1
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Kang B, Park SV, Oh SS. Ionic liquid-caged nucleic acids enable active folding-based molecular recognition with hydrolysis resistance. Nucleic Acids Res 2024; 52:73-86. [PMID: 37994697 PMCID: PMC10783497 DOI: 10.1093/nar/gkad1093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 11/07/2023] [Indexed: 11/24/2023] Open
Abstract
Beyond storage and transmission of genetic information in cellular life, nucleic acids can perform diverse interesting functions, including specific target recognition and biochemical reaction acceleration; the versatile biopolymers, however, are acutely vulnerable to hydrolysis-driven degradation. Here, we demonstrate that the cage effect of choline dihydrogen phosphate permits active folding of nucleic acids like water, but prevents their phosphodiester hydrolysis unlike water. The choline-based ionic liquid not only serves as a universal inhibitor of nucleases, exceptionally extending half-lives of nucleic acids up to 6 500 000 times, but highly useful tasks of nucleic acids (e.g. mRNA detection of molecular beacons, ligand recognition of aptamers, and transesterification reaction of ribozymes) can be also conducted with well-conserved affinities and specificities. As liberated from the function loss and degradation risk, the presence of undesired and unknown nucleases does not undermine desired molecular functions of nucleic acids without hydrolysis artifacts even in nuclease cocktails and human saliva.
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Affiliation(s)
- Byunghwa Kang
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk 37673, South Korea
| | - Soyeon V Park
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk 37673, South Korea
| | - Seung Soo Oh
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk 37673, South Korea
- Institute for Convergence Research and Education in Advanced Technology (I-CREATE), Yonsei University, Incheon 21983, South Korea
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2
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Arteaga S, Dolenz BJ, Znosko BM. Competitive Influence of Alkali Metals in the Ion Atmosphere on Nucleic Acid Duplex Stability. ACS OMEGA 2024; 9:1287-1297. [PMID: 38222622 PMCID: PMC10785066 DOI: 10.1021/acsomega.3c07563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 01/16/2024]
Abstract
The nonspecific atmosphere around nucleic acids, often termed the ion atmosphere, encompasses a collection of weak ion-nucleic acid interactions. Although nonspecific, the ion atmosphere has been shown to influence nucleic acid folding and structural stability. Studies investigating the composition of the ion atmosphere have shown competitive occupancy of the atmosphere between metal ions in the same solution. Many studies have investigated single ion effects on nucleic acid secondary structure stability; however, no comprehensive studies have investigated how the competitive occupancy of mixed ions in the ion atmosphere influences nucleic acid secondary structure stability. Here, six oligonucleotides were optically melted in buffers containing molar quantities, or mixtures, of either XCl (X = Li, K, Rb, or Cs) or NaCl. A correction factor was developed to better predict RNA duplex stability in solutions containing mixed XCl/NaCl. For solutions containing a 1:1 mixture of XCl/NaCl, one alkali metal chloride contributed more to duplex stability than the other. Overall, there was a 54% improvement in predictive capabilities with the correction factor compared with the standard 1.0 M NaCl nearest-neighbor models. This correction factor can be used in models to better predict RNA secondary structure in solutions containing mixed XCl/NaCl.
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Affiliation(s)
- Sebastian
J. Arteaga
- Department of Chemistry, Saint Louis University, Saint
Louis, Missouri 63103, United States
| | - Bruce J. Dolenz
- Department of Chemistry, Saint Louis University, Saint
Louis, Missouri 63103, United States
| | - Brent M. Znosko
- Department of Chemistry, Saint Louis University, Saint
Louis, Missouri 63103, United States
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3
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Patki GM, Rajamani S. Nonenzymatic RNA replication in a mixture of 'spent' nucleotides. FEBS Lett 2023; 597:3125-3134. [PMID: 38058189 DOI: 10.1002/1873-3468.14785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/23/2023] [Accepted: 11/19/2023] [Indexed: 12/08/2023]
Abstract
Nonenzymatic template-directed replication would have been affected by co-solutes in a heterogeneous prebiotic soup due to lack of enzymatic machinery. Unlike in contemporary biology, these reactions use chemically activated nucleotides, which undergo rapid hydrolysis forming nucleoside monophosphates ('spent' monomers). These co-solutes cannot extend the primer but continue to base pair with the template, thereby interfering with replication. We, therefore, aimed to understand how a mixture of 'spent' ribonucleotides would affect nonenzymatic replication. We observed the inhibition of replication in the mixture, wherein the predominant contribution came from the cognate Watson-Crick monomer, showing potential sequence dependence. Our study highlights how nonenzymatic RNA replication would have been directly affected by co-solutes, with ramifications for the emergence of functional polymers in an RNA World.
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Affiliation(s)
- Gauri M Patki
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, India
| | - Sudha Rajamani
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, India
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4
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Tants JN, Schlundt A. Advances, Applications, and Perspectives in Small-Angle X-ray Scattering of RNA. Chembiochem 2023; 24:e202300110. [PMID: 37466350 DOI: 10.1002/cbic.202300110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/22/2023] [Indexed: 07/20/2023]
Abstract
RNAs exhibit a plethora of functions far beyond transmitting genetic information. Often, RNA functions are entailed in their structure, be it as a regulatory switch, protein binding site, or providing catalytic activity. Structural information is a prerequisite for a full understanding of RNA-regulatory mechanisms. Owing to the inherent dynamics, size, and instability of RNA, its structure determination remains challenging. Methods such as NMR spectroscopy, X-ray crystallography, and cryo-electron microscopy can provide high-resolution structures; however, their limitations make structure determination, even for small RNAs, cumbersome, if at all possible. Although at a low resolution, small-angle X-ray scattering (SAXS) has proven valuable in advancing structure determination of RNAs as a complementary method, which is also applicable to large-sized RNAs. Here, we review the technological and methodological advancements of RNA SAXS. We provide examples of the powerful inclusion of SAXS in structural biology and discuss possible future applications to large RNAs.
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Affiliation(s)
- Jan-Niklas Tants
- Goethe University Frankfurt, Institute for Molecular Biosciences and Biomagnetic Resonance Centre (BMRZ), Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Andreas Schlundt
- Goethe University Frankfurt, Institute for Molecular Biosciences and Biomagnetic Resonance Centre (BMRZ), Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
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5
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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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6
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Dai J, Peng Z, Shen S, Huang B, Ren L, Liu J, Chen CH, Chen G. Evaluation of exogenous therapeutic protein activity under confinement and crowding effects. NANOSCALE 2023; 15:13450-13458. [PMID: 37548227 DOI: 10.1039/d3nr02968a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Dysfunction of intracellular proteins is frequently associated with various diseases, such as cancer. The exogenous proteins in cells are usually assembled with specific configurations due to physiological confinement/crowding to exhibit novel features in the protein structure, folding or conformational stability, distinguished with their behaviors in buffer solutions. Here, we synthesized exogenous proteins under confined/crowded conditions, to explore protein activity within cells. The findings suggested that the confinement and crowding effects on protein activity are heterogeneous; they showed an inhibitory effect on HRP by decreasing Km from ∼9.5- and ∼21.7-fold and Vmax from ∼6.8- and ∼20.2-fold lower than that of dilute solutions. Interestingly, the effects on Cyt C seem to be more complicated, and crowding exerts a positive effect by increasing Km ∼ 3.6-fold and Vmax ∼ 1.5-fold higher than that of dilute solutions; however, confinement exhibits a negative effect by decreasing Km ∼2.0 and Vmax ∼8.3 times. Additionally, in contrast to traditional nanoparticle-based confinement models, we synthesized a biodegradable nanoparticle to mimic the confined space, and the biggest advantage of this novel model is that the particles can be degraded and thus it can provide more intuitive observations of the properties of the target proteins under confinement and after release. Furthermore, we also evaluated protein activity in different cellular environments, indicating that the exogenous protein activity was closely related to the crowdedness of cellular environments, and the inhibition of protein activity in MDA-MB-231 cancer cells was more obvious than in HEK293 normal cells. Finally, SAXS analysis revealed the correlation between the protein conformation and the different environments. Our work will provide a unique method for precisely assessing whether the target cellular environments are native matrix in which specific exogenous protein drugs are delivered to function or whether they display a therapeutic role, which is of great significance for screening and development of new drugs.
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Affiliation(s)
- Jie Dai
- School of Pharmaceutical Sciences, Nanjing Tech University, 30th Puzhu South Road, Nanjing 211816, China.
| | - Zhiyi Peng
- School of Pharmaceutical Sciences, Nanjing Tech University, 30th Puzhu South Road, Nanjing 211816, China.
| | - Shuwei Shen
- School of Pharmaceutical Sciences, Nanjing Tech University, 30th Puzhu South Road, Nanjing 211816, China.
| | - Binbin Huang
- School of Pharmaceutical Sciences, Nanjing Tech University, 30th Puzhu South Road, Nanjing 211816, China.
| | - Lili Ren
- School of Pharmaceutical Sciences, Nanjing Tech University, 30th Puzhu South Road, Nanjing 211816, China.
| | - Jia Liu
- School of Pharmaceutical Sciences, Nanjing Tech University, 30th Puzhu South Road, Nanjing 211816, China.
| | - Chia-Hung Chen
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China.
| | - Guoguang Chen
- School of Pharmaceutical Sciences, Nanjing Tech University, 30th Puzhu South Road, Nanjing 211816, China.
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7
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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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8
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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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9
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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: 0] [Impact Index Per Article: 0] [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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10
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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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11
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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: 1] [Impact Index Per Article: 0.5] [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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12
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Lai YC, Liu Z, Chen IA. Encapsulation of ribozymes inside model protocells leads to faster evolutionary adaptation. Proc Natl Acad Sci U S A 2021; 118:e2025054118. [PMID: 34001592 PMCID: PMC8166191 DOI: 10.1073/pnas.2025054118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Functional biomolecules, such as RNA, encapsulated inside a protocellular membrane are believed to have comprised a very early, critical stage in the evolution of life, since membrane vesicles allow selective permeability and create a unit of selection enabling cooperative phenotypes. The biophysical environment inside a protocell would differ fundamentally from bulk solution due to the microscopic confinement. However, the effect of the encapsulated environment on ribozyme evolution has not been previously studied experimentally. Here, we examine the effect of encapsulation inside model protocells on the self-aminoacylation activity of tens of thousands of RNA sequences using a high-throughput sequencing assay. We find that encapsulation of these ribozymes generally increases their activity, giving encapsulated sequences an advantage over nonencapsulated sequences in an amphiphile-rich environment. In addition, highly active ribozymes benefit disproportionately more from encapsulation. The asymmetry in fitness gain broadens the distribution of fitness in the system. Consistent with Fisher's fundamental theorem of natural selection, encapsulation therefore leads to faster adaptation when the RNAs are encapsulated inside a protocell during in vitro selection. Thus, protocells would not only provide a compartmentalization function but also promote activity and evolutionary adaptation during the origin of life.
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Affiliation(s)
- Yei-Chen Lai
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Ziwei Liu
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Irene A Chen
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095;
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
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13
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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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14
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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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15
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Hautke AC, Ebbinghaus S. Folding Stability and Self‐Association of a Triplet‐Repeat (CAG)
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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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16
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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: 22] [Impact Index Per Article: 5.5] [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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17
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NMR analysis of nucleotide π-stacking in prebiotically relevant crowded environment. Commun Chem 2020; 3:51. [PMID: 36703483 PMCID: PMC9814533 DOI: 10.1038/s42004-020-0300-7] [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: 06/23/2019] [Accepted: 04/07/2020] [Indexed: 01/29/2023] Open
Abstract
The prebiotic soup of a putative 'RNA World' would have been replete with a plethora of molecules resulting from complex chemical syntheses and exogeneous delivery. The presence of background molecules could lead to molecular crowding, potentially affecting the course of the reactions facilitated therein. Using NMR spectroscopy, we have analyzed the effect of crowding on the stacking ability of RNA monomers. Our findings corroborate that the purines stack more efficiently than the pyrimidine ribonucleotides. This competence is further enhanced in the presence of a crowding agent. This enhanced stacking could result in greater sequestration of the purine monomers, putting their ready availability for relevant nonenzymatic reactions into question. Thus, this study demonstrates the need for systematic characterization of molecular crowding in the context of prebiotically pertinent processes. Unraveling such phenomena is essential for our understanding of the transition from abiotic to biotic, during the origin of life.
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18
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Abstract
Molecular crowding promotes RNA folding and catalysis and could have played vital roles in the evolution of primordial ribozymes and protocells.
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Affiliation(s)
- Saurja DasGupta
- Howard Hughes Medical Institute
- Massachusetts General Hospital
- Boston
- USA
- Department of Molecular Biology
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19
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Gao Y, Liu X, Sun L, Xu Y, Yang S, Fan C, Li D. Alleviated Inhibition of Single Enzyme in Confined and Crowded Environment. J Phys Chem Lett 2019; 10:82-89. [PMID: 30565943 DOI: 10.1021/acs.jpclett.8b03736] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Most proteins perform functions in intracellular milieu. The crowding, compartmentalized cytosol environment affects the protein structure, folding, conformational stability, substrate diffusion, and substrate-enzyme binding. Moreover, enzymes are available at single or very low copy numbers in a cell, and thus the conformation fluctuations of a single enzyme in a crowding environment could also greatly influence its kinetics. However, the crowding effect is poorly understood in the kinetical aspect of enzymatic reactions. In the present study, individual horseradish peroxidase (HRP) is encapsulated in a liposome containing crowding reagents as mimics of viscous cytosol. The confined crowding environment possesses a profound influence on both the catalytic activity and the product inhibition of enzymes. By analyzing the correlation between product generation and product inhibition, we find that the allosteric noncompetitive inhibition of HRP is alleviated in the crowded and confined milieu. Small-angle X-ray scattering experiments provide straightforward proofs of structural changes of enzymes in crowding environments, which are responsible for the reduced enzyme activity and increased enzyme-substrate affinity. We expect that this work may deepen the understanding of correlations between enzymatic conformations and activity performance in real cellular environments.
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Affiliation(s)
- Yanjing Gao
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Lele Sun
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Yan Xu
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
- National Engineering Research Center for Nanotechnology , Shanghai 200241 , China
| | - Sichun Yang
- Center for Proteomics and Department of Nutrition , Case Western Reserve University , Cleveland , Ohio 44106 , United States
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Di Li
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
- School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200241 , China
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20
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Paudel BP, Fiorini E, Börner R, Sigel RKO, Rueda DS. Optimal molecular crowding accelerates group II intron folding and maximizes catalysis. Proc Natl Acad Sci U S A 2018; 115:11917-11922. [PMID: 30397128 PMCID: PMC6255197 DOI: 10.1073/pnas.1806685115] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Unlike in vivo conditions, group II intron ribozymes are known to require high magnesium(II) concentrations ([Mg2+]) and high temperatures (42 °C) for folding and catalysis in vitro. A possible explanation for this difference is the highly crowded cellular environment, which can be mimicked in vitro by macromolecular crowding agents. Here, we combined bulk activity assays and single-molecule Förster Resonance Energy Transfer (smFRET) to study the influence of polyethylene glycol (PEG) on catalysis and folding of the ribozyme. Our activity studies reveal that PEG reduces the [Mg2+] required, and we found an "optimum" [PEG] that yields maximum activity. smFRET experiments show that the most compact state population, the putative active state, increases with increasing [PEG]. Dynamic transitions between folded states also increase. Therefore, this study shows that optimal molecular crowding concentrations help the ribozyme not only to reach the native fold but also to increase its in vitro activity to approach that in physiological conditions.
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Affiliation(s)
- Bishnu P Paudel
- Molecular Virology, Department of Medicine, Imperial College London, London W12 0NN, United Kingdom
- Single Molecule Imaging, Medical Research Council London Institute of Medical Sciences, London W12 0NN, United Kingdom
| | - Erica Fiorini
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Richard Börner
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Roland K O Sigel
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
| | - David S Rueda
- Molecular Virology, Department of Medicine, Imperial College London, London W12 0NN, United Kingdom;
- Single Molecule Imaging, Medical Research Council London Institute of Medical Sciences, London W12 0NN, United Kingdom
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21
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Saha R, Verbanic S, Chen IA. Lipid vesicles chaperone an encapsulated RNA aptamer. Nat Commun 2018; 9:2313. [PMID: 29899431 PMCID: PMC5998061 DOI: 10.1038/s41467-018-04783-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 05/22/2018] [Indexed: 01/08/2023] Open
Abstract
The organization of molecules into cells is believed to have been critical for the emergence of living systems. Early protocells likely consisted of RNA functioning inside vesicles made of simple lipids. However, little is known about how encapsulation would affect the activity and folding of RNA. Here we find that confinement of the malachite green RNA aptamer inside fatty acid vesicles increases binding affinity and locally stabilizes the bound conformation of the RNA. The vesicle effectively ‘chaperones’ the aptamer, consistent with an excluded volume mechanism due to confinement. Protocellular organization thereby leads to a direct benefit for the RNA. Coupled with previously described mechanisms by which encapsulated RNA aids membrane growth, this effect illustrates how the membrane and RNA might cooperate for mutual benefit. Encapsulation could thus increase RNA fitness and the likelihood that functional sequences would emerge during the origin of life. So far little is known about how encapsulation affects the activity and folding of RNA, which is of interest for understanding the origin of cellular life. Here the authors show that encapsulation of functional RNA in vesicles increases RNA activity and improves RNA folding through a biophysical confinement effect.
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Affiliation(s)
- Ranajay Saha
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA
| | - Samuel Verbanic
- Program in Biomolecular Sciences and Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Irene A Chen
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA. .,Program in Biomolecular Sciences and Engineering, University of California, Santa Barbara, CA, 93106, USA.
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22
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Cellular conditions of weakly chelated magnesium ions strongly promote RNA stability and catalysis. Nat Commun 2018; 9:2149. [PMID: 29858572 PMCID: PMC5984629 DOI: 10.1038/s41467-018-04415-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/23/2018] [Indexed: 01/06/2023] Open
Abstract
Most RNA folding studies have been performed under non-physiological conditions of high concentrations (≥10 mM) of Mg2+free, while actual cellular concentrations of Mg2+free are only ~1 mM in a background of greater than 50 mM Mg2+total. To uncover cellular behavior of RNA, we devised cytoplasm mimic systems that include biological concentrations of amino acids, which weakly chelate Mg2+. Amino acid-chelated Mg2+ (aaCM) of ~15 mM dramatically increases RNA folding and prevents RNA degradation. Furthermore, aaCM enhance self-cleavage of several different ribozymes, up to 100,000-fold at Mg2+free of just 0.5 mM, indirectly through RNA compaction. Other metabolites that weakly chelate magnesium offer similar beneficial effects, which implies chelated magnesium may enhance RNA function in the cell in the same way. Overall, these results indicate that the states of Mg2+ should not be limited to free and bound only, as weakly bound Mg2+ strongly promotes RNA function under cellular conditions.
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23
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Leamy KA, Yennawar NH, Bevilacqua PC. Molecular Mechanism for Folding Cooperativity of Functional RNAs in Living Organisms. Biochemistry 2018; 57:2994-3002. [PMID: 29733204 PMCID: PMC6726375 DOI: 10.1021/acs.biochem.8b00345] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A diverse set of organisms has adapted to live under extreme conditions. The molecular origin of the stability is unclear, however. It is not known whether the adaptation of functional RNAs, which have intricate tertiary structures, arises from strengthening of tertiary or secondary structure. Herein we evaluate effects of sequence changes on the thermostability of tRNAphe using experimental and computational approaches. To separate out effects of secondary and tertiary structure on thermostability, we modify base pairing strength in the acceptor stem, which does not participate in tertiary structure. In dilute solution conditions, strengthening secondary structure leads to non-two-state thermal denaturation curves and has small effects on thermostability, or the temperature at which tertiary structure and function are lost. In contrast, under cellular conditions with crowding and Mg2+-chelated amino acids, where two-state cooperative unfolding is maintained, strengthening secondary structure enhances thermostability. Investigation of stabilities of each tRNA stem across 44 organisms with a range of optimal growing temperatures revealed that organisms that grow in warmer environments have more stable stems. We also used Shannon entropies to identify positions of higher and lower information content, or sequence conservation, in tRNAphe and found that secondary structures have modest information content allowing them to drive thermal adaptation, while tertiary structures have maximal information content hindering them from participating in thermal adaptation. Base-paired regions with no tertiary structure and modest information content thus offer a facile evolutionary route to enhancing the thermostability of functional RNA by the simple molecular rules of base pairing.
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Affiliation(s)
- Kathleen A Leamy
- Department of Chemistry , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
- Center for RNA Molecular Biology , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Neela H Yennawar
- Huck Institutes of the Life Sciences , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Philip C Bevilacqua
- Department of Chemistry , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
- Center for RNA Molecular Biology , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
- Department of Biochemistry and Molecular Biology , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
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24
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Marianelli AM, Miller BM, Keating CD. Impact of macromolecular crowding on RNA/spermine complex coacervation and oligonucleotide compartmentalization. SOFT MATTER 2018; 14:368-378. [PMID: 29265152 DOI: 10.1039/c7sm02146a] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We report the effect of neutral macromolecular crowders poly(ethylene glycol) (PEG) (8 kDa) and Ficoll (70 kDa) on liquid-liquid phase separation in a polyuridylic acid (polyU)/spermine complex coacervate system. The addition of PEG decreased both the amount of spermine required for phase separation and the coacervation temperature (TC). We interpret these effects on phase behavior as arising due to excluded volume and preferential interactions on both the secondary structure/condensation of spermine-associated polyU molecules and on the association of soluble polyU/spermine polyelectrolyte complexes to form coacervate droplets. Examination of coacervates formed in the presence of fluorescently-labeled PEG or Ficoll crowders indicated that Ficoll is accumulated while PEG is excluded from the coacervate phase, which provides further insight into the differences in phase behavior. Crowding agents impact distribution of a biomolecular solute: partitioning of a fluorescently-labeled U15 RNA oligomer into the polyU/spermine coacervates was increased approximately two-fold by 20 wt% Ficoll 70 kDa and by more than two orders of magnitude by 20 wt% PEG 8 kDa. The volume of the coacervate phase decreased in the presence of crowder relative to a dilute buffer solution. These findings indicate that potential impacts of macromolecular crowding on phase behavior and solute partitioning should be considered in model systems for intracellular membraneless organelles.
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Affiliation(s)
- A M Marianelli
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA.
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25
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Daher M, Widom JR, Tay W, Walter NG. Soft Interactions with Model Crowders and Non-canonical Interactions with Cellular Proteins Stabilize RNA Folding. J Mol Biol 2017; 430:509-523. [PMID: 29128594 DOI: 10.1016/j.jmb.2017.10.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/22/2017] [Accepted: 10/30/2017] [Indexed: 12/18/2022]
Abstract
Living cells contain diverse biopolymers, creating a heterogeneous crowding environment, the impact of which on RNA folding is poorly understood. Here, we have used single-molecule fluorescence resonance energy transfer to monitor tertiary structure formation of the hairpin ribozyme as a model to probe the effects of polyethylene glycol and yeast cell extract as crowding agents. As expected, polyethylene glycol stabilizes the docked, catalytically active state of the ribozyme, in part through excluded volume effects; unexpectedly, we found evidence that it additionally displays soft, non-specific interactions with the ribozyme. Yeast extract has a profound effect on folding at protein concentrations 1000-fold lower than found intracellularly, suggesting the dominance of specific interactions over volume exclusion. Gel shift assays and affinity pull-down followed by mass spectrometry identified numerous non-canonical RNA-binding proteins that stabilize ribozyme folding; the apparent chaperoning activity of these ubiquitous proteins significantly compensates for the low-counterion environment of the cell.
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Affiliation(s)
- May Daher
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Julia R Widom
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Wendy Tay
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109-1055, USA.
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26
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The 2D Structure of the T. brucei Preedited RPS12 mRNA Is Not Affected by Macromolecular Crowding. J Nucleic Acids 2017; 2017:6067345. [PMID: 28698807 PMCID: PMC5494072 DOI: 10.1155/2017/6067345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/04/2017] [Indexed: 11/17/2022] Open
Abstract
Mitochondrial transcript maturation in African trypanosomes requires RNA editing to convert sequence-deficient pre-mRNAs into translatable mRNAs. The different pre-mRNAs have been shown to adopt highly stable 2D folds; however, it is not known whether these structures resemble the in vivo folds given the extreme "crowding" conditions within the mitochondrion. Here, we analyze the effects of macromolecular crowding on the structure of the mitochondrial RPS12 pre-mRNA. We use high molecular mass polyethylene glycol as a macromolecular cosolute and monitor the structure of the RNA globally and with nucleotide resolution. We demonstrate that crowding has no impact on the 2D fold and we conclude that the MFE structure in dilute solvent conditions represents a good proxy for the folding of the pre-mRNA in its mitochondrial solvent context.
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27
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Leamy KA, Yennawar NH, Bevilacqua PC. Cooperative RNA Folding under Cellular Conditions Arises From Both Tertiary Structure Stabilization and Secondary Structure Destabilization. Biochemistry 2017; 56:3422-3433. [PMID: 28657303 DOI: 10.1021/acs.biochem.7b00325] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
RNA folding has been studied extensively in vitro, typically under dilute solution conditions and abiologically high salt concentrations of 1 M Na+ or 10 mM Mg2+. The cellular environment is very different, with 20-40% crowding and only 10-40 mM Na+, 140 mM K+, and 0.5-2.0 mM Mg2+. As such, RNA structures and functions can be radically altered under cellular conditions. We previously reported that tRNAphe secondary and tertiary structures unfold together in a cooperative two-state fashion under crowded in vivo-like ionic conditions, but in a noncooperative multistate fashion under dilute in vitro ionic conditions unless in nonphysiologically high concentrations of Mg2+. The mechanistic basis behind these effects remains unclear, however. To address the mechanism that drives RNA folding cooperativity, we probe effects of cellular conditions on structures and stabilities of individual secondary structure fragments comprising the full-length RNA. We elucidate effects of a diverse set of crowders on tRNA secondary structural fragments and full-length tRNA at three levels: at the nucleotide level by temperature-dependent in-line probing, at the tertiary structure level by small-angle X-ray scattering, and at the global level by thermal denaturation. We conclude that cooperative RNA folding is induced by two overlapping mechanisms: increased stability and compaction of tertiary structure through effects of Mg2+, and decreased stability of certain secondary structure elements through the effects of molecular crowders. These findings reveal that despite having very different chemical makeups RNA and protein can both have weak secondary structures in vivo leading to cooperative folding.
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Affiliation(s)
- Kathleen A Leamy
- Department of Chemistry, ‡Center for RNA Molecular Biology, §Huck Institutes of the Life Sciences, and ⊥Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Neela H Yennawar
- Department of Chemistry, ‡Center for RNA Molecular Biology, §Huck Institutes of the Life Sciences, and ⊥Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Philip C Bevilacqua
- Department of Chemistry, ‡Center for RNA Molecular Biology, §Huck Institutes of the Life Sciences, and ⊥Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States
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28
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Abstract
In addition to continuous rapid progress in RNA structure determination, probing, and biophysical studies, the past decade has seen remarkable advances in the development of a new generation of RNA folding theories and models. In this article, we review RNA structure prediction models and models for ion-RNA and ligand-RNA interactions. These new models are becoming increasingly important for a mechanistic understanding of RNA function and quantitative design of RNA nanotechnology. We focus on new methods for physics-based, knowledge-based, and experimental data-directed modeling for RNA structures and explore the new theories for the predictions of metal ion and ligand binding sites and metal ion-dependent RNA stabilities. The integration of these new methods with theories about the cellular environment effects in RNA folding, such as molecular crowding and cotranscriptional kinetic effects, may ultimately lead to an all-encompassing RNA folding model.
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Affiliation(s)
- Li-Zhen Sun
- Department of Physics, Department of Biochemistry, and MU Informatics Institute, University of Missouri, Columbia, Missouri 65211;
| | - Dong Zhang
- Department of Physics, Department of Biochemistry, and MU Informatics Institute, University of Missouri, Columbia, Missouri 65211;
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and MU Informatics Institute, University of Missouri, Columbia, Missouri 65211;
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29
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Ferreira LA, Uversky VN, Zaslavsky BY. Role of solvent properties of water in crowding effects induced by macromolecular agents and osmolytes. MOLECULAR BIOSYSTEMS 2017; 13:2551-2563. [DOI: 10.1039/c7mb00436b] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Dipolarity/polarizability of water in polymer mixtures may be additive, reduced or enhanced depending on the composition of the mixture.
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Affiliation(s)
| | - V. N. Uversky
- Department of Molecular Medicine
- Morsant College of Medicine
- University of South Florida
- Tampa
- USA
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30
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Yu T, Zhu Y, He Z, Chen SJ. Predicting Molecular Crowding Effects in Ion-RNA Interactions. J Phys Chem B 2016; 120:8837-44. [PMID: 27490487 DOI: 10.1021/acs.jpcb.6b05625] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We develop a new statistical mechanical model to predict the molecular crowding effects in ion-RNA interactions. By considering discrete distributions of the crowders, the model can treat the main crowder-induced effects, such as the competition with ions for RNA binding, changes of electrostatic interaction due to crowder-induced changes in the dielectric environment, and changes in the nonpolar hydration state of the crowder-RNA system. To enhance the computational efficiency, we sample the crowder distribution using a hybrid approach: For crowders in the close vicinity of RNA surface, we sample their discrete distributions; for crowders in the bulk solvent away from the RNA surface, we use a continuous mean-field distribution for the crowders. Moreover, using the tightly bound ion (TBI) model, we account for ion fluctuation and correlation effects in the calculation for ion-RNA interactions. Applications of the model to a variety of simple RNA structures such as RNA helices show a crowder-induced increase in free energy and decrease in ion binding. Such crowding effects tend to contribute to the destabilization of RNA structure. Further analysis indicates that these effects are associated with the crowder-ion competition in RNA binding and the effective decrease in the dielectric constant. This simple ion effect model may serve as a useful framework for modeling more realistic crowders with larger, more complex RNA structures.
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Affiliation(s)
- Tao Yu
- Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri , Columbia, Missouri 65211, United States.,Department of Physics, Jianghan University , Wuhan, Hubei 430056, China
| | - Yuhong Zhu
- Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri , Columbia, Missouri 65211, United States.,Department of Physics, Hangzhou Normal University , Hangzhou, Zhejiang 310036, China
| | - Zhaojian He
- Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri , Columbia, Missouri 65211, United States
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri , Columbia, Missouri 65211, United States
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31
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Kilburn D, Behrouzi R, Lee HT, Sarkar K, Briber RM, Woodson SA. Entropic stabilization of folded RNA in crowded solutions measured by SAXS. Nucleic Acids Res 2016; 44:9452-9461. [PMID: 27378777 PMCID: PMC5100557 DOI: 10.1093/nar/gkw597] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 06/21/2016] [Indexed: 01/29/2023] Open
Abstract
Non-coding RNAs must fold into specific structures that are stabilized by metal ions and other co-solutes in the cell's interior. Large crowder molecules such as PEG stabilize a bacterial group I ribozyme so that the RNA folds in low Mg2+ concentrations typical of the cell's interior. To understand the thermodynamic origins of stabilization by crowder molecules, small angle X-ray scattering was used to measure the folding and helix assembly of a bacterial group I ribozyme at different temperatures and in different MgCl2 and polyethylene glycol (PEG) concentrations. The resulting phase diagrams show that perturbations to folding by each variable do not overlap. A favorable enthalpy change drives the formation of compact, native-like structures, but requires Mg2+ ions at all temperatures studied (5–55°C). PEG reduces the entropic cost of helix assembly and increases correlations between RNA segments at all temperatures. The phase diagrams also revealed a semi-compact intermediate between the unfolded and folded ensemble that is locally more flexible than the unfolded state, as judged by SHAPE modification. These results suggest that environmental variables such as temperature and solute density will favor different types of RNA structures.
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Affiliation(s)
- Duncan Kilburn
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Reza Behrouzi
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Hui-Ting Lee
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Krishnarjun Sarkar
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Robert M Briber
- Department of Materials Science and Engineering, University of Maryland, College Park, MD 20742, USA
| | - Sarah A Woodson
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
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Abstract
Deciphering the folding pathways and predicting the structures of complex three-dimensional biomolecules is central to elucidating biological function. RNA is single-stranded, which gives it the freedom to fold into complex secondary and tertiary structures. These structures endow RNA with the ability to perform complex chemistries and functions ranging from enzymatic activity to gene regulation. Given that RNA is involved in many essential cellular processes, it is critical to understand how it folds and functions in vivo. Within the last few years, methods have been developed to probe RNA structures in vivo and genome-wide. These studies reveal that RNA often adopts very different structures in vivo and in vitro, and provide profound insights into RNA biology. Nonetheless, both in vitro and in vivo approaches have limitations: studies in the complex and uncontrolled cellular environment make it difficult to obtain insight into RNA folding pathways and thermodynamics, and studies in vitro often lack direct cellular relevance, leaving a gap in our knowledge of RNA folding in vivo. This gap is being bridged by biophysical and mechanistic studies of RNA structure and function under conditions that mimic the cellular environment. To date, most artificial cytoplasms have used various polymers as molecular crowding agents and a series of small molecules as cosolutes. Studies under such in vivo-like conditions are yielding fresh insights, such as cooperative folding of functional RNAs and increased activity of ribozymes. These observations are accounted for in part by molecular crowding effects and interactions with other molecules. In this review, we report milestones in RNA folding in vitro and in vivo and discuss ongoing experimental and computational efforts to bridge the gap between these two conditions in order to understand how RNA folds in the cell.
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Gao M, Gnutt D, Orban A, Appel B, Righetti F, Winter R, Narberhaus F, Müller S, Ebbinghaus S. Faltung einer RNA-Haarnadel in der dicht gedrängten Zelle. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201510847] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Mimi Gao
- Lehrstuhl für Physikalische Chemie II; Ruhr-Universität Bochum; Universitätsstr. 150 44801 Bochum Deutschland
| | - David Gnutt
- Lehrstuhl für Physikalische Chemie II; Ruhr-Universität Bochum; Universitätsstr. 150 44801 Bochum Deutschland
| | - Axel Orban
- Institut für Biochemie; Ernst-Moritz-Arndt-Universität Greifswald; Felix-Hausdorff-Str. 4 17487 Greifswald Deutschland
| | - Bettina Appel
- Institut für Biochemie; Ernst-Moritz-Arndt-Universität Greifswald; Felix-Hausdorff-Str. 4 17487 Greifswald Deutschland
| | - Francesco Righetti
- Biologie der Mikroorganismen; Ruhr-Universität Bochum; Universitätsstr. 150 44801 Bochum Deutschland
| | - Roland Winter
- Lehrstuhl für Physikalische Chemie I; TU Dortmund; Otto-Hahn-Str. 4a 44227 Dortmund Deutschland
| | - Franz Narberhaus
- Biologie der Mikroorganismen; Ruhr-Universität Bochum; Universitätsstr. 150 44801 Bochum Deutschland
| | - Sabine Müller
- Institut für Biochemie; Ernst-Moritz-Arndt-Universität Greifswald; Felix-Hausdorff-Str. 4 17487 Greifswald Deutschland
| | - Simon Ebbinghaus
- Lehrstuhl für Physikalische Chemie II; Ruhr-Universität Bochum; Universitätsstr. 150 44801 Bochum Deutschland
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34
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Gao M, Gnutt D, Orban A, Appel B, Righetti F, Winter R, Narberhaus F, Müller S, Ebbinghaus S. RNA Hairpin Folding in the Crowded Cell. Angew Chem Int Ed Engl 2016; 55:3224-8. [PMID: 26833452 PMCID: PMC4762321 DOI: 10.1002/anie.201510847] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Indexed: 12/02/2022]
Abstract
Precise secondary and tertiary structure formation is critically important for the cellular functionality of ribonucleic acids (RNAs). RNA folding studies were mainly conducted in vitro, without the possibility of validating these experiments inside cells. Here, we directly resolve the folding stability of a hairpin‐structured RNA inside live mammalian cells. We find that the stability inside the cell is comparable to that in dilute physiological buffer. On the contrary, the addition of in vitro artificial crowding agents, with the exception of high‐molecular‐weight PEG, leads to a destabilization of the hairpin structure through surface interactions and reduction in water activity. We further show that RNA stability is highly variable within cell populations as well as within subcellular regions of the cytosol and nucleus. We conclude that inside cells the RNA is subject to (localized) stabilizing and destabilizing effects that lead to an on average only marginal modulation compared to diluted buffer.
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Affiliation(s)
- Mimi Gao
- Physical Chemistry II, Ruhr-Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - David Gnutt
- Physical Chemistry II, Ruhr-Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Axel Orban
- Institute for Biochemistry, Ernst-Moritz-Arndt-University Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Bettina Appel
- Institute for Biochemistry, Ernst-Moritz-Arndt-University Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Francesco Righetti
- Microbial Biology, Ruhr-Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Roland Winter
- Physical Chemistry I, Technical University Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Franz Narberhaus
- Microbial Biology, Ruhr-Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Sabine Müller
- Institute for Biochemistry, Ernst-Moritz-Arndt-University Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Simon Ebbinghaus
- Physical Chemistry II, Ruhr-Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany.
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35
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Effect of Co-solutes on Template-Directed Nonenzymatic Replication of Nucleic Acids. J Mol Evol 2015; 81:72-80. [DOI: 10.1007/s00239-015-9700-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 09/23/2015] [Indexed: 12/14/2022]
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36
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Yu H, Rathore SS, Shen C, Liu Y, Ouyang Y, Stowell MH, Shen J. Reconstituting Intracellular Vesicle Fusion Reactions: The Essential Role of Macromolecular Crowding. J Am Chem Soc 2015; 137:12873-83. [PMID: 26431309 DOI: 10.1021/jacs.5b08306] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Intracellular vesicle fusion is mediated by SNAREs and Sec1/Munc18 (SM) proteins. Despite intensive efforts, the SNARE-SM mediated vesicle fusion reaction has not been faithfully reconstituted in biochemical assays. Here, we present an unexpected discovery that macromolecular crowding is required for reconstituting the vesicle fusion reaction in vitro. Macromolecular crowding is known to profoundly influence the kinetic and thermodynamic behaviors of macromolecules, but its role in membrane transport processes such as vesicle fusion remains unexplored. We introduced macromolecular crowding agents into reconstituted fusion reactions to mimic the crowded cellular environment. In this crowded assay, SNAREs and SM proteins acted in concert to drive efficient membrane fusion. In uncrowded assays, by contrast, SM proteins failed to associate with the SNAREs and the fusion rate decreased more than 30-fold, close to undetectable levels. The activities of SM proteins were strictly specific to their cognate SNARE isoforms and sensitive to biologically relevant mutations, further supporting that the crowded fusion assay accurately recapitulates the vesicle fusion reaction. Using this crowded fusion assay, we also showed that the SNARE-SM mediated fusion reaction can be modulated by two additional factors: NSF and α-SNAP. These findings suggest that the vesicle fusion machinery likely has been evolutionarily selected to function optimally in the crowded milieu of the cell. Accordingly, macromolecular crowding should constitute an integral element of any reconstituted fusion assay.
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Affiliation(s)
- Haijia Yu
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder , Boulder, Colorado 80309, United States
| | - Shailendra S Rathore
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder , Boulder, Colorado 80309, United States
| | - Chong Shen
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder , Boulder, Colorado 80309, United States
| | - Yinghui Liu
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder , Boulder, Colorado 80309, United States
| | - Yan Ouyang
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder , Boulder, Colorado 80309, United States
| | - Michael H Stowell
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder , Boulder, Colorado 80309, United States
| | - Jingshi Shen
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder , Boulder, Colorado 80309, United States
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37
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Chaudhuri BN. Emerging applications of small angle solution scattering in structural biology. Protein Sci 2015; 24:267-76. [PMID: 25516491 PMCID: PMC4353354 DOI: 10.1002/pro.2624] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 12/05/2014] [Indexed: 12/12/2022]
Abstract
Small angle solution X-ray and neutron scattering recently resurfaced as powerful tools to address an array of biological problems including folding, intrinsic disorder, conformational transitions, macromolecular crowding, and self or hetero-assembling of biomacromolecules. In addition, small angle solution scattering complements crystallography, nuclear magnetic resonance spectroscopy, and other structural methods to aid in the structure determinations of multidomain or multicomponent proteins or nucleoprotein assemblies. Neutron scattering with hydrogen/deuterium contrast variation, or X-ray scattering with sucrose contrast variation to a certain extent, is a convenient tool for characterizing the organizations of two-component systems such as a nucleoprotein or a lipid-protein assembly. Time-resolved small and wide-angle solution scattering to study biological processes in real time, and the use of localized heavy-atom labeling and anomalous solution scattering for applications as FRET-like molecular rulers, are amongst promising newer developments. Despite the challenges in data analysis and interpretation, these X-ray/neutron solution scattering based approaches hold great promise for understanding a wide variety of complex processes prevalent in the biological milieu.
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Affiliation(s)
- Barnali N Chaudhuri
- Faculty of Life Sciences and Biotechnology, South Asian UniversityAkbar Bhawan, Chanakyapuri, New Delhi, India
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38
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Lee HT, Kilburn D, Behrouzi R, Briber RM, Woodson SA. Molecular crowding overcomes the destabilizing effects of mutations in a bacterial ribozyme. Nucleic Acids Res 2015; 43:1170-6. [PMID: 25541198 PMCID: PMC4333387 DOI: 10.1093/nar/gku1335] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 12/01/2014] [Accepted: 12/05/2014] [Indexed: 11/13/2022] Open
Abstract
The native structure of the Azoarcus group I ribozyme is stabilized by the cooperative formation of tertiary interactions between double helical domains. Thus, even single mutations that break this network of tertiary interactions reduce ribozyme activity in physiological Mg(2+) concentrations. Here, we report that molecular crowding comparable to that in the cell compensates for destabilizing mutations in the Azoarcus ribozyme. Small angle X-ray scattering, native polyacrylamide gel electrophoresis and activity assays were used to compare folding free energies in dilute and crowded solutions containing 18% PEG1000. Crowder molecules allowed the wild-type and mutant ribozymes to fold at similarly low Mg(2+) concentrations and stabilized the active structure of the mutant ribozymes under physiological conditions. This compensation helps explains why ribozyme mutations are often less deleterious in the cell than in the test tube. Nevertheless, crowding did not rescue the high fraction of folded but less active structures formed by double and triple mutants. We conclude that crowding broadens the fitness landscape by stabilizing compact RNA structures without improving the specificity of self-assembly.
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Affiliation(s)
- Hui-Ting Lee
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Duncan Kilburn
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA Center for Neutron Scattering Research, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, MD 20899, USA
| | - Reza Behrouzi
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Robert M Briber
- Department of Materials Science and Engineering, University of Maryland, College Park, MD 20742, USA
| | - Sarah A Woodson
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
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39
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Abstract
A diverse population of large RNA molecules controls every aspect of cellular function, and yet we know very little about their molecular structures. However, robust technologies developed for visualizing ribozymes and riboswitches, together with new approaches for mapping RNA inside cells, provide the foundation for visualizing the structures of long noncoding RNAs, mRNAs, and viral RNAs, thereby facilitating new mechanistic insights.
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Affiliation(s)
- Anna Marie Pyle
- Department of Molecular, Cellular and Developmental Biology and Department of Chemistry, Yale University, New Haven, CT 06520, USA.
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40
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Saha R, Pohorille A, Chen IA. Molecular crowding and early evolution. ORIGINS LIFE EVOL B 2014; 44:319-24. [PMID: 25585804 DOI: 10.1007/s11084-014-9392-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 10/31/2014] [Indexed: 10/24/2022]
Abstract
The environment of protocells might have been crowded with small molecules and functional and non-specific polymers. In addition to altering conformational equilibria, affecting reaction rates and changing the structure and activity of water, crowding might have enhanced the capabilities of protocells for evolutionary innovation through the creation of extended neutral networks in the fitness landscape.
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Affiliation(s)
- Ranajay Saha
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
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41
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Abstract
![]()
All biological processes take place
in highly crowded cellular
environments. However, the effect that molecular crowding agents have
on the folding and catalytic properties of RNA molecules remains largely
unknown. Here, we have combined single-molecule fluorescence resonance
energy transfer (smFRET) and bulk cleavage assays to determine the
effect of a molecular crowding agents on the folding and catalysis
of a model RNA enzyme, the hairpin ribozyme. Our single-molecule data
reveal that PEG favors the formation of the docked (active) structure
by increasing the docking rate constant with increasing PEG concentrations.
Furthermore, Mg2+ ion-induced folding in the presence of
PEG occurs at concentrations ∼7-fold lower than in the absence
of PEG, near the physiological range (∼1 mM). Lastly, bulk
cleavage assays in the presence of the crowding agent show that the
ribozyme’s activity increases while the heterogeneity decreases.
Our data is consistent with the idea that molecular crowding plays
an important role in the stabilization of ribozyme active conformations in vivo.
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Affiliation(s)
- Bishnu P Paudel
- Department of Medicine, Section of Virology, and Single Molecule Imaging Group, MRC-Clinical Sciences Centre, Imperial College London , Du Cane Road, London W12 0NN, U.K
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42
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Mustoe AM, Brooks CL, Al-Hashimi HM. Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity. Nucleic Acids Res 2014; 42:11792-804. [PMID: 25217593 PMCID: PMC4191394 DOI: 10.1093/nar/gku807] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Recent studies have shown that basic steric and connectivity constraints encoded at the secondary structure level are key determinants of 3D structure and dynamics in simple two-way RNA junctions. However, the role of these topological constraints in higher order RNA junctions remains poorly understood. Here, we use a specialized coarse-grained molecular dynamics model to directly probe the thermodynamic contributions of topological constraints in defining the 3D architecture and dynamics of transfer RNA (tRNA). Topological constraints alone restrict tRNA's allowed conformational space by over an order of magnitude and strongly discriminate against formation of non-native tertiary contacts, providing a sequence independent source of folding specificity. Topological constraints also give rise to long-range correlations between the relative orientation of tRNA's helices, which in turn provides a mechanism for encoding thermodynamic cooperativity between distinct tertiary interactions. These aspects of topological constraints make it such that only several tertiary interactions are needed to confine tRNA to its native global structure and specify functionally important 3D dynamics. We further show that topological constraints are conserved across tRNA's different naturally occurring secondary structures. Taken together, our results emphasize the central role of secondary-structure-encoded topological constraints in defining RNA 3D structure, dynamics and folding.
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Affiliation(s)
- Anthony M Mustoe
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Charles L Brooks
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Chemistry, Duke University School of Medicine, Durham, NC 27710, USA
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43
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Song Y, Liu KJ, Wang TH. Elimination of ligation dependent artifacts in T4 RNA ligase to achieve high efficiency and low bias microRNA capture. PLoS One 2014; 9:e94619. [PMID: 24722341 PMCID: PMC3983213 DOI: 10.1371/journal.pone.0094619] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 03/18/2014] [Indexed: 01/22/2023] Open
Abstract
Adapter ligation is a critical first step in many microRNA analysis methods including microarray, qPCR, and sequencing. Previous studies have shown that ligation bias can have dramatic effects on both the fidelity of expression profiles and reproducibility across samples. We have developed a method for high efficiency and low bias microRNA capture by 3′ adapter ligation using T4 RNA ligase that does not require pooled adapters. Using a panel of 20 microRNA, we investigated the effects of ligase type, PEG concentration, ligase amount, adapter concentration, incubation time, incubation temperature, and adapter design on capture efficiency and bias. Of these factors, high PEG% was found to be critical in suppressing ligation bias. We obtained high average capture efficiency and low CV across the 20 microRNA panel, both in idealized buffer conditions (86%±10%) and total RNA spiking conditions (64%±17%). We demonstrate that this method is reliable across microRNA species that previous studies have had difficulty capturing and that our adapter design performs significantly better than the common adapter designs. Further, we demonstrate that the optimization methodology must be specifically designed for minimizing bias in order to obtain the ideal reaction parameters.
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Affiliation(s)
- Yunke Song
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Kelvin J. Liu
- Mechanical Engineering Department, Johns Hopkins University, Baltimore, Maryland, United States of America
- Circulomics Inc, Baltimore, Maryland, United States of America
- * E-mail: (THW); (KJL)
| | - Tza-Huei Wang
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, Maryland, United States of America
- Mechanical Engineering Department, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail: (THW); (KJL)
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44
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Strulson CA, Boyer JA, Whitman EE, Bevilacqua PC. Molecular crowders and cosolutes promote folding cooperativity of RNA under physiological ionic conditions. RNA (NEW YORK, N.Y.) 2014; 20:331-47. [PMID: 24442612 PMCID: PMC3923128 DOI: 10.1261/rna.042747.113] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Accepted: 11/22/2013] [Indexed: 05/21/2023]
Abstract
Folding mechanisms of functional RNAs under idealized in vitro conditions of dilute solution and high ionic strength have been well studied. Comparatively little is known, however, about mechanisms for folding of RNA in vivo where Mg(2+) ion concentrations are low, K(+) concentrations are modest, and concentrations of macromolecular crowders and low-molecular-weight cosolutes are high. Herein, we apply a combination of biophysical and structure mapping techniques to tRNA to elucidate thermodynamic and functional principles that govern RNA folding under in vivo-like conditions. We show by thermal denaturation and SHAPE studies that tRNA folding cooperativity increases in physiologically low concentrations of Mg(2+) (0.5-2 mM) and K(+) (140 mM) if the solution is supplemented with physiological amounts (∼ 20%) of a water-soluble neutral macromolecular crowding agent such as PEG or dextran. Low-molecular-weight cosolutes show varying effects on tRNA folding cooperativity, increasing or decreasing it based on the identity of the cosolute. For those additives that increase folding cooperativity, the gain is manifested in sharpened two-state-like folding transitions for full-length tRNA over its secondary structural elements. Temperature-dependent SHAPE experiments in the absence and presence of crowders and cosolutes reveal extent of cooperative folding of tRNA on a nucleotide basis and are consistent with the melting studies. Mechanistically, crowding agents appear to promote cooperativity by stabilizing tertiary structure, while those low molecular cosolutes that promote cooperativity stabilize tertiary structure and/or destabilize secondary structure. Cooperative folding of functional RNA under physiological-like conditions parallels the behavior of many proteins and has implications for cellular RNA folding kinetics and evolution.
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Affiliation(s)
- Christopher A. Strulson
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Joshua A. Boyer
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Elisabeth E. Whitman
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Philip C. Bevilacqua
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Corresponding authorE-mail
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45
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Desai R, Kilburn D, Lee HT, Woodson SA. Increased ribozyme activity in crowded solutions. J Biol Chem 2013; 289:2972-7. [PMID: 24337582 DOI: 10.1074/jbc.m113.527861] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Noncoding RNAs must function in the crowded environment of the cell. Previous small-angle x-ray scattering experiments showed that molecular crowders stabilize the structure of the Azoarcus group I ribozyme, allowing the ribozyme to fold at low physiological Mg(2+) concentrations. Here, we used an RNA cleavage assay to show that the PEG and Ficoll crowder molecules increased the biochemical activity of the ribozyme, whereas sucrose did not. Crowding lowered the Mg(2+) threshold at which activity was detected and increased total RNA cleavage at high Mg(2+) concentrations sufficient to fold the RNA in crowded or dilute solution. After correcting for solution viscosity, the observed reaction rate was proportional to the fraction of active ribozyme. We conclude that molecular crowders stabilize the native ribozyme and favor the active structure relative to compact inactive folding intermediates.
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Affiliation(s)
- Ravi Desai
- From the T. C. Jenkins Department of Biophysics, The Johns Hopkins University, Baltimore, Maryland 21218
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