1
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Moller AL, Middleton IA, Maynard GE, Cox LB, Wang A, Li HL, Thordarson P. Discrimination between Purine and Pyrimidine-Rich RNA in Liquid-Liquid Phase-Separated Condensates with Cationic Peptides and the Effect of Artificial Crowding Agents. Biomacromolecules 2024. [PMID: 39661936 DOI: 10.1021/acs.biomac.4c01282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2024]
Abstract
Membraneless organelles, often referred to as condensates or coacervates, are liquid-liquid phase-separated systems formed between noncoding RNAs and intrinsically disordered proteins. While the importance of different amino acid residues in short peptide-based condensates has been investigated, the role of the individual nucleobases or the type of heterocyclic structures, the purine vs pyrimidine nucleobases, is less researched. The cell's crowded environment has been mimicked in vitro to demonstrate its ability to induce the formation of condensates, but more research in this area is required, especially with respect to RNA-facilitated phase separation and the properties of the crowding agent, poly(ethylene glycol) (PEG). Herein, we have shown that the nucleotide base sequence of RNA can greatly influence its propensity to undergo phase separation with cationic peptides, with the purine-only RNA decamer (AG)5 readily doing so while the pyrimidine-only (CU)5 does not. Furthermore, we show that the presence and size of a PEG macromolecular crowder affects both the ability to phase separate and the stability of coacervates formed, possibly due to co-condensation of PEG with the RNA and peptides. This work sheds light on the presence of low-complexity long purine- or pyrimidine-rich noncomplementary repeat (AG or CU) sequences in various noncoding RNAs found in biology.
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Affiliation(s)
- Anika L Moller
- School of Chemistry and the UNSW RNA Institute, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Isis A Middleton
- School of Chemistry and the UNSW RNA Institute, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Grace E Maynard
- School of Chemistry and the UNSW RNA Institute, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Lachlan B Cox
- School of Chemistry and the UNSW RNA Institute, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Anna Wang
- School of Chemistry and the UNSW RNA Institute, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Hsiu L Li
- School of Chemistry and the UNSW RNA Institute, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Pall Thordarson
- School of Chemistry and the UNSW RNA Institute, UNSW Sydney, Sydney, NSW 2052, Australia
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2
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Marzano N, Johnston B, Paudel BP, Schmidberger J, Jergic S, Böcking T, Agostino M, Small I, van Oijen AM, Bond CS. Single-molecule visualization of sequence-specific RNA binding by a designer PPR protein. Nucleic Acids Res 2024; 52:14154-14170. [PMID: 39530228 DOI: 10.1093/nar/gkae984] [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: 05/29/2024] [Revised: 10/01/2024] [Accepted: 10/16/2024] [Indexed: 11/16/2024] Open
Abstract
Pentatricopeptide repeat proteins (PPR) are a large family of modular RNA-binding proteins, whereby each module can be modified to bind to a specific ssRNA nucleobase. As such, there is interest in developing 'designer' PPRs (dPPRs) for a range of biotechnology applications, including diagnostics or in vivo localization of ssRNA species; however, the mechanistic details regarding how PPRs search for and bind to target sequences is unclear. To address this, we determined the structure of a dPPR bound to its target sequence and used two- and three-color single-molecule fluorescence resonance energy transfer to interrogate the mechanism of ssRNA binding to individual dPPRs in real time. We demonstrate that dPPRs are slower to bind longer ssRNA sequences (or could not bind at all) and that this is, in part, due to their propensity to form stable secondary structures that sequester the target sequence from dPPR. Importantly, dPPR binds only to its target sequence (i.e. it does not associate with non-target ssRNA sequences) and does not 'scan' longer ssRNA oligonucleotides for the target sequence. The kinetic constraints imposed by random 3D diffusion may explain the long-standing conundrum of why PPR proteins are abundant in organelles, but almost unknown outside them (i.e. in the cytosol and nucleus).
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Affiliation(s)
- Nicholas Marzano
- University of Wollongong, School of Chemistry and Molecular Bioscience, Molecular Horizons, Northfields Avenue, Wollongong, NSW 2500, Australia
| | - Brady Johnston
- University of Western Australia, School of Molecular Sciences, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Bishnu P Paudel
- University of Wollongong, School of Chemistry and Molecular Bioscience, Molecular Horizons, Northfields Avenue, Wollongong, NSW 2500, Australia
| | - Jason Schmidberger
- University of Western Australia, School of Molecular Sciences, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Slobodan Jergic
- University of Wollongong, School of Chemistry and Molecular Bioscience, Molecular Horizons, Northfields Avenue, Wollongong, NSW 2500, Australia
| | - Till Böcking
- University of New South Wales, Department of Molecular Medicine, EMBL Australia Node in Single Molecule Science, Gate 11, Botany St, Sydney, NSW 2052, Australia
| | - Mark Agostino
- Curtin University, Curtin Medical School, Curtin Health Innovation Research Institute, and Curtin Institute for Computation, Kent St, Bentley, WA 6102, Australia
| | - Ian Small
- University of Western Australia, School of Molecular Sciences, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Antoine M van Oijen
- University of Sydney, Faculty of Medicine and Health, G02 Jane Foss Russell Building, Sydney, NSW 2006, Australia
| | - Charles S Bond
- University of Western Australia, School of Molecular Sciences, 35 Stirling Highway, Crawley, WA 6009, Australia
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3
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Kawai K, Jang SH, Igarashi Y, Yazawa K, Gotoh K, Kikkawa J, Yamada A, Tateyama Y, Okubo M. Proton Intercalation into an Open-Tunnel Bronze Phase with Near-Zero Volume Change. Angew Chem Int Ed Engl 2024:e202410971. [PMID: 39205395 DOI: 10.1002/anie.202410971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 07/30/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024]
Abstract
Managing safety and supply-chain risks associated with lithium-ion batteries (LIBs) is an urgent task for sustainable development. Aqueous proton batteries are attractive alternatives to LIBs because using water and protons addresses these two risks. However, most host materials undergo large volume changes upon H+ intercalation, which induces intraparticle cracking to accelerates parasitic reactions. Herein, we report that Mo3Nb2O14 bronze exhibits reversible H+ intercalation (200 mAh g-1) with a Coulombic efficiency of 99.7 % owing to near-zero volume change and solid-solution-type phase transition. Combination of experimental and theoretical analyses clarifies that rotation and shrinkage of open tunnels, which consist of flexible corner-sharing Mo/NbOn polyhedra, relieve local structural distortions upon H+ intercalation to suppress intraparticle cracking. The prototype full cell of an aqueous proton battery with a Mo3Nb2O14 anode operates stably over 1000 charge/discharge cycles. This study reveals the importance of implementing distortion-relieving voids in host materials to reduce volume change upon charge/discharge.
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Grants
- JPMJCR21O6 Core Research for Evolutional Science and Technology
- JPMXP1121467561 Ministry of Education, Culture, Sports, Science and Technology
- JPMXP1020200301 Ministry of Education, Culture, Sports, Science and Technology
- JPMXP1020230325 Ministry of Education, Culture, Sports, Science and Technology
- JP24H02204 Ministry of Education, Culture, Sports, Science and Technology
- Kazuchika Okura Memorial Foundation
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Affiliation(s)
- Kosuke Kawai
- Department of Electrical Engineering and Bioscience, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Seong-Hoon Jang
- Research Center for Energy and Environmental Materials (GREEN), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan
- Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Yuta Igarashi
- Department of Electrical Engineering and Bioscience, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Koji Yazawa
- JEOL Ltd., 3-1-2 Musashino, Akishima, Tokyo, 196-8558, Japan
| | - Kazuma Gotoh
- Center for Nano Materials and Technology (CNMT), Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa, 923-1292, Japan
| | - Jun Kikkawa
- Center for Basic Research on Materials (CBRM), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan
| | - Atsuo Yamada
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
- Sungkyunkwan University Institute of Energy Science & Technology (SIEST), Sungkyunkwan University, Suwon, 16419, Korea
| | - Yoshitaka Tateyama
- Research Center for Energy and Environmental Materials (GREEN), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan
- Tokyo Institute of Technology (Tokyo Tech), 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan
| | - Masashi Okubo
- Department of Electrical Engineering and Bioscience, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
- Kagami Memorial Research Institute for Material Science and Technology, Waseda University, Tokyo, 169-0051, Japan
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4
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Saha R, Choi JA, Chen IA. Protocell Effects on RNA Folding, Function, and Evolution. Acc Chem Res 2024; 57:2058-2066. [PMID: 39005057 PMCID: PMC11308369 DOI: 10.1021/acs.accounts.4c00174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 06/03/2024] [Accepted: 07/03/2024] [Indexed: 07/16/2024]
Abstract
ConspectusCreating a living system from nonliving matter is a great challenge in chemistry and biophysics. The early history of life can provide inspiration from the idea of the prebiotic "RNA World" established by ribozymes, in which all genetic and catalytic activities were executed by RNA. Such a system could be much simpler than the interdependent central dogma characterizing life today. At the same time, cooperative systems require a mechanism such as cellular compartmentalization in order to survive and evolve. Minimal cells might therefore consist of simple vesicles enclosing a prebiotic RNA metabolism.The internal volume of a vesicle is a distinctive environment due to its closed boundary, which alters diffusion and available volume for macromolecules and changes effective molecular concentrations, among other considerations. These physical effects are mechanistically distinct from chemical interactions, such as electrostatic repulsion, that might also occur between the membrane boundary and encapsulated contents. Both indirect and direct interactions between the membrane and RNA can give rise to nonintuitive, "emergent" behaviors in the model protocell system. We have been examining how encapsulation inside membrane vesicles would affect the folding and activity of entrapped RNA.Using biophysical techniques such as FRET, we characterized ribozyme folding and activity inside vesicles. Encapsulation inside model protocells generally promoted RNA folding, consistent with an excluded volume effect, independently of chemical interactions. This energetic stabilization translated into increased ribozyme activity in two different systems that were studied (hairpin ribozyme and self-aminoacylating RNAs). A particularly intriguing finding was that encapsulation could rescue the activity of mutant ribozymes, suggesting that encapsulation could affect not only folding and activity but also evolution. To study this further, we developed a high-throughput sequencing assay to measure the aminoacylation kinetics of many thousands of ribozyme variants in parallel. The results revealed an unexpected tendency for encapsulation to improve the better ribozyme variants more than worse variants. During evolution, this effect would create a tilted playing field, so to speak, that would give additional fitness gains to already-high-activity variants. According to Fisher's Fundamental Theorem of Natural Selection, the increased variance in fitness should manifest as faster evolutionary adaptation. This prediction was borne out experimentally during in vitro evolution, where we observed that the initially diverse ribozyme population converged more quickly to the most active sequences when they were encapsulated inside vesicles.The studies in this Account have expanded our understanding of emergent protocell behavior, by showing how simply entrapping an RNA inside a vesicle, which could occur spontaneously during vesicle formation, might profoundly affect the evolutionary landscape of the RNA. Because of the exponential dynamics of replication and selection, even small changes to activity and function could lead to major evolutionary consequences. By closely studying the details of minimal yet surprisingly complex protocells, we might one day trace a pathway from encapsulated RNA to a living system.
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Affiliation(s)
- Ranajay Saha
- Department of Chemical and Biomolecular
Engineering, Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095-1592, United States
| | - Jongseok A. Choi
- Department of Chemical and Biomolecular
Engineering, Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095-1592, United States
| | - Irene A. Chen
- Department of Chemical and Biomolecular
Engineering, Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095-1592, United States
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5
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Saha R, Vázquez-Salazar A, Nandy A, Chen IA. Fitness Landscapes and Evolution of Catalytic RNA. Annu Rev Biophys 2024; 53:109-125. [PMID: 39013026 DOI: 10.1146/annurev-biophys-030822-025038] [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: 07/18/2024]
Abstract
The relationship between genotype and phenotype, or the fitness landscape, is the foundation of genetic engineering and evolution. However, mapping fitness landscapes poses a major technical challenge due to the amount of quantifiable data that is required. Catalytic RNA is a special topic in the study of fitness landscapes due to its relatively small sequence space combined with its importance in synthetic biology. The combination of in vitro selection and high-throughput sequencing has recently provided empirical maps of both complete and local RNA fitness landscapes, but the astronomical size of sequence space limits purely experimental investigations. Next steps are likely to involve data-driven interpolation and extrapolation over sequence space using various machine learning techniques. We discuss recent progress in understanding RNA fitness landscapes, particularly with respect to protocells and machine representations of RNA. The confluence of technical advances may significantly impact synthetic biology in the near future.
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Affiliation(s)
- Ranajay Saha
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California, USA; ,
| | - Alberto Vázquez-Salazar
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California, USA; ,
| | - Aditya Nandy
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California, USA; ,
- Department of Chemistry, The University of Chicago, Chicago, Illinois, USA
- The James Franck Institute, The University of Chicago, Chicago, Illinois, USA
| | - Irene A Chen
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California, USA; ,
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA
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6
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Li H, Chen Z, Zheng L, Wang J, Adenusi H, Passerini S, Zhang H. Electrolyte Strategies Facilitating Anion-Derived Solid-Electrolyte Interphases for Aqueous Zinc-Metal Batteries. SMALL METHODS 2024; 8:e2300554. [PMID: 37421218 DOI: 10.1002/smtd.202300554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/20/2023] [Indexed: 07/10/2023]
Abstract
Rechargeable aqueous zinc-metal batteries (AZBs) are a promising complimentary technology to the existing lithium-ion batteries and the re-emerging lithium-metal batteries to satisfy the increasing demands on energy storage. Despite considerable progress achieved in the past years, the fundamental understanding of the solid-electrolyte interphase (SEI) formation and how its composition influences the SEI properties are limited. This review highlights the functionalities of anion-tuned SEI on the reversibility of zinc-metal anode, with a specific emphasis on new structural insights obtained through advanced characterizations and computational techniques. Recent efforts in terms of key variables that govern the interfacial behaviors to improve the long-term stability of zinc anode, i.e., Coulombic efficiency, plating morphology, dendrite formation, and side-reactions, are comprehensively reviewed. Lastly, the remaining challenges and future perspectives are presented, providing insights into the rational design of practical high-performance AZBs.
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Affiliation(s)
- Huihua Li
- Key Laboratory of Engineering Dielectric and Applications (Ministry of Education), School of Electrical and Electronic Engineering, Harbin University of Science and Technology, Harbin, 150080, P. R. China
| | - Zhen Chen
- Key Laboratory of Engineering Dielectric and Applications (Ministry of Education), School of Electrical and Electronic Engineering, Harbin University of Science and Technology, Harbin, 150080, P. R. China
| | - Leilei Zheng
- Institute of Flexible Electronics, Northwestern Polytechnical University, Xi'an, 710072, P. R. China
| | - Jian Wang
- Helmholtz Institute Ulm (HIU), D-89081, Ulm, Germany
- Karlsruhe Institute of Technology (KIT), D-76021, Karlsruhe, Germany
| | - Henry Adenusi
- Department of Chemistry, The University of Hong Kong, Hong Kong, P. R. China
- Hong Kong Quantum AI Lab, Hong Kong, P. R. China
| | - Stefano Passerini
- Helmholtz Institute Ulm (HIU), D-89081, Ulm, Germany
- Karlsruhe Institute of Technology (KIT), D-76021, Karlsruhe, Germany
- Chemistry Department, Sapienza University of Rome, Rome, 00185, Italy
| | - Huang Zhang
- Institute of Flexible Electronics, Northwestern Polytechnical University, Xi'an, 710072, P. R. China
- Chongqing Innovation Center, Northwestern Polytechnical University, Chongqing, 401135, P. R. China
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7
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Djalali-Cuevas A, Rettel M, Stein F, Savitski M, Kearns S, Kelly J, Biggs M, Skoufos I, Tzora A, Prassinos N, Diakakis N, Zeugolis DI. Macromolecular crowding in human tenocyte and skin fibroblast cultures: A comparative analysis. Mater Today Bio 2024; 25:100977. [PMID: 38322661 PMCID: PMC10846491 DOI: 10.1016/j.mtbio.2024.100977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/22/2023] [Accepted: 01/24/2024] [Indexed: 02/08/2024] Open
Abstract
Although human tenocytes and dermal fibroblasts have shown promise in tendon engineering, no tissue engineered medicine has been developed due to the prolonged ex vivo time required to develop an implantable device. Considering that macromolecular crowding has the potential to substantially accelerate the development of functional tissue facsimiles, herein we compared human tenocyte and dermal fibroblast behaviour under standard and macromolecular crowding conditions to inform future studies in tendon engineering. Basic cell function analysis made apparent the innocuousness of macromolecular crowding for both cell types. Gene expression analysis of the without macromolecular crowding groups revealed expression of tendon related molecules in human dermal fibroblasts and tenocytes. Protein electrophoresis and immunocytochemistry analyses showed significantly increased and similar deposition of collagen fibres by macromolecular crowding in the two cell types. Proteomics analysis demonstrated great similarities between human tenocyte and dermal fibroblast cultures, as well as the induction of haemostatic, anti-microbial and tissue-protective proteins by macromolecular crowding in both cell populations. Collectively, these data rationalise the use of either human dermal fibroblasts or tenocytes in combination with macromolecular crowding in tendon engineering.
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Affiliation(s)
- Adrian Djalali-Cuevas
- Laboratory of Animal Science, Nutrition and Biotechnology, School of Agriculture, University of Ioannina, Arta, Greece
- School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Regenerative, Modular & Developmental Engineering Laboratory (REMODEL), Charles Institute of Dermatology, Conway Institute of Biomolecular & Biomedical Research and School of Mechanical & Materials Engineering, University College Dublin (UCD), Dublin, Ireland
| | - Mandy Rettel
- Proteomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Mikhail Savitski
- Proteomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Jack Kelly
- Galway University Hospital, Galway, Ireland
| | - Manus Biggs
- Science Foundation Ireland (SFI) Centre for Research in Medical Devices (CÚRAM), Biomedical Sciences Building, University of Galway, Galway, Ireland
| | - Ioannis Skoufos
- Laboratory of Animal Science, Nutrition and Biotechnology, School of Agriculture, University of Ioannina, Arta, Greece
| | - Athina Tzora
- Laboratory of Animal Science, Nutrition and Biotechnology, School of Agriculture, University of Ioannina, Arta, Greece
| | - Nikitas Prassinos
- School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Nikolaos Diakakis
- School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dimitrios I. Zeugolis
- Regenerative, Modular & Developmental Engineering Laboratory (REMODEL), Charles Institute of Dermatology, Conway Institute of Biomolecular & Biomedical Research and School of Mechanical & Materials Engineering, University College Dublin (UCD), Dublin, Ireland
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8
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Alfano C, Fichou Y, Huber K, Weiss M, Spruijt E, Ebbinghaus S, De Luca G, Morando MA, Vetri V, Temussi PA, Pastore A. Molecular Crowding: The History and Development of a Scientific Paradigm. Chem Rev 2024; 124:3186-3219. [PMID: 38466779 PMCID: PMC10979406 DOI: 10.1021/acs.chemrev.3c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 02/13/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024]
Abstract
It is now generally accepted that macromolecules do not act in isolation but "live" in a crowded environment, that is, an environment populated by numerous different molecules. The field of molecular crowding has its origins in the far 80s but became accepted only by the end of the 90s. In the present issue, we discuss various aspects that are influenced by crowding and need to consider its effects. This Review is meant as an introduction to the theme and an analysis of the evolution of the crowding concept through time from colloidal and polymer physics to a more biological perspective. We introduce themes that will be more thoroughly treated in other Reviews of the present issue. In our intentions, each Review may stand by itself, but the complete collection has the aspiration to provide different but complementary perspectives to propose a more holistic view of molecular crowding.
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Affiliation(s)
- Caterina Alfano
- Structural
Biology and Biophysics Unit, Fondazione
Ri.MED, 90100 Palermo, Italy
| | - Yann Fichou
- CNRS,
Bordeaux INP, CBMN UMR 5248, IECB, University
of Bordeaux, F-33600 Pessac, France
| | - Klaus Huber
- Department
of Chemistry, University of Paderborn, 33098 Paderborn, Germany
| | - Matthias Weiss
- Experimental
Physics I, Physics of Living Matter, University
of Bayreuth, 95440 Bayreuth, Germany
| | - Evan Spruijt
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Simon Ebbinghaus
- Lehrstuhl
für Biophysikalische Chemie and Research Center Chemical Sciences
and Sustainability, Research Alliance Ruhr, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Giuseppe De Luca
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | | | - Valeria Vetri
- Dipartimento
di Fisica e Chimica − Emilio Segrè, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | | | - Annalisa Pastore
- King’s
College London, Denmark
Hill Campus, SE5 9RT London, United Kingdom
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9
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Miyagawa A, Ueda Y, Nakatani K. Molecular crowding effect in Hantzch pyridine synthesis in polyethylene glycol aqueous solution. Phys Chem Chem Phys 2024; 26:5615-5620. [PMID: 38288480 DOI: 10.1039/d3cp06104c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
In a molecular crowding environment, the kinetics and thermodynamics differ from those in a diluted solution. Although the molecular crowding effect has been extensively investigated, its fundamental kinetics and thermodynamics remain unclear. In this study, we investigated the change in the rate constant (k) of the Hantzch pyridine reaction in a molecular crowding environment using polyethylene glycol (PEG). While the k value increased to a PEG concentration (CPEG) of 10 vol%, a decreasing trend was observed for CPEG > 20 vol%. This intriguing behavior was analyzed based on the increase in reactant activity due to volume exclusion and the decrease in water activity due to osmotic pressure. Volume exclusion and osmotic pressure had opposing effects on the reaction, which were positive for volume exclusion and negative for osmotic pressure. We found that k decreased when the negative effect of the osmotic pressure surpassed the volume exclusion effect.
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Affiliation(s)
- Akihisa Miyagawa
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Yasuyuki Ueda
- Institute of Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba 263-8555, Japan
| | - Kiyoharu Nakatani
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
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10
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Shandilya E, Bains AS, Maiti S. Enzyme-Mediated Temporal Control over the Conformational Disposition of a Condensed Protein in Macromolecular Crowded Media. J Phys Chem B 2023; 127:10508-10517. [PMID: 38052045 DOI: 10.1021/acs.jpcb.3c07074] [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: 12/07/2023]
Abstract
Temporal regulation between input and output signals is one of the hallmarks of complex biological processes. Herein, we report that the conformational disposition of a protein in macromolecularly crowded media can be controlled with time using enzymes. First, we demonstrate the pH dependence of bovine serum albumin (BSA) condensation and conformational alteration in the presence of poly(ethylene glycol) as a crowder. However, by exploiting the strength of pH-modulatory enzymatic reactions (glucose oxidase and urease), the conversion time between the condensed and free forms can be tuned. Additionally, we demonstrate that the trapping of intermediate states with respect to the overall system at a particular α-helix or β-sheet composition and rotational mobility can be possible simply by altering the substrate concentration. Finally, we show that the intrinsic catalytic ability of BSA toward the Kemp elimination (KE) reaction is inhibited in the aggregated form but regained in the free form. In fact, the rate of KE reaction can also be actuated enzymatically in a temporal fashion, therefore demonstrating the programmability of a cascade of biochemical events in crowded media.
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Affiliation(s)
- Ekta Shandilya
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
| | - Arshdeep Singh Bains
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
| | - Subhabrata Maiti
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
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11
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Ji D, Kim J. Trend of Developing Aqueous Liquid and Gel Electrolytes for Sustainable, Safe, and High-Performance Li-Ion Batteries. NANO-MICRO LETTERS 2023; 16:2. [PMID: 37930432 PMCID: PMC10628089 DOI: 10.1007/s40820-023-01220-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/28/2023] [Indexed: 11/07/2023]
Abstract
Current lithium-ion batteries (LIBs) rely on organic liquid electrolytes that pose significant risks due to their flammability and toxicity. The potential for environmental pollution and explosions resulting from battery damage or fracture is a critical concern. Water-based (aqueous) electrolytes have been receiving attention as an alternative to organic electrolytes. However, a narrow electrochemical-stability window, water decomposition, and the consequent low battery operating voltage and energy density hinder the practical use of aqueous electrolytes. Therefore, developing novel aqueous electrolytes for sustainable, safe, high-performance LIBs remains challenging. This Review first commences by summarizing the roles and requirements of electrolytes-separators and then delineates the progression of aqueous electrolytes for LIBs, encompassing aqueous liquid and gel electrolyte development trends along with detailed principles of the electrolytes. These aqueous electrolytes are progressed based on strategies using superconcentrated salts, concentrated diluents, polymer additives, polymer networks, and artificial passivation layers, which are used for suppressing water decomposition and widening the electrochemical stability window of water of the electrolytes. In addition, this Review discusses potential strategies for the implementation of aqueous Li-metal batteries with improved electrolyte-electrode interfaces. A comprehensive understanding of each strategy in the aqueous system will assist in the design of an aqueous electrolyte and the development of sustainable and safe high-performance batteries.
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Affiliation(s)
- Donghwan Ji
- School of Chemical Engineering, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
- Department of NanoEngineering, University of California San Diego, La Jolla, San Diego, CA, 92093, USA
| | - Jaeyun Kim
- School of Chemical Engineering, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea.
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology (SAIHST), Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea.
- Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea.
- Institute of Quantum Biophysics (IQB), Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea.
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12
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Dandekar BR, Majumdar BB, Mondal J. Nonmonotonic Modulation of the Protein-Ligand Recognition Event by Inert Crowders. J Phys Chem B 2023; 127:7449-7461. [PMID: 37590118 DOI: 10.1021/acs.jpcb.3c03946] [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: 08/19/2023]
Abstract
The ubiquitous event of a protein recognizing small molecules or ligands at its native binding site is crucial for initiating major biological processes. However, how a crowded environment, as is typically represented by a cellular interior, would modulate the protein-ligand search process is largely debated. Excluded volume-based theory suggests that the presence of an inert crowder would reinforce a steady stabilization and enhancement of the protein-ligand recognition process. Here, we counter this long-held perspective via the molecular dynamics simulation and Markov state model of the protein-ligand recognition event in the presence of inert crowders. Specifically, we demonstrate that, depending on concentration, even purely inert crowders can exert a nonmonotonic effect via either stabilizing or destabilizing the protein-ligand binding event. Analysis of the kinetic network of binding pathways reveals that the crowders would either modulate precedent non-native on-pathway intermediates or would devise additional ones in a multistate recognition event across a wide range of concentrations. As an important insight, crowders gradually shift the relative transitional preference of these intermediates toward a native-bound state, with ligand residence time at the binding pocket dictating the trend of nonmonotonic concentration dependence by simple inert crowders.
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13
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Menon S, Mondal J. Conformational Plasticity in α-Synuclein and How Crowded Environment Modulates It. J Phys Chem B 2023; 127:4032-4049. [PMID: 37114769 DOI: 10.1021/acs.jpcb.3c00982] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
A 140-residue intrinsically disordered protein (IDP), α-synuclein (αS), is known to adopt conformations that are vastly plastic and susceptible to environmental cues and crowders. However, the inherently heterogeneous nature of αS has precluded a clear demarcation of its monomeric precursor between aggregation-prone and functionally relevant aggregation-resistant states and how a crowded environment could modulate their mutual dynamic equilibrium. Here, we identify an optimal set of distinct metastable states of αS in aqueous media by dissecting a 73 μs-long molecular dynamics ensemble via building a comprehensive Markov state model (MSM). Notably, the most populated metastable state corroborates with the dimension obtained from PRE-NMR studies of αS monomer, and it undergoes kinetic transition at diverse time scales with a weakly populated random-coil-like ensemble and a globular protein-like state. However, subjecting αS to a crowded environment results in a nonmonotonic compaction of these metastable conformations, thereby skewing the ensemble by either introducing new tertiary contacts or by reinforcing the innate contacts. The early stage of dimerization process is found to be considerably expedited in the presence of crowders, albeit promoting nonspecific interactions. Together with this, using an extensively sampled ensemble of αS, this exposition demonstrates that crowded environments can potentially modulate the conformational preferences of IDP that can either promote or inhibit aggregation events.
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Affiliation(s)
- Sneha Menon
- Tata Institute of Fundamental Research Hyderabad, Telangana 500046, India
| | - Jagannath Mondal
- Tata Institute of Fundamental Research Hyderabad, Telangana 500046, India
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14
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Lai WJC, Zhu M, Belinite M, Ballard G, Mathews DH, Ermolenko DN. Intrinsically Unstructured Sequences in the mRNA 3' UTR Reduce the Ability of Poly(A) Tail to Enhance Translation. J Mol Biol 2022; 434:167877. [PMID: 36368412 PMCID: PMC9750134 DOI: 10.1016/j.jmb.2022.167877] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 09/27/2022] [Accepted: 11/01/2022] [Indexed: 11/09/2022]
Abstract
The 5' cap and 3' poly(A) tail of mRNA are known to synergistically stimulate translation initiation via the formation of the cap•eIF4E•eIF4G•PABP•poly(A) complex. Most mRNA sequences have an intrinsic propensity to fold into extensive intramolecular secondary structures that result in short end-to-end distances. The inherent compactness of mRNAs might stabilize the cap•eIF4E•eIF4G•PABP•poly(A) complex and enhance cap-poly(A) translational synergy. Here, we test this hypothesis by introducing intrinsically unstructured sequences into the 5' or 3' UTRs of model mRNAs. We found that the introduction of unstructured sequences into the 3' UTR, but not the 5' UTR, decreases mRNA translation in cell-free wheat germ and yeast extracts without affecting mRNA stability. The observed reduction in protein synthesis results from the diminished ability of the poly(A) tail to stimulate translation. These results suggest that base pair formation by the 3' UTR enhances the cap-poly(A) synergy in translation initiation.
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Affiliation(s)
- Wan-Jung C Lai
- Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, United States
| | - Mingyi Zhu
- Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, United States
| | - Margarita Belinite
- Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, United States
| | - Gregory Ballard
- Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, United States
| | - David H Mathews
- Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, United States
| | - Dmitri N Ermolenko
- Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, United States.
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15
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Miyagawa A, Komatsu H, Nagatomo S, Nakatani K. Thermodynamic Complexation Mechanism of Zinc Ion with 8-Hydroxyquinoline-5-Sulfonic Acid in Molecular Crowding Environment. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.121181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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16
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Sieg JP, McKinley LN, Huot MJ, Yennawar NH, Bevilacqua PC. The Metabolome Weakens RNA Thermodynamic Stability and Strengthens RNA Chemical Stability. Biochemistry 2022; 61:2579-2591. [PMID: 36306436 PMCID: PMC9669196 DOI: 10.1021/acs.biochem.2c00488] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We examined the complex network of interactions among RNA, the metabolome, and divalent Mg2+ under conditions that mimic the Escherichia coli cytoplasm. We determined Mg2+ binding constants for the top 15 E. coli metabolites, comprising 80% of the metabolome by concentration at physiological pH and monovalent ion concentrations. These data were used to inform the development of an artificial cytoplasm that mimics in vivo E. coli conditions, which we term "Eco80". We empirically determined that the mixture of E. coli metabolites in Eco80 approximated single-site binding behavior toward Mg2+ in the biologically relevant free Mg2+ range of ∼0.5 to 3 mM Mg2+, using a Mg2+-sensitive fluorescent dye. Effects of Eco80 conditions on the thermodynamic stability, chemical stability, structure, and catalysis of RNA were examined. We found that Eco80 conditions lead to opposing effects on the thermodynamic and chemical stabilities of RNA. In particular, the thermodynamic stability of RNA helices was weakened by 0.69 ± 0.12 kcal/mol, while the chemical stability was enhanced ∼2-fold, which can be understood using the speciation of Mg2+ between weak and strong Mg2+-metabolite complexes in Eco80. Overall, the use of Eco80 reflects RNA function in vivo and enhances the biological relevance of mechanistic studies of RNA.
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Affiliation(s)
- Jacob P. Sieg
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802
| | - Lauren N. McKinley
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802
| | - Melanie J. Huot
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802
- Department of Biology, Pennsylvania State University, University Park, PA 16802
| | - Neela H. Yennawar
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Philip C. Bevilacqua
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802
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17
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Quinn SD, Dresser L, Graham S, Conteduca D, Shepherd J, Leake MC. Crowding-induced morphological changes in synthetic lipid vesicles determined using smFRET. Front Bioeng Biotechnol 2022; 10:958026. [PMID: 36394015 PMCID: PMC9650091 DOI: 10.3389/fbioe.2022.958026] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/13/2022] [Indexed: 12/02/2022] Open
Abstract
Lipid vesicles are valuable mesoscale molecular confinement vessels for studying membrane mechanics and lipid-protein interactions, and they have found utility among bio-inspired technologies, including drug delivery vehicles. While vesicle morphology can be modified by changing the lipid composition and introducing fusion or pore-forming proteins and detergents, the influence of extramembrane crowding on vesicle morphology has remained under-explored owing to a lack of experimental tools capable of capturing morphological changes on the nanoscale. Here, we use biocompatible polymers to simulate molecular crowding in vitro, and through combinations of FRET spectroscopy, lifetime analysis, dynamic light scattering, and single-vesicle imaging, we characterize how crowding regulates vesicle morphology. We show that both freely diffusing and surface-tethered vesicles fluorescently tagged with the DiI and DiD FRET pair undergo compaction in response to modest concentrations of sorbitol, polyethylene glycol, and Ficoll. A striking observation is that sorbitol results in irreversible compaction, whereas the influence of high molecular weight PEG-based crowders was found to be reversible. Regulation of molecular crowding allows for precise control of the vesicle architecture in vitro, with vast implications for drug delivery and vesicle trafficking systems. Furthermore, our observations of vesicle compaction may also serve to act as a mechanosensitive readout of extramembrane crowding.
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Affiliation(s)
- Steven D. Quinn
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
- York Biomedical Research Institute, University of York, York, United Kingdom
| | - Lara Dresser
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
| | - Sarah Graham
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
| | - Donato Conteduca
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
| | - Jack Shepherd
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
- Department of Biology, University of York, York, United Kingdom
| | - Mark C. Leake
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
- York Biomedical Research Institute, University of York, York, United Kingdom
- Department of Biology, University of York, York, United Kingdom
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18
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Gupta P, Khadake RM, Panja S, Shinde K, Rode AB. Alternative RNA Conformations: Companion or Combatant. Genes (Basel) 2022; 13:1930. [PMID: 36360167 PMCID: PMC9689429 DOI: 10.3390/genes13111930] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/19/2022] [Accepted: 10/19/2022] [Indexed: 09/06/2024] Open
Abstract
RNA molecules, in one form or another, are involved in almost all aspects of cell physiology, as well as in disease development. The diversity of the functional roles of RNA comes from its intrinsic ability to adopt complex secondary and tertiary structures, rivaling the diversity of proteins. The RNA molecules form dynamic ensembles of many interconverting conformations at a timescale of seconds, which is a key for understanding how they execute their cellular functions. Given the crucial role of RNAs in various cellular processes, we need to understand the RNA molecules from a structural perspective. Central to this review are studies aimed at revealing the regulatory role of conformational equilibria in RNA in humans to understand genetic diseases such as cancer and neurodegenerative diseases, as well as in pathogens such as bacteria and viruses so as to understand the progression of infectious diseases. Furthermore, we also summarize the prior studies on the use of RNA structures as platforms for the rational design of small molecules for therapeutic applications.
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Affiliation(s)
| | | | | | | | - Ambadas B. Rode
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad—Gurugram Expressway, Faridabad 121001, India
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19
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J-aggregation of 5, 10, 15, 20-tetraphenyl-21H, 23H-porphinetetrasulfonic acid in a molecular crowding environment simulated using dextran. ANAL SCI 2022; 38:1505-1512. [PMID: 36050568 DOI: 10.1007/s44211-022-00185-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/23/2022] [Indexed: 11/01/2022]
Abstract
In a molecular crowding environment, different thermodynamics is often observed in a dilute solution. One such example is the promotion of the formation of amyloids, which are causal agents of Alzheimer's disease. Although a considerable number of molecular crowding studies have been reported, its effect remains unclear. In this study, we investigated a J-aggregation of a porphyrin derivative, 5, 10, 15, 20-tetraphenyl-21H,23H-porphinetetrasulfonic acid (TPPS), in a molecular crowding environment simulated by dextran (Dex) in HClO4, HCl, and NaCl solutions. The changes in the number of monomers in the J-aggregate (n) with the concentration of Dex (CDex) depended on the type of solution. No change in n was observed in the NaCl solution, which indicated that the Dex solution did not affect the J-aggregation because of the ionic strength effect. In the HCl solution, the aggregation behavior changed with the pH. Further, at a low pH, the electrostatic interactions promoted J-aggregation by the volume exclusion of Dex, while the aggregation was suppressed at a high pH owing to steric hindrance. A different aggregation mechanism, involving the hydrogen bonding between NH in the center of the TPPS macrocyclic frame and the SO3H and ClO4- functional groups, was responsible for the J-aggregation in the HClO4 solution. Moreover, the n value increased owing to the volume exclusion effect. We expect that this study will be useful for further elucidation of the molecular crowding effect.
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20
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Yoo H, Davis CM. An in vitro cytomimetic of in-cell RNA folding. Chembiochem 2022; 23:e202200406. [PMID: 35999178 DOI: 10.1002/cbic.202200406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/21/2022] [Indexed: 11/07/2022]
Abstract
To discover the cytomimetic that accounts for cytoplasmic crowding and sticking on RNA stability, we conducted a two-dimensional scan of mixtures of artificial crowding and sticking agents, PEG10k and M-PERTM. As our model RNA, we investigate the fourU RNA thermometer motif of Salmonella, a hairpin-structured RNA that regulates translation by unfolding and exposing its RBS in response to temperature perturbations. We found that the addition of artificial crowding and sticking agents leads to a stabilization and destabilization of RNA folding, respectively, through the excluded volume effect and surface interactions. FRET-labels were added to the fourU RNA and Fast Relaxation Imaging (FReI), fluorescence microscopy coupled to temperature-jump spectroscopy, probed differences between folding stability of RNA inside single living cells and in vitro. Our results suggest that the cytoplasmic environment affecting RNA folding is comparable to a combination of 20% v/v M-PERTM and 150 g/L PEG10k.
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Affiliation(s)
- Hyejin Yoo
- Yale University, Chemistry, 225 Prospect St, 06511, New Haven, UNITED STATES
| | - Caitlin M Davis
- Yale University, Chemistry, 225 Prospect St., 06511, New Haven, UNITED STATES
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21
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Sung HL, Nesbitt DJ. Synergism in the Molecular Crowding of Ligand-Induced Riboswitch Folding: Kinetic/Thermodynamic Insights from Single-Molecule Spectroscopy. J Phys Chem B 2022; 126:6419-6427. [PMID: 35981263 DOI: 10.1021/acs.jpcb.2c03507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Conformational dynamics in riboswitches involves ligand binding and folding of RNA, each of which can be influenced by excluded volume effects under "crowded" in vivo cellular conditions and thus incompletely characterized by in vitro studies under dilute buffer conditions. In this work, temperature-dependent single-molecule fluorescence resonance energy transfer (FRET) spectroscopy is used to characterize the thermodynamics of (i) cognate ligand and (ii) molecular crowders (PEG, polyethylene glycol) on folding of the B. subtilis LysC lysine riboswitch. With the help of detailed kinetic analysis, we isolate and study the effects of PEG on lysine binding and riboswitch folding steps individually, from which we find that PEG crowding facilitates riboswitch folding primarily via a surprising increase in affinity for the cognate ligand. This is furthermore confirmed by temperature-dependent studies, which reveal that PEG crowding is not purely entropic and instead significantly impacts both enthalpic and entropic contributions to the free energy landscape for folding. The results indicate that PEG molecular crowding/stabilization of the lysine riboswitch is more mechanistically complex and requires extension beyond the conventional picture of purely repulsive solvent-solute steric interactions arising from excluded volume and entropy. Instead, the current experimental FRET data support an alternative multistep mechanism, whereby PEG first entropically crowds the unfolded riboswitch into a "pre-folded" conformation, which in turn greatly increases the ligand binding affinity and thereby enhances the overall equilibrium for riboswitch folding.
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Affiliation(s)
- Hsuan-Lei Sung
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, United States.,Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - David J Nesbitt
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, United States.,Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States.,Department of Physics, University of Colorado, Boulder, Colorado 80309, United States
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22
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Miyagawa A, Komatsu H, Nagatomo S, Nakatani K. Acid Dissociation Behavior of 8-Hydroxyquinoline-5-Sulfonic Acid in Molecular Crowding Environment Modeled Using Polyethylene Glycol. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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23
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Basu M, Mishra PP. Kineto-Mechanistic Investigation of Effect of Macromolecular Crowding on the Breathing of DNA Bubble. J Phys Chem B 2022; 126:1375-1387. [PMID: 35143192 DOI: 10.1021/acs.jpcb.1c08206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Macromolecular crowding along with hydrogen bonding or stacking interactions and hydration reportedly has enormous repercussions on elementary biochemical processes, such as the folding of proteins or nucleic acids involving the stability of DNA base pairing. By using the mismatch-induced DNA bubble as a mesoscopic model, the complex interplay of macromolecular crowding on the dynamical fluctuations at the bubble region within the thermodynamic limit has been monitored using single-molecule fluorescence resonance energy transfer (sm-FRET). These single-molecule experimental results have been further corroborated using physical models such as "scaled particle theory" (SPT) and "Gaussian cloud model" (GCM), to predict the biological activity of DNA. The two-state fluctuation of the DNA bubble has been visualized as a function of the nature, size, and concentration of the crowder. The influence of crowders on the DNA conformation has been investigated with the help of the m-factor, the eccentricity, and the kinetic and thermodynamic parameters without any prior assumption. The clear effect of crowding on the dynamics of such a simple biomolecular system emphasizes the power of single-molecule methods and the dependency of the radius of gyration of the co-solute as well as the preferential interaction with the crowder on the distinct conformational states adopted by the bubble. This study provides an idea and hypothesizes the preferential propensity of the DNA bubble to adopt a conformation with the single-stranded domains being far apart, independent of the crowder size, that may be beneficial for efficient recognition by proteins for an uninterrupted procession of the biological process of the central dogma.
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Affiliation(s)
- Manali Basu
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India.,Homi Bhaba National Institute, Mumbai, Maharashtra 400094, India
| | - Padmaja Prasad Mishra
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India.,Homi Bhaba National Institute, Mumbai, Maharashtra 400094, India
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24
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Abstract
The roots of biological homochirality remain unknown despite decades of study. A commonly proposed path includes an initial small enantiomeric excess that was amplified over time, but a satisfactory source of the excess and a plausible amplification process have yet to be described. We propose here a route to oligonucleotide homochirality from unactivated racemic sources based upon the facts that duplex structures are inherently homochiral and their synthesis from strands of complementary string nucleotide subunits is both uncommonly rapid and exergonic. Simulations employing available kinetic and thermochemical data in an iterated sequence of three equilibria in dry/wet cycles running from unactivated and racemic RNA monomers through oligonucleotides to duplex structures have shown that the exceptional association rate distorts the otherwise simple equilibrium string and overcomes the severe kinetic and stoichiometric barriers to the pairing of the statistically scant homochiral fractions. The simulations reveal widespread deracemization and the full conversion of racemic monomers to populations of L- and D-duplexes in a succession of growth in which the initially formed duplexes are replaced over time with increasingly larger descendants. This claim is open to experimental testing.
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Affiliation(s)
- David Ross
- Retired, formerly SRI International, Menlo Park, California, USA
| | - David Deamer
- Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA
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25
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Peng H, Lelievre A, Landenfeld K, Müller S, Chen IA. Vesicle encapsulation stabilizes intermolecular association and structure formation of functional RNA and DNA. Curr Biol 2022; 32:86-96.e6. [PMID: 34762821 PMCID: PMC8752491 DOI: 10.1016/j.cub.2021.10.047] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/02/2021] [Accepted: 10/21/2021] [Indexed: 01/12/2023]
Abstract
During the origin of life, encapsulation of RNA inside vesicles is believed to have been a defining feature of the earliest cells (protocells). The confined biophysical environment provided by membrane encapsulation differs from that of bulk solution and has been shown to increase activity as well as evolutionary rate for functional RNA. However, the structural basis of the effect on RNA has not been clear. Here, we studied how encapsulation of the hairpin ribozyme inside model protocells affects ribozyme kinetics, ribozyme folding into the active conformation, and cleavage and ligation activities. We further examined the effect of encapsulation on the folding of a stem-loop RNA structure and on the formation of a triplex structure in a pH-sensitive DNA switch. The results indicate that encapsulation promotes RNA-RNA association, both intermolecular and intramolecular, and also stabilizes tertiary folding, including the docked conformation characteristic of the active hairpin ribozyme and the triplex structure. The effects of encapsulation were sufficient to rescue the activity of folding-deficient mutants of the hairpin ribozyme. Stabilization of multiple modes of nucleic acid folding and interaction thus enhanced the activity of encapsulated nucleic acids. Increased association between RNA molecules may facilitate the formation of more complex structures and cooperative interactions. These effects could promote the emergence of biological functions in an "RNA world" and may have utility in the construction of minimal synthetic cells.
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Affiliation(s)
- Huan Peng
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
| | - Amandine Lelievre
- Institute of Biochemistry, University of Greifswald, 17487 Greifswald, Germany
| | | | - Sabine Müller
- Institute of Biochemistry, University of Greifswald, 17487 Greifswald, Germany
| | - Irene A. Chen
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA,Lead Contact:
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26
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Chen J, Sun L, Wang S, Tian F, Zhu H, Zhang R, Dai L. Crowding-induced polymer trapping in a channel. Phys Rev E 2021; 104:054502. [PMID: 34942690 DOI: 10.1103/physreve.104.054502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 10/20/2021] [Indexed: 11/07/2022]
Abstract
In this work, we report an intriguing phenomenon: crowding-induced polymer trapping in a channel. Using Langevin dynamics simulations and analytical calculations, we find that for a polymer confined in a channel, crowding particles can push a polymer into the channel corner through inducing an effective polymer-corner attraction due to the depletion effect. This phenomenon is referred to as polymer trapping. The occurrence of polymer trapping requires a minimum volume fraction of crowders, ϕ^{*}, which scales as ϕ^{*}∼(a_{c}/L_{p})^{1/3} for a_{c}≫a_{m} and ϕ^{*}∼(a_{c}/L_{p})^{1/3}(a_{c}/a_{m})^{1/2} for a_{c}≪a_{m}, where a_{c} is the crowder diameter, a_{m} is the monomer diameter, and L_{p} is the polymer persistence length. For DNA, ϕ^{*} is estimated to be around 0.25 for crowders with a_{c}=2nm. We find that ϕ^{*} also strongly depends on the shape of the channel cross section, and ϕ^{*} is much smaller for a triangle channel than a square channel. The polymer trapping leads to a nearly fully stretched polymer conformation along a channel corner, which may have practical applications, such as full stretching of DNA for the nanochannel-based genome mapping technology.
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Affiliation(s)
- Jialu Chen
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Liang Sun
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Simin Wang
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Fujia Tian
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Haoqi Zhu
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Ruiqin Zhang
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Hong Kong, China
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27
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Sung HL, Nesbitt DJ. Effects of Molecular Crowders on Single-Molecule Nucleic Acid Folding: Temperature-Dependent Studies Reveal True Crowding vs Enthalpic Interactions. J Phys Chem B 2021; 125:13147-13157. [PMID: 34813337 DOI: 10.1021/acs.jpcb.1c07852] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Biomolecular folding in cells can be strongly influenced by spatial overlap/excluded volume interactions (i.e., "crowding") with intracellular solutes. As a result, traditional in vitro experiments with dilute buffers may not accurately recapitulate biomolecule folding behavior in vivo. In order to account for such ubiquitous excluded volume effects, biologically inert polyethylene glycol (PEG) and polysaccharides (dextran and Ficoll) are often used as in vitro crowding agents to mimic in vivo crowding conditions, with a common observation that high concentrations of these polymers stabilize the more compact biomolecule conformation. However, such an analysis can be distorted by differences in polymer interactions with the folded vs unfolded conformers, requiring temperature-dependent analysis of the thermodynamics to reliably assess competing enthalpic vs entropic contributions and thus the explicit role of excluded volume. In this work, temperature-controlled single-molecule fluorescence resonance energy transfer (smFRET) is used to characterize the thermodynamic interaction between nucleic acids and common polymer crowders PEG, dextran, and Ficoll. The results reveal that PEG promotes secondary and tertiary nucleic acid folding by simultaneously increasing the folding rate while decreasing the unfolding rate, with temperature-dependent studies confirming that the source of PEG stabilization is predominantly entropic and consistent with a true excluded volume crowding mechanism. By way of contrast, neither dextran nor Ficoll induces any significant concentration-dependent change in nucleic acid folding stability at room temperature, but instead, stabilization effects gradually appear with a temperature increase. Such a thermal response indicates that both folding enthalpies and entropies are impacted by dextran and Ficoll. A detailed thermodynamic analysis of the kinetics suggests that, instead of true entropic molecular crowding, dextran and Ficoll associate preferentially with the unfolded vs folded nucleic acid conformer as a result of larger solvent accessible surface area, thereby skewing the free energy landscapes through both significant entropic/enthalpic contributions that compete and fortuitously cancel near room temperature.
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Affiliation(s)
- Hsuan-Lei Sung
- JILA, National Institute of Standards and Technology, University of Colorado, Boulder, Colorado 80309, United States.,Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - David J Nesbitt
- JILA, National Institute of Standards and Technology, University of Colorado, Boulder, Colorado 80309, United States.,Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States.,Department of Physics, University of Colorado, Boulder, Colorado 80309, United States
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28
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Mukherjee SK, Knop JM, Winter RHA. Modulation of the Conformational Space of SARS-CoV-2 RNA Quadruplex RG-1 by Cellular Components and the Amyloidogenic Peptides α-Synuclein and hIAPP. Chemistry 2021; 28:e202104182. [PMID: 34882862 PMCID: PMC9015630 DOI: 10.1002/chem.202104182] [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: 11/21/2021] [Indexed: 11/10/2022]
Abstract
Given the emergence of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), which particularly threatens older people with comorbidities such as diabetes mellitus and dementia, understanding the relationship between Covid-19 and other diseases is an important factor for treatment. Possible targets for medical intervention include G-quadruplexes (G4Qs) and their protein interaction partners. We investigated the stability and conformational space of the RG-1 RNA-G-quadruplex of the SARS-CoV-2 N-gene in the presence of salts, cosolutes, crowders and intrinsically disordered peptides, focusing on α-Synuclein and the human islet amyloid polypeptide, which are involved in Parkinson's disease (PD) and type-II diabetes mellitus (T2DM), respectively. We found that the conformational dynamics of the RG-1 G4Q is strongly affected by the various solution conditions. Further, the amyloidogenic peptides were found to strongly modulate the conformational equilibrium of the RG-1. Considerable changes are observed with respect to their interaction with human telomeric G4Qs, which adopt different topologies. These results may therefore shed more light on the relationship between PD as well as T2DM and the SARS-CoV-2 disease and their molecular underpinnings. Since dysregulation of G4Q formation by rationally designed targeting compounds affects the control of cellular processes, this study should contribute to the development of specific ligands for intervention.
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Affiliation(s)
- Sanjib K Mukherjee
- TU Dortmund University: Technische Universitat Dortmund, Chemistry and Chemical Biology, GERMANY
| | - Jim-Marcel Knop
- TU Dortmund University: Technische Universitat Dortmund, Chemistry and Chemical Biology, GERMANY
| | - Roland Hermann Alfons Winter
- TU Dortmund University, Chemistry and Chemical Biology, Otto-Hahn Str. 4a, Physical Chemistry I, 44227, Dortmund, GERMANY
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29
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Hohmann KF, Blümler A, Heckel A, Fürtig B. The RNA chaperone StpA enables fast RNA refolding by destabilization of mutually exclusive base pairs within competing secondary structure elements. Nucleic Acids Res 2021; 49:11337-11349. [PMID: 34614185 PMCID: PMC8565331 DOI: 10.1093/nar/gkab876] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/13/2021] [Accepted: 09/17/2021] [Indexed: 11/14/2022] Open
Abstract
In bacteria RNA gene regulatory elements refold dependent on environmental clues between two or more long-lived conformational states each associated with a distinct regulatory state. The refolding kinetics are strongly temperature-dependent and especially at lower temperatures they reach timescales that are biologically not accessible. To overcome this problem, RNA chaperones have evolved. However, the precise molecular mechanism of how these proteins accelerate RNA refolding reactions remains enigmatic. Here we show how the RNA chaperone StpA of Escherichia coli leads to an acceleration of a bistable RNA's refolding kinetics through the selective destabilization of key base pairing interactions. We find in laser assisted real-time NMR experiments on photocaged bistable RNAs that the RNA chaperone leads to a two-fold increase in refolding rates at low temperatures due to reduced stability of ground state conformations. Further, we can show that upon interaction with StpA, base pairing interactions in the bistable RNA are modulated to favor refolding through the dominant pseudoknotted transition pathway. Our results shed light on the molecular mechanism of the interaction between RNA chaperones and bistable RNAs and are the first step into a functional classification of chaperones dependent on their biophysical mode of operation.
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Affiliation(s)
- Katharina F Hohmann
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance BMRZ, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438 Frankfurt/Main, Germany
| | - Anja Blümler
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438 Frankfurt/Main, Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438 Frankfurt/Main, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance BMRZ, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438 Frankfurt/Main, Germany
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30
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Miyagawa A, Komatsu H, Nagatomo S, Nakatani K. Effect of Molecular Crowding on Complexation of Metal Ions and 8-Quinolinol-5-Sulfonic Acid. J Phys Chem B 2021; 125:9853-9859. [PMID: 34410719 DOI: 10.1021/acs.jpcb.1c05851] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The effect of molecular crowding on macromolecular reactions has been revealed by many researchers. In this study, we investigate the complexation of metal ions (Zn, Co, and Cd) with 8-quinolinol-5-sulfonic acid as a model of small-molecular reactions in molecular crowding. The complexation constants for 1:1, 1:2, and total complexation in the presence of polyethylene glycol (PEG, a molecular crowding reagent) are evaluated based on the increase in the reactant activity by volume exclusion and the decrease in the water activity due to the change in osmotic pressure. All complexation constants are enhanced by increasing the concentration of PEG. Its mechanisms differ for 1:1, 1:2, and total complexation. The 1:1 complexation is promoted only by the influence of the water activity, while the reactant and water activities influence the increase in the 1:2 complexation constant. Increasing the molecular weight of PEG further increases the complexation constants, as dehydration of the complex is promoted by a higher hydration number of PEG. Because this study gives the fundamental knowledge for the protein-metal interaction, in which solvation is an important factor, in molecular crowding, it provides new insights into molecular crowding studies and should attract the attention of a broad spectrum of biochemistry researchers.
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Affiliation(s)
- Akihisa Miyagawa
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Hiroyuki Komatsu
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Shigenori Nagatomo
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Kiyoharu Nakatani
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
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31
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Tom AM, Kim WK, Hyeon C. Polymer brush-induced depletion interactions and clustering of membrane proteins. J Chem Phys 2021; 154:214901. [PMID: 34240971 DOI: 10.1063/5.0048554] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We investigate the effect of mobile polymer brushes on proteins embedded in biological membranes by employing both Asakura-Oosawa type of theoretical model and coarse-grained molecular dynamics simulations. The brush polymer-induced depletion attraction between proteins changes non-monotonically with the size of brush. The depletion interaction, which is determined by the ratio of the protein size to the grafting distance between brush polymers, increases linearly with the brush size as long as the polymer brush height is shorter than the protein size. When the brush height exceeds the protein size, however, the depletion attraction among proteins is slightly reduced. We also explore the possibility of the brush polymer-induced assembly of a large protein cluster, which can be related to one of many molecular mechanisms underlying recent experimental observations of integrin nanocluster formation and signaling.
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Affiliation(s)
- Anvy Moly Tom
- Korea Institute for Advanced Study, Seoul 02455, South Korea
| | - Won Kyu Kim
- Korea Institute for Advanced Study, Seoul 02455, South Korea
| | - Changbong Hyeon
- Korea Institute for Advanced Study, Seoul 02455, South Korea
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32
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Dobirul Islam M, Motiar Rahman M, Matsumura S, Ikawa Y. Effects of chain length of polyethylene glycol molecular crowders on a mutant Tetrahymena group I ribozyme lacking large peripheral module. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2021; 40:867-883. [PMID: 34402751 DOI: 10.1080/15257770.2021.1956531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
While current group I ribozymes use several distinct strategies to function under conditions of low Mg2+ concentration (≤ 3 mM), a deletion mutant of the Tetrahymena ribozyme (ΔP5 ribozyme) is virtually inactive with 3 mM Mg2+ due to removal of the large peripheral module, P5abc, supporting the active conformation of the core module. We investigated the molecular crowding effects of synthetic polyethylene glycols (PEGs) on the activity of the ΔP5 ribozyme. Among PEG molecules with different chain lengths, PEG600 improved the activity of the ΔP5 ribozyme most effectively in the presence of 3 mM Mg2+.
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Affiliation(s)
- Md Dobirul Islam
- Graduate School of Innovative Life Science, University of Toyama, Toyama, Japan
| | - Md Motiar Rahman
- Graduate School of Innovative Life Science, University of Toyama, Toyama, Japan
| | - Shigeyoshi Matsumura
- Graduate School of Innovative Life Science, University of Toyama, Toyama, Japan.,Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | - Yoshiya Ikawa
- Graduate School of Innovative Life Science, University of Toyama, Toyama, Japan.,Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
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33
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Shape changes and cooperativity in the folding of the central domain of the 16S ribosomal RNA. Proc Natl Acad Sci U S A 2021; 118:2020837118. [PMID: 33658370 DOI: 10.1073/pnas.2020837118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Both the small and large subunits of the ribosome, the molecular machine that synthesizes proteins, are complexes of ribosomal RNAs (rRNAs) and a number of proteins. In bacteria, the small subunit has a single 16S rRNA whose folding is the first step in its assembly. The central domain of the 16S rRNA folds independently, driven either by Mg2+ ions or by interaction with ribosomal proteins. To provide a quantitative description of ion-induced folding of the ∼350-nucleotide rRNA, we carried out extensive coarse-grained molecular simulations spanning Mg2+ concentration between 0 and 30 mM. The Mg2+ dependence of the radius of gyration shows that globally the rRNA folds cooperatively. Surprisingly, various structural elements order at different Mg2+ concentrations, indicative of the heterogeneous assembly even within a single domain of the rRNA. Binding of Mg2+ ions is highly specific, with successive ion condensation resulting in nucleation of tertiary structures. We also predict the Mg2+-dependent protection factors, measurable in hydroxyl radical footprinting experiments, which corroborate the specificity of Mg2+-induced folding. The simulations, which agree quantitatively with several experiments on the folding of a three-way junction, show that its folding is preceded by formation of other tertiary contacts in the central junction. Our work provides a starting point in simulating the early events in the assembly of the small subunit of the ribosome.
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34
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The effect of macromolecular crowders on dielecric constant of aqueous electrolyte solutions. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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Yamagami R, Sieg JP, Bevilacqua PC. Functional Roles of Chelated Magnesium Ions in RNA Folding and Function. Biochemistry 2021; 60:2374-2386. [PMID: 34319696 DOI: 10.1021/acs.biochem.1c00012] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RNA regulates myriad cellular events such as transcription, translation, and splicing. To perform these essential functions, RNA often folds into complex tertiary structures in which its negatively charged ribose-phosphate backbone interacts with metal ions. Magnesium, the most abundant divalent metal ion in cells, neutralizes the backbone, thereby playing essential roles in RNA folding and function. This has been known for more than 50 years, and there are now thousands of in vitro studies, most of which have used ≥10 mM free Mg2+ ions to achieve optimal RNA folding and function. In the cell, however, concentrations of free Mg2+ ions are much lower, with most Mg2+ ions chelated by metabolites. In this Perspective, we curate data from a number of sources to provide extensive summaries of cellular concentrations of metabolites that bind Mg2+ and to estimate cellular concentrations of metabolite-chelated Mg2+ species, in the representative prokaryotic and eukaryotic systems Escherichia coli, Saccharomyces cerevisiae, and iBMK cells. Recent research from our lab and others has uncovered the fact that such weakly chelated Mg2+ ions can enhance RNA function, including its thermodynamic stability, chemical stability, and catalysis. We also discuss how metabolite-chelated Mg2+ complexes may have played roles in the origins of life. It is clear from this analysis that bound Mg2+ should not be simply considered non-RNA-interacting and that future RNA research, as well as protein research, could benefit from considering chelated magnesium.
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Affiliation(s)
- Ryota Yamagami
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Jacob P Sieg
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Philip C Bevilacqua
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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36
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Sung HL, Sengupta A, Nesbitt D. Smaller molecules crowd better: Crowder size dependence revealed by single-molecule FRET studies and depletion force modeling analysis. J Chem Phys 2021; 154:155101. [PMID: 33887926 DOI: 10.1063/5.0045492] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The cell is an extremely crowded environment, which is known to have a profound impact on the thermodynamics, functionality, and conformational stability of biomolecules. Speculations from recent theoretical molecular dynamics studies suggest an intriguing size dependence to such purely entropic crowding effects, whereby small molecular weight crowders under constant enthalpy conditions are more effective than larger crowders on a per volume basis. If experimentally confirmed, this would be profoundly significant, as the cellular cytoplasm is also quite concentrated in smaller molecular weight solutes such as inorganic ions, amino acids, and various metabolites. The challenge is to perform such studies isolating entropic effects under isoenthalpic conditions. In this work, we first present results from single-molecule FRET spectroscopy (smFRET) on the molecular size-dependent crowding stabilization of a simple RNA tertiary motif (the GAAA tetraloop-tetraloop receptor), indeed providing evidence in support of the surprising notion in the crowding literature that "smaller is better." Specifically, systematic smFRET studies as a function of crowder solute size reveal that smaller molecules both significantly increase the RNA tertiary folding rate and, yet, simultaneously decrease the unfolding rate, predicting strongly size-dependent stabilization of RNA tertiary structures under crowded cellular conditions. The size dependence of these effects has been explored via systematic variation of crowder size over a broad range of molecular weights (90-3000 amu). Furthermore, corresponding temperature dependent studies indicate the systematic changes in the folding equilibrium to be predominantly entropic in origin, i.e., consistent with a fundamental picture of entropic molecular crowding without additional enthalpic interactions. Most importantly, all trends in the single-molecule crowding data can be quantitatively recapitulated by a simple analytic depletion force model, whereby excluded volume interactions represent the major thermodynamic driving force toward folding. Our study, thus, not only provides experimental evidence and theoretical support for small molecule crowding but also predicts further enhancement of crowding effects for even smaller molecules on a per volume basis.
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Affiliation(s)
- Hsuan-Lei Sung
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, USA
| | - Abhigyan Sengupta
- Biophysics Department, Technical University of Munich, Garching, Germany
| | - David Nesbitt
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, USA
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37
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Feng C, Tan YL, Cheng YX, Shi YZ, Tan ZJ. Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement. Front Mol Biosci 2021; 8:666369. [PMID: 33928126 PMCID: PMC8078894 DOI: 10.3389/fmolb.2021.666369] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/17/2021] [Indexed: 12/27/2022] Open
Abstract
Macromolecules, such as RNAs, reside in crowded cell environments, which could strongly affect the folded structures and stability of RNAs. The emergence of RNA-driven phase separation in biology further stresses the potential functional roles of molecular crowding. In this work, we employed the coarse-grained model that was previously developed by us to predict 3D structures and stability of the mouse mammary tumor virus (MMTV) pseudoknot under different spatial confinements over a wide range of salt concentrations. The results show that spatial confinements can not only enhance the compactness and stability of MMTV pseudoknot structures but also weaken the dependence of the RNA structure compactness and stability on salt concentration. Based on our microscopic analyses, we found that the effect of spatial confinement on the salt-dependent RNA pseudoknot stability mainly comes through the spatial suppression of extended conformations, which are prevalent in the partially/fully unfolded states, especially at low ion concentrations. Furthermore, our comprehensive analyses revealed that the thermally unfolding pathway of the pseudoknot can be significantly modulated by spatial confinements, since the intermediate states with more extended conformations would loss favor when spatial confinements are introduced.
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Affiliation(s)
- Chenjie Feng
- Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, Center for Theoretical Physics, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Ya-Lan Tan
- Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, Center for Theoretical Physics, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Yu-Xuan Cheng
- Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, Center for Theoretical Physics, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Ya-Zhou Shi
- Research Center of Nonlinear Science, School of Mathematics and Computer Science, Wuhan Textile University, Wuhan, China
| | - Zhi-Jie Tan
- Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, Center for Theoretical Physics, School of Physics and Technology, Wuhan University, Wuhan, China
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38
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Subadini S, Bera K, Hritz J, Sahoo H. Polyethylene glycol perturbs the unfolding of CRABP I: A correlation between experimental and theoretical approach. Colloids Surf B Biointerfaces 2021; 202:111696. [PMID: 33770701 DOI: 10.1016/j.colsurfb.2021.111696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/25/2021] [Accepted: 03/11/2021] [Indexed: 10/21/2022]
Abstract
The importance of macromolecules paves the way towards a detailed molecular level investigation as all most all cellular processes occurring at the interior of cells in the form of proteins, enzymes, and other biological molecules are significantly affected because of their crowding. Thus, exploring the role of crowding environment on the denaturation and renaturation kinetics of protein molecules is of great importance. Here, CRABP I (cellular retinoic acid binding protein I) is employed as a model protein along with different molecular weights of Polyethylene glycol (PEG) as molecular crowders. The experimental evaluations are done by accessing the protein secondary structure analysis using circular dichroism (CD) spectroscopy and unfolding kinetics using intrinsic fluorescence of CRABP I at 37 °C to mimic the in vivo crowding environment. The unfolding kinetics results indicated that both PEG 2000 and PEG 4000 act as stabilizers by retarding the unfolding kinetic rates. Both kinetic and stability outcomes presented the importance of crowding environment on stability and kinetics of CRABP I. The molecular dynamics (MD) studies revealed that thirteen PEG 2000 molecules assembled during the 500 ns simulation, which increases the stability and percentage of β-sheet. The experimental findings are well supported by the molecular dynamics simulation results.
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Affiliation(s)
- Suchismita Subadini
- Biophysical and Protein Chemistry Lab, Department of Chemistry, NIT Rourkela, Rourkela, 769008, India
| | - Krishnendu Bera
- CEITEC MU, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Jozef Hritz
- CEITEC MU, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic; Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Harekrushna Sahoo
- Biophysical and Protein Chemistry Lab, Department of Chemistry, NIT Rourkela, Rourkela, 769008, India; Center of Nanomaterials, NIT Rourkela, Rourkela, 769008, India.
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39
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Roden C, Gladfelter AS. RNA contributions to the form and function of biomolecular condensates. Nat Rev Mol Cell Biol 2021; 22:183-195. [PMID: 32632317 PMCID: PMC7785677 DOI: 10.1038/s41580-020-0264-6] [Citation(s) in RCA: 350] [Impact Index Per Article: 116.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2020] [Indexed: 01/08/2023]
Abstract
Biomolecular condensation partitions cellular contents and has important roles in stress responses, maintaining homeostasis, development and disease. Many nuclear and cytoplasmic condensates are rich in RNA and RNA-binding proteins (RBPs), which undergo liquid-liquid phase separation (LLPS). Whereas the role of RBPs in condensates has been well studied, less attention has been paid to the contribution of RNA to LLPS. In this Review, we discuss the role of RNA in biomolecular condensation and highlight considerations for designing condensate reconstitution experiments. We focus on RNA properties such as composition, length, structure, modifications and expression level. These properties can modulate the biophysical features of native condensates, including their size, shape, viscosity, liquidity, surface tension and composition. We also discuss the role of RNA-protein condensates in development, disease and homeostasis, emphasizing how their properties and function can be determined by RNA. Finally, we discuss the multifaceted cellular functions of biomolecular condensates, including cell compartmentalization through RNA transport and localization, supporting catalytic processes, storage and inheritance of specific molecules, and buffering noise and responding to stress.
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Affiliation(s)
- Christine Roden
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- The Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Amy S Gladfelter
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- The Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
- Whitman Center, Marine Biology Laboratory, Woods Hole, MA, USA.
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40
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Hautke AC, Ebbinghaus S. Folding Stability and Self‐Association of a Triplet‐Repeat (CAG)
20
RNA Hairpin in Cytomimetic Media. CHEMSYSTEMSCHEM 2020. [DOI: 10.1002/syst.202000052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Alexander Christoph Hautke
- Institut für Physikalische und Theoretische Chemie TU Braunschweig Rebenring 56 38106 Braunschweig Germany
| | - Simon Ebbinghaus
- Institut für Physikalische und Theoretische Chemie TU Braunschweig Rebenring 56 38106 Braunschweig Germany
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41
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Kartje ZJ, Janis HI, Mukhopadhyay S, Gagnon KT. Revisiting T7 RNA polymerase transcription in vitro with the Broccoli RNA aptamer as a simplified real-time fluorescent reporter. J Biol Chem 2020; 296:100175. [PMID: 33303627 PMCID: PMC7948468 DOI: 10.1074/jbc.ra120.014553] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 12/03/2020] [Accepted: 12/10/2020] [Indexed: 11/06/2022] Open
Abstract
Methods for rapid and high-throughput screening of transcription in vitro to examine reaction conditions, enzyme mutants, promoter variants, and small molecule modulators can be extremely valuable tools. However, these techniques may be difficult to establish or inaccessible to many researchers. To develop a straightforward and cost-effective platform for assessing transcription in vitro, we used the "Broccoli" RNA aptamer as a direct, real-time fluorescent transcript readout. To demonstrate the utility of our approach, we screened the effect of common reaction conditions and components on bacteriophage T7 RNA polymerase (RNAP) activity using a common quantitative PCR instrument for fluorescence detection. Several essential conditions for in vitro transcription by T7 RNAP were confirmed with this assay, including the importance of enzyme and substrate concentrations, covariation of magnesium and nucleoside triphosphates, and the effects of several typical additives. When we used this method to assess all possible point mutants of a canonical T7 RNAP promoter, our results coincided well with previous reports. This approach should translate well to a broad variety of bacteriophage in vitro transcription systems and provides a platform for developing fluorescence-based readouts of more complex transcription systems in vitro.
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Affiliation(s)
- Zachary J Kartje
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois, USA
| | - Helen I Janis
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois, USA
| | - Shaoni Mukhopadhyay
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois, USA
| | - Keith T Gagnon
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois, USA; Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois, USA.
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42
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Hong F, Schreck JS, Šulc P. Understanding DNA interactions in crowded environments with a coarse-grained model. Nucleic Acids Res 2020; 48:10726-10738. [PMID: 33045749 PMCID: PMC7641764 DOI: 10.1093/nar/gkaa854] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/29/2020] [Accepted: 10/01/2020] [Indexed: 01/01/2023] Open
Abstract
Nucleic acid interactions under crowded environments are of great importance for biological processes and nanotechnology. However, the kinetics and thermodynamics of nucleic acid interactions in a crowded environment remain poorly understood. We use a coarse-grained model of DNA to study the kinetics and thermodynamics of DNA duplex and hairpin formation in crowded environments. We find that crowders can increase the melting temperature of both an 8-mer DNA duplex and a hairpin with a stem of 6-nt depending on the excluded volume fraction of crowders in solution and the crowder size. The crowding induced stability originates from the entropic effect caused by the crowding particles in the system. Additionally, we study the hybridization kinetics of DNA duplex formation and the formation of hairpin stems, finding that the reaction rate kon is increased by the crowding effect, while koff is changed only moderately. The increase in kon mostly comes from increasing the probability of reaching a transition state with one base pair formed. A DNA strand displacement reaction in a crowded environment is also studied with the model and we find that rate of toehold association is increased, with possible applications to speeding up strand displacement cascades in nucleic acid nanotechnology.
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Affiliation(s)
- Fan Hong
- School of Molecular Sciences and Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - John S Schreck
- School of Molecular Sciences and Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.,Department of Chemistry, Drexel University, Philadelphia, PA 19104, USA
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.,Center for Biological Physics, Arizona State University, Tempe, AZ 85287, USA
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43
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Abstract
RNA enzymes or ribozymes catalyze some of the most important reactions in biology and are thought to have played a central role in the origin and evolution of life on earth. Catalytic function in RNA has evolved in crowded cellular environments that are different from dilute solutions in which most in vitro assays are performed. The presence of molecules such as amino acids, polypeptides, alcohols, and sugars in the cell introduces forces that modify the kinetics and thermodynamics of ribozyme-catalyzed reactions. Synthetic molecules are routinely used in in vitro studies to better approximate the properties of biomolecules under in vivo conditions. This review discusses the various forces that operate within simulated crowded solutions in the context of RNA structure, folding, and catalysis. It also explores ideas about how crowding could have been beneficial to the evolution of functional RNAs and the development of primitive cellular systems in a prebiotic milieu.
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Affiliation(s)
- Saurja DasGupta
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.
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44
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Xie J, Liang Z, Lu YC. Molecular crowding electrolytes for high-voltage aqueous batteries. NATURE MATERIALS 2020; 19:1006-1011. [PMID: 32313263 DOI: 10.1038/s41563-020-0667-y] [Citation(s) in RCA: 181] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 03/05/2020] [Indexed: 06/11/2023]
Abstract
Developing low-cost and eco-friendly aqueous electrolytes with a wide voltage window is critical to achieve safe, high-energy and sustainable Li-ion batteries. Emerging approaches using highly concentrated salts (21-55 m (mol kg-1)) create artificial solid-electrode interfaces and improve water stability; however, these approaches raise concerns about cost and toxicity. Molecular crowding is a common phenomenon in living cells where water activity is substantially suppressed by molecular crowding agents through altering the hydrogen-bonding structure. Here we demonstrate a 'molecular crowding' electrolyte using the water-miscible polymer poly(ethylene glycol) as the crowding agent to decrease water activity, thereby achieving a wide electrolyte operation window (3.2 V) with low salt concentration (2 m). Aqueous Li4Ti5O12/LiMn2O4 full cells with stable specific energies between 75 and 110 W h kg-1 were demonstrated over 300 cycles. Online electrochemical mass spectroscopy revealed that common side reactions in aqueous Li-ion batteries (hydrogen/oxygen evolution reactions) are virtually eliminated. This work provides a path for designing high-voltage aqueous electrolytes for low-cost and sustainable energy storage.
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Affiliation(s)
- Jing Xie
- Electrochemical Energy and Interfaces Laboratory, Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Zhuojian Liang
- Electrochemical Energy and Interfaces Laboratory, Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Yi-Chun Lu
- Electrochemical Energy and Interfaces Laboratory, Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China.
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45
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Li X, Liang QX, Lin JR, Peng J, Yang JH, Yi C, Yu Y, Zhang QC, Zhou KR. Epitranscriptomic technologies and analyses. SCIENCE CHINA-LIFE SCIENCES 2020; 63:501-515. [DOI: 10.1007/s11427-019-1658-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 02/12/2020] [Indexed: 01/28/2023]
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46
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Ganser LR, Kelly ML, Herschlag D, Al-Hashimi HM. The roles of structural dynamics in the cellular functions of RNAs. Nat Rev Mol Cell Biol 2020; 20:474-489. [PMID: 31182864 DOI: 10.1038/s41580-019-0136-0] [Citation(s) in RCA: 295] [Impact Index Per Article: 73.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
RNAs fold into 3D structures that range from simple helical elements to complex tertiary structures and quaternary ribonucleoprotein assemblies. The functions of many regulatory RNAs depend on how their 3D structure changes in response to a diverse array of cellular conditions. In this Review, we examine how the structural characterization of RNA as dynamic ensembles of conformations, which form with different probabilities and at different timescales, is improving our understanding of RNA function in cells. We discuss the mechanisms of gene regulation by microRNAs, riboswitches, ribozymes, post-transcriptional RNA modifications and RNA-binding proteins, and how the cellular environment and processes such as liquid-liquid phase separation may affect RNA folding and activity. The emerging RNA-ensemble-function paradigm is changing our perspective and understanding of RNA regulation, from in vitro to in vivo and from descriptive to predictive.
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Affiliation(s)
- Laura R Ganser
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Megan L Kelly
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford ChEM-H Chemistry, Engineering, and Medicine for Human Health, Stanford University, Stanford, CA, USA.,Department of Chemical Engineering, Stanford ChEM-H Chemistry, Engineering, and Medicine for Human Health, Stanford University, Stanford, CA, USA.,Department of Chemistry, Stanford ChEM-H Chemistry, Engineering, and Medicine for Human Health, Stanford University, Stanford, CA, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA. .,Department of Chemistry, Duke University, Durham, NC, USA.
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47
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Shi L, Cao F, Zhang L, Tian Y. I-motif Formed at Physiological pH Triggered by Spatial Confinement of Nanochannels: An Electrochemical Platform for pH Monitoring in Brain Microdialysates. Anal Chem 2020; 92:4535-4540. [PMID: 32052626 DOI: 10.1021/acs.analchem.9b05732] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The development of switches responding to specific pH changes was particularly useful in wide application fields. Owing to flexible switches simulated by pH, i-motif DNAs are widely used as a pH sensor. But its character of structure transition strongly dependent on acidic pH severely hampers the application of i-motif DNA in physiological media. Herein, we report the stable i-motif structure formed at a physiological pH triggered by spatial confinement of silica nanochannels. Three classic DNA chains containing 21-mer i-motif domain base-pairs and a single-stranded multiply (T)n spacer, 5'-COOH-(T)n-CCCTAACCCTAACCCTAACCC-3', were employed to evaluate the enhanced stability of i-motif structure. Compared to their free states in a dilute solution, the transition pH of all i-motif DNAs decorated in nanochannels remarkably shifts toward a neutral pH. Moreover, the transition midpoint can be tuned sensitively over the physiologically relevant pH range through slightly varying the length of T base spacer. Density functional theory (DFT) calculations validate that the increased proton density in a nanochannel triggers the formation of an i-motif structure under a neutral pH. Finally, this i-motif DNA based nanochannels electrode was successfully employed to monitor pH in brain microdialysates followed by cerebral ischemia. The present approach is not limited by fundamental investigation for DNA conformation but may extend toward the manipulation of i-motif based structures for artificial molecular machines and signaling systems.
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Affiliation(s)
- Lu Shi
- School of Chemistry and Molecular Engineering, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Feifei Cao
- School of Chemistry and Molecular Engineering, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Limin Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Yang Tian
- School of Chemistry and Molecular Engineering, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
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48
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Sagar A, Svergun D, Bernadó P. Structural Analyses of Intrinsically Disordered Proteins by Small-Angle X-Ray Scattering. Methods Mol Biol 2020; 2141:249-269. [PMID: 32696361 DOI: 10.1007/978-1-0716-0524-0_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Small-angle X-ray scattering (SAXS) is a low-resolution method for the structural characterization of biological macromolecules in solution. Information about the overall structural features provided by SAXS is highly complementary to X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy, which are high-resolution methods. SAXS not only provides the shape, oligomeric state, and quaternary structure of folded proteins and protein complexes but also allows for quantitative analysis of flexible biomolecules. In this chapter, the most relevant SAXS procedures for structural characterization of flexible macromolecules, including intrinsically disordered proteins (IDPs), are presented. The sample requirements for SAXS experiments on protein solutions and the sequence of steps in data collection and processing are described. The use of the advanced data analysis tools to quantitatively characterize flexible proteins is presented in detail. Typical experimental issues and potential problems encountered during SAXS data measurements and analyses are discussed.
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Affiliation(s)
- Amin Sagar
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, France.
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Hamburg, Germany
| | - Pau Bernadó
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, France.
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49
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Bashardanesh Z, Elf J, Zhang H, van der Spoel D. Rotational and Translational Diffusion of Proteins as a Function of Concentration. ACS OMEGA 2019; 4:20654-20664. [PMID: 31858051 PMCID: PMC6906769 DOI: 10.1021/acsomega.9b02835] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/14/2019] [Indexed: 05/21/2023]
Abstract
Atomistic simulations of three different proteins at different concentrations are performed to obtain insight into protein mobility as a function of protein concentration. We report on simulations of proteins from diluted to the physiological water concentration (about 70% of the mass). First, the viscosity was computed and found to increase by a factor of 7-9 going from pure water to the highest protein concentration, in excellent agreement with in vivo nuclear magnetic resonance results. At a physiological concentration of proteins, the translational diffusion is found to be slowed down to about 30% of the in vitro values. The slow-down of diffusion found here using atomistic models is slightly more than that of a hard sphere model that neglects the electrostatic interactions. Interestingly, rotational diffusion of proteins is slowed down somewhat more (by about 80-95% compared to in vitro values) than translational diffusion, in line with experimental findings and consistent with the increased viscosity. The finding that rotation is retarded more than translation is attributed to solvent-separated clustering. No direct interactions between the proteins are found, and the clustering can likely be attributed to dispersion interactions that are stronger between proteins than between protein and water. Based on these simulations, we can also conclude that the internal dynamics of the proteins in our study are affected only marginally under crowding conditions, and the proteins become somewhat more stable at higher concentrations. Simulations were performed using a force field that was tuned for dealing with crowding conditions by strengthening the protein-water interactions. This force field seems to lead to a reproducible partial unfolding of an α-helix in one of the proteins, an effect that was not observed in the unmodified force field.
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Affiliation(s)
- Zahedeh Bashardanesh
- Uppsala
Center for Computational Chemistry, Science for Life Laboratory, Department
of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box
596, SE-75124 Uppsala, Sweden
| | - Johan Elf
- Uppsala
Center for Computational Chemistry, Science for Life Laboratory, Department
of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box
596, SE-75124 Uppsala, Sweden
| | - Haiyang Zhang
- Department
of Biological Science and Engineering, School of Chemistry and Biological
Engineering, University of Science and Technology
Beijing, 100083 Beijing, China
| | - David van der Spoel
- Uppsala
Center for Computational Chemistry, Science for Life Laboratory, Department
of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box
596, SE-75124 Uppsala, Sweden
- E-mail: . Phone: +46 18 4714205
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50
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Ward FR, Watson ZL, Ad O, Schepartz A, Cate JHD. Defects in the Assembly of Ribosomes Selected for β-Amino Acid Incorporation. Biochemistry 2019; 58:4494-4504. [PMID: 31607123 PMCID: PMC8435211 DOI: 10.1021/acs.biochem.9b00746] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ribosome engineering has emerged as a promising field in synthetic biology, particularly concerning the production of new sequence-defined polymers. Mutant ribosomes have been developed that improve the incorporation of several nonstandard monomers including d-amino acids, dipeptides, and β-amino acids into polypeptide chains. However, there remains little mechanistic understanding of how these ribosomes catalyze incorporation of these new substrates. Here, we probed the properties of a mutant ribosome-P7A7-evolved for better in vivo β-amino acid incorporation through in vitro biochemistry and cryo-electron microscopy. Although P7A7 is a functional ribosome in vivo, it is inactive in vitro, and assembles poorly into 70S ribosome complexes. Structural characterization revealed large regions of disorder in the peptidyltransferase center and nearby features, suggesting a defect in assembly. Comparison of RNA helix and ribosomal protein occupancy with other assembly intermediates revealed that P7A7 is stalled at a late stage in ribosome assembly, explaining its weak activity. These results highlight the importance of ensuring efficient ribosome assembly during ribosome engineering toward new catalytic abilities.
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Affiliation(s)
- Fred R. Ward
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA
| | - Zoe L. Watson
- Department of Chemistry, University of California-Berkeley, Berkeley, CA
| | - Omer Ad
- Department of Chemistry, Yale University, New Haven, CT
| | - Alanna Schepartz
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA
- Department of Chemistry, University of California-Berkeley, Berkeley, CA
- Department of Chemistry, Yale University, New Haven, CT
| | - Jamie H. D. Cate
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA
- Department of Chemistry, University of California-Berkeley, Berkeley, CA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA
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