ArgRS activity led to catastrophic impacts on arginine biosynthesis due to underexpressed N-acetylglutamate synthase, where translation depends on repeated CGG codons. Overall, the expanded E. coli model deepens understanding of how translation operates in an in vivo context.
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Affiliation(s)
- Heejo Choi
- Department of Bioengineering, Stanford University, 443 Via Ortega, Stanford, CA 94305, USA
| | - Markus W Covert
- Department of Bioengineering, Stanford University, 443 Via Ortega, Stanford, CA 94305, USA
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21
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Uzhytchak M, Smolková B, Frtús A, Stupakov A, Lunova M, Scollo F, Hof M, Jurkiewicz P, Sullivan GJ, Dejneka A, Lunov O. Sensitivity of endogenous autofluorescence in HeLa cells to the application of external magnetic fields. Sci Rep 2023; 13:10818. [PMID: 37402779 DOI: 10.1038/s41598-023-38015-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 06/30/2023] [Indexed: 07/06/2023] Open
Abstract
Dramatically increased levels of electromagnetic radiation in the environment have raised concerns over the potential health hazards of electromagnetic fields. Various biological effects of magnetic fields have been proposed. Despite decades of intensive research, the molecular mechanisms procuring cellular responses remain largely unknown. The current literature is conflicting with regards to evidence that magnetic fields affect functionality directly at the cellular level. Therefore, a search for potential direct cellular effects of magnetic fields represents a cornerstone that may propose an explanation for potential health hazards associated with magnetic fields. It has been proposed that autofluorescence of HeLa cells is magnetic field sensitive, relying on single-cell imaging kinetic measurements. Here, we investigate the magnetic field sensitivity of an endogenous autofluorescence in HeLa cells. Under the experimental conditions used, magnetic field sensitivity of an endogenous autofluorescence was not observed in HeLa cells. We present a number of arguments indicating why this is the case in the analysis of magnetic field effects based on the imaging of cellular autofluorescence decay. Our work indicates that new methods are required to elucidate the effects of magnetic fields at the cellular level.
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Affiliation(s)
- Mariia Uzhytchak
- Department of Optical and Biophysical Systems, Institute of Physics of the Czech Academy of Sciences, Prague, 18221, Czech Republic
| | - Barbora Smolková
- Department of Optical and Biophysical Systems, Institute of Physics of the Czech Academy of Sciences, Prague, 18221, Czech Republic
| | - Adam Frtús
- Department of Optical and Biophysical Systems, Institute of Physics of the Czech Academy of Sciences, Prague, 18221, Czech Republic
| | - Alexandr Stupakov
- Department of Optical and Biophysical Systems, Institute of Physics of the Czech Academy of Sciences, Prague, 18221, Czech Republic
| | - Mariia Lunova
- Department of Optical and Biophysical Systems, Institute of Physics of the Czech Academy of Sciences, Prague, 18221, Czech Republic
- Institute for Clinical and Experimental Medicine (IKEM), Prague, 14021, Czech Republic
| | - Federica Scollo
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, 18223, Czech Republic
| | - Martin Hof
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, 18223, Czech Republic
| | - Piotr Jurkiewicz
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, 18223, Czech Republic
| | - Gareth John Sullivan
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- Department of Pediatric Research, Oslo University Hospital, Oslo, Norway
- Department of Immunology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Alexandr Dejneka
- Department of Optical and Biophysical Systems, Institute of Physics of the Czech Academy of Sciences, Prague, 18221, Czech Republic
| | - Oleg Lunov
- Department of Optical and Biophysical Systems, Institute of Physics of the Czech Academy of Sciences, Prague, 18221, Czech Republic.
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22
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Affiliation(s)
- Alana P Gudinas
- Department of Physics, Stanford University, Stanford, CA, USA
| | - Danielle J Mai
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA.
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23
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Ruan Z, Li S, Grigoropoulos A, Amiri H, Hilburg SL, Chen H, Jayapurna I, Jiang T, Gu Z, Alexander-Katz A, Bustamante C, Huang H, Xu T. Population-based heteropolymer design to mimic protein mixtures. Nature 2023; 615:251-258. [PMID: 36890370 PMCID: PMC10468399 DOI: 10.1038/s41586-022-05675-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 12/21/2022] [Indexed: 03/10/2023]
Abstract
Biological fluids, the most complex blends, have compositions that constantly vary and cannot be molecularly defined1. Despite these uncertainties, proteins fluctuate, fold, function and evolve as programmed2-4. We propose that in addition to the known monomeric sequence requirements, protein sequences encode multi-pair interactions at the segmental level to navigate random encounters5,6; synthetic heteropolymers capable of emulating such interactions can replicate how proteins behave in biological fluids individually and collectively. Here, we extracted the chemical characteristics and sequential arrangement along a protein chain at the segmental level from natural protein libraries and used the information to design heteropolymer ensembles as mixtures of disordered, partially folded and folded proteins. For each heteropolymer ensemble, the level of segmental similarity to that of natural proteins determines its ability to replicate many functions of biological fluids including assisting protein folding during translation, preserving the viability of fetal bovine serum without refrigeration, enhancing the thermal stability of proteins and behaving like synthetic cytosol under biologically relevant conditions. Molecular studies further translated protein sequence information at the segmental level into intermolecular interactions with a defined range, degree of diversity and temporal and spatial availability. This framework provides valuable guiding principles to synthetically realize protein properties, engineer bio/abiotic hybrid materials and, ultimately, realize matter-to-life transformations.
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Affiliation(s)
- Zhiyuan Ruan
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Shuni Li
- Department of Statistics, University of California Berkeley, Berkeley, CA, USA
| | - Alexandra Grigoropoulos
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Hossein Amiri
- Institute for Quantitative Biosciences-QB3, University of California, Berkeley, CA, USA
| | - Shayna L Hilburg
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Haotian Chen
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Ivan Jayapurna
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Tao Jiang
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, CA, USA
- Department of Chemistry, Xiamen University and The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen, China
| | - Zhaoyi Gu
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, CA, USA
- Departments of Chemistry and Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Alfredo Alexander-Katz
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Carlos Bustamante
- Institute for Quantitative Biosciences-QB3, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
- Department of Physics, University of California Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA
| | - Haiyan Huang
- Department of Statistics, University of California Berkeley, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Ting Xu
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, CA, USA.
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA.
- Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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24
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Honegger P, Steinhauser O, Schröder C. Collective Spectroscopy of Solvation Phenomena: Conflicts, Challenges, and Opportunities. J Phys Chem Lett 2023; 14:609-618. [PMID: 36634000 DOI: 10.1021/acs.jpclett.2c03574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Different spectroscopy types reveal different aspects of molecular processes in soft matter. In particular, collective observables can provide insights into intermolecular correlations invisible to the more popular single-particle methods. In this perspective we feature the dielectric relaxation spectroscopy (DRS) with an emphasis on the proper interpretation of this complex observable aided by computational spectroscopy. While we focus on the history and recent advances of DRS in the fields of biomolecular hydration and nanoconfinement, the discussion transcends this particular field and provides a guide for how collective spectroscopy types supported by computational decomposition can be employed to further our understanding of soft matter phenomena.
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Affiliation(s)
- Philipp Honegger
- University of Vienna,Faculty of Chemistry, Department of Computational Biological Chemistry, Wien, 1090, Austria
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, BostonMassachusetts02115, United States
| | - Othmar Steinhauser
- University of Vienna,Faculty of Chemistry, Department of Computational Biological Chemistry, Wien, 1090, Austria
| | - Christian Schröder
- University of Vienna,Faculty of Chemistry, Department of Computational Biological Chemistry, Wien, 1090, Austria
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25
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Scott S, Weiss M, Selhuber-Unkel C, Barooji YF, Sabri A, Erler JT, Metzler R, Oddershede LB. Extracting, quantifying, and comparing dynamical and biomechanical properties of living matter through single particle tracking. Phys Chem Chem Phys 2023; 25:1513-1537. [PMID: 36546878 DOI: 10.1039/d2cp01384c] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A panoply of new tools for tracking single particles and molecules has led to an explosion of experimental data, leading to novel insights into physical properties of living matter governing cellular development and function, health and disease. In this Perspective, we present tools to investigate the dynamics and mechanics of living systems from the molecular to cellular scale via single-particle techniques. In particular, we focus on methods to measure, interpret, and analyse complex data sets that are associated with forces, materials properties, transport, and emergent organisation phenomena within biological and soft-matter systems. Current approaches, challenges, and existing solutions in the associated fields are outlined in order to support the growing community of researchers at the interface of physics and the life sciences. Each section focuses not only on the general physical principles and the potential for understanding living matter, but also on details of practical data extraction and analysis, discussing limitations, interpretation, and comparison across different experimental realisations and theoretical frameworks. Particularly relevant results are introduced as examples. While this Perspective describes living matter from a physical perspective, highlighting experimental and theoretical physics techniques relevant for such systems, it is also meant to serve as a solid starting point for researchers in the life sciences interested in the implementation of biophysical methods.
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Affiliation(s)
- Shane Scott
- Institute of Physiology, Kiel University, Hermann-Rodewald-Straße 5, 24118 Kiel, Germany
| | - Matthias Weiss
- Experimental Physics I, University of Bayreuth, Universitätsstr. 30, D-95447 Bayreuth, Germany
| | - Christine Selhuber-Unkel
- Institute for Molecular Systems Engineering, Heidelberg University, D-69120 Heidelberg, Germany.,Max Planck School Matter to Life, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Younes F Barooji
- Niels Bohr Institute, Blegdamsvej 17, DK-2100 Copenhagen, Denmark.
| | - Adal Sabri
- Experimental Physics I, University of Bayreuth, Universitätsstr. 30, D-95447 Bayreuth, Germany
| | - Janine T Erler
- BRIC, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark.
| | - Ralf Metzler
- Institute of Physics and Astronomy, University of Potsdam, Karl-Liebknecht Str. 24/25, D-14476 Potsdam, Germany.,Asia Pacific Center for Theoretical Physics, Pohang 37673, Republic of Korea
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26
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Saini B, Mukherjee TK. Biomolecular Condensates Regulate Enzymatic Activity under a Crowded Milieu: Synchronization of Liquid-Liquid Phase Separation and Enzymatic Transformation. J Phys Chem B 2023; 127:180-193. [PMID: 36594499 DOI: 10.1021/acs.jpcb.2c07684] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Cellular crowding plays a key role in regulating the enzymatic reactivity in physiological conditions, which is challenging to realize in the dilute phase. Enzymes drive a wide range of complex metabolic reactions with high efficiency and selectivity under extremely heterogeneous and crowded cellular environments. However, the molecular interpretation behind the enhanced enzymatic reactivity under a crowded milieu is poorly understood. Herein, using the horseradish peroxidase (HRP) and glucose oxidase (GOx) cascade pair, we demonstrate for the first time that macromolecular crowding induces liquid-liquid phase separation (LLPS) via the formation of liquid-like condensates/droplets and thereby increases the intrinsic catalytic efficiencies of HRP and GOx. Both these enzymes undergo crowding induced homotypic LLPS via enthalpically driven multivalent electrostatic as well as hydrophobic interactions. Using a set of kinetic and microscopic experiments, we show that precise synchronization of spontaneous LLPS and enzymatic transformations is key to realize the enhanced enzymatic activity under the crowded environments. Our findings reveal an unprecedented enhancement (91- to 205-fold) in the catalytic efficiency (kcat/Km) of HRP at pH 4.0 within the droplet phase relative to that in the bulk aqueous phase in the presence of different crowders. In addition, we have shown that other enzymes also undergo spontaneous LLPS under macromolecular crowding, signifying the generality of this phenomenon under the crowded environments. More importantly, coalescence driven highly regulated GOx/HRP cascade reactions within the fused droplets have been demonstrated with enhanced activity and specificity under the crowded environments. The present discovery highlights the active role of membraneless condensates in regulating the enzymatic efficacy for complex metabolic reactions under the crowded cellular environments and may find significant importance in the field of biocatalysis.
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Affiliation(s)
- Bhawna Saini
- Department of Chemistry, Indian Institute of Technology Indore, Simrol, Indore453552Madhya Pradesh, India
| | - Tushar Kanti Mukherjee
- Department of Chemistry, Indian Institute of Technology Indore, Simrol, Indore453552Madhya Pradesh, India
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27
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Cammarata M, Piazza F, Rivas G, Schirò G, Temussi PA, Pastore A. Revitalizing an important field in biophysics: The new frontiers of molecular crowding. Front Mol Biosci 2023; 10:1153996. [PMID: 36923640 PMCID: PMC10010569 DOI: 10.3389/fmolb.2023.1153996] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 02/13/2023] [Indexed: 03/02/2023] Open
Abstract
Taking into account the presence of the crowded environment of a macromolecule has been an important goal of biology over the past 20 years. Molecular crowding affects the motions, stability and the kinetic behaviour of proteins. New powerful approaches have recently been developed to study molecular crowding, some of which make use of the synchrotron radiation light. The meeting "New Frontiers in Molecular Crowding" was organized in July 2022at the European Synchrotron Radiation facility of Grenoble to discuss the new frontiers of molecular crowding. The workshop brought together researchers from different disciplines to highlight the new developments of the field, including areas where new techniques allow the scientists to gain unprecedently expected information. A key conclusion of the meeting was the need to build an international and interdisciplinary research community through enhanced communication, resource-sharing, and educational initiatives that could let the molecular crowding field flourish further.
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Affiliation(s)
- Marco Cammarata
- Experiment Division, European Synchrotron Radiation Facility, 71 Ave des Martyrs, Grenoble, France
| | - Francesco Piazza
- Department of Physics & Astronomy, University of Florence and INFN Sezione di Firenze, Sesto Fiorentino, Italy
| | - Germán Rivas
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Giorgio Schirò
- CNRS, CEA, IBS, University Grenoble Alpes, Grenoble, France
| | - Piero Andrea Temussi
- Dipartimento di Scienze Chimiche, University "Federico II" of Naples, via Cynthia, Naples, Italy
| | - Annalisa Pastore
- Experiment Division, European Synchrotron Radiation Facility, 71 Ave des Martyrs, Grenoble, France
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28
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Raina N, Hassan MI, Ahmad F, Islam A, Singh AK. PEG mediated destabilization of holo α-lactalbumin probed by in silico and in vitro studies: deviation from excluded volume effect. J Biomol Struct Dyn 2022; 40:13265-13277. [PMID: 34726117 DOI: 10.1080/07391102.2021.1987990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Crowded and confined macromolecular milieus surround proteins, and both are stabilizing if the nature of the interaction between crowder and proteins are considered hard-core repulsive interactions. However, non-specific chemical interactions between a protein and its surroundings also play a significant role and the sum effect of both hard-core repulsion and soft interaction balances the overall effect of crowding/confinement. Previous studies showing the effect of polyethylene glycol (PEG) on protein and nucleic acid may be interpreted as either primarily excluded volume effect or, in some cases, chemical effect by changing solvent properties. In case of destabilizing interactions, charge-charge and hydrophobic contact have to gain more attention. For instance, in vitro and in vivo studies using protein as crowding agent revealed the destabilization of proteins induced by charge-charge interactions. To investigate the effect of PEG 10 kDa on holo α-lactalbumin (holo α-LA), structure and thermal stability of the protein were measured at different pH values using several techniques. Structural characterization by Trp-fluorescence, near-UV CD and far-UV measurements at different pH values clearly shows perturbation of tertiary and secondary structure of holo α-LA by PEG 10 kDa. Furthermore, the dynamic light scattering measurement shows that the protein is homogeneous under all experimental conditions. Analysis of the heat-induced denaturation profile in the presence of the crowder shows destabilization of the protein in terms of Tm (midpoint of denaturation) and ΔGD0 (Gibbs free energy change at 25 °C). To evaluate the interaction of PEG 10 kDa with holo α-LA and stability of PEG-α-LA complex, docking and molecular dynamic simulation were carried out for 100 ns.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Neha Raina
- Department of Biotechnology, Sharda University, Greater Noida, Uttar Pradesh, India.,Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, Delhi, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, Delhi, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, Delhi, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, Delhi, India
| | - Amit Kumar Singh
- Department of Biotechnology, Sharda University, Greater Noida, Uttar Pradesh, India
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29
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Dutta P, Roy P, Sengupta N. Effects of External Perturbations on Protein Systems: A Microscopic View. ACS OMEGA 2022; 7:44556-44572. [PMID: 36530249 PMCID: PMC9753117 DOI: 10.1021/acsomega.2c06199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Protein folding can be viewed as the origami engineering of biology resulting from the long process of evolution. Even decades after its recognition, research efforts worldwide focus on demystifying molecular factors that underlie protein structure-function relationships; this is particularly relevant in the era of proteopathic disease. A complex co-occurrence of different physicochemical factors such as temperature, pressure, solvent, cosolvent, macromolecular crowding, confinement, and mutations that represent realistic biological environments are known to modulate the folding process and protein stability in unique ways. In the current review, we have contextually summarized the substantial efforts in unveiling individual effects of these perturbative factors, with major attention toward bottom-up approaches. Moreover, we briefly present some of the biotechnological applications of the insights derived from these studies over various applications including pharmaceuticals, biofuels, cryopreservation, and novel materials. Finally, we conclude by summarizing the challenges in studying the combined effects of multifactorial perturbations in protein folding and refer to complementary advances in experiment and computational techniques that lend insights to the emergent challenges.
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Affiliation(s)
- Pallab Dutta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
| | - Priti Roy
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma74078, United States
| | - Neelanjana Sengupta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
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30
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Saini B, Mukherjee TK. Synthetic Protocell as Efficient Bioreactor: Enzymatic Superactivity and Ultrasensitive Glucose Sensing in Urine. ACS APPLIED MATERIALS & INTERFACES 2022; 14:53462-53474. [PMID: 36404589 DOI: 10.1021/acsami.2c13112] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
It is believed that membraneless cellular condensates play a critical role in accelerating various slow and thermodynamically unfavorable biochemical processes. However, the exact mechanisms behind the enhanced activity within biocondensates remain poorly understood. Here, we report the fabrication of a high-performance integrated cascade bioplatform based on synthetic droplets for ultrasensitive glucose sensing. Using a horseradish peroxidase (HRP) and glucose oxidase (GOx) cascade pair, we report an unprecedented enhancement in the catalytic activity of HRP inside the synthetic membraneless droplet. Liquidlike membraneless droplets have been prepared via multivalent electrostatic interactions between adenosine triphosphate (ATP) and poly(diallyldimethylammonium chloride) (PDADMAC) in an aqueous medium. Compartmentalized enzymes (GOx/HRP@Droplet) exhibit high encapsulation efficiency, low leakage, prolong retention of activity, and exceptional stability toward protease digestion. Using an HRP@Droplet composite, we have shown that the enzymatic reaction within the droplet follows the classical Michaelis-Menten model. Our findings reveal remarkable enhancement in the catalytic activity of up to 100- and 51-fold for HRP@Droplet and GOx/HRP@Droplet, respectively. These enhanced activities have been explained on the basis of increased local concentrations of enzymes and substrates, along with altered conformations of sequestered enzymes. Furthermore, we have utilized highly efficient and recyclable GOx/HRP@Droplet composite to demonstrate ultrasensitive glucose sensing with a limit of detection of 228 nM. Finally, the composite platform has been exploited to detect glucose in spiked urine samples in solution and filter paper. Our present study illustrates the unprecedented activity of the compartmentalized enzymes and paves the way for next-generation composite bioreactors for a wide range of applications.
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Affiliation(s)
- Bhawna Saini
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Simrol, Indore453552, Madhya Pradesh, India
| | - Tushar Kanti Mukherjee
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Simrol, Indore453552, Madhya Pradesh, India
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31
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Parray ZA, Naqvi AAT, Ahanger IA, Shahid M, Ahmad F, Hassan MI, Islam A. Measuring Structural Changes in Cytochrome c under Crowded Conditions Using In Vitro and In Silico Approaches. Polymers (Basel) 2022; 14:polym14224808. [PMID: 36432935 PMCID: PMC9692323 DOI: 10.3390/polym14224808] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 11/11/2022] Open
Abstract
It is known from in vitro studies that macromolecular crowding in the cell effects protein structure, stability and function; but predictive studies are relatively unexplored. There are few reports where the effect of various crowder mixtures has been exploited to discern their combined effect on the structural stability of proteins. These studies are more significant because their effect can mimicked with in vivo conditions, where the environment is heterogeneous. Effects of two crowders, polyethylene glycol (PEG 400 Da), and its monomer ethylene glycol (EG) alone and in mixture on the structural stability of cytochrome c (cyt c) were determined using various spectroscopic and bioinformatics tools. The main conclusions of our study are (i) the monomer EG has a kosmotropic effect on the protein (stabilizes the protein), and has no significant effect on the tertiary structure; (ii) PEG 400 destabilizes the structure as well as the stability of the protein; and (iii) EG counteracts the destabilizing effect of PEG 400. From this investigation, it seems evident that proteins may fold or unfold in the crowded environment of the cell where various interactions assist them to maintain their structure for their functions. Bioinformatics approaches were also used to support all of the in vitro observations. Cyt c is functional protein; if the structure of the protein is modulated due to change in the environment its nature of function will also change. Our research addresses the question by modulating the environment around the protein, and the macromolecule (protein) conformation dynamics and interaction study via in vitro and in silico approaches which indirectly compares with that of the environment in-cellular milieu, which is highly crowded.
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Affiliation(s)
- Zahoor Ahmad Parray
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
- Department of Chemistry, Indian Institute of Technology Delhi, IIT Campus, Hauz Khas, New Delhi 110016, India
| | - Ahmad Abu Turab Naqvi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Ishfaq Ahmad Ahanger
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
- Department of Chemistry, Biochemistry and Forensic Science, Amity School of Applied Sciences, Amity University Haryana, Gurugram 122413, India
| | - Mohammad Shahid
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam Bin Abdulaziz University, Al Kharj 11942, Saudi Arabia
| | - Faizan Ahmad
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
- Correspondence: ; Tel.: +91-9312812007
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32
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O'Shea JM, Goutou A, Brydon J, Sethna CR, Wood CW, Greiss S. Generation of Photocaged Nanobodies for Intracellular Applications in an Animal Using Genetic Code Expansion and Computationally Guided Protein Engineering. Chembiochem 2022; 23:e202200321. [PMID: 35731601 PMCID: PMC9542635 DOI: 10.1002/cbic.202200321] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Indexed: 11/12/2022]
Abstract
Nanobodies are becoming increasingly popular as tools for manipulating and visualising proteins in vivo. The ability to control nanobody/antigen interactions using light could provide precise spatiotemporal control over protein function. We develop a general approach to engineer photo-activatable nanobodies using photocaged amino acids that are introduced into the target binding interface by genetic code expansion. Guided by computational alanine scanning and molecular dynamics simulations, we tune nanobody/target binding affinity to eliminate binding before uncaging. Upon photo-activation using 365 nm light, binding is restored. We use this approach to generate improved photocaged variants of two anti-GFP nanobodies that function robustly when directly expressed in a complex intracellular environment together with their antigen. We apply them to control subcellular protein localisation in the nematode worm Caenorhabditis elegans. Our approach applies predictions derived from computational modelling directly in a living animal and demonstrates the importance of accounting for in vivo effects on protein-protein interactions.
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Affiliation(s)
- Jack M O'Shea
- Centre for Discovery Brain Sciences, University of Edinburgh, Hugh Robson Building George Square, Edinburgh, EH8 9XD, UK
| | - Angeliki Goutou
- Centre for Discovery Brain Sciences, University of Edinburgh, Hugh Robson Building George Square, Edinburgh, EH8 9XD, UK
| | - Jack Brydon
- MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital Crewe Road South, Edinburgh, EH4 2XR, UK
| | - Cyrus R Sethna
- Centre for Discovery Brain Sciences, University of Edinburgh, Hugh Robson Building George Square, Edinburgh, EH8 9XD, UK
| | - Christopher W Wood
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Roger Land Building King's Buildings, Edinburgh, EH9 3JQ, UK
| | - Sebastian Greiss
- Centre for Discovery Brain Sciences, University of Edinburgh, Hugh Robson Building George Square, Edinburgh, EH8 9XD, UK
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33
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Strobl K, Selivanovitch E, Ibáñez-Freire P, Moreno-Madrid F, Schaap IAT, Delgado-Buscalioni R, Douglas T, de Pablo PJ. Electromechanical Photophysics of GFP Packed Inside Viral Protein Cages Probed by Force-Fluorescence Hybrid Single-Molecule Microscopy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2200059. [PMID: 35718881 PMCID: PMC9528512 DOI: 10.1002/smll.202200059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Packing biomolecules inside virus capsids has opened new avenues for the study of molecular function in confined environments. These systems not only mimic the highly crowded conditions in nature, but also allow their manipulation at the nanoscale for technological applications. Here, green fluorescent proteins are packed in virus-like particles derived from P22 bacteriophage procapsids. The authors explore individual virus cages to monitor their emission signal with total internal reflection fluorescence microscopy while simultaneously changing the microenvironment with the stylus of atomic force microscopy. The mechanical and electronic quenching can be decoupled by ≈10% each using insulator and conductive tips, respectively. While with conductive tips the fluorescence quenches and recovers regardless of the structural integrity of the capsid, with the insulator tips quenching only occurs if the green fluorescent proteins remain organized inside the capsid. The electronic quenching is associated with the coupling of the protein fluorescence emission with the tip surface plasmon resonance. In turn, the mechanical quenching is a consequence of the unfolding of the aggregated proteins during the mechanical disruption of the capsid.
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Affiliation(s)
- Klara Strobl
- Department of Condensed Matter Physics, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | | | - Pablo Ibáñez-Freire
- Department of Condensed Matter Physics, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Francisco Moreno-Madrid
- Department of Condensed Matter Physics, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | | | - Rafael Delgado-Buscalioni
- Department of Condensed Matter Physics, Universidad Autónoma de Madrid, Madrid, 28049, Spain
- Institute of Condensed Matter Physics (IFIMAC), Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Trevor Douglas
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Pedro J de Pablo
- Department of Condensed Matter Physics, Universidad Autónoma de Madrid, Madrid, 28049, Spain
- Institute of Condensed Matter Physics (IFIMAC), Universidad Autónoma de Madrid, Madrid, 28049, Spain
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34
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Del Galdo S, Chiarini M, Casieri C, Daidone I. High density water clusters observed at high concentrations of the macromolecular crowder PEG400. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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35
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Heimsch KC, Gertzen CGW, Schuh AK, Nietzel T, Rahlfs S, Przyborski JM, Gohlke H, Schwarzländer M, Becker K, Fritz-Wolf K. Structure and Function of Redox-Sensitive Superfolder Green Fluorescent Protein Variant. Antioxid Redox Signal 2022; 37:1-18. [PMID: 35072524 PMCID: PMC9293687 DOI: 10.1089/ars.2021.0234] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Aims: Genetically encoded green fluorescent protein (GFP)-based redox biosensors are widely used to monitor specific and dynamic redox processes in living cells. Over the last few years, various biosensors for a variety of applications were engineered and enhanced to match the organism and cellular environments, which should be investigated. In this context, the unicellular intraerythrocytic parasite Plasmodium, the causative agent of malaria, represents a challenge, as the small size of the organism results in weak fluorescence signals that complicate precise measurements, especially for cell compartment-specific observations. To address this, we have functionally and structurally characterized an enhanced redox biosensor superfolder roGFP2 (sfroGFP2). Results: SfroGFP2 retains roGFP2-like behavior, yet with improved fluorescence intensity (FI) in cellulo. SfroGFP2-based redox biosensors are pH insensitive in a physiological pH range and show midpoint potentials comparable with roGFP2-based redox biosensors. Using crystallography and rigidity theory, we identified the superfolding mutations as being responsible for improved structural stability of the biosensor in a redox-sensitive environment, thus explaining the improved FI in cellulo. Innovation: This work provides insight into the structure and function of GFP-based redox biosensors. It describes an improved redox biosensor (sfroGFP2) suitable for measuring oxidizing effects within small cells where applicability of other redox sensor variants is limited. Conclusion: Improved structural stability of sfroGFP2 gives rise to increased FI in cellulo. Fusion to hGrx1 (human glutaredoxin-1) provides the hitherto most suitable biosensor for measuring oxidizing effects in Plasmodium. This sensor is of major interest for studying glutathione redox changes in small cells, as well as subcellular compartments in general. Antioxid. Redox Signal. 37, 1-18.
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Affiliation(s)
- Kim C Heimsch
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen, Germany
| | - Christoph G W Gertzen
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Anna Katharina Schuh
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen, Germany
| | - Thomas Nietzel
- Institute of Plant Biology and Biotechnology, University of Münster, Münster, Germany
| | - Stefan Rahlfs
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen, Germany
| | - Jude M Przyborski
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,John von Neumann Institute of Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Markus Schwarzländer
- Institute of Plant Biology and Biotechnology, University of Münster, Münster, Germany
| | - Katja Becker
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen, Germany
| | - Karin Fritz-Wolf
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen, Germany.,Max-Planck Institute of Medical Research, Heidelberg, Germany
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36
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Matsumoto S, Takahashi S, Bhowmik S, Ohyama T, Sugimoto N. Volumetric Strategy for Quantitatively Elucidating a Local Hydration Network around a G-Quadruplex. Anal Chem 2022; 94:7400-7407. [PMID: 35535999 DOI: 10.1021/acs.analchem.2c01075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydration around nucleic acids, such as DNA and RNA, is an important factor not only for the stability of nucleic acids but also for their interaction with binding molecules. Thus, it is necessary to quantitatively elucidate the hydration properties of nucleic acids around a certain structure. In this study, volumetric changes in G-quadruplex (G4) RNA formation were investigated by systematically changing the number of G-quartet stacks under high pressure. The volumetric contribution at the level of each G4 structural unit revealed that the core G4 helix was significantly more dehydrated than the other parts, including the edges of G-quartets and loops. These findings will help in predicting the binding of G4 ligands on the surface of G4, depending on the chemical structure of the ligand and solution environment. Therefore, the preset volumetric parameter provides information that can predict molecular interactions in G4 formations during molecular crowding in cells.
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Affiliation(s)
- Saki Matsumoto
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Shuntaro Takahashi
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Sudipta Bhowmik
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.,Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
| | - Tatsuya Ohyama
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Naoki Sugimoto
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.,FIRST (Graduate School of Frontiers of Innovative Research in Science and Technology), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
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Malcı K, Walls LE, Rios-Solis L. Rational Design of CRISPR/Cas12a-RPA Based One-Pot COVID-19 Detection with Design of Experiments. ACS Synth Biol 2022; 11:1555-1567. [PMID: 35363475 PMCID: PMC9016756 DOI: 10.1021/acssynbio.1c00617] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
Simple
and effective molecular diagnostic methods have gained importance
due to the devastating effects of the COVID-19 pandemic. Various isothermal
one-pot COVID-19 detection methods have been proposed as favorable
alternatives to standard RT-qPCR methods as they do not require sophisticated
and/or expensive devices. However, as one-pot reactions are highly
complex with a large number of variables, determining the optimum
conditions to maximize sensitivity while minimizing diagnostic cost
can be cumbersome. Here, statistical design of experiments (DoE) was
employed to accelerate the development and optimization of a CRISPR/Cas12a-RPA-based
one-pot detection method for the first time. Using a definitive screening
design, factors with a significant effect on performance were elucidated
and optimized, facilitating the detection of two copies/μL of
full-length SARS-CoV-2 (COVID-19) genome using simple instrumentation.
The screening revealed that the addition of a reverse transcription
buffer and an RNase inhibitor, components generally omitted in one-pot
reactions, improved performance significantly, and optimization of
reverse transcription had a critical impact on the method’s
sensitivity. This strategic method was also applied in a second approach
involving a DNA sequence of the N gene from the COVID-19 genome. The
slight differences in optimal conditions for the methods using RNA
and DNA templates highlight the importance of reaction-specific optimization
in ensuring robust and efficient diagnostic performance. The proposed
detection method is automation-compatible, rendering it suitable for
high-throughput testing. This study demonstrated the benefits of DoE
for the optimization of complex one-pot molecular diagnostics methods
to increase detection sensitivity.
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Affiliation(s)
- Koray Malcı
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Kings Buildings, Edinburgh EH9 3BF, United Kingdom
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, Edinburgh EH9 3BD, United Kingdom
| | - Laura E. Walls
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Kings Buildings, Edinburgh EH9 3BF, United Kingdom
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, Edinburgh EH9 3BD, United Kingdom
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Kings Buildings, Edinburgh EH9 3BF, United Kingdom
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, Edinburgh EH9 3BD, United Kingdom
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K
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38
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Molines AT, Lemière J, Gazzola M, Steinmark IE, Edrington CH, Hsu CT, Real-Calderon P, Suhling K, Goshima G, Holt LJ, Thery M, Brouhard GJ, Chang F. Physical properties of the cytoplasm modulate the rates of microtubule polymerization and depolymerization. Dev Cell 2022; 57:466-479.e6. [PMID: 35231427 PMCID: PMC9319896 DOI: 10.1016/j.devcel.2022.02.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 11/01/2021] [Accepted: 01/31/2022] [Indexed: 11/20/2022]
Abstract
The cytoplasm is a crowded, visco-elastic environment whose physical properties change according to physiological or developmental states. How the physical properties of the cytoplasm impact cellular functions in vivo remains poorly understood. Here, we probe the effects of cytoplasmic concentration on microtubules by applying osmotic shifts to fission yeast, moss, and mammalian cells. We show that the rates of both microtubule polymerization and depolymerization scale linearly and inversely with cytoplasmic concentration; an increase in cytoplasmic concentration decreases the rates of microtubule polymerization and depolymerization proportionally, whereas a decrease in cytoplasmic concentration leads to the opposite. Numerous lines of evidence indicate that these effects are due to changes in cytoplasmic viscosity rather than cellular stress responses or macromolecular crowding per se. We reconstituted these effects on microtubules in vitro by tuning viscosity. Our findings indicate that, even in normal conditions, the viscosity of the cytoplasm modulates the reactions that underlie microtubule dynamic behaviors.
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Affiliation(s)
- Arthur T Molines
- Department of Cell and Tissue Biology, University of California, San Francisco, USA; Marine Biological Laboratory, Woods Hole, MA 02543, USA.
| | - Joël Lemière
- Department of Cell and Tissue Biology, University of California, San Francisco, USA
| | - Morgan Gazzola
- University of Grenoble-Alpes, CEA, CNRS, INRA, Interdisciplinary Research Institute of Grenoble, Laboratoire de Phyiologie Cellulaire & Vegétale, CytoMorpho Lab, 38054 Grenoble, France
| | | | | | - Chieh-Ting Hsu
- Department of Physics, McGill University, Montréal, Quebec, Canada
| | - Paula Real-Calderon
- Department of Cell and Tissue Biology, University of California, San Francisco, USA
| | - Klaus Suhling
- Department of Physics, King's College London, London, UK
| | - Gohta Goshima
- Sugashima Marine Biological Laboratory and Division of Biological Science, Graduate School of Science, Nagoya University, Toba City, Mie, Japan; Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA; Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Manuel Thery
- University of Grenoble-Alpes, CEA, CNRS, INRA, Interdisciplinary Research Institute of Grenoble, Laboratoire de Phyiologie Cellulaire & Vegétale, CytoMorpho Lab, 38054 Grenoble, France; Université de Paris, INSERM, CEA, Institut de Recherche Saint Louis, U 976, CytoMorpho Lab, 75010 Paris, France
| | - Gary J Brouhard
- Department of Biology, McGill University, Montréal, Quebec, Canada
| | - Fred Chang
- Department of Cell and Tissue Biology, University of California, San Francisco, USA; Marine Biological Laboratory, Woods Hole, MA 02543, USA.
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39
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A new visual design language for biological structures in a cell. Structure 2022; 30:485-497.e3. [DOI: 10.1016/j.str.2022.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/28/2021] [Accepted: 01/04/2022] [Indexed: 01/16/2023]
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40
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Wang C, Yang J, Lu Y. Modularize and Unite: Toward Creating a Functional Artificial Cell. Front Mol Biosci 2021; 8:781986. [PMID: 34912849 PMCID: PMC8667554 DOI: 10.3389/fmolb.2021.781986] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/17/2021] [Indexed: 11/17/2022] Open
Abstract
An artificial cell is a simplified model of a living system, bringing breakthroughs into both basic life science and applied research. The bottom-up strategy instructs the construction of an artificial cell from nonliving materials, which could be complicated and interdisciplinary considering the inherent complexity of living cells. Although significant progress has been achieved in the past 2 decades, the area is still facing some problems, such as poor compatibility with complex bio-systems, instability, and low standardization of the construction method. In this review, we propose creating artificial cells through the integration of different functional modules. Furthermore, we divide the function requirements of an artificial cell into four essential parts (metabolism, energy supplement, proliferation, and communication) and discuss the present researches. Then we propose that the compartment and the reestablishment of the communication system would be essential for the reasonable integration of functional modules. Although enormous challenges remain, the modular construction would facilitate the simplification and standardization of an artificial cell toward a natural living system. This function-based strategy would also broaden the application of artificial cells and represent the steps of imitating and surpassing nature.
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Affiliation(s)
- Chen Wang
- Key Laboratory of Industrial Biocatalysis, Department of Chemical Engineering, Ministry of Education, Tsinghua University, Beijing, China
| | - Junzhu Yang
- Key Laboratory of Industrial Biocatalysis, Department of Chemical Engineering, Ministry of Education, Tsinghua University, Beijing, China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Department of Chemical Engineering, Ministry of Education, Tsinghua University, Beijing, China
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41
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Ghassemi Z, Ruesing S, Leach JB, Zustiak SP. Stability of proteins encapsulated in Michael-type addition polyethylene glycol hydrogels. Biotechnol Bioeng 2021; 118:4840-4853. [PMID: 34606089 PMCID: PMC8585711 DOI: 10.1002/bit.27949] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/30/2021] [Accepted: 09/12/2021] [Indexed: 11/12/2022]
Abstract
Degradable polyethylene glycol (PEG) hydrogels are excellent vehicles for sustained drug release due to their biocompatibility, tunable physical properties, and customizable degradation. However, protein therapeutics are unstable under physiological conditions and releasing degraded or inactive therapeutics can induce immunogenic effects. While controlling protein release from PEG hydrogels has been extensively investigated, few studies have detailed protein stability long-term or under stress conditions. Here, lysozyme and alcohol dehydrogenase (ADH) stability were explored upon encapsulation in PEG hydrogels formed through Michael-type addition. The stability and structure of the two model proteins were monitored by measuring the free energy of unfolding and fluoresce quenching when confined in a hydrogel and compared to PEG solution and buffer. Hydrogels destabilized lysozyme structure at low denaturant concentrations but prevented complete unfolding at high concentrations. ADH was stabilized as the confining mesh size approached the protein radius of gyration. Both proteins retained enzymatic activity within the hydrogels under stress conditions, including denaturant, high temperature, and agitation. Conjugation between lysozyme and PEG-acrylate was identified at long reaction times but no conjugation was observed in the time required for complete gelation. Studies of protein stability in PEG hydrogels, as the one detailed here, can lead to designer technologies for the improved formulation, storage, and delivery of protein therapeutics.
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Affiliation(s)
- Zahra Ghassemi
- Chemical, Biochemical, and Environmental Engineering, University of Maryland, Baltimore County, 1000 Hilltop Circle, Engineering 314, Baltimore, MD 21250, USA
| | - Sam Ruesing
- Biomedical Engineering, Saint Louis University, 3507 Lindell Blvd, St. Louis, MO 63103, USA
| | - Jennie B Leach
- Chemical, Biochemical, and Environmental Engineering, University of Maryland, Baltimore County, 1000 Hilltop Circle, Engineering 314, Baltimore, MD 21250, USA
| | - Silviya P Zustiak
- Biomedical Engineering, Saint Louis University, 3507 Lindell Blvd, St. Louis, MO 63103, USA
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42
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Lecinski S, Shepherd JW, Frame L, Hayton I, MacDonald C, Leake MC. Investigating molecular crowding during cell division and hyperosmotic stress in budding yeast with FRET. CURRENT TOPICS IN MEMBRANES 2021; 88:75-118. [PMID: 34862033 PMCID: PMC7612257 DOI: 10.1016/bs.ctm.2021.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Cell division, aging, and stress recovery triggers spatial reorganization of cellular components in the cytoplasm, including membrane bound organelles, with molecular changes in their compositions and structures. However, it is not clear how these events are coordinated and how they integrate with regulation of molecular crowding. We use the budding yeast Saccharomyces cerevisiae as a model system to study these questions using recent progress in optical fluorescence microscopy and crowding sensing probe technology. We used a Förster Resonance Energy Transfer (FRET) based sensor, illuminated by confocal microscopy for high throughput analyses and Slimfield microscopy for single-molecule resolution, to quantify molecular crowding. We determine crowding in response to cellular growth of both mother and daughter cells, in addition to osmotic stress, and reveal hot spots of crowding across the bud neck in the burgeoning daughter cell. This crowding might be rationalized by the packing of inherited material, like the vacuole, from mother cells. We discuss recent advances in understanding the role of crowding in cellular regulation and key current challenges and conclude by presenting our recent advances in optimizing FRET-based measurements of crowding while simultaneously imaging a third color, which can be used as a marker that labels organelle membranes. Our approaches can be combined with synchronized cell populations to increase experimental throughput and correlate molecular crowding information with different stages in the cell cycle.
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Affiliation(s)
- Sarah Lecinski
- Department of Physics, University of York, York, United Kingdom
| | - Jack W Shepherd
- Department of Physics, University of York, York, United Kingdom; Department of Biology, University of York, York, United Kingdom
| | - Lewis Frame
- School of Natural Sciences, University of York, York, United Kingdom
| | - Imogen Hayton
- Department of Biology, University of York, York, United Kingdom
| | - Chris MacDonald
- Department of Biology, University of York, York, United Kingdom
| | - Mark C Leake
- Department of Physics, University of York, York, United Kingdom; Department of Biology, University of York, York, United Kingdom.
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43
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Fan R, Zachariah GT, Padding JT, Hartkamp R. Real-time temperature measurement in stochastic rotation dynamics. Phys Rev E 2021; 104:034124. [PMID: 34654203 DOI: 10.1103/physreve.104.034124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/03/2021] [Indexed: 11/07/2022]
Abstract
Many physical and chemical processes involve energy change with rates that depend sensitively on local temperature. Important examples include heterogeneously catalyzed reactions and activated desorption. Because of the multiscale nature of such systems, it is desirable to connect the macroscopic world of continuous hydrodynamic and temperature fields to mesoscopic particle-based simulations with discrete particle events. In this work we show how to achieve real-time measurement of the local temperature in stochastic rotation dynamics (SRD), a mesoscale method particularly well suited for problems involving hydrodynamic flows with thermal fluctuations. We employ ensemble averaging to achieve local temperature measurement in dynamically changing environments. After validation by heat diffusion between two isothermal plates, heating of walls by a hot strip, and by temperature programed desorption, we apply the method to a case of a model flow reactor with temperature-sensitive heterogeneously catalyzed reactions on solid spherical catalysts. In this model, adsorption, chemical reactions, and desorption are explicitly tracked on the catalyst surface. This work opens the door for future projects where SRD is used to couple hydrodynamic flows and thermal fluctuations to solids with complex temperature-dependent surface mechanisms.
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Affiliation(s)
- Rong Fan
- Complex Fluid Processing, Process and Energy Department, Delft University of Technology, 2628 CB Delft, The Netherlands
| | - Githin T Zachariah
- Complex Fluid Processing, Process and Energy Department, Delft University of Technology, 2628 CB Delft, The Netherlands
| | - Johan T Padding
- Complex Fluid Processing, Process and Energy Department, Delft University of Technology, 2628 CB Delft, The Netherlands
| | - Remco Hartkamp
- Complex Fluid Processing, Process and Energy Department, Delft University of Technology, 2628 CB Delft, The Netherlands
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44
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Bao Y, Ertbjerg P, Estévez M, Yuan L, Gao R. Freezing of meat and aquatic food: Underlying mechanisms and implications on protein oxidation. Compr Rev Food Sci Food Saf 2021; 20:5548-5569. [PMID: 34564951 DOI: 10.1111/1541-4337.12841] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 07/03/2021] [Accepted: 08/24/2021] [Indexed: 12/24/2022]
Abstract
Over the recent decades,protein oxidation in muscle foods has gained increasing research interests as it is known that protein oxidation can affect eating quality and nutritional value of meat and aquatic products. Protein oxidation occurs during freezing/thawing and frozen storage of muscle foods, leading to irreversible physicochemical changes and impaired quality traits. Controlling oxidative damage to muscle foods during such technological processes requires a deeper understanding of the mechanisms of freezing-induced protein oxidation. This review focus on key physicochemical factors in freezing/thawing and frozen storage of muscle foods, such as formation of ice crystals, freeze concentrating and macromolecular crowding effect, instability of proteins at the ice-water interface, freezer burn, lipid oxidation, and so on. Possible relationships between these physicochemical factors and protein oxidation are thoroughly discussed. In addition, the occurrence of protein oxidation, the impact on eating quality and nutrition, and controlling methods are also briefly reviewed. This review will shed light on the complicated mechanism of protein oxidation in frozen muscle foods.
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Affiliation(s)
- Yulong Bao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Per Ertbjerg
- Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
| | - Mario Estévez
- Meat and Meat Products Research Institute, University of Extremadura, Cáceres, Spain
| | - Li Yuan
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Ruichang Gao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
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45
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Baverstock K. The gene: An appraisal. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 164:46-62. [PMID: 33979646 DOI: 10.1016/j.pbiomolbio.2021.04.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/14/2021] [Accepted: 04/22/2021] [Indexed: 11/29/2022]
Abstract
The gene can be described as the foundational concept of modern biology. As such, it has spilled over into daily discourse, yet it is acknowledged among biologists to be ill-defined. Here, following a short history of the gene, I analyse critically its role in inheritance, evolution, development, and morphogenesis. Wilhelm Johannsen's genotype-conception, formulated in 1910, has been adopted as the foundation stone of genetics, giving the gene a higher degree of prominence than is justified by the evidence. An analysis of the results of the Long-Term Evolution Experiment (LTEE) with E. coli bacteria, grown over 60,000 generations, does not support spontaneous gene mutation as the source of variance for natural selection. From this it follows that the gene is not Mendel's unit of inheritance: that must be Johannsen's transmission-conception at the gamete phenotype level, a form of inheritance that Johannsen did not consider. Alternatively, I contend that biology viewed on the bases of thermodynamics, complex system dynamics and self-organisation, provides a new framework for the foundations of biology. In this framework, the gene plays a passive role as a vital information store: it is the phenotype that plays the active role in inheritance, evolution, development, and morphogenesis.
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Affiliation(s)
- Keith Baverstock
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio Campus, Kuopio, Finland.
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46
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Nikitin AA, Yurenya AY, Gabbasov RR, Cherepanov VM, Polikarpov MA, Chuev MA, Majouga AG, Panchenko VY, Abakumov MA. Effects of Macromolecular Crowding on Nanoparticle Diffusion: New Insights from Mössbauer Spectroscopy. J Phys Chem Lett 2021; 12:6804-6811. [PMID: 34270251 DOI: 10.1021/acs.jpclett.1c01984] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In this work, we used Mössbauer spectroscopy as a new approach for experimental quantification of the self-diffusion coefficient (DMössbauer) and hydrodynamic (HD) size of iron-containing nanoparticles (NPs) in complex crowded solutions, mimicking cell cytoplasm. As a probe, we used 9 nm cobalt ferrite NPs (CFNs) dispersed in solutions of bovine serum albumin (BSA) with a volume fraction (φBSA) of 0-0.2. Our results show that the broadening of Mössbauer spectra is highly sensitive to the diffusion of CFNs, while when φBSA = 0.2, the CFN-normalized diffusivity is reduced by 86% compared to that of a protein-free solution. CFN colloids were also studied by dynamic light scattering (DLS). Comparison of the experimental data shows that DLS significantly underestimates the diffusion coefficient of CFNs and, consequently, overestimates the HD size of CFNs at φBSA > 0, which cannot be attributed to the formation of the BSA monolayer on the surface of CFNs.
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Affiliation(s)
- Aleksey A Nikitin
- National University of Science and Technology MISiS, Moscow 119049, Russian Federation
| | - Anton Yu Yurenya
- Lomonosov Moscow State University, Moscow 119991, Russian Federation
- National Research Centre "Kurchatov Institute", Moscow 123182, Russian Federation
| | - Raul R Gabbasov
- National Research Centre "Kurchatov Institute", Moscow 123182, Russian Federation
| | - Valeriy M Cherepanov
- National Research Centre "Kurchatov Institute", Moscow 123182, Russian Federation
| | - Mikhail A Polikarpov
- National Research Centre "Kurchatov Institute", Moscow 123182, Russian Federation
| | - Michael A Chuev
- Valiev Institute of Physics and Technology, Russian Academy of Sciences, Moscow 117218, Russian Federation
| | - Alexander G Majouga
- D. Mendeleev University of Chemical Technology of Russia, Moscow 125047, Russian Federation
| | - Vladislav Ya Panchenko
- Lomonosov Moscow State University, Moscow 119991, Russian Federation
- National Research Centre "Kurchatov Institute", Moscow 123182, Russian Federation
| | - Maxim A Abakumov
- National University of Science and Technology MISiS, Moscow 119049, Russian Federation
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47
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Rastogi H, Chowdhury PK. Understanding enzyme behavior in a crowded scenario through modulation in activity, conformation and dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140699. [PMID: 34298166 DOI: 10.1016/j.bbapap.2021.140699] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/08/2021] [Accepted: 07/19/2021] [Indexed: 01/25/2023]
Abstract
Macromolecular crowding, inside the physiological interior, modulates the energy landscape of biological macromolecules in multiple ways. Amongst these, enzymes occupy a special place and hence understanding the function of the same in the crowded interior is of utmost importance. In this study, we have investigated the manner in which the multidomain enzyme, AK3L1 (PDB ID: 1ZD8), an isoform of adenylate kinase, has its features affected in presence of commonly used crowders (PEG 8, Dextran 40, Dextran 70, and Ficoll 70). Michaelis Menten plots reveal that the crowders in general enhance the activity of the enzyme, with the Km and Vmax values showing significant variations. Ficoll 70, induced the maximum activity for AK3L1 at 100 g/L, beyond which the activity reduced. Ensemble FRET studies were performed to provide insights into the relative domain (LID and CORE) displacements in presence of the crowders. Solvation studies reveal that the protein matrix surrounding the probe CPM (7-diethylamino-3-(4-maleimido-phenyl)-4-methylcoumarin) gets restricted in presence of the crowders, with Ficoll 70 providing the maximum rigidity, the same being linked to the decrease in the activity of the enzyme. Through our multipronged approach, we have observed a distinct correlation between domain displacement, enzyme activity and associated dynamics. Thus, keeping in mind the complex nature of enzyme activity and the surrounding bath of dense soup that the biological entity remains immersed in, indeed more such approaches need to be undertaken to have a better grasp of the "enzymes in the crowd".
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Affiliation(s)
- Harshita Rastogi
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Pramit K Chowdhury
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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48
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Yu J, Ramirez LM, Premo A, Busch DB, Lin Q, Burz DS, Shekhtman A. Ribosome-Amplified Metabolism, RAMBO, Measured by NMR Spectroscopy. Biochemistry 2021; 60:1885-1895. [PMID: 34081430 PMCID: PMC11299219 DOI: 10.1021/acs.biochem.1c00074] [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] [Indexed: 11/28/2022]
Abstract
NMR spectroscopy was used to investigate the phenomenon of ribosome-amplified metabolism or RAMBO between pyruvate kinase and ribosomes. Because the concentration of ribosomes increases as the cell grows, ribosome binding interactions may regulate metabolic fluxes by altering the distribution of bound and free enzymes. Pyruvate kinase (PK) catalyzes the last step of glycolysis and represents a major drug target for controlling bacterial infections. The binding of metabolic enzymes to ribosomes creates protein quinary structures with altered catalytic activities. NMR spectroscopy and chemical cross-linking combined with high-resolution mass spectrometry were used to establish that PK binds to ribosome at three independent sites, the L1 stalk, the A site, and the mRNA entry pore. The bioanalytical methodology described characterizes the altered kinetics and confirms the specificity of pyruvate kinase-ribosome interaction, affording an opportunity to investigate the ribosome dependence of metabolic reactions under solution conditions that closely mimic the cytosol. Expanding on the concept of ribosomal heterogeneity, which describes variations in ribosomal constituents that contribute to the specificity of cellular processes, this work firmly establishes the reciprocal process by which ribosome-dependent quinary interactions affect metabolic activity.
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Affiliation(s)
- JianChao Yu
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Lisa M Ramirez
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Aaron Premo
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Devin B Busch
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Qishan Lin
- RNA Epitranscriptomics & Proteomics Resource, University at Albany, State University of New York, Albany, New York 12222, United States
| | - David S Burz
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Alexander Shekhtman
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
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49
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Reinhardt M, Bruce NJ, Kokh DB, Wade RC. Brownian Dynamics Simulations of Proteins in the Presence of Surfaces: Long-Range Electrostatics and Mean-Field Hydrodynamics. J Chem Theory Comput 2021; 17:3510-3524. [PMID: 33784462 DOI: 10.1021/acs.jctc.0c01312] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Simulations of macromolecular diffusion and adsorption in confined environments can offer valuable mechanistic insights into numerous biophysical processes. In order to model solutes at atomic detail on relevant time scales, Brownian dynamics simulations can be carried out with the approximation of rigid body solutes moving through a continuum solvent. This allows the precomputation of interaction potential grids for the solutes, thereby allowing the computationally efficient calculation of forces. However, hydrodynamic and long-range electrostatic interactions cannot be fully treated with grid-based approaches alone. Here, we develop a treatment of both hydrodynamic and electrostatic interactions to include the presence of surfaces by modeling grid-based and long-range interactions. We describe its application to simulate the self-association and many-molecule adsorption of the well-characterized protein hen egg-white lysozyme to mica-like and silica-like surfaces. We find that the computational model can recover a number of experimental observables of the adsorption process and provide insights into their determinants. The computational model is implemented in the Simulation of Diffusional Association (SDA) software package.
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Affiliation(s)
- Martin Reinhardt
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Neil J Bruce
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Daria B Kokh
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Center for Molecular Biology (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
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50
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Szatkowski L, Varikoti RA, Dima RI. Modeling the Mechanical Response of Microtubule Lattices to Pressure. J Phys Chem B 2021; 125:5009-5021. [PMID: 33970630 DOI: 10.1021/acs.jpcb.1c01770] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microtubules, the largest and stiffest filaments of the cytoskeleton, have to be well adapted to the high levels of crowdedness in cells to perform their multitude of functions. Furthermore, fundamental processes that involve microtubules, such as the maintenance of the cellular shape and cellular motion, are known to be highly dependent on external pressure. In light of the importance of pressure for the functioning of microtubules, numerous studies interrogated the response of these cytoskeletal filaments to osmotic pressure, resulting from crowding by osmolytes, such as poly(ethylene glycol)/poly(ethylene oxide) (PEG/PEO) molecules, or to direct applied pressure. The interpretation of experiments is usually based on the assumptions that PEG molecules have unfavorable interactions with the microtubule lattices and that the behavior of microtubules under pressure can be described by using continuous models. We probed directly these two assumptions. First, we characterized the interaction between the main interfaces in a microtubule filament and PEG molecules of various sizes using a combination of docking and molecular dynamics simulations. Second, we studied the response of a microtubule filament to compression using a coarse-grained model that allows for the breaking of lattice interfaces. Our results show that medium length PEG molecules do not alter the energetics of the lateral interfaces in microtubules but rather target and can penetrate into the voids between tubulin monomers at these interfaces, which can lead to a rapid loss of lateral interfaces under pressure. Compression of a microtubule under conditions corresponding to high osmotic pressure results in the formation of the deformed phase found in experiments. Our simulations show that the breaking of lateral interfaces, rather than the buckling of the filament inferred from the continuous models, accounts for the deformation.
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Affiliation(s)
- Lukasz Szatkowski
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States.,Division of Science, Mathematics, and Engineering, University of South Carolina Sumter, Sumter, South Carolina 29150, United States
| | - Rohith Anand Varikoti
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Ruxandra I Dima
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
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