1
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Alston JJ, Soranno A. Condensation Goes Viral: A Polymer Physics Perspective. J Mol Biol 2023; 435:167988. [PMID: 36709795 PMCID: PMC10368797 DOI: 10.1016/j.jmb.2023.167988] [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: 10/18/2022] [Revised: 01/18/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023]
Abstract
The past decade has seen a revolution in our understanding of how the cellular environment is organized, where an incredible body of work has provided new insights into the role played by membraneless organelles. These rapid advancements have been made possible by an increasing awareness of the peculiar physical properties that give rise to such bodies and the complex biology that enables their function. Viral infections are not extraneous to this. Indeed, in host cells, viruses can harness existing membraneless compartments or, even, induce the formation of new ones. By hijacking the cellular machinery, these intracellular bodies can assist in the replication, assembly, and packaging of the viral genome as well as in the escape of the cellular immune response. Here, we provide a perspective on the fundamental polymer physics concepts that may help connect and interpret the different observed phenomena, ranging from the condensation of viral genomes to the phase separation of multicomponent solutions. We complement the discussion of the physical basis with a description of biophysical methods that can provide quantitative insights for testing and developing theoretical and computational models.
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Affiliation(s)
- Jhullian J Alston
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA; Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130 Saint Louis, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA; Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130 Saint Louis, MO, USA.
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2
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Henning-Knechtel A, Thirumalai D, Kirmizialtin S. Differences in ion-RNA binding modes due to charge density variations explain the stability of RNA in monovalent salts. SCIENCE ADVANCES 2022; 8:eabo1190. [PMID: 35857829 PMCID: PMC9299541 DOI: 10.1126/sciadv.abo1190] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The stability of RNA increases as the charge density of the alkali metal cations increases. The molecular mechanism for this phenomenon remains elusive. To fill this gap, we performed all-atom molecular dynamics pulling simulations of HIV-1 trans-activation response RNA. We first established that the free energy landscape obtained in the simulations is in excellent agreement with the single-molecule optical tweezer experiments. The origin of the stronger stability in sodium compared to potassium is found to be due to the differences in the charge density-related binding modes. The smaller hydrated sodium ion preferentially binds to the highly charged phosphates that have high surface area. In contrast, the larger potassium ions interact with the major grooves. As a result, more cations condense around phosphate groups in the case of sodium ions, leading to the reduction of electrostatic repulsion. Because the proposed mechanism is generic, we predict that the same conclusions are valid for divalent alkaline earth metal cations.
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Affiliation(s)
| | - D. Thirumalai
- Department of Chemistry, University of Texas, Austin, TX 78712, USA
- Corresponding author. (D.T.); (S.K.)
| | - Serdal Kirmizialtin
- Chemistry Program, Math and Sciences, New York University Abu Dhabi, Abu Dhabi, UAE
- Corresponding author. (D.T.); (S.K.)
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3
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Poblete S, Božič A, Kanduč M, Podgornik R, Guzman HV. RNA Secondary Structures Regulate Adsorption of Fragments onto Flat Substrates. ACS OMEGA 2021; 6:32823-32831. [PMID: 34901632 PMCID: PMC8655909 DOI: 10.1021/acsomega.1c04774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/04/2021] [Indexed: 06/14/2023]
Abstract
RNA is a functionally rich molecule with multilevel, hierarchical structures whose role in the adsorption to molecular substrates is only beginning to be elucidated. Here, we introduce a multiscale simulation approach that combines a tractable coarse-grained RNA structural model with an interaction potential of a structureless flat adsorbing substrate. Within this approach, we study the specific role of stem-hairpin and multibranch RNA secondary structure motifs on its adsorption phenomenology. Our findings identify a dual regime of adsorption for short RNA fragments with and without the secondary structure and underline the adsorption efficiency in both cases as a function of the surface interaction strength. The observed behavior results from an interplay between the number of contacts formed at the surface and the conformational entropy of the RNA molecule. The adsorption phenomenology of RNA seems to persist also for much longer RNAs as qualitatively observed by comparing the trends of our simulations with a theoretical approach based on an ideal semiflexible polymer chain.
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Affiliation(s)
- Simón Poblete
- Instituto
de Ciencias Físicas y Matemáticas, Universidad Austral de Chile, Valdivia 5091000, Chile
- Computational
Biology Lab, Fundación Ciencia &
Vida, Santiago 7780272, Chile
| | - Anže Božič
- Department
of Theoretical Physics, Jožef Stefan
Institute, SI-1000 Ljubljana, Slovenia
| | - Matej Kanduč
- Department
of Theoretical Physics, Jožef Stefan
Institute, SI-1000 Ljubljana, Slovenia
| | - Rudolf Podgornik
- School
of Physical Sciences and Kavli Institute for Theoretical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Institute
of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Wenzhou
Institute of the University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
- Department
of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Horacio V. Guzman
- Department
of Theoretical Physics, Jožef Stefan
Institute, SI-1000 Ljubljana, Slovenia
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4
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Cetnar DP, Salis HM. Systematic Quantification of Sequence and Structural Determinants Controlling mRNA stability in Bacterial Operons. ACS Synth Biol 2021; 10:318-332. [PMID: 33464822 DOI: 10.1021/acssynbio.0c00471] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
mRNA degradation is a central process that affects all gene expression levels, and yet, the determinants that control mRNA decay rates remain poorly characterized. Here, we applied a synthetic biology, learn-by-design approach to elucidate the sequence and structural determinants that control mRNA stability in bacterial operons. We designed, constructed, and characterized 82 operons in Escherichia coli, systematically varying RNase binding site characteristics, translation initiation rates, and transcriptional terminator efficiencies in the 5' untranslated region (UTR), intergenic, and 3' UTR regions, followed by measuring their mRNA levels using reverse transcription quantitative polymerase chain reaction (RT-qPCR) assays during exponential growth. We show that introducing long single-stranded RNA into 5' UTRs reduced mRNA levels by up to 9.4-fold and that lowering translation rates reduced mRNA levels by up to 11.8-fold. We also found that RNase binding sites in intergenic regions had much lower effects on mRNA levels. Surprisingly, changing the transcriptional termination efficiency or introducing long single-stranded RNA into 3' UTRs had no effect on upstream mRNA levels. From these measurements, we developed and validated biophysical models of ribosome protection and RNase activity with excellent quantitative agreement. We also formulated design rules to rationally control a mRNA's stability, facilitating the automated design of engineered genetic systems with desired functionalities.
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5
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Re-entrant swelling and redissolution of polyelectrolytes arises from an increased electrostatic decay length at high salt concentrations. J Colloid Interface Sci 2020; 579:369-378. [DOI: 10.1016/j.jcis.2020.06.072] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 11/24/2022]
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6
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Jobbins AM, Reichenbach LF, Lucas CM, Hudson AJ, Burley GA, Eperon IC. The mechanisms of a mammalian splicing enhancer. Nucleic Acids Res 2019; 46:2145-2158. [PMID: 29394380 PMCID: PMC5861446 DOI: 10.1093/nar/gky056] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/19/2018] [Indexed: 12/21/2022] Open
Abstract
Exonic splicing enhancer (ESE) sequences are bound by serine & arginine-rich (SR) proteins, which in turn enhance the recruitment of splicing factors. It was inferred from measurements of splicing around twenty years ago that Drosophila doublesex ESEs are bound stably by SR proteins, and that the bound proteins interact directly but with low probability with their targets. However, it has not been possible with conventional methods to demonstrate whether mammalian ESEs behave likewise. Using single molecule multi-colour colocalization methods to study SRSF1-dependent ESEs, we have found that that the proportion of RNA molecules bound by SRSF1 increases with the number of ESE repeats, but only a single molecule of SRSF1 is bound. We conclude that initial interactions between SRSF1 and an ESE are weak and transient, and that these limit the activity of a mammalian ESE. We tested whether the activation step involves the propagation of proteins along the RNA or direct interactions with 3' splice site components by inserting hexaethylene glycol or abasic RNA between the ESE and the target 3' splice site. These insertions did not block activation, and we conclude that the activation step involves direct interactions. These results support a model in which regulatory proteins bind transiently and in dynamic competition, with the result that each ESE in an exon contributes independently to the probability that an activator protein is bound and in close proximity to a splice site.
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Affiliation(s)
- Andrew M Jobbins
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, UK
| | | | - Christian M Lucas
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, UK
| | - Andrew J Hudson
- Leicester Institute of Structural & Chemical Biology and Department of Chemistry, University of Leicester, UK
| | - Glenn A Burley
- Department of Pure and Applied Chemistry, University of Strathclyde, UK
| | - Ian C Eperon
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, UK
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7
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Sarkar S, Maity A, Sarma Phukon A, Ghosh S, Chakrabarti R. Salt Induced Structural Collapse, Swelling, and Signature of Aggregation of Two ssDNA Strands: Insights from Molecular Dynamics Simulation. J Phys Chem B 2018; 123:47-56. [DOI: 10.1021/acs.jpcb.8b09098] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Soham Sarkar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Atanu Maity
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Aditya Sarma Phukon
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Soumadwip Ghosh
- Beckman Research Institute of the City of Hope National Medical Center, 1500 East Duarte Road, Duarte, California 91010, United States
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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8
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Liu L, Hyeon C. From octopus to dendrite—Semiflexible polyelectrolyte brush condensates in trivalent counterion solution. J Chem Phys 2018; 149:163302. [DOI: 10.1063/1.5027161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
- Lei Liu
- Korea Institute for Advanced Study, Seoul 02455, South Korea
| | - Changbong Hyeon
- Korea Institute for Advanced Study, Seoul 02455, South Korea
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9
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Zhang X, Bao L, Wu YY, Zhu XL, Tan ZJ. Radial distribution function of semiflexible oligomers with stretching flexibility. J Chem Phys 2018; 147:054901. [PMID: 28789545 DOI: 10.1063/1.4991689] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The radial distribution of the end-to-end distance Ree is crucial for quantifying the global size and flexibility of a linear polymer. For semiflexible polymers, several analytical formulas have been derived for the radial distribution of Ree ignoring the stretching flexibility. However, for semiflexible oligomers, such as DNA or RNA, the stretching flexibility can be rather pronounced and can significantly affect the radial distribution of Ree. In this study, we obtained an extended formula that includes the stretch modulus to describe the distribution of Ree for semiflexible oligomers on the basis of previous formulas for semiflexible polymers without stretching flexibility. The extended formula was validated by extensive Monte Carlo simulations over wide ranges of the stretch modulus and persistence length, as well as all-atom molecular dynamics simulations of short DNAs and RNAs. Additionally, our analyses showed that the effect of stretching flexibility on the distribution of Ree becomes negligible for DNAs longer than ∼130 base pairs and RNAs longer than ∼240 base pairs.
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Affiliation(s)
- Xi Zhang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Lei Bao
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Yuan-Yan Wu
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Xiao-Long Zhu
- Department of Physics, School of Physics and Information Engineering, Jianghan University, Wuhan 430056, China
| | - Zhi-Jie Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
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10
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Manz C, Kobitski AY, Samanta A, Jäschke A, Nienhaus GU. The multi-state energy landscape of the SAM-I riboswitch: A single-molecule Förster resonance energy transfer spectroscopy study. J Chem Phys 2018; 148:123324. [DOI: 10.1063/1.5003783] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Christoph Manz
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
- HEiKA–Heidelberg Karlsruhe Research Partnership, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Andrei Yu. Kobitski
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
| | - Ayan Samanta
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Andres Jäschke
- HEiKA–Heidelberg Karlsruhe Research Partnership, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - G. Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
- HEiKA–Heidelberg Karlsruhe Research Partnership, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Nanotechnology and Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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11
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Pathak AK, Bandyopadhyay T. Water isotope effect on the thermostability of a polio viral RNA hairpin: A metadynamics study. J Chem Phys 2017; 146:165104. [DOI: 10.1063/1.4982049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Arup K. Pathak
- Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Tusar Bandyopadhyay
- Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
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12
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Castellanos MM, McAuley A, Curtis JE. Investigating Structure and Dynamics of Proteins in Amorphous Phases Using Neutron Scattering. Comput Struct Biotechnol J 2016; 15:117-130. [PMID: 28138368 PMCID: PMC5257034 DOI: 10.1016/j.csbj.2016.12.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 12/10/2016] [Accepted: 12/13/2016] [Indexed: 02/07/2023] Open
Abstract
In order to increase shelf life and minimize aggregation during storage, many biotherapeutic drugs are formulated and stored as either frozen solutions or lyophilized powders. However, characterizing amorphous solids can be challenging with the commonly available set of biophysical measurements used for proteins in liquid solutions. Therefore, some questions remain regarding the structure of the active pharmaceutical ingredient during freezing and drying of the drug product and the molecular role of excipients. Neutron scattering is a powerful technique to study structure and dynamics of a variety of systems in both solid and liquid phases. Moreover, neutron scattering experiments can generally be correlated with theory and molecular simulations to analyze experimental data. In this article, we focus on the use of neutron techniques to address problems of biotechnological interest. We describe the use of small-angle neutron scattering to study the solution structure of biological molecules and the packing arrangement in amorphous phases, that is, frozen glasses and freeze-dried protein powders. In addition, we discuss the use of neutron spectroscopy to measure the dynamics of glassy systems at different time and length scales. Overall, we expect that the present article will guide and prompt the use of neutron scattering to provide unique insights on many of the outstanding questions in biotechnology.
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Affiliation(s)
- Maria Monica Castellanos
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, United States; Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, United States
| | - Arnold McAuley
- Department of Drug Product Development, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320, United States
| | - Joseph E Curtis
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, United States
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13
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Chremos A, Douglas JF. Influence of higher valent ions on flexible polyelectrolyte stiffness and counter-ion distribution. J Chem Phys 2016; 144:164904. [DOI: 10.1063/1.4947221] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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14
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Wang FH, Wu YY, Tan ZJ. Salt contribution to the flexibility of single-stranded nucleic acid offinite length. Biopolymers 2016; 99:370-81. [PMID: 23529689 DOI: 10.1002/bip.22189] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 11/18/2012] [Indexed: 12/15/2022]
Abstract
Nucleic acids are negatively charged macromolecules and their structure properties are strongly coupled to metal ions in solutions. In this article, the salt effects on the flexibility of single-stranded (ss) nucleic acid chain ranging from 12 to 120 nucleotides are investigated systematically by the coarse-grained Monte Carlo simulations where the salt ions are considered explicitly and the ss chain is modeled with the virtual-bond structural model. Our calculations show that, the increase of ion concentration causes the structural collapse of ss chain and multivalent ions are much more efficient in causing such collapse, and both trivalent/small divalent ions can induce more compact state than a random relaxation state. We found that monovalent, divalent, and trivalent ions can all overcharge ss chain, and the dominating source for such overcharging changes from ion-exclusion-volume effect to ion Coulomb correlations. In addition, the predicted Na(+) and Mg(2+)-dependent persistence length l(p)'s of ss nucleic acid are in accordance with the available experimental data, and through systematic calculations, we obtained the empirical formulas for l(p) as a function of [Na(+)], [Mg(2+)] and chain length.
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Affiliation(s)
- Feng-Hua Wang
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, 430072, China
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15
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Wu YY, Bao L, Zhang X, Tan ZJ. Flexibility of short DNA helices with finite-length effect: From base pairs to tens of base pairs. J Chem Phys 2016; 142:125103. [PMID: 25833610 DOI: 10.1063/1.4915539] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Flexibility of short DNA helices is important for the biological functions such as nucleosome formation and DNA-protein recognition. Recent experiments suggest that short DNAs of tens of base pairs (bps) may have apparently higher flexibility than those of kilo bps, while there is still the debate on such high flexibility. In the present work, we have studied the flexibility of short DNAs with finite-length of 5-50 bps by the all-atomistic molecular dynamics simulations and Monte Carlo simulations with the worm-like chain model. Our microscopic analyses reveal that short DNAs have apparently high flexibility which is attributed to the significantly strong bending and stretching flexibilities of ∼6 bps at each helix end. Correspondingly, the apparent persistence length lp of short DNAs increases gradually from ∼29 nm to ∼45 nm as DNA length increases from 10 to 50 bps, in accordance with the available experimental data. Our further analyses show that the short DNAs with excluding ∼6 bps at each helix end have the similar flexibility with those of kilo bps and can be described by the worm-like chain model with lp ∼ 50 nm.
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Affiliation(s)
- Yuan-Yan Wu
- Department of Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Lei Bao
- Department of Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Xi Zhang
- Department of Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Zhi-Jie Tan
- Department of Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
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16
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Roh JH. Dynamics of Biopolymers: Role of Hydration and Electrostatic Interactions. MACROMOL CHEM PHYS 2015. [DOI: 10.1002/macp.201500279] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Joon Ho Roh
- Institute for Basic Science; Center for Self-Assembly and Complexity; 77 Cheongam-Ro Nam-gu Pohang 790-784 South Korea
- Biomolecular Science; University of Science and Technology; 217 Gajeong-ro Yuseong-gu Daejeon 305-350 South Korea
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17
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Ghosh S, Dixit H, Chakrabarti R. Ion assisted structural collapse of a single stranded DNA: A molecular dynamics approach. Chem Phys 2015. [DOI: 10.1016/j.chemphys.2015.07.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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18
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Kang H, Toan NM, Hyeon C, Thirumalai D. Unexpected Swelling of Stiff DNA in a Polydisperse Crowded Environment. J Am Chem Soc 2015; 137:10970-8. [PMID: 26267166 DOI: 10.1021/jacs.5b04531] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We investigate the conformations of DNA-like stiff chains, characterized by contour length (L) and persistence length (lp), in a variety of crowded environments containing monodisperse soft spherical (SS) and spherocylindrical (SC) particles, a mixture of SS and SC, and a milieu mimicking the composition of proteins in the Escherichia coli cytoplasm. The stiff chain, whose size modestly increases in SS crowders up to ϕ ≈ 0.1, is considerably more compact at low volume fractions (ϕ ≤ 0.2) in monodisperse SC particles than in a medium containing SS particles. A 1:1 mixture of SS and SC crowders induces greater chain compaction than the pure SS or SC crowders at the same ϕ, with the effect being highly nonadditive. We also discover a counterintuitive result that the polydisperse crowding environment, mimicking the composition of a cell lysate, swells the DNA-like polymer, which is in stark contrast to the size reduction of flexible polymers in the same milieu. Trapping of the stiff chain in a fluctuating tube-like environment created by large-sized crowders explains the dramatic increase in size and persistence length of the stiff chain. In the polydisperse medium, mimicking the cellular environment, the size of the DNA (or related RNA) is determined by L/lp. At low L/lp, the size of the polymer is unaffected, whereas there is a dramatic swelling at an intermediate value of L/lp. We use these results to provide insights into recent experiments on crowding effects on RNA and also make testable predictions.
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Affiliation(s)
| | | | | | - D Thirumalai
- Korea Institute for Advanced Study , Seoul 130-722, Korea
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19
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Tsai MY, Zheng W, Balamurugan D, Schafer NP, Kim BL, Cheung MS, Wolynes PG. Electrostatics, structure prediction, and the energy landscapes for protein folding and binding. Protein Sci 2015; 25:255-69. [PMID: 26183799 DOI: 10.1002/pro.2751] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 07/14/2015] [Indexed: 11/09/2022]
Abstract
While being long in range and therefore weakly specific, electrostatic interactions are able to modulate the stability and folding landscapes of some proteins. The relevance of electrostatic forces for steering the docking of proteins to each other is widely acknowledged, however, the role of electrostatics in establishing specifically funneled landscapes and their relevance for protein structure prediction are still not clear. By introducing Debye-Hückel potentials that mimic long-range electrostatic forces into the Associative memory, Water mediated, Structure, and Energy Model (AWSEM), a transferable protein model capable of predicting tertiary structures, we assess the effects of electrostatics on the landscapes of thirteen monomeric proteins and four dimers. For the monomers, we find that adding electrostatic interactions does not improve structure prediction. Simulations of ribosomal protein S6 show, however, that folding stability depends monotonically on electrostatic strength. The trend in predicted melting temperatures of the S6 variants agrees with experimental observations. Electrostatic effects can play a range of roles in binding. The binding of the protein complex KIX-pKID is largely assisted by electrostatic interactions, which provide direct charge-charge stabilization of the native state and contribute to the funneling of the binding landscape. In contrast, for several other proteins, including the DNA-binding protein FIS, electrostatics causes frustration in the DNA-binding region, which favors its binding with DNA but not with its protein partner. This study highlights the importance of long-range electrostatics in functional responses to problems where proteins interact with their charged partners, such as DNA, RNA, as well as membranes.
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Affiliation(s)
- Min-Yeh Tsai
- Department of Chemistry, Rice University, Houston, Texas, 77005.,Center for Theoretical Biological Physics, Rice University, Houston, Texas, 77005.,Department of Physics, University of Houston, Houston, Texas, 77204
| | - Weihua Zheng
- Department of Chemistry, Rice University, Houston, Texas, 77005.,Center for Theoretical Biological Physics, Rice University, Houston, Texas, 77005
| | - D Balamurugan
- Computation Institute, University of Chicago, Chicago, Illinois, 60637
| | - Nicholas P Schafer
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus C, Denmark
| | - Bobby L Kim
- Department of Chemistry, Rice University, Houston, Texas, 77005.,Center for Theoretical Biological Physics, Rice University, Houston, Texas, 77005
| | - Margaret S Cheung
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, 77005.,Department of Physics, University of Houston, Houston, Texas, 77204
| | - Peter G Wolynes
- Department of Chemistry, Rice University, Houston, Texas, 77005.,Center for Theoretical Biological Physics, Rice University, Houston, Texas, 77005.,Physics and Astronomy, Rice University, Houston, Texas, 77005
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20
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Kim J, Wu J. A molecular thermodynamic model for the stability of hepatitis B capsids. J Chem Phys 2015; 140:235101. [PMID: 24952568 DOI: 10.1063/1.4882068] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Self-assembly of capsid proteins and genome encapsidation are two critical steps in the life cycle of most plant and animal viruses. A theoretical description of such processes from a physiochemical perspective may help better understand viral replication and morphogenesis thus provide fresh insights into the experimental studies of antiviral strategies. In this work, we propose a molecular thermodynamic model for predicting the stability of Hepatitis B virus (HBV) capsids either with or without loading nucleic materials. With the key components represented by coarse-grained thermodynamic models, the theoretical predictions are in excellent agreement with experimental data for the formation free energies of empty T4 capsids over a broad range of temperature and ion concentrations. The theoretical model predicts T3/T4 dimorphism also in good agreement with the capsid formation at in vivo and in vitro conditions. In addition, we have studied the stability of the viral particles in response to physiological cellular conditions with the explicit consideration of the hydrophobic association of capsid subunits, electrostatic interactions, molecular excluded volume effects, entropy of mixing, and conformational changes of the biomolecular species. The course-grained model captures the essential features of the HBV nucleocapsid stability revealed by recent experiments.
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Affiliation(s)
- Jehoon Kim
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, USA
| | - Jianzhong Wu
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, USA
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21
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Schefer L, Usov I, Mezzenga R. Anomalous Stiffening and Ion-Induced Coil–Helix Transition of Carrageenans under Monovalent Salt Conditions. Biomacromolecules 2015; 16:985-91. [DOI: 10.1021/bm501874k] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Larissa Schefer
- Department of Health Sciences
and Technology, ETH Zurich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| | - Ivan Usov
- Department of Health Sciences
and Technology, ETH Zurich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| | - Raffaele Mezzenga
- Department of Health Sciences
and Technology, ETH Zurich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
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22
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Jacobson DR, McIntosh DB, Saleh OA. The snakelike chain character of unstructured RNA. Biophys J 2014; 105:2569-76. [PMID: 24314087 DOI: 10.1016/j.bpj.2013.10.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 10/16/2013] [Accepted: 10/23/2013] [Indexed: 01/30/2023] Open
Abstract
In the absence of base-pairing and tertiary structure, ribonucleic acid (RNA) assumes a random-walk conformation, modulated by the electrostatic self-repulsion of the charged, flexible backbone. This behavior is often modeled as a Kratky-Porod "wormlike chain" (WLC) with a Barrat-Joanny scale-dependent persistence length. In this study we report measurements of the end-to-end extension of poly(U) RNA under 0.1 to 10 pN applied force and observe two distinct elastic-response regimes: a low-force, power-law regime characteristic of a chain of swollen blobs on long length scales and a high-force, salt-valence-dependent regime consistent with ion-stabilized crumpling on short length scales. This short-scale structure is additionally supported by force- and salt-dependent quantification of the RNA ion atmosphere composition, which shows that ions are liberated under stretching; the number of ions liberated increases with increasing bulk salt concentration. Both this result and the observation of two elastic-response regimes directly contradict the WLC model, which predicts a single elastic regime across all forces and, when accounting for scale-dependent persistence length, the opposite trend in ion release with salt concentration. We conclude that RNA is better described as a "snakelike chain," characterized by smooth bending on long length scales and ion-stabilized crumpling on short length scales. In monovalent salt, these two regimes are separated by a characteristic length that scales with the Debye screening length, highlighting the determining importance of electrostatics in RNA conformation.
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Affiliation(s)
- David R Jacobson
- Department of Physics, University of California, Santa Barbara, CA
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23
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Sinner C, Lutz B, John S, Reinartz I, Verma A, Schug A. Simulating Biomolecular Folding and Function by Native-Structure-Based/Go-Type Models. Isr J Chem 2014. [DOI: 10.1002/ijch.201400012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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24
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Yoon J, Lin JC, Hyeon C, Thirumalai D. Dynamical Transition and Heterogeneous Hydration Dynamics in RNA. J Phys Chem B 2014; 118:7910-9. [DOI: 10.1021/jp500643u] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jeseong Yoon
- Korea Institute for Advanced Study, 130-722 Seoul, Korea
| | - Jong-Chin Lin
- Department
of Chemistry and Biochemistry, and Biophysics
Program, Institute for Physical Sciences and Technology, University of Maryland, College
Park, Maryland 20742, United States
| | | | - D. Thirumalai
- Department
of Chemistry and Biochemistry, and Biophysics
Program, Institute for Physical Sciences and Technology, University of Maryland, College
Park, Maryland 20742, United States
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25
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Bosco A, Camunas-Soler J, Ritort F. Elastic properties and secondary structure formation of single-stranded DNA at monovalent and divalent salt conditions. Nucleic Acids Res 2014; 42:2064-74. [PMID: 24225314 PMCID: PMC3919573 DOI: 10.1093/nar/gkt1089] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 10/16/2013] [Accepted: 10/17/2013] [Indexed: 11/16/2022] Open
Abstract
Single-stranded DNA (ssDNA) plays a major role in several biological processes. It is therefore of fundamental interest to understand how the elastic response and the formation of secondary structures are modulated by the interplay between base pairing and electrostatic interactions. Here we measure force-extension curves (FECs) of ssDNA molecules in optical tweezers set up over two orders of magnitude of monovalent and divalent salt conditions, and obtain its elastic parameters by fitting the FECs to semiflexible models of polymers. For both monovalent and divalent salts, we find that the electrostatic contribution to the persistence length is proportional to the Debye screening length, varying as the inverse of the square root of cation concentration. The intrinsic persistence length is equal to 0.7 nm for both types of salts, and the effectivity of divalent cations in screening electrostatic interactions appears to be 100-fold as compared with monovalent salt, in line with what has been recently reported for single-stranded RNA. Finally, we propose an analysis of the FECs using a model that accounts for the effective thickness of the filament at low salt condition and a simple phenomenological description that quantifies the formation of non-specific secondary structure at low forces.
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Affiliation(s)
- Alessandro Bosco
- SISSA - Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, 34136 Trieste, Italy, Elettra-Sincrotrone Trieste S.C.p.A., Strada Statale 14 - km 163,5 in AREA Science Park, 34149 Basovizza Trieste, Italy, Departament de Física Fonamental, Universitat de Barcelona, Diagonal 647, 08028 Barcelona, Spain and CIBER de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Madrid, Spain
| | - Joan Camunas-Soler
- SISSA - Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, 34136 Trieste, Italy, Elettra-Sincrotrone Trieste S.C.p.A., Strada Statale 14 - km 163,5 in AREA Science Park, 34149 Basovizza Trieste, Italy, Departament de Física Fonamental, Universitat de Barcelona, Diagonal 647, 08028 Barcelona, Spain and CIBER de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Madrid, Spain
| | - Felix Ritort
- SISSA - Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, 34136 Trieste, Italy, Elettra-Sincrotrone Trieste S.C.p.A., Strada Statale 14 - km 163,5 in AREA Science Park, 34149 Basovizza Trieste, Italy, Departament de Física Fonamental, Universitat de Barcelona, Diagonal 647, 08028 Barcelona, Spain and CIBER de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Madrid, Spain
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26
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Abstract
A common theoretical approach to calculating reaction kinetics is to approximate a high-dimensional conformational search with a one-dimensional diffusion along an effective reaction coordinate. We employed Brownian dynamics simulations to test the validity of this approximation for loop formation kinetics in the worm-like chain polymer model. This model is often used to describe polymers that exhibit backbone stiffness beyond the monomer length scale. We find that one-dimensional diffusion models overestimate the looping time and do not predict the quantitatively correct dependence of looping time on chain length or capture radius. Our findings highlight the difficulty of describing high-dimensional polymers with simple kinetic theories.
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Affiliation(s)
- Reza Afra
- Department of Physics, Purdue University, West Lafayette, Indiana 47907, USA
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27
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Faber M, Klumpp S. Kinetic Monte Carlo approach to RNA folding dynamics using structure-based models. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:052701. [PMID: 24329290 DOI: 10.1103/physreve.88.052701] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 09/03/2013] [Indexed: 06/03/2023]
Abstract
RNA molecules form three-dimensional structures via base pairing that determine the function and biochemical activity of the molecule. Here we introduce a structure-based method for studying the folding dynamics of RNA secondary structures. The approach focuses on native contacts that are parametrized with standard empirical free energies. Kinetic Monte Carlo simulations for free folding of simple hairpins and complex structures such as a tRNA as well as for folding in the presence of an external force show good agreement with experimental data. A systematic comparison of simulated and experimental folding rates for various structures shows a strong correlation, indicating that the approach can predict folding rates within about an order of magnitude.
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Affiliation(s)
- Michael Faber
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany
| | - Stefan Klumpp
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany
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28
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Kilburn D, Roh JH, Behrouzi R, Briber RM, Woodson SA. Crowders perturb the entropy of RNA energy landscapes to favor folding. J Am Chem Soc 2013; 135:10055-63. [PMID: 23773075 DOI: 10.1021/ja4030098] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Biological macromolecules have evolved to fold and operate in the crowded environment of the cell. We have shown previously that molecular crowding stabilizes folded RNA structures. Here we report SAXS measurements on a 64 kDa bacterial group I ribozyme in the presence of mono- and divalent ions and PEG crowders of different molecular weight. These experiments show that crowders always stabilize the folded RNA, but this stabilization is weaker in NaCl solutions than MgCl2 solutions. Additionally, we find that RNAs with the same global structure, parametrized by Rg, have different scattering functions depending upon the ratio of electrostatic and entropic stabilization by ions and crowders, respectively. We quantify this difference using the scattering length per scattering volume and find that this ratio is larger for RNAs that fold in lower ionic strength solutions due to the higher crowder content. We conclude that lower RNA flexibility, or reduced configurational entropy, widens the free energy gap between the unfolded and folded RNA in crowded MgCl2 solutions.
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Affiliation(s)
- Duncan Kilburn
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
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29
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Seaton DT, Schnabel S, Landau DP, Bachmann M. From flexible to stiff: systematic analysis of structural phases for single semiflexible polymers. PHYSICAL REVIEW LETTERS 2013; 110:028103. [PMID: 23383941 DOI: 10.1103/physrevlett.110.028103] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2012] [Indexed: 06/01/2023]
Abstract
Inspired by recent studies revealing unexpected pliability of semiflexible biomolecules like RNA and DNA, we systematically investigate the range of structural phases by means of a simple generic polymer model. Using a two-dimensional variant of Wang-Landau sampling to explore the conformational space in energy and stiffness within a single simulation, we identify the entire diversity of structures existing from the well-studied limit of flexible polymers to that of wormlike chains. We also discuss, in detail, the influence of finite-size effects in the formation of crystalline structures that are virtually inaccessible via conventional computational approaches.
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Affiliation(s)
- Daniel T Seaton
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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30
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Toan NM, Thirumalai D. On the origin of the unusual behavior in the stretching of single-stranded DNA. J Chem Phys 2012; 136:235103. [PMID: 22779622 DOI: 10.1063/1.4729371] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Force-extension curves (FECs), which quantify the response of a variety of biomolecules subject to mechanical force (f), are often quantitatively fit using worm-like chain (WLC) or freely jointed chain (FJC) models. These models predict that the chain extension, x, normalized by the contour length increases linearly at small f and at high forces scale as x ~ (1 - f(-α)), where α = 0.5 for WLC and unity for FJC. In contrast, experiments on single-stranded DNA (ssDNA) show that over a range of f and ionic concentration, x scales as x ~ ln f, which cannot be explained using WLC or FJC models. Using theory and simulations we show that this unusual behavior in FEC in ssDNA is due to sequence-independent polyelectrolyte effects. We show that the x ~ ln f arises because in the absence of force the tangent correlation function, quantifying chain persistence, decays algebraically on length scales on the order of the Debye length. Our theory, which is most appropriate for monovalent salts, quantitatively fits the experimental data and further predicts that such a regime is not discernible in double-stranded DNA.
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Affiliation(s)
- Ngo Minh Toan
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland at College Park, College Park, Maryland 20742, USA
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31
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de Almeida Ribeiro E, Beich-Frandsen M, Konarev PV, Shang W, Večerek B, Kontaxis G, Hämmerle H, Peterlik H, Svergun DI, Bläsi U, Djinović-Carugo K. Structural flexibility of RNA as molecular basis for Hfq chaperone function. Nucleic Acids Res 2012; 40:8072-84. [PMID: 22718981 PMCID: PMC3439903 DOI: 10.1093/nar/gks510] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 05/05/2012] [Accepted: 05/09/2012] [Indexed: 12/22/2022] Open
Abstract
In enteric bacteria, many small regulatory RNAs (sRNAs) associate with the RNA chaperone host factor Q (Hfq) and often require the protein for regulation of target mRNAs. Previous studies suggested that the hexameric Escherichia coli Hfq (Hfq(Ec)) binds sRNAs on the proximal site, whereas the distal site has been implicated in Hfq-mRNA interactions. Employing a combination of small angle X-ray scattering, nuclear magnetic resonance and biochemical approaches, we report the structural analysis of a 1:1 complex of Hfq(Ec) with a 34-nt-long subsequence of a natural substrate sRNA, DsrA (DsrA(34)). This sRNA is involved in post-transcriptional regulation of the E. coli rpoS mRNA encoding the stationary phase sigma factor RpoS. The molecular envelopes of Hfq(Ec) in complex with DsrA(34) revealed an overall asymmetric shape of the complex in solution with the protein maintaining its doughnut-like structure, whereas the extended DsrA(34) is flexible and displays an ensemble of different spatial arrangements. These results are discussed in terms of a model, wherein the structural flexibility of RNA ligands bound to Hfq stochastically facilitates base pairing and provides the foundation for the RNA chaperone function inherent to Hfq.
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Affiliation(s)
- Euripedes de Almeida Ribeiro
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Mads Beich-Frandsen
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Petr V. Konarev
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Weifeng Shang
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Branislav Večerek
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Georg Kontaxis
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Hermann Hämmerle
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Herwig Peterlik
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Dmitri I. Svergun
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Udo Bläsi
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Kristina Djinović-Carugo
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
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32
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Wessig P, Möllnitz K. Building Blocks for Oligospiroketal (OSK) Rods and Evaluation of Their Influence on Rod Rigidity. J Org Chem 2012; 77:3907-20. [DOI: 10.1021/jo300266b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pablo Wessig
- Universität Potsdam, Institut für Chemie, Karl-Liebknecht-Str. 24-25, D-14476
Potsdam, Germany
| | - Kristian Möllnitz
- Universität Potsdam, Institut für Chemie, Karl-Liebknecht-Str. 24-25, D-14476
Potsdam, Germany
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33
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Gopal A, Zhou ZH, Knobler CM, Gelbart WM. Visualizing large RNA molecules in solution. RNA (NEW YORK, N.Y.) 2012; 18:284-99. [PMID: 22190747 PMCID: PMC3264915 DOI: 10.1261/rna.027557.111] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 11/12/2011] [Indexed: 05/24/2023]
Abstract
Single-stranded RNAs (ssRNAs) longer than a few hundred nucleotides do not have a unique structure in solution. Their equilibrium properties therefore reflect the average of an ensemble of structures. We use cryo-electron microscopy to image projections of individual long ssRNA molecules and characterize the anisotropy of their ensembles in solution. A flattened prolate volume is found to best represent the shapes of these ensembles. The measured sizes and anisotropies are in good agreement with complementary determinations using small-angle X-ray scattering and coarse-grained molecular dynamics simulations. A long viral ssRNA is compared with shorter noncoding transcripts to demonstrate that prolate geometry and flatness are generic properties independent of sequence length and origin. The anisotropy persists under physiological as well as low-ionic-strength conditions, revealing a direct correlation between secondary structure asymmetry and 3D shape and size. We discuss the physical origin of the generic anisotropy and its biological implications.
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Affiliation(s)
- Ajaykumar Gopal
- Department of Chemistry and Biochemistry, University of California-Los Angeles, CA 90095, USA.
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34
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Mao Y, Zhang J. Understanding thermodynamic competitivity between biopolymer folding and misfolding under large-scale intermolecular interactions. J Am Chem Soc 2011; 134:631-9. [PMID: 22126310 DOI: 10.1021/ja209534c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cooperativity is a hallmark of spontaneous biopolymer folding. The presence of intermolecular interactions could create off-pathway misfolding structures and suppress folding cooperativity. This raises the hypothesis that thermodynamic competitivity between off-pathway misfolding and on-pathway folding may intervene with cooperativity and govern biopolymer folding dynamics under conditions permitting large-scale intermolecular interactions. Here we report direct imaging and theoretical modeling of thermodynamic competitivity between biopolymer folding and misfolding under such conditions, using a two-dimensional array of proton-fueled DNA molecular motors packed at the maximal density as a model system. Time-resolved liquid-phase atomic force microscopy with enhanced phase contrast revealed that the misfolding and folding intermediates transiently self-organize into spatiotemporal patterns on the nanoscale in thermodynamic states far away from equilibrium as a result of thermodynamic competitivity. Computer simulations using a novel cellular-automaton network model provide quantitative insights into how large-scale intermolecular interactions correlate the structural dynamics of individual biomolecules together at the systems level.
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Affiliation(s)
- Youdong Mao
- Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02215, USA.
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35
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Roh JH, Tyagi M, Briber RM, Woodson SA, Sokolov AP. The Dynamics of Unfolded versus Folded tRNA: The Role of Electrostatic Interactions. J Am Chem Soc 2011; 133:16406-9. [DOI: 10.1021/ja207667u] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Joon Ho Roh
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland, United States
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, United States
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland, United States
| | - Madhu Tyagi
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland, United States
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland, United States
| | - R. M. Briber
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland, United States
| | - Sarah A. Woodson
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, United States
| | - Alexei P. Sokolov
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee, United States
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36
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Abstract
Positively charged ions, atoms, or molecules compensate the high negative charge of the nucleic acid backbone. Their presence is critical to the biological function of DNA and RNA. This review focuses on experimental studies probing (a) interactions between small ions and nucleic acids and (b) ion-mediated interactions between nucleic acid duplexes. Experimental results on these simple model systems can be compared with specific theoretical models to validate their predictions. Small angle X-ray scattering (SAXS) provides unique insight into these interactions. Anomalous SAXS reports the spatial correlations of condensed (e.g., locally concentrated) counterions to individual DNA or RNA duplexes. SAXS very effectively reports interactions between nucleic acid helices, which range from strongly repulsive to strongly attractive depending on the ionic species present. The sign and strength of interparticle interactions are easily deduced from dramatic changes in the scattering profiles of interacting duplexes.
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Affiliation(s)
- Lois Pollack
- School of Applied & Engineering Physics, Cornell University, Ithaca, NY 14853, USA.
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37
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Pereyaslavets LB, Baranov MV, Leonova EI, Galzitskaya OV. Prediction of folding nuclei in tRNA molecules. BIOCHEMISTRY (MOSCOW) 2011; 76:236-44. [PMID: 21568857 DOI: 10.1134/s0006297911020106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Prediction of folding nuclei in RNA molecules allows one to look in a new way at the problem of possible RNA base sequence folding and at problems associated with incorrect RNA folding, as well as at RNA structure stability. We have chosen a model and energy parameters for description of RNA structure. The algorithm for studying processes including protein folding/unfolding was successfully applied to calculations on tRNA. Four tRNA molecules were considered whose structures were obtained in the free state (tRNA(Phe), tRNA(Asp), tRNA(fMet), and tRNA(Lys)). The calculated Φ-values for tRNA molecules correlate with experimental data showing that nucleotide residues in the D and T hairpin regions are involved in tRNA structure last, or more exactly, they are not included in the tRNA folding nucleus. High Φ-values in the anticodon hairpin region show that the nucleus of tRNA folding is localized just in that place.
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Affiliation(s)
- L B Pereyaslavets
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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38
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Chen WH, Fu JY, Kourentzi K, Willson RC. Nucleic acid affinity of clustered-charge anion exchange adsorbents: Effects of ionic strength and ligand density. J Chromatogr A 2011; 1218:258-62. [DOI: 10.1016/j.chroma.2010.11.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Revised: 11/08/2010] [Accepted: 11/11/2010] [Indexed: 10/18/2022]
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39
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Fluegel S, Fischer K, McDaniel JR, Chilkoti A, Schmidt M. Chain stiffness of elastin-like polypeptides. Biomacromolecules 2010; 11:3216-8. [PMID: 20961120 DOI: 10.1021/bm100965y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sabine Fluegel
- Institute of Physical Chemistry, University of Mainz, 55099 Mainz, Germany, and Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
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40
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Roh JH, Guo L, Kilburn JD, Briber RM, Irving T, Woodson SA. Multistage collapse of a bacterial ribozyme observed by time-resolved small-angle X-ray scattering. J Am Chem Soc 2010; 132:10148-54. [PMID: 20597502 PMCID: PMC2918669 DOI: 10.1021/ja103867p] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ribozymes must fold into compact, native structures to function properly in the cell. The first step in forming the RNA tertiary structure is the neutralization of the phosphate charge by cations, followed by collapse of the unfolded molecules into more compact structures. The specificity of the collapse transition determines the structures of the folding intermediates and the folding time to the native state. However, the forces that enable specific collapse in RNA are not understood. Using time-resolved SAXS, we report that upon addition of 5 mM Mg(2+) to the Azoarcus group I ribozyme up to 80% of chains form compact structures in less than 1 ms. In 1 mM Mg(2+), the collapse transition produces extended structures that slowly approach the folded state, while > or = 1.5 mM Mg(2+) leads to an ensemble of random coils that fold with multistage kinetics. Increased flexibility of molecules in the intermediate ensemble correlates with a Mg(2+)-dependent increase in the fast folding population and a previously unobserved crossover in the collapse kinetics. Partial denaturation of the unfolded RNA with urea also increases the fraction of chains following the fast-folding pathway. These results demonstrate that the preferred collapse mechanism depends on the extent of Mg(2+)-dependent charge neutralization and that non-native interactions within the unfolded ensemble contribute to the heterogeneity of the ribozyme folding pathways at the very earliest stages of tertiary structure formation.
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Affiliation(s)
- Joon Ho Roh
- Department of Materials Science and Engineering, University of Maryland, College Park, MD 20742, USA
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
- NIST Center for Neutron Scattering Research, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Liang Guo
- BioCAT, CSRRI and Department of BCPS, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - J. Duncan Kilburn
- 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
| | - Thomas Irving
- BioCAT, CSRRI and Department of BCPS, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Sarah A. Woodson
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
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41
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Abstract
We provide a unified theory for the high force entropic elasticity of biopolymers solely in terms of the persistence length, ξp , and the monomer spacing, a. When the force f>ℱ h ~ kBTξp /a2 the biopolymers behave as freely jointed chains (FJCs) while in the range ℱ l ~ kBT/ξp <f<ℱ h the worm-like chain (WLC) is a better model. We show that ξp can be estimated from the force extension curve (FEC) at the extension x ≈ 1/2 (normalized by the contour length of the biopolymer). After validating the theory using simulations, we provide a quantitative analysis of the FECs for a diverse set of biopolymers (dsDNA, ssRNA, ssDNA, polysaccharides, and unstructured PEVK domain of titin) for x ≥ 1/2. The success of a specific polymer model (FJC or WLC) to describe the FEC of a given biopolymer is naturally explained by the theory. Only by probing the response of biopolymers over a wide range of forces can the f-dependent elasticity be fully described.
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Affiliation(s)
- Ngo Minh Toan
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland at College Park, College Park, Maryland 20742
| | - D Thirumalai
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland at College Park, College Park, Maryland 20742.,Department of Chemistry and Biochemistry, University of Maryland at College Park, College Park, Maryland 20742
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42
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Moghaddam S, Caliskan G, Chauhan S, Hyeon C, Briber RM, Thirumalai D, Woodson SA. Metal ion dependence of cooperative collapse transitions in RNA. J Mol Biol 2009; 393:753-64. [PMID: 19712681 PMCID: PMC2772878 DOI: 10.1016/j.jmb.2009.08.044] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Revised: 08/18/2009] [Accepted: 08/18/2009] [Indexed: 10/20/2022]
Abstract
Positively charged counterions drive RNA molecules into compact configurations that lead to their biologically active structures. To understand how the valence and size of the cations influences the collapse transition in RNA, small-angle X-ray scattering was used to follow the decrease in the radius of gyration (R(g)) of the Azoarcus and Tetrahymena ribozymes in different cations. Small, multivalent cations induced the collapse of both ribozymes more efficiently than did monovalent ions. Thus, the cooperativity of the collapse transition depends on the counterion charge density. Singular value decomposition of the scattering curves showed that folding of the smaller and more thermostable Azoarcus ribozyme is well described by two components, whereas collapse of the larger Tetrahymena ribozyme involves at least one intermediate. The ion-dependent persistence length, extracted from the distance distribution of the scattering vectors, shows that the Azoarcus ribozyme is less flexible at the midpoint of transition in low-charge-density ions than in high-charge-density ions. We conclude that the formation of sequence-specific tertiary interactions in the Azoarcus ribozyme overlaps with neutralization of the phosphate charge, while tertiary folding of the Tetrahymena ribozyme requires additional counterions. Thus, the stability of the RNA structure determines its sensitivity to the valence and size of the counterions.
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Affiliation(s)
- Sarvin Moghaddam
- Dept. of Materials Science and Engineering, University of Maryland, College Park, MD 20472
| | - Gokhan Caliskan
- T. C. Jenkins Dept. of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218-2685
| | - Seema Chauhan
- Dept. of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218-2685
| | - Changbong Hyeon
- Dept. of Chemistry, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - R. M. Briber
- Dept. of Materials Science and Engineering, University of Maryland, College Park, MD 20472
| | - D. Thirumalai
- Biophysics Program, Institute for Physical Sciences and Technology, University of Maryland, College Park, MD 20472 USA
| | - Sarah A. Woodson
- T. C. Jenkins Dept. of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218-2685
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43
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McIntosh DB, Ribeck N, Saleh OA. Detailed scaling analysis of low-force polyelectrolyte elasticity. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 80:041803. [PMID: 19905329 DOI: 10.1103/physreve.80.041803] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Indexed: 05/28/2023]
Abstract
Single-molecule force-extension data are typically compared to ideal models of polymer behavior that ignore the effects of self-avoidance. Here, we demonstrate a link between single-molecule data and the scaling pictures of a real polymer. We measure a low-force elasticity regime where the extension L of chemically denatured single-stranded DNA grows as a power law with force f : L approximately f;{gamma} , with gamma approximately 0.60-0.69 . This compares favorably with the "tensile-blob" model of a self-avoiding polymer, which predicts gamma=2/3 . We show that the transition out of the low-force regime is highly salt dependent, and use the tensile-blob model to relate this effect to the salt dependence of the polymer's Kuhn length and excluded-volume parameter. We find that, contrary to the well-known Odijk-Skolnick-Fixman theory, the Kuhn length of single-stranded DNA is linearly proportional to the Debye length of the solution. Finally, we show that the low-force elasticity becomes linear (gamma=1) at approximately 3 M salt, and interpret this as a Theta point of the polymer. At this point, the force-extension data is best described by the wormlike chain model, from which we estimate the bare (nonelectrostatic) persistence length of the polymer to be approximately 0.6 nm .
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Affiliation(s)
- D B McIntosh
- Physics Department, University of California, Santa Barbara, California 93106, USA
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44
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Choudhury PK, Bagchi D, Menon R. π-conjugation and conformation in a semiconducting polymer: small angle x-ray scattering study. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2009; 21:195801. [PMID: 21825496 DOI: 10.1088/0953-8984/21/19/195801] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Small angle x-ray scattering (SAXS) in a poly[2-methoxy-5-(2'-ethyl-hexyloxy)-1,4-phenylene vinylene] (MEH-PPV) solution has shown the important role of π-electron conjugation in controlling the chain conformation and assembly. By increasing the extent of conjugation from 30 to 100%, the persistence length (l(p)) increases from 20 to 66 Å. Moreover, a pronounced second peak in the pair distribution function has been observed in a fully conjugated chain, at larger length scales. This feature indicates that the chain segments tend to self-assemble as the conjugation along the chain increases. Xylene enhances the rigidity of the PPV backbone to yield extended structures, while tetrahydrofuran solvates the side groups to form compact coils in which the l(p) is much shorter.
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45
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Werner A, Konarev PV, Svergun DI, Hahn U. Characterization of a fluorophore binding RNA aptamer by fluorescence correlation spectroscopy and small angle X-ray scattering. Anal Biochem 2009; 389:52-62. [PMID: 19303859 DOI: 10.1016/j.ab.2009.03.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2009] [Accepted: 03/12/2009] [Indexed: 01/14/2023]
Abstract
Using fluorescence correlation spectroscopy (FCS), we have established an in vitro assay to study RNA dynamics by analyzing fluorophore binding RNA aptamers at the single molecule level. The RNA aptamer SRB2m, a minimized variant of the initially selected aptamer SRB-2, has a high affinity to the disulfonated triphenylmethane dye sulforhodamine B. A mobility shift of sulforhodamine B after binding to SRB2m was measured. In contrast, patent blue V (PBV) is visible only if complexed with SRB2m due to increased molecular brightness and minimal background. With small angle X-ray scattering (SAXS), the three-dimensional structure of the RNA aptamer was characterized at low resolution to analyze the effect of fluorophore binding. The aptamer and sulforhodamine B-aptamer complex was found to be predominantly dimeric in solution. Interaction of PBV with SRB2m led to a dissociation of SRB2m dimers into monomers. Radii of gyration and hydrodynamic radii, gained from dynamic light scattering, FCS, and fluorescence cross-correlation experiments, led to comparable conclusions. Our study demonstrates how RNA-aptamer fluorophore complexes can be simultaneously structurally and photophysically characterized by FCS. Furthermore, fluorophore binding RNA aptamers provide a tool for visualizing single RNA molecules.
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Affiliation(s)
- Arne Werner
- Institute for Biochemistry and Molecular Biology, Department of Chemistry, Faculty of Mathematics, Informatics, and Natural Sciences, Hamburg University, D-20146 Hamburg, Germany
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46
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Fogarty K, McPhee JT, Scott E, Van Orden A. Probing the ionic atmosphere of single-stranded DNA using continuous flow capillary electrophoresis and fluorescence correlation spectroscopy. Anal Chem 2009; 81:465-72. [PMID: 19117467 DOI: 10.1021/ac8019416] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Two-beam fluorescence cross-correlation spectroscopy coupled with continuous flow capillary electrophoresis (2bFCCS-CFCE) was used to study the relationship between diffusion and effective charge of a fluorescently labeled 40-base polythymine single-stranded DNA (ssDNA) as a function of Mg2+ concentration. Cross-correlation analysis of the fluorescence monitored from two spatially offset microscopic detection volumes revealed the diffusion and electrophoretic migration of ssDNA at a range of Mg2+ concentrations and electric field strengths. The effective charge of the ssDNA could then be determined using simple calculations. It was found that as the Mg2+ concentration in the buffer solution increased, the diffusion of the ssDNA also increased, while the effective charge of the ssDNA decreased. This was believed to be caused by increased association of the Mg2+ counterions with the negatively charged backbone of the ssDNA, which partially neutralized the negatively charged functional groups and allowed the ssDNA to adopt a more compact structure. To our knowledge, this is the first demonstration of the measurement of effective charge of ssDNA in relation to Mg2+ concentration.
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Affiliation(s)
- Keir Fogarty
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA
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47
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Abstract
The unfolded states in proteins and nucleic acids remain weakly understood despite their importance in folding processes; misfolding diseases (Parkinson's and Alzheimer's); natively unfolded proteins (as many as 30% of eukaryotic proteins, according to Fink); and the study of ribozymes. Research has been hindered by the inability to quantify the residual (native) structure present in an unfolded protein or nucleic acid. Here, a scaling model is proposed to quantify the molar degree of folding and the unfolded state. The model takes a global view of protein structure and can be applied to a number of analytic methods and to simulations. Three examples are given of application to small-angle scattering from pressure-induced unfolding of SNase, from acid-unfolded cytochrome c, and from folding of Azoarcus ribozyme. These examples quantitatively show three characteristic unfolded states for proteins, the statistical nature of a protein folding pathway, and the relationship between extent of folding and chain size during folding for charge-driven folding in RNA.
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48
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Schlatterer JC, Kwok LW, Lamb JS, Park HY, Andresen K, Brenowitz M, Pollack L. Hinge stiffness is a barrier to RNA folding. J Mol Biol 2008; 379:859-70. [PMID: 18471829 DOI: 10.1016/j.jmb.2008.04.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2008] [Revised: 04/03/2008] [Accepted: 04/03/2008] [Indexed: 11/27/2022]
Abstract
Cation-mediated RNA folding from extended to compact, biologically active conformations relies on a temporal balance of forces. The Mg2 +-mediated folding of the Tetrahymena thermophila ribozyme is characterized by rapid nonspecific collapse followed by tertiary-contact-induced compaction. This article focuses on an autonomously folding portion of the Tetrahymena ribozyme, its P4-P6 domain, in order to probe one facet of the rapid collapse: chain flexibility. The time evolution of P4-P6 folding was followed by global and local measures as a function of Mg2 + concentration. While all concentrations of Mg2 + studied are sufficient to screen the charge on the helices, the rates of compaction and tertiary contact formation diverge as the concentration of Mg2 + increases; collapse is greatly accelerated by Mg2 +, while tertiary contact formation is not. These studies highlight the importance of chain stiffness to RNA folding; at 10 mM Mg2 +, a stiff hinge limits the rate of P4-P6 folding. At higher magnesium concentrations, the rate-limiting step shifts from hinge bending to tertiary contact formati
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Affiliation(s)
- Jörg C Schlatterer
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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49
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Abstract
Nucleic acids are highly charged polyanionic molecules; thus, the ionic conditions are crucial for nucleic acid structural changes such as bending. We use the tightly bound ion theory, which explicitly accounts for the correlation and ensemble effects for counterions, to calculate the electrostatic free energy landscapes for DNA helix bending. The electrostatic free energy landscapes show that DNA bending energy is strongly dependent on ion concentration, valency, and size. In a Na(+) solution, DNA bending is electrostatically unfavorable because of the strong charge repulsion on backbone. With the increase of the Na(+) concentration, the electrostatic bending repulsion is reduced and thus the bending becomes less unfavorable. In contrast, in an Mg(2+) solution, ion correlation induces a possible attractive force between the different parts of the helical strands, resulting in bending. The electrostatically most favorable and unfavorable bending directions are toward the major and minor grooves, respectively. Decreasing the size of the divalent ions enhances the electrostatic bending attraction, causing an increased bending angle, and shifts the most favorable bending to the direction toward the minor groove. The microscopic analysis on ion-binding distribution reveals that the divalent ion-induced helix bending attraction may come from the correlated distribution of the ions across the grooves in the bending direction.
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50
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Skewis LR, Reinhard BM. Spermidine modulated ribonuclease activity probed by RNA plasmon rulers. NANO LETTERS 2008; 8:214-220. [PMID: 18052230 DOI: 10.1021/nl0725042] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We extend the scope of nanometer distance measurements based on coupled pairs of gold nanoparticles, or plasmon rulers, to individual RNA molecules. These sensors were used to monitor the influence of spermidine on the cleavage kinetics of RNA by ribonuclease A. Time-resolved cleavage experiments of individual RNA plasmon rulers reveal transiently stabilized RNA sub-populations at increased spermidine concentrations that indicate spermidine-induced stabilization of weak secondary and tertiary structural elements.
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Affiliation(s)
- Lynell R Skewis
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
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