1
|
Halder A, Kumar S, Valsson O, Reddy G. Mg 2+ Sensing by an RNA Fragment: Role of Mg 2+-Coordinated Water Molecules. J Chem Theory Comput 2020; 16:6702-6715. [PMID: 32941038 DOI: 10.1021/acs.jctc.0c00589] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RNA molecules selectively bind to specific metal ions to populate their functional active states, making it important to understand their source of ion selectivity. In large RNA systems, metal ions interact with the RNA at multiple locations, making it difficult to decipher the precise role of ions in folding. To overcome this complexity, we studied the role of different metal ions (Mg2+, Ca2+, and K+) in the folding of a small RNA hairpin motif (5'-ucCAAAga-3') using unbiased all-atom molecular dynamics simulations. The advantage of studying this system is that it requires specific binding of a single metal ion to fold to its native state. We find that even for this small RNA, the folding free energy surface (FES) is multidimensional as different metal ions present in the solution can simultaneously facilitate folding. The FES shows that specific binding of a metal ion is indispensable for its folding. We further show that in addition to the negatively charged phosphate groups, the spatial organization of electronegative nucleobase atoms drives the site-specific binding of the metal ions. Even though the binding site cannot discriminate between different metal ions, RNA folds efficiently only in a Mg2+ solution. We show that the rigid network of Mg2+-coordinated water molecules facilitates the formation of important interactions in the transition state. The other metal ions such as K+ and Ca2+ cannot facilitate the formation of such interactions. These results allow us to hypothesize possible metal-sensing mechanisms in large metalloriboswitches and also provide useful insights into the design of appropriate collective variables for studying large RNA molecules using enhanced sampling methods.
Collapse
Affiliation(s)
- Antarip Halder
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Sunil Kumar
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Omar Valsson
- Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| |
Collapse
|
2
|
Wu P, Yu Y, McGhee CE, Tan LH, Lu Y. Applications of synchrotron-based spectroscopic techniques in studying nucleic acids and nucleic acid-functionalized nanomaterials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2014; 26:7849-72. [PMID: 25205057 PMCID: PMC4275547 DOI: 10.1002/adma.201304891] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 06/02/2014] [Indexed: 05/22/2023]
Abstract
In this review, we summarize recent progress in the application of synchrotron-based spectroscopic techniques for nucleic acid research that takes advantage of high-flux and high-brilliance electromagnetic radiation from synchrotron sources. The first section of the review focuses on the characterization of the structure and folding processes of nucleic acids using different types of synchrotron-based spectroscopies, such as X-ray absorption spectroscopy, X-ray emission spectroscopy, X-ray photoelectron spectroscopy, synchrotron radiation circular dichroism, X-ray footprinting and small-angle X-ray scattering. In the second section, the characterization of nucleic acid-based nanostructures, nucleic acid-functionalized nanomaterials and nucleic acid-lipid interactions using these spectroscopic techniques is summarized. Insights gained from these studies are described and future directions of this field are also discussed.
Collapse
Affiliation(s)
- Peiwen Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yang Yu
- Center of Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Claire E. McGhee
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Li Huey Tan
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yi Lu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Center of Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| |
Collapse
|
3
|
Bohon J, D’Mello R, Ralston C, Gupta S, Chance MR. Synchrotron X-ray footprinting on tour. JOURNAL OF SYNCHROTRON RADIATION 2014; 21:24-31. [PMID: 24365913 PMCID: PMC3874017 DOI: 10.1107/s1600577513024715] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 09/04/2013] [Indexed: 05/22/2023]
Abstract
Synchrotron footprinting is a valuable technique in structural biology for understanding macromolecular solution-state structure and dynamics of proteins and nucleic acids. Although an extremely powerful tool, there is currently only a single facility in the USA, the X28C beamline at the National Synchrotron Light Source (NSLS), dedicated to providing infrastructure, technology development and support for these studies. The high flux density of the focused white beam and variety of specialized exposure environments available at X28C enables footprinting of highly complex biological systems; however, it is likely that a significant fraction of interesting experiments could be performed at unspecialized facilities. In an effort to investigate the viability of a beamline-flexible footprinting program, a standard sample was taken on tour around the nation to be exposed at several US synchrotrons. This work describes how a relatively simple and transportable apparatus can allow beamlines at the NSLS, CHESS, APS and ALS to be used for synchrotron footprinting in a general user mode that can provide useful results.
Collapse
Affiliation(s)
- Jen Bohon
- Center for Synchrotron Biosciences, Case Western Reserve University, National Synchrotron Light Source, Brookhaven National Laboratory, Upton, NY 11973, USA
- Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Correspondence e-mail:
| | - Rhijuta D’Mello
- Center for Synchrotron Biosciences, Case Western Reserve University, National Synchrotron Light Source, Brookhaven National Laboratory, Upton, NY 11973, USA
- Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Corie Ralston
- Berkeley Center for Structural Biology, Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Sayan Gupta
- Berkeley Center for Structural Biology, Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Mark R. Chance
- Center for Synchrotron Biosciences, Case Western Reserve University, National Synchrotron Light Source, Brookhaven National Laboratory, Upton, NY 11973, USA
- Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| |
Collapse
|
4
|
Holmstrom ED, Fiore JL, Nesbitt DJ. Thermodynamic origins of monovalent facilitated RNA folding. Biochemistry 2012; 51:3732-43. [PMID: 22448852 DOI: 10.1021/bi201420a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cations have long been associated with formation of native RNA structure and are commonly thought to stabilize the formation of tertiary contacts by favorably interacting with the electrostatic potential of the RNA, giving rise to an "ion atmosphere". A significant amount of information regarding the thermodynamics of structural transitions in the presence of an ion atmosphere has accumulated and suggests stabilization is dominated by entropic terms. This work provides an analysis of how RNA-cation interactions affect the entropy and enthalpy associated with an RNA tertiary transition. Specifically, temperature-dependent single-molecule fluorescence resonance energy transfer studies have been exploited to determine the free energy (ΔG°), enthalpy (ΔH°), and entropy (ΔS°) of folding for an isolated tetraloop-receptor tertiary interaction as a function of Na(+) concentration. Somewhat unexpectedly, increasing the Na(+) concentration changes the folding enthalpy from a strongly exothermic process [e.g., ΔH° = -26(2) kcal/mol at 180 mM] to a weakly exothermic process [e.g., ΔH° = -4(1) kcal/mol at 630 mM]. As a direct corollary, it is the strong increase in folding entropy [Δ(ΔS°) > 0] that compensates for this loss of exothermicity for the achievement of more favorable folding [Δ(ΔG°) < 0] at higher Na(+) concentrations. In conjunction with corresponding measurements of the thermodynamics of the transition state barrier, these data provide a detailed description of the folding pathway associated with the GAAA tetraloop-receptor interaction as a function of Na(+) concentration. The results support a potentially universal mechanism for monovalent facilitated RNA folding, whereby an increasing monovalent concentration stabilizes tertiary structure by reducing the entropic penalty for folding.
Collapse
Affiliation(s)
- Erik D Holmstrom
- JILA, University of Colorado and National Institute of Standards and Technology, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0440, USA
| | | | | |
Collapse
|
5
|
Quarta G, Sin K, Schlick T. Dynamic energy landscapes of riboswitches help interpret conformational rearrangements and function. PLoS Comput Biol 2012; 8:e1002368. [PMID: 22359488 PMCID: PMC3280964 DOI: 10.1371/journal.pcbi.1002368] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 12/19/2011] [Indexed: 11/23/2022] Open
Abstract
Riboswitches are RNAs that modulate gene expression by ligand-induced conformational changes. However, the way in which sequence dictates alternative folding pathways of gene regulation remains unclear. In this study, we compute energy landscapes, which describe the accessible secondary structures for a range of sequence lengths, to analyze the transcriptional process as a given sequence elongates to full length. In line with experimental evidence, we find that most riboswitch landscapes can be characterized by three broad classes as a function of sequence length in terms of the distribution and barrier type of the conformational clusters: low-barrier landscape with an ensemble of different conformations in equilibrium before encountering a substrate; barrier-free landscape in which a direct, dominant “downhill” pathway to the minimum free energy structure is apparent; and a barrier-dominated landscape with two isolated conformational states, each associated with a different biological function. Sharing concepts with the “new view” of protein folding energy landscapes, we term the three sequence ranges above as the sensing, downhill folding, and functional windows, respectively. We find that these energy landscape patterns are conserved in various riboswitch classes, though the order of the windows may vary. In fact, the order of the three windows suggests either kinetic or thermodynamic control of ligand binding. These findings help understand riboswitch structure/function relationships and open new avenues to riboswitch design. Riboswitches are RNAs that modulate gene expression by ligand-induced conformational changes. However, the way that sequence dictates alternative folding pathways of gene regulation remains unclear. In this study, we mimic transcription by computing energy landscapes which describe accessible secondary structures for a range of sequence lengths. Consistent with experimental evidence, we find that most riboswitch landscapes can be characterized by three broad classes as a function of sequence length in terms of the distribution and barrier type of the conformational clusters: Low-barrier landscape with an ensemble of conformations in equilibrium before encountering a substrate; barrier-free landscape with a dominant “downhill” pathway to the minimum free energy structure; and barrier-dominated landscape with two isolated conformational states with different functions. Sharing concepts with the “new view” of protein folding energy landscapes, we term the three sequence ranges above as the sensing, downhill folding, and functional windows, respectively. We find that these energy landscape patterns are conserved between riboswitch classes, though the order of the windows may vary. In fact, the order of the three windows suggests either kinetic or thermodynamic control of ligand binding. These findings help understand riboswitch structure/function relationships and open new avenues to riboswitch design.
Collapse
Affiliation(s)
- Giulio Quarta
- Department of Chemistry, New York University, New York, New York, United States of America
- Howard Hughes Medical Institute - Medical Research Fellows Program, Chevy Chase, Maryland, United States of America
| | - Ken Sin
- Department of Chemistry, New York University, New York, New York, United States of America
| | - Tamar Schlick
- Department of Chemistry, New York University, New York, New York, United States of America
- Courant Institute of Mathematical Sciences, New York University, New York, New York, United States of America
- * E-mail:
| |
Collapse
|
6
|
Benz-Moy TL, Herschlag D. Structure-function analysis from the outside in: long-range tertiary contacts in RNA exhibit distinct catalytic roles. Biochemistry 2011; 50:8733-55. [PMID: 21815635 PMCID: PMC3186870 DOI: 10.1021/bi2008245] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The conserved catalytic core of the Tetrahymena group I ribozyme is encircled by peripheral elements. We have conducted a detailed structure-function study of the five long-range tertiary contacts that fasten these distal elements together. Mutational ablation of each of the tertiary contacts destabilizes the folded ribozyme, indicating a role of the peripheral elements in overall stability. Once folded, three of the five tertiary contact mutants exhibit defects in overall catalysis that range from 20- to 100-fold. These and the subsequent results indicate that the structural ring of peripheral elements does not act as a unitary element; rather, individual connections have distinct roles as further revealed by kinetic and thermodynamic dissection of the individual reaction steps. Ablation of P14 or the metal ion core/metal ion core receptor (MC/MCR) destabilizes docking of the substrate-containing P1 helix into tertiary interactions with the ribozyme's conserved core. In contrast, ablation of the L9/P5 contact weakens binding of the guanosine nucleophile by slowing its association, without affecting P1 docking. The P13 and tetraloop/tetraloop receptor (TL/TLR) mutations had little functional effect and small, local structural changes, as revealed by hydroxyl radical footprinting, whereas the P14, MC/MCR, and L9/P5 mutants show structural changes distal from the mutation site. These changes extended into regions of the catalytic core involved in docking or guanosine binding. Thus, distinct allosteric pathways couple the long-range tertiary contacts to functional sites within the conserved core. This modular functional specialization may represent a fundamental strategy in RNA structure-function interrelationships.
Collapse
Affiliation(s)
- Tara L. Benz-Moy
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - Daniel Herschlag
- Department of Chemistry, Stanford University, Stanford, California 94305
- Department of Biochemistry, Stanford University, Stanford, California 94305
| |
Collapse
|
7
|
Mitra S, Laederach A, Golden BL, Altman RB, Brenowitz M. RNA molecules with conserved catalytic cores but variable peripheries fold along unique energetically optimized pathways. RNA (NEW YORK, N.Y.) 2011; 17:1589-1603. [PMID: 21712400 PMCID: PMC3153981 DOI: 10.1261/rna.2694811] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 05/19/2011] [Indexed: 05/31/2023]
Abstract
Functional and kinetic constraints must be efficiently balanced during the folding process of all biopolymers. To understand how homologous RNA molecules with different global architectures fold into a common core structure we determined, under identical conditions, the folding mechanisms of three phylogenetically divergent group I intron ribozymes. These ribozymes share a conserved functional core defined by topologically equivalent tertiary motifs but differ in their primary sequence, size, and structural complexity. Time-resolved hydroxyl radical probing of the backbone solvent accessible surface and catalytic activity measurements integrated with structural-kinetic modeling reveal that each ribozyme adopts a unique strategy to attain the conserved functional fold. The folding rates are not dictated by the size or the overall structural complexity, but rather by the strength of the constituent tertiary motifs which, in turn, govern the structure, stability, and lifetime of the folding intermediates. A fundamental general principle of RNA folding emerges from this study: The dominant folding flux always proceeds through an optimally structured kinetic intermediate that has sufficient stability to act as a nucleating scaffold while retaining enough conformational freedom to avoid kinetic trapping. Our results also suggest a potential role of naturally selected peripheral A-minor interactions in balancing RNA structural stability with folding efficiency.
Collapse
Affiliation(s)
- Somdeb Mitra
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Barbara L. Golden
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Russ B. Altman
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Michael Brenowitz
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| |
Collapse
|
8
|
Rocca-Serra P, Bellaousov S, Birmingham A, Chen C, Cordero P, Das R, Davis-Neulander L, Duncan CD, Halvorsen M, Knight R, Leontis NB, Mathews DH, Ritz J, Stombaugh J, Weeks KM, Zirbel CL, Laederach A. Sharing and archiving nucleic acid structure mapping data. RNA (NEW YORK, N.Y.) 2011; 17:1204-12. [PMID: 21610212 PMCID: PMC3138558 DOI: 10.1261/rna.2753211] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Nucleic acids are particularly amenable to structural characterization using chemical and enzymatic probes. Each individual structure mapping experiment reveals specific information about the structure and/or dynamics of the nucleic acid. Currently, there is no simple approach for making these data publically available in a standardized format. We therefore developed a standard for reporting the results of single nucleotide resolution nucleic acid structure mapping experiments, or SNRNASMs. We propose a schema for sharing nucleic acid chemical probing data that uses generic public servers for storing, retrieving, and searching the data. We have also developed a consistent nomenclature (ontology) within the Ontology of Biomedical Investigations (OBI), which provides unique identifiers (termed persistent URLs, or PURLs) for classifying the data. Links to standardized data sets shared using our proposed format along with a tutorial and links to templates can be found at http://snrnasm.bio.unc.edu.
Collapse
Affiliation(s)
| | - Stanislav Bellaousov
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | | | - Chunxia Chen
- Biology Department, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
| | - Pablo Cordero
- Biochemistry Department, Stanford University, Stanford, California 94305, USA
| | - Rhiju Das
- Biochemistry Department, Stanford University, Stanford, California 94305, USA
| | - Lauren Davis-Neulander
- Biology Department, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
| | - Caia D.S. Duncan
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
| | - Matthew Halvorsen
- Biology Department, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
| | - Rob Knight
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA
- Howard Hughes Medical Institute, Boulder, Colorado 80309, USA
| | - Neocles B. Leontis
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, USA
| | - David H. Mathews
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Justin Ritz
- Biology Department, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
| | - Jesse Stombaugh
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA
| | - Kevin M. Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
| | - Craig L. Zirbel
- Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, Ohio 43403, USA
| | - Alain Laederach
- Biology Department, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
- Corresponding author.E-mail .
| |
Collapse
|
9
|
Mitra S. Using analytical ultracentrifugation (AUC) to measure global conformational changes accompanying equilibrium tertiary folding of RNA molecules. Methods Enzymol 2009; 469:209-36. [PMID: 20946791 DOI: 10.1016/s0076-6879(09)69010-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Analytical ultracentrifugation (AUC) is a powerful technique to determine the global conformational changes in RNA molecules mediated by cations or small molecule ligands. Although most of the developments in the field of AUC have been centered on studies involving protein molecules, the experimental methods as well as the analytical approaches have been successfully adapted and applied to the study of a variety of RNA molecules ranging from small riboswitches to large ribozymes. Most often AUC studies are performed in conjunction with other structural probing techniques that provide complementary information on local changes in the solvent accessibilities at specific regions within RNA molecules. This chapter provides a brief theoretical background, working knowledge of instrumentation, practical considerations for experimental setup, and guidelines for data analysis procedures to enable the design, execution, and interpretation of sedimentation velocity experiments that detect changes in the global dimensions of an RNA molecule during its equilibrium folding.
Collapse
Affiliation(s)
- Somdeb Mitra
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| |
Collapse
|
10
|
Shcherbakova I, Mitra S. Hydroxyl-radical footprinting to probe equilibrium changes in RNA tertiary structure. Methods Enzymol 2009; 468:31-46. [PMID: 20946763 DOI: 10.1016/s0076-6879(09)68002-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Hydroxyl-radical footprinting utilizes the ability of a highly reactive species to nonspecifically cleave the solvent accessible regions of a nucleic acid backbone. Thus, changes in a nucleic acids structure can be probed either as a function of time or of a reagent's concentration. When combined with techniques that allow single nucleotide resolution of the resulting fragments, footprinting experiments provide richly detailed information about local changes in tertiary structure of a nucleic acid accompanying its folding or ligand binding. In this chapter, we present two protocols of equilibrium hydroxyl-radical footprinting based on peroxidative and oxidative Fenton chemistry and discuss how to adjust the Fenton reagent concentrations for a specific experimental condition. We also discuss the choice of the techniques to separate the reaction products and specifics of the data analysis for equilibrium footprinting experiments. Protocols addressing the use of peroxidative Fenton chemistry for time-resolved studies have been published [Schlatterer and Brenowitz, 2009. Methods; Shcherbakova and Brenowitz, 2008. Nat. Protoc.3(2), 288-302; Shcherbakova et al., 2006. Nucleic Acids Res.34(6), e48; Shcherbakova et al., 2007. Methods Cell Biol.84, 589-615].
Collapse
Affiliation(s)
- Inna Shcherbakova
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | | |
Collapse
|
11
|
Shcherbakova I, Mitra S, Laederach A, Brenowitz M. Energy barriers, pathways, and dynamics during folding of large, multidomain RNAs. Curr Opin Chem Biol 2008; 12:655-66. [PMID: 18926923 DOI: 10.1016/j.cbpa.2008.09.017] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Revised: 08/22/2008] [Accepted: 09/16/2008] [Indexed: 10/21/2022]
Abstract
Large, multidomain RNA molecules are generally thought to fold following multiple pathways down rugged landscapes populated with intermediates and traps. A challenge to understanding RNA folding reactions is the complex relationships that exist between the structure of the RNA and its folding landscape. The identification of intermediate species that populate folding landscapes and characterization of elements of their structures are the key components to solving the RNA folding problem. This review explores recent studies that characterize the dominant pathways by which RNA folds, structural and dynamic features of intermediates that populate the folding landscape, and the energy barriers that separate the distinct steps of the folding process.
Collapse
Affiliation(s)
- Inna Shcherbakova
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | | | | | | |
Collapse
|
12
|
Shcherbakova I, Mitra S, Beer RH, Brenowitz M. Following molecular transitions with single residue spatial and millisecond time resolution. Methods Cell Biol 2008; 84:589-615. [PMID: 17964944 DOI: 10.1016/s0091-679x(07)84019-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
"Footprinting" describes assays in which ligand binding or structure formation protects polymers such as nucleic acids and proteins from either cleavage or modification; footprinting allows the accessibility of individual residues to be mapped in solution. Equilibrium and time-dependent footprinting links site-specific structural information with thermodynamic and kinetic transitions, respectively. The hydroxyl radical (*OH) is a uniquely insightful footprinting probe by virtue of it being among the most reactive chemical oxidants; it reports the solvent accessibility of reactive sites on macromolecules with as fine as a single residue resolution. A novel method of millisecond time-resolved *OH footprinting is presented based on the Fenton reaction, Fe(II) + H(2)O(2) --> Fe(III) + *OH + OH(-). It is implemented using a standard three-syringe quench-flow mixer. The utility of this method is demonstrated by its application to the studies on RNA folding. Its applicability to a broad range of biological questions involving the function of DNA, RNA, and proteins is discussed.
Collapse
Affiliation(s)
- Inna Shcherbakova
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | | | | | | |
Collapse
|
13
|
Abstract
RNA folds to a myriad of three-dimensional structures and performs an equally diverse set of functions. The ability of RNA to fold and function in vivo is all the more remarkable because, in vitro, RNA has been shown to have a strong propensity to adopt misfolded, non-functional conformations. A principal factor underlying the dominance of RNA misfolding is that local RNA structure can be quite stable even in the absence of enforcing global tertiary structure. This property allows non-native structure to persist, and it also allows native structure to form and stabilize non-native contacts or non-native topology. In recent years it has become clear that one of the central reasons for the apparent disconnect between the capabilities of RNA in vivo and its in vitro folding properties is the presence of RNA chaperones, which facilitate conformational transitions of RNA and therefore mitigate the deleterious effects of RNA misfolding. Over the past two decades, it has been demonstrated that several classes of non-specific RNA binding proteins possess profound RNA chaperone activity in vitro and when overexpressed in vivo, and at least some of these proteins appear to function as chaperones in vivo. More recently, it has been shown that certain DExD/H-box proteins function as general chaperones to facilitate folding of group I and group II introns. These proteins are RNA-dependent ATPases and have RNA helicase activity, and are proposed to function by using energy from ATP binding and hydrolysis to disrupt RNA structure and/or to displace proteins from RNA-protein complexes. This review outlines experimental studies that have led to our current understanding of the range of misfolded RNA structures, the physical origins of RNA misfolding, and the functions and mechanisms of putative RNA chaperone proteins.
Collapse
Affiliation(s)
- Rick Russell
- Department of Chemistry and Biochemistry, The Institute For Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
| |
Collapse
|
14
|
Laederach A, Shcherbakova I, Jonikas MA, Altman RB, Brenowitz M. Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding. Proc Natl Acad Sci U S A 2007; 104:7045-50. [PMID: 17438287 PMCID: PMC1855354 DOI: 10.1073/pnas.0608765104] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We distinguish the contribution of the electrostatic environment, initial conformational ensemble, and macromolecular stability on the folding mechanism of a large RNA using a combination of time-resolved "Fast Fenton" hydroxyl radical footprinting and exhaustive kinetic modeling. This integrated approach allows us to define the folding landscape of the L-21 Tetrahymena thermophila group I intron structurally and kinetically from its earliest steps with unprecedented accuracy. Distinct parallel pathways leading the RNA to its native form upon its Mg(2+)-induced folding are observed. The structures of the intermediates populating the pathways are not affected by variation of the concentration and type of background monovalent ions (electrostatic environment) but are altered by a mutation that destabilizes one domain of the ribozyme. Experiments starting from different conformational ensembles but folding under identical conditions show that whereas the electrostatic environment modulates molecular flux through different pathways, the initial conformational ensemble determines the partitioning of the flux. This study showcases a robust approach for the development of kinetic models from collections of local structural probes.
Collapse
Affiliation(s)
| | - Inna Shcherbakova
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461
| | | | - Russ B. Altman
- Departments of *Genetics and
- To whom correspondence may be addressed. E-mail: or
| | - Michael Brenowitz
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461
- To whom correspondence may be addressed. E-mail: or
| |
Collapse
|
15
|
Russell R, Tijerina P, Chadee AB, Bhaskaran H. Deletion of the P5abc peripheral element accelerates early and late folding steps of the Tetrahymena group I ribozyme. Biochemistry 2007; 46:4951-61. [PMID: 17419589 PMCID: PMC2582984 DOI: 10.1021/bi0620149] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The P5abc peripheral element stabilizes the Tetrahymena group I ribozyme and enhances its catalytic activity. Despite its beneficial effects on the native structure, prior studies have shown that early formation of P5abc structure during folding can slow later folding steps. Here we use a P5abc deletion variant E(deltaP5abc) to systematically probe the role of P5abc throughout tertiary folding. Time-resolved hydroxyl radical footprinting shows that E(deltaP5abc) forms its earliest stable tertiary structure on the millisecond time scale, approximately 5-fold faster than the wild-type ribozyme, and stable structure spreads throughout E(deltaP5abc) in seconds. Nevertheless, activity measurements show that the earliest detectable formation of native E(deltaP5abc) ribozyme is much slower (approximately 0.6 min(-1)), in a manner similar to that of the wild type. Also similar, only a small fraction of E(deltaP5abc) attains the native state on this time scale under standard conditions at 25 degrees C, whereas the remainder misfolds; footprinting experiments show that the misfolded conformer shares structural features with the long-lived misfolded conformer of the wild-type ribozyme. Thus, P5abc does not have a large overall effect on the rate-limiting step(s) along this pathway. However, once misfolded, E(deltaP5abc) refolds to the native state 80-fold faster than the wild-type ribozyme and is less accelerated by urea, indicating that P5abc stabilizes the misfolded structure relative to the less-ordered transition state for refolding. Together, the results suggest that, under these conditions, even the earliest tertiary folding intermediates of the wild-type ribozyme represent misfolded species and that P5abc is principally a liability during the tertiary folding process.
Collapse
Affiliation(s)
- Rick Russell
- Department of Chemistry and Biochemistry and Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA.
| | | | | | | |
Collapse
|
16
|
Shcherbakova I, Mitra S, Beer RH, Brenowitz M. Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins. Nucleic Acids Res 2006; 34:e48. [PMID: 16582097 PMCID: PMC1421499 DOI: 10.1093/nar/gkl055] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2006] [Revised: 02/14/2006] [Accepted: 02/24/2006] [Indexed: 11/20/2022] Open
Abstract
'Footprinting' describes assays in which ligand binding or structure formation protects polymers such as nucleic acids and proteins from either cleavage or modification; footprinting allows the accessibility of individual residues to be mapped in solution. Equilibrium and time-dependent footprinting links site-specific structural information with thermodynamic and kinetic transitions. The hydroxyl radical (*OH) is a particularly valuable footprinting probe by virtue of it being among the most reactive of chemical oxidants; it reports the solvent accessibility of reactive sites on macromolecules with as fine as a single residue resolution. A novel method of millisecond time-resolved .OH footprinting has been developed based on the Fenton reaction, Fe(II) + H2O2 --> Fe(III) + *OH + OH-. This method can be implemented in laboratories using widely available three-syringe quench flow mixers and inexpensive reagents to study local changes in the solvent accessibility of DNA, RNA and proteins associated with their biological function.
Collapse
Affiliation(s)
- Inna Shcherbakova
- Department of Biochemistry, Albert Einstein College of Medicine1300 Morris Park Avenue, Bronx, NY 10461, USA
- Department of Chemistry, Fordham University441 East Fordham Road, Bronx, NY 10458, USA
| | - Somdeb Mitra
- Department of Biochemistry, Albert Einstein College of Medicine1300 Morris Park Avenue, Bronx, NY 10461, USA
- Department of Chemistry, Fordham University441 East Fordham Road, Bronx, NY 10458, USA
| | - Robert H. Beer
- Department of Chemistry, Fordham University441 East Fordham Road, Bronx, NY 10458, USA
| | - Michael Brenowitz
- To whom correspondence should be addressed. Tel: 00 1 718 430 3179; Fax: 00 1 718 430 8565;
| |
Collapse
|
17
|
Laederach A, Shcherbakova I, Liang MP, Brenowitz M, Altman RB. Local kinetic measures of macromolecular structure reveal partitioning among multiple parallel pathways from the earliest steps in the folding of a large RNA molecule. J Mol Biol 2006; 358:1179-90. [PMID: 16574145 PMCID: PMC2621361 DOI: 10.1016/j.jmb.2006.02.075] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2005] [Revised: 02/24/2006] [Accepted: 02/27/2006] [Indexed: 10/24/2022]
Abstract
At the heart of the RNA folding problem is the number, structures, and relationships among the intermediates that populate the folding pathways of most large RNA molecules. Unique insight into the structural dynamics of these intermediates can be gleaned from the time-dependent changes in local probes of macromolecular conformation (e.g. reports on individual nucleotide solvent accessibility offered by hydroxyl radical (()OH) footprinting). Local measures distributed around a macromolecule individually illuminate the ensemble of separate changes that constitute a folding reaction. Folding pathway reconstruction from a multitude of these individual measures is daunting due to the combinatorial explosion of possible kinetic models as the number of independent local measures increases. Fortunately, clustering of time progress curves sufficiently reduces the dimensionality of the data so as to make reconstruction computationally tractable. The most likely folding topology and intermediates can then be identified by exhaustively enumerating all possible kinetic models on a super-computer grid. The folding pathways and measures of the relative flux through them were determined for Mg(2+) and Na(+)-mediated folding of the Tetrahymena thermophila group I intron using this combined experimental and computational approach. The flux during Mg(2+)-mediated folding is divided among numerous parallel pathways. In contrast, the flux during the Na(+)-mediated reaction is predominantly restricted through three pathways, one of which is without detectable passage through intermediates. Under both conditions, the folding reaction is highly parallel with no single pathway accounting for more than 50% of the molecular flux. This suggests that RNA folding is non-sequential under a variety of different experimental conditions even at the earliest stages of folding. This study provides a template for the systematic analysis of the time-evolution of RNA structure from ensembles of local measures that will illuminate the chemical and physical characteristics of each step in the process. The applicability of this analysis approach to other macromolecules is discussed.
Collapse
Affiliation(s)
- Alain Laederach
- Department of Genetics, Stanford University, 300 Pasteur Dr. Stanford, Ca. 94305
| | - Inna Shcherbakova
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461
| | - Mike P. Liang
- Department of Genetics, Stanford University, 300 Pasteur Dr. Stanford, Ca. 94305
| | - Michael Brenowitz
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461
- to whom correspondence may be addressed, Tel: (650) 725−3394 Fax: (650) 725−3863, e-mail: and Tel: (718) 430−3179 Fax: (718) 430−8565,
| | - Russ B. Altman
- Department of Genetics, Stanford University, 300 Pasteur Dr. Stanford, Ca. 94305
- to whom correspondence may be addressed, Tel: (650) 725−3394 Fax: (650) 725−3863, e-mail: and Tel: (718) 430−3179 Fax: (718) 430−8565,
| |
Collapse
|
18
|
Kwok LW, Shcherbakova I, Lamb JS, Park HY, Andresen K, Smith H, Brenowitz M, Pollack L. Concordant exploration of the kinetics of RNA folding from global and local perspectives. J Mol Biol 2005; 355:282-93. [PMID: 16303138 DOI: 10.1016/j.jmb.2005.10.070] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2005] [Revised: 10/21/2005] [Accepted: 10/25/2005] [Indexed: 11/16/2022]
Abstract
Time-resolved small-angle X-ray scattering (SAXS) with millisecond time-resolution reveals two discrete phases of global compaction upon Mg2+-mediated folding of the Tetrahymena thermophila ribozyme. Electrostatic relaxation of the RNA occurs rapidly and dominates the first phase of compaction during which the observed radius of gyration (R(g)) decreases from 75 angstroms to 55 angstroms. A further decrease in R(g) to 45 angstroms occurs in a well-defined second phase. An analysis of mutant ribozymes shows that the latter phase depends upon the formation of long-range tertiary contacts within the P4-P6 domain of the ribozyme; disruption of the three remaining long-range contacts linking the peripheral helices has no effect on the 55-45 angstroms compaction transition. A better understanding of the role of specific tertiary contacts in compaction was obtained by concordant time-resolved hydroxyl radical (OH) analyses that report local changes in the solvent accessibility of the RNA backbone. Comparison of the global and local measures of folding shows that formation of a subset of native tertiary contacts (i.e. those defining the ribozyme core) can occur within a highly compact ensemble whose R(g) is close to that of the fully folded ribozyme. Analyses of additional ribozyme mutants and reaction conditions establish the generality of the rapid formation of a partially collapsed state with little to no detectable tertiary structure. These studies directly link global RNA compaction with formation of tertiary structure as the molecule acquires its biologically active structure, and underscore the strong dependence on salt of both local and global measures of folding kinetics.
Collapse
Affiliation(s)
- Lisa W Kwok
- School of Applied & Engineering Physics, Cornell University, Ithaca NY 14853, USA
| | | | | | | | | | | | | | | |
Collapse
|
19
|
Shcherbakova I, Brenowitz M. Perturbation of the hierarchical folding of a large RNA by the destabilization of its Scaffold's tertiary structure. J Mol Biol 2005; 354:483-96. [PMID: 16242711 DOI: 10.1016/j.jmb.2005.09.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2005] [Revised: 09/06/2005] [Accepted: 09/09/2005] [Indexed: 10/25/2022]
Abstract
The P4-P6 domain serves as a scaffold against which the periphery and catalytic core organize and fold during Mg2+-mediated folding of the Tetrahymena thermophila ribozyme. The most prominent structural motif of the P4-P6 domain is the tetraloop-tetraloop receptor interaction which "clamps" the distal parts of its hairpin-like structure. Destabilization of the tertiary structure of the P4-P6 domain by perturbation of the tetraloop-tetraloop receptor interaction alters the Mg2+-mediated folding pathway. The folding hierarchy of P5c approximately P4-P6 > periphery > catalytic core that is a striking attribute of the folding of the wild-type RNA is abolished. The initial steps in folding of the mutant RNA are > or =50-fold faster than those of the wild-type ribozyme with the earliest observed tertiary contacts forming around regions known to specifically bind Mg2+. The interaction between the mutant tetraloop and the tetraloop receptor appears coincidently with slowly forming catalytic core tertiary contacts. Thus, the stability conferred upon the P4-P6 domain by the tetraloop-tetraloop receptor interaction dictates the preferred folding pathway by stabilizing an early intermediate. A sub-denaturing concentration of urea diminishes the early barrier to folding the wild-type ribozyme along with complex effects on the subsequent steps of folding the wild-type and mutant RNA.
Collapse
Affiliation(s)
- Inna Shcherbakova
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | |
Collapse
|
20
|
Guan JQ, Takamoto K, Almo SC, Reisler E, Chance MR. Structure and dynamics of the actin filament. Biochemistry 2005; 44:3166-75. [PMID: 15736927 DOI: 10.1021/bi048021j] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structures of filamentous Mg-ATP-actin (F actin) in the presence and absence of KCl have been mapped with hydroxyl radicals (*OH) generated by synchrotron X-ray radiolysis. Proteolysis and mass spectrometry (MS) analysis revealed 52 reactive side-chain sites from 27 distinct peptides within actin. The reactivities of these probe sites with *OH in the F-actin states are compared with those of Mg-ATP-G-actin (monomers) analyzed previously [Guan, J.-Q. et al. (2003) Biochemistry 42, 11992-12000]. Filament-dependent protection within subdomains 2, 3, and 4 and at the C terminus is consistent with longitudinal contacts of monomers within the filament helical structure as predicted by the Holmes model. In the absence of KCl, the extent of filament-dependent protection rarely reached 3-fold, consistent with a highly dynamic filament characterized by relatively weak interactions between actin protomers. However, in the presence of KCl, the extents of protection are significantly increased, consistent with a well-ordered, more tightly packed filament structure. Filament-dependent enhancements of reactivity not predicted by the Holmes model are seen for a peptide that overlaps the "hydrophobic plug" (H-plug) region and for a peptide that forms contacts with the polyphosphate moiety of the bound nucleotide. Overall, these data are both consistent with and complementary to a recent deuterium-exchange MS study of filamentous actin [Chik, J. K., and Schriemer, D.C. (2003) J. Mol. Biol. 334, 373-385], which also did not detect any burial of the H plug upon formation of filaments.
Collapse
Affiliation(s)
- Jing-Qu Guan
- Center for Synchrotron Biosciences, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, New York 10461, USA
| | | | | | | | | |
Collapse
|
21
|
Abstract
Metal ions are required to stabilize RNA tertiary structure and to begin the folding process. How different metal ions enable RNAs to fold depends on the electrostatic potential of the RNA and correlated fluctuations in the positions of the ions themselves. Theoretical models, fluorescence spectroscopy, small angle scattering and structural biology reveal that metal ions alter the RNA dynamics and folding transition states. Specifically coordinated divalent metal ions mediate conformational rearrangements within ribozyme active sites.
Collapse
Affiliation(s)
- Sarah A Woodson
- TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218-2685, USA.
| |
Collapse
|
22
|
Das R, Laederach A, Pearlman SM, Herschlag D, Altman RB. SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. RNA (NEW YORK, N.Y.) 2005; 11:344-54. [PMID: 15701734 PMCID: PMC1262685 DOI: 10.1261/rna.7214405] [Citation(s) in RCA: 265] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2004] [Accepted: 12/07/2004] [Indexed: 05/18/2023]
Abstract
Footprinting is a powerful and widely used tool for characterizing the structure, thermodynamics, and kinetics of nucleic acid folding and ligand binding reactions. However, quantitative analysis of the gel images produced by footprinting experiments is tedious and time-consuming, due to the absence of informatics tools specifically designed for footprinting analysis. We have developed SAFA, a semi-automated footprinting analysis software package that achieves accurate gel quantification while reducing the time to analyze a gel from several hours to 15 min or less. The increase in analysis speed is achieved through a graphical user interface that implements a novel methodology for lane and band assignment, called "gel rectification," and an optimized band deconvolution algorithm. The SAFA software yields results that are consistent with published methodologies and reduces the investigator-dependent variability compared to less automated methods. These software developments simplify the analysis procedure for a footprinting gel and can therefore facilitate the use of quantitative footprinting techniques in nucleic acid laboratories that otherwise might not have considered their use. Further, the increased throughput provided by SAFA may allow a more comprehensive understanding of molecular interactions. The software and documentation are freely available for download at http://safa.stanford.edu.
Collapse
Affiliation(s)
- Rhiju Das
- Department of Physics, Stanford University, Stanford, CA 94305,USA
| | | | | | | | | |
Collapse
|
23
|
Shcherbakova I, Gupta S, Chance MR, Brenowitz M. Monovalent ion-mediated folding of the Tetrahymena thermophila ribozyme. J Mol Biol 2004; 342:1431-42. [PMID: 15364572 DOI: 10.1016/j.jmb.2004.07.092] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2004] [Revised: 07/26/2004] [Accepted: 07/27/2004] [Indexed: 11/23/2022]
Abstract
The time-course of monovalent cation-induced folding of the L-21 Sca1 Tetrahymena thermophila ribozyme and a selected mutant was quantitatively followed using synchrotron X-ray (.OH) footprinting. Initiating folding by increasing the concentration of either Na+ or K+ to 1.5M from an initial condition of approximately 0.008 M Na+ at 42 degrees C resulted in the complete formation of tertiary contacts within the P5abc subdomain and between the peripheral helices within the dead time of our measurements (k>50 s(-1)). These results contrast with folding rates of 2-0.2 s(-1) previously observed for formation of these contacts in 10mM Mg2+ from the same initial condition. Thus, the initial formation of native tertiary contacts is inhibited by divalent but not monovalent cations. The native contacts within the catalytic core form without a detectable burst phase at rates of 0.4-1.0 s(-1) in a manner reminiscent of the Mg2+-dependent folding behavior, although tenfold faster. The tertiary interactions stabilizing the catalytic core interaction with P4-P6 and P2.1, as well as one of the protections internal for the P4-P6 domain, display progress curves with appreciable burst amplitudes and a phase comparable in rate to that of the catalytic core. That the slow folding of the ribozyme's core is a consequence of the alt-P3 secondary structure is shown by the 100% burst phase amplitudes that are observed for folding of the U273A mutant ribozyme within which the native secondary structure (P3) is strengthened. Thus, formation of a misfolded intermediate(s) resulting from the alt-P3 secondary structure is independent of ion valency while the rate at which the respective intermediates are resolved is sensitive to ion valency. The overall portrait painted by these results is that ion valency differentially affects steps in the folding process and that folding in monovalent ion alone for the U273A mutant Tetrahymena ribozyme is fast and direct.
Collapse
Affiliation(s)
- Inna Shcherbakova
- Department of Biochemistry and Center for Synchrotron Biosciences, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | | | | | | |
Collapse
|
24
|
Takamoto K, Das R, He Q, Doniach S, Brenowitz M, Herschlag D, Chance MR. Principles of RNA Compaction: Insights from the Equilibrium Folding Pathway of the P4-P6 RNA Domain in Monovalent Cations. J Mol Biol 2004; 343:1195-206. [PMID: 15491606 DOI: 10.1016/j.jmb.2004.08.080] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2004] [Revised: 08/24/2004] [Accepted: 08/26/2004] [Indexed: 11/28/2022]
Abstract
Counterions are required for RNA folding, and divalent metal ions such as Mg(2+) are often critical. To dissect the role of counterions, we have compared global and local folding of wild-type and mutant variants of P4-P6 RNA derived from the Tetrahymena group I ribozyme in monovalent and in divalent metal ions. A remarkably simple picture of the folding thermodynamics emerges. The equilibrium folding pathway in monovalent ions displays two phases. In the first phase, RNA molecules that are initially in an extended conformation enforced by charge-charge repulsion are relaxed by electrostatic screening to a state with increased flexibility but without formation of long-range tertiary contacts. At higher concentrations of monovalent ions, a state that is nearly identical to the native folded state in the presence of Mg(2+) is formed, with tertiary contacts that involve base and backbone interactions but without the subset of interactions that involve specific divalent metal ion-binding sites. The folding model derived from these and previous results provides a robust framework for understanding the equilibrium and kinetic folding of RNA.
Collapse
Affiliation(s)
- Keiji Takamoto
- Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, New York, NY 10461, USA
| | | | | | | | | | | | | |
Collapse
|
25
|
Brown TS, Chadalavada DM, Bevilacqua PC. Design of a highly reactive HDV ribozyme sequence uncovers facilitation of RNA folding by alternative pairings and physiological ionic strength. J Mol Biol 2004; 341:695-712. [PMID: 15288780 DOI: 10.1016/j.jmb.2004.05.071] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2004] [Revised: 05/18/2004] [Accepted: 05/21/2004] [Indexed: 11/23/2022]
Abstract
The hepatitis delta virus (HDV) ribozyme is a self-cleaving RNA that resides in the HDV genome and regulates its replication. The native fold of the ribozyme is complex, having two pseudoknots. Earlier work implicated four non-native pairings in slowing pseudoknot formation: Alt 1, Alt 2, Alt 3, and Alt P1. The goal of the present work was design of a kinetically simplified and maximally reactive construct for in vitro mechanistic and structural studies. The initial approach chosen was site-directed mutagenesis in which known alternative pairings were destabilized while leaving the catalytic core intact. Based on prior studies, the G11C/U27Delta double mutant was prepared. However, biphasic kinetics and antisense oligonucleotide response trends opposite those of the well-studied G11C mutant were observed suggesting that new alternative pairings with multiple registers, termed Alt X and Alt Y, had been created. Enzymatic structure mapping of oligonucleotide models supported this notion. This led to a model wherein Alt 2 and the phylogenetically conserved Alt 3 act as "folding guides", facilitating folding of the major population of the RNA molecules by hindering formation of the Alt X and Alt Y registers. Attempts to eliminate the strongest of the Alt X pairings by rational design of a quadruple mutant only resulted in more complex kinetic behavior. In an effort to simultaneously destabilize multiple alternative pairings, studies were carried out on G11C/U27Delta in the presence of urea or increased monovalent ion concentration. Inclusion of physiological ionic strength allowed the goal of monophasic, fast-folding (kobs approximately 60 min(-1)) kinetics to be realized. To account for this, a model is developed wherein Na+, which destabilizes secondary and tertiary structures in the presence of Mg2+, facilitates native folding by destabilizing the multiple alternative secondary structures with a higher-order dependence.
Collapse
Affiliation(s)
- Trevor S Brown
- The Huck Institutes of the Life, The Pennsylvania State University, University Park, PA 16802, USA
| | | | | |
Collapse
|
26
|
Sanchez ER, Caudle MT. Evidence for ditopic coordination of phosphate diesters to [Mg(15-crown-5)]2+. Implications for magnesium biocoordination chemistry. J Biol Inorg Chem 2004; 9:724-32. [PMID: 15241659 DOI: 10.1007/s00775-004-0568-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2004] [Accepted: 05/27/2004] [Indexed: 10/26/2022]
Abstract
The interaction of a series of phosphate diesters and triesters (1=diphenyl phosphate,2=dimethyl phosphate,3=bis(2-ethylhexyl) phosphate,4=trimethyl phosphate,5=methyldiphenyl phosphate,6=triphenyl phosphate) with [Mg(15-crown-5)](2+) (15-crown-5=1,4,7,10,13-pentaoxocyclopentadecane) was studied as a simplified model for the interaction of aqueous Mg(2+) ion with phosphate-containing biomolecules such as RNA. Using electrospray mass spectrometry, we confirm the formation of 1:1 adducts in the gas phase. Proton and (31)P NMR titration data were used to construct binding isotherms, and a 1:1 binding equilibrium was fit to the isotherms at room temperature to estimate the binding affinities. The binding affinity data are consistent with ditopic coordination of neutral dialkyl phosphate ligands to the [Mg(15-crown-5)](2+) unit. This involves inner-sphere coordination to the Mg(2+) via an oxygen atom, which is complemented by a weak hydrogen-bonding interaction with the crown ether ligand. Ditopic interaction is consistent with low-temperature NMR spectra showing four different configurations for1 coordinated to [Mg(15-crown-5)](2+), which are interpreted in terms of hindered rotation around the Mg-O(phos) bond. Thermochemical analysis of the binding affinity data suggests that the second-shell interaction contributes only about 1 kcal/mol to the binding free energy, so additional factors, such as steric constraints, must be operative to give a preferred phosphate orientation in this system. However, the experimental data do suggest that second-shell interactions contribute as much as 40% of the total binding energy, consistent with the pronounced ability of aqueous Mg(2+) to form salt-bridges linking secondary and tertiary elements of RNA structure.
Collapse
Affiliation(s)
- Elizabeth R Sanchez
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-1604, USA
| | | |
Collapse
|
27
|
Perez-Salas UA, Rangan P, Krueger S, Briber RM, Thirumalai D, Woodson SA. Compaction of a bacterial group I ribozyme coincides with the assembly of core helices. Biochemistry 2004; 43:1746-53. [PMID: 14769052 DOI: 10.1021/bi035642o] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Counterions are critical to the self-assembly of RNA tertiary structure because they neutralize the large electrostatic forces which oppose the folding process. Changes in the size and shape of the Azoarcus group I ribozyme as a function of Mg(2+) and Na(+) concentration were followed by small angle neutron scattering. In low salt buffer, the RNA was expanded, with an average radius of gyration (R(g)) of 53 +/- 1 A. A highly cooperative transition to a compact form (R(g) = 31.5 +/- 0.5 A) was observed between 1.6 and 1.7 mM MgCl(2). The collapse transition, which is unusually sharp in Mg(2+), has the characteristics of a first-order phase transition. Partial digestion with ribonuclease T1 under identical conditions showed that this transition correlated with the assembly of double helices in the ribozyme core. Fivefold higher Mg(2+) concentrations were required for self-splicing, indicating that compaction occurs before native tertiary interactions are fully stabilized. No further decrease in R(g) was observed between 1.7 and 20 mM MgCl(2), indicating that the intermediates have the same dimensions as the native ribozyme, within the uncertainty of the data (+/-1 A). A more gradual transition to a final R(g) of approximately 33.5 A was observed between 0.45 and 2 M NaCl. This confirms the expectation that monovalent ions not only are less efficient in charge neutralization but also contract the RNA less efficiently than multivalent ions.
Collapse
Affiliation(s)
- Ursula A Perez-Salas
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8562, USA.
| | | | | | | | | | | |
Collapse
|
28
|
Abstract
With the advent of functional genomics and the shift of interest towards sequence-based therapeutics, the past decades have witnessed intense research efforts on nucleic acid-mediated gene regulation technologies. Today, RNA interference is emerging as a groundbreaking discovery, holding promise for development of genetic modulators of unprecedented potency. Twenty-five years after the discovery of antisense RNA and ribozymes, gene control therapeutics are still facing developmental difficulties, with only one US FDA-approved antisense drug currently available in the clinic. Limited predictability of target site selection models is recognized as one major stumbling block that is shared by all of the so-called complementary technologies, slowing the progress towards a commercial product. Currently employed in vitro systems for target site selection include RNAse H-based mapping, antisense oligonucleotide microarrays, and functional screening approaches using libraries of catalysts with randomized target-binding arms to identify optimal ribozyme/DNAzyme cleavage sites. Individually, each strategy has its drawbacks from a drug development perspective. Utilization of message-modulating sequences as therapeutic agents requires that their action on a given target transcript meets criteria of potency and selectivity in the natural physiological environment. In addition to sequence-dependent characteristics, other factors will influence annealing reactions and duplex stability, as well as nucleic acid-mediated catalysis. Parallel consideration of physiological selection systems thus appears essential for screening for nucleic acid compounds proposed for therapeutic applications. Cellular message-targeting studies face issues relating to efficient nucleic acid delivery and appropriate analysis of response. For reliability and simplicity, prokaryotic systems can provide a rapid and cost-effective means of studying message targeting under pseudo-cellular conditions, but such approaches also have limitations. To streamline nucleic acid drug discovery, we propose a multi-model strategy integrating high-throughput-adapted bacterial screening, followed by reporter-based and/or natural cellular models and potentially also in vitro assays for characterization of the most promising candidate sequences, before final in vivo testing.
Collapse
Affiliation(s)
- Isabelle Gautherot
- Virology Platform, Industrialization and Process Development, AVENTIS PASTEUR, Marcy l'Etoile, France.
| | | |
Collapse
|
29
|
Xu G, Takamoto K, Chance MR. Radiolytic Modification of Basic Amino Acid Residues in Peptides: Probes for Examining Protein−Protein Interactions. Anal Chem 2003; 75:6995-7007. [PMID: 14670063 DOI: 10.1021/ac035104h] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein footprinting utilizing hydroxyl radicals coupled with mass spectrometry has become a powerful technique for mapping the solvent accessible surface of proteins and examining protein-protein interactions in solution. Hydroxyl radicals generated by radiolysis or chemical methods efficiently react with many amino acid residue side chains, including the aromatic and sulfur-containing residues along with proline and leucine, generating stable oxidation products that are valuable probes for examining protein structure. In this study, we examine the radiolytic oxidation chemistry of histidine, lysine, and arginine for comparison with their metal-catalyzed oxidation products. Model peptides containing arginine, histidine, and lysine were irradiated using white light from a synchrotron X-ray source or a cesium-137 gamma-ray source. The rates of oxidation and the radiolysis products were primarily characterized by electrospray mass spectrometry including tandem mass spectrometry. Arginine is very sensitive to radiolytic oxidation, giving rise to a characteristic product with a 43 Da mass reduction as a result of the loss of guanidino group and conversion to gamma-glutamyl semialdehyde, consistent with previous metal-catalyzed oxidation studies. Histidine was oxidized to generate a mixture of products with characteristic mass changes primarily involving rupture of and addition to the imidazole ring. Lysine was converted to hydroxylysine or carbonylysine by radiolysis. The development of methods to probe these residues due to their high frequency of occurrence, their typical presence on the protein surface, and their frequent participation in protein-protein interactions considerably extends the utility of protein footprinting.
Collapse
Affiliation(s)
- Guozhong Xu
- Department of Physiology & Biophysics, Department of Biochemistry, and Center for Synchrotron Biosciences, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461-1602, USA
| | | | | |
Collapse
|
30
|
Das R, Kwok LW, Millett IS, Bai Y, Mills TT, Jacob J, Maskel GS, Seifert S, Mochrie SGJ, Thiyagarajan P, Doniach S, Pollack L, Herschlag D. The fastest global events in RNA folding: electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme. J Mol Biol 2003; 332:311-9. [PMID: 12948483 DOI: 10.1016/s0022-2836(03)00854-4] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Large RNAs can collapse into compact conformations well before the stable formation of the tertiary contacts that define their final folds. This study identifies likely physical mechanisms driving these early compaction events in RNA folding. We have employed time-resolved small-angle X-ray scattering to monitor the fastest global shape changes of the Tetrahymena ribozyme under different ionic conditions and with RNA mutations that remove long-range tertiary contacts. A partial collapse in each of the folding time-courses occurs within tens of milliseconds with either monovalent or divalent cations. Combined with comparison to predictions from structural models, this observation suggests a relaxation of the RNA to a more compact but denatured conformational ensemble in response to enhanced electrostatic screening at higher ionic concentrations. Further, the results provide evidence against counterion-correlation-mediated attraction between RNA double helices, a recently proposed model for early collapse. A previous study revealed a second 100 ms phase of collapse to a globular state. Surprisingly, we find that progression to this second early folding intermediate requires RNA sequence motifs that eventually mediate native long-range tertiary interactions, even though these regions of the RNA were observed to be solvent-accessible in previous footprinting studies under similar conditions. These results help delineate an analogy between the early conformational changes in RNA folding and the "burst phase" changes and molten globule formation in protein folding.
Collapse
Affiliation(s)
- Rhiju Das
- Department of Physics, Stanford University, Stanford, CA 94305-4060, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Abstract
Intrinsic events during RNA folding include conformational search and metal ion binding. Several experimentally testable models have been proposed to explain how large ribozymes accomplish folding. Future challenges include the validation of these models, and the correlation of experimental results and theoretical simulations.
Collapse
Affiliation(s)
- Tobin R Sosnick
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.
| | | |
Collapse
|