1
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Bonilla SL, Jang K. Challenges, advances, and opportunities in RNA structural biology by Cryo-EM. Curr Opin Struct Biol 2024; 88:102894. [PMID: 39121532 DOI: 10.1016/j.sbi.2024.102894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 07/03/2024] [Accepted: 07/15/2024] [Indexed: 08/12/2024]
Abstract
RNAs are remarkably versatile molecules that can fold into intricate three-dimensional (3D) structures to perform diverse cellular and viral functions. Despite their biological importance, relatively few RNA 3D structures have been solved, and our understanding of RNA structure-function relationships remains in its infancy. This limitation partly arises from challenges posed by RNA's complex conformational landscape, characterized by structural flexibility, formation of multiple states, and a propensity to misfold. Recently, cryo-electron microscopy (cryo-EM) has emerged as a powerful tool for the visualization of conformationally dynamic RNA-only 3D structures. However, RNA's characteristics continue to pose challenges. We discuss experimental methods developed to overcome these hurdles, including the engineering of modular modifications that facilitate the visualization of small RNAs, improve particle alignment, and validate structural models.
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Affiliation(s)
- Steve L Bonilla
- Laboratory of RNA Structural Biology and Biophysics, The Rockefeller University, New York, NY, 10065, USA.
| | - Karen Jang
- Laboratory of RNA Structural Biology and Biophysics, The Rockefeller University, New York, NY, 10065, USA
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2
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Choi T, Li Z, Song G, Chen HF. Comprehensive Comparison and Critical Assessment of RNA-Specific Force Fields. J Chem Theory Comput 2024; 20:2676-2688. [PMID: 38447040 DOI: 10.1021/acs.jctc.4c00066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Molecular dynamics simulations play a pivotal role in elucidating the dynamic behaviors of RNA structures, offering a valuable complement to traditional methods such as nuclear magnetic resonance or X-ray. Despite this, the current precision of RNA force fields lags behind that of protein force fields. In this work, we systematically compared the performance of four RNA force fields (ff99bsc0χOL3, AMBERDES, ff99OL3_CMAP1, AMBERMaxEnt) across diverse RNA structures. Our findings highlight significant challenges in maintaining stability, particularly with regard to cross-strand and cross-loop hydrogen bonds. Furthermore, we observed the limitations in accurately describing the conformations of nonhelical structural motif, terminal nucleotides, and also base pairing and base stacking interactions by the tested RNA force fields. The identified deficiencies in existing RNA force fields provide valuable insights for subsequent force field development. Concurrently, these findings offer recommendations for selecting appropriate force fields in RNA simulations.
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Affiliation(s)
- Taeyoung Choi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhengxin Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ge Song
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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3
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Roy R, Geng A, Shi H, Merriman DK, Dethoff EA, Salmon L, Al-Hashimi HM. Kinetic Resolution of the Atomic 3D Structures Formed by Ground and Excited Conformational States in an RNA Dynamic Ensemble. J Am Chem Soc 2023; 145:22964-22978. [PMID: 37831584 DOI: 10.1021/jacs.3c04614] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
Knowing the 3D structures formed by the various conformations populating the RNA free-energy landscape, their relative abundance, and kinetic interconversion rates is required to obtain a quantitative and predictive understanding of how RNAs fold and function at the atomic level. While methods integrating ensemble-averaged experimental data with computational modeling are helping define the most abundant conformations in RNA ensembles, elucidating their kinetic rates of interconversion and determining the 3D structures of sparsely populated short-lived RNA excited conformational states (ESs) remains challenging. Here, we developed an approach integrating Rosetta-FARFAR RNA structure prediction with NMR residual dipolar couplings and relaxation dispersion that simultaneously determines the 3D structures formed by the ground-state (GS) and ES subensembles, their relative abundance, and kinetic rates of interconversion. The approach is demonstrated on HIV-1 TAR, whose six-nucleotide apical loop was previously shown to form a sparsely populated (∼13%) short-lived (lifetime ∼ 45 μs) ES. In the GS, the apical loop forms a broad distribution of open conformations interconverting on the pico-to-nanosecond time scale. Most residues are unpaired and preorganized to bind the Tat-superelongation protein complex. The apical loop zips up in the ES, forming a narrow distribution of closed conformations, which sequester critical residues required for protein recognition. Our work introduces an approach for determining the 3D ensemble models formed by sparsely populated RNA conformational states, provides a rare atomic view of an RNA ES, and kinetically resolves the atomic 3D structures of RNA conformational substates, interchanging on time scales spanning 6 orders of magnitude, from picoseconds to microseconds.
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Affiliation(s)
- Rohit Roy
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Ainan Geng
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Dawn K Merriman
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Elizabeth A Dethoff
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Loïc Salmon
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
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4
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Herbst EC, Eberhard EA, Hutchinson JR, Richards CT. Spherical frame projections for visualising joint range of motion, and a complementary method to capture mobility data. J Anat 2022; 241:1054-1065. [PMID: 35819977 PMCID: PMC9482700 DOI: 10.1111/joa.13717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/13/2022] [Accepted: 06/06/2022] [Indexed: 12/16/2022] Open
Abstract
Quantifying joint range of motion (RoM), the reachable poses at a joint, has many applications in research and clinical care. Joint RoM measurements can be used to investigate the link between form and function in extant and extinct animals, to diagnose musculoskeletal disorders and injuries or monitor rehabilitation progress. However, it is difficult to visually demonstrate how the rotations of the joint axes interact to produce joint positions. Here, we introduce the spherical frame projection (SFP), which is a novel 3D visualisation technique, paired with a complementary data collection approach. SFP visualisations are intuitive to interpret in relation to the joint anatomy because they 'trace' the motion of the coordinate system of the distal bone at a joint relative to the proximal bone. Furthermore, SFP visualisations incorporate the interactions of degrees of freedom, which is imperative to capture the full joint RoM. For the collection of such joint RoM data, we designed a rig using conventional motion capture systems, including live audio-visual feedback on torques and sampled poses. Thus, we propose that our visualisation and data collection approach can be adapted for wide use in the study of joint function.
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Affiliation(s)
- Eva C. Herbst
- Palaeontological Institute and MuseumUniversity of ZurichZurichSwitzerland
- Structure and Motion LaboratoryRoyal Veterinary CollegeLondonUK
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5
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Wiedemann J, Kaczor J, Milostan M, Zok T, Blazewicz J, Szachniuk M, Antczak M. RNAloops: a database of RNA multiloops. Bioinformatics 2022; 38:4200-4205. [PMID: 35809063 PMCID: PMC9438955 DOI: 10.1093/bioinformatics/btac484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/26/2022] [Accepted: 07/06/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Knowledge of the 3D structure of RNA supports discovering its functions and is crucial for designing drugs and modern therapeutic solutions. Thus, much attention is devoted to experimental determination and computational prediction targeting the global fold of RNA and its local substructures. The latter include multi-branched loops-functionally significant elements that highly affect the spatial shape of the entire molecule. Unfortunately, their computational modeling constitutes a weak point of structural bioinformatics. A remedy for this is in collecting these motifs and analyzing their features. RESULTS RNAloops is a self-updating database that stores multi-branched loops identified in the PDB-deposited RNA structures. A description of each loop includes angular data-planar and Euler angles computed between pairs of adjacent helices to allow studying their mutual arrangement in space. The system enables search and analysis of multiloops, presents their structure details numerically and visually, and computes data statistics. AVAILABILITY AND IMPLEMENTATION RNAloops is freely accessible at https://rnaloops.cs.put.poznan.pl. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jakub Wiedemann
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Jacek Kaczor
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Maciej Milostan
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland,Poznan Supercomputing and Networking Center, 61-131 Poznan, Poland
| | - Tomasz Zok
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland,Poznan Supercomputing and Networking Center, 61-131 Poznan, Poland
| | - Jacek Blazewicz
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland,Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
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6
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He W, Naleem N, Kleiman D, Kirmizialtin S. Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix-Junction-Helix RNA. J Phys Chem Lett 2022; 13:3400-3408. [PMID: 35404614 PMCID: PMC9036580 DOI: 10.1021/acs.jpclett.2c00359] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
The growing recognition of the functional and therapeutic roles played by RNA and the difficulties in gaining atomic-level insights by experiments are paving the way for all-atom simulations of RNA. One of the main impediments to the use of all-atom simulations is the imbalance between the energy terms of the RNA force fields. Through exhaustive sampling of an RNA helix-junction-helix (HJH) model using enhanced sampling, we critically assessed the select Amber force fields against small-angle X-ray scattering (SAXS) experiments. The tested AMBER99SB, DES-AMBER, and CUFIX force fields show deviations from measured profiles. First, we identified parameters leading to inconsistencies. Then, as a way to balance the forces governing RNA folding, we adopted strategies to refine hydrogen bonding, backbone, and base-stacking parameters. We validated the modified force field (HB-CUFIX) against SAXS data of the HJH model in different ionic strengths. Moreover, we tested a set of independent RNA systems to cross-validate the force field. Overall, HB-CUFIX demonstrates improved performance in studying thermodynamics and structural properties of realistic RNA motifs.
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Affiliation(s)
- Weiwei He
- Chemistry
Program, Science Division, New York University, P.O. Box 129188, Abu Dhabi, United Arab Emirates
- Department
of Chemistry, New York University, New York, New York 10003United States
| | - Nawavi Naleem
- Chemistry
Program, Science Division, New York University, P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Diego Kleiman
- Chemistry
Program, Science Division, New York University, P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Serdal Kirmizialtin
- Chemistry
Program, Science Division, New York University, P.O. Box 129188, Abu Dhabi, United Arab Emirates
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7
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Medeiros Selegato D, Bracco C, Giannelli C, Parigi G, Luchinat C, Sgheri L, Ravera E. Comparison of Different Reweighting Approaches for the Calculation of Conformational Variability of Macromolecules from Molecular Simulations. Chemphyschem 2020; 22:127-138. [DOI: 10.1002/cphc.202000714] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/14/2020] [Indexed: 11/07/2022]
Affiliation(s)
- Denise Medeiros Selegato
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Dipartimento di Chimica “Ugo Schiff” Università degli Studi di Firenze Via della Lastruccia 3 50019 Sesto Fiorentino Italy
- Present address: Fundación MEDINA, Centro de Excelentia en Investigación de Medicamentos Innovadores and Andalucía MSD España Granada Spain
| | - Cesare Bracco
- Dipartimento di Matematica e Informatica “U. Dini” Università degli Studi di Firenze Viale Morgagni 67/a 50134 Florence Italy
| | - Carlotta Giannelli
- Dipartimento di Matematica e Informatica “U. Dini” Università degli Studi di Firenze Viale Morgagni 67/a 50134 Florence Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Dipartimento di Chimica “Ugo Schiff” Università degli Studi di Firenze Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Dipartimento di Chimica “Ugo Schiff” Università degli Studi di Firenze Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Luca Sgheri
- Istituto per le Applicazioni del Calcolo (CNR) sede di Firenze via Madonna del Piano 10 50019 Sesto Fiorentino Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Dipartimento di Chimica “Ugo Schiff” Università degli Studi di Firenze Via della Lastruccia 3 50019 Sesto Fiorentino Italy
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8
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Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction. Nat Commun 2020; 11:5531. [PMID: 33139729 PMCID: PMC7608651 DOI: 10.1038/s41467-020-19371-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 10/07/2020] [Indexed: 11/08/2022] Open
Abstract
Biomolecules form dynamic ensembles of many inter-converting conformations which are key for understanding how they fold and function. However, determining ensembles is challenging because the information required to specify atomic structures for thousands of conformations far exceeds that of experimental measurements. We addressed this data gap and dramatically simplified and accelerated RNA ensemble determination by using structure prediction tools that leverage the growing database of RNA structures to generate a conformation library. Refinement of this library with NMR residual dipolar couplings provided an atomistic ensemble model for HIV-1 TAR, and the model accuracy was independently supported by comparisons to quantum-mechanical calculations of NMR chemical shifts, comparison to a crystal structure of a substate, and through designed ensemble redistribution via atomic mutagenesis. Applications to TAR bulge variants and more complex tertiary RNAs support the generality of this approach and the potential to make the determination of atomic-resolution RNA ensembles routine. Determining dynamic ensembles of biomolecules is still challenging. Here the authors present an approach for rapid RNA ensemble determination that combines RNA structure prediction tools and NMR residual dipolar coupling data and use it to determine atomistic ensemble models for a variety of RNAs.
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9
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Afek A, Shi H, Rangadurai A, Sahay H, Senitzki A, Xhani S, Fang M, Salinas R, Mielko Z, Pufall MA, Poon GMK, Haran TE, Schumacher MA, Al-Hashimi HM, Gordân R. DNA mismatches reveal conformational penalties in protein-DNA recognition. Nature 2020; 587:291-296. [PMID: 33087930 PMCID: PMC7666076 DOI: 10.1038/s41586-020-2843-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 09/17/2020] [Indexed: 12/17/2022]
Abstract
Transcription factors recognize specific genomic sequences to regulate complex gene-expression programs. Although it is well-established that transcription factors bind to specific DNA sequences using a combination of base readout and shape recognition, some fundamental aspects of protein-DNA binding remain poorly understood1,2. Many DNA-binding proteins induce changes in the structure of the DNA outside the intrinsic B-DNA envelope. However, how the energetic cost that is associated with distorting the DNA contributes to recognition has proven difficult to study, because the distorted DNA exists in low abundance in the unbound ensemble3-9. Here we use a high-throughput assay that we term SaMBA (saturation mismatch-binding assay) to investigate the role of DNA conformational penalties in transcription factor-DNA recognition. In SaMBA, mismatched base pairs are introduced to pre-induce structural distortions in the DNA that are much larger than those induced by changes in the Watson-Crick sequence. Notably, approximately 10% of mismatches increased transcription factor binding, and for each of the 22 transcription factors that were examined, at least one mismatch was found that increased the binding affinity. Mismatches also converted non-specific sites into high-affinity sites, and high-affinity sites into 'super sites' that exhibit stronger affinity than any known canonical binding site. Determination of high-resolution X-ray structures, combined with nuclear magnetic resonance measurements and structural analyses, showed that many of the DNA mismatches that increase binding induce distortions that are similar to those induced by protein binding-thus prepaying some of the energetic cost incurred from deforming the DNA. Our work indicates that conformational penalties are a major determinant of protein-DNA recognition, and reveals mechanisms by which mismatches can recruit transcription factors and thus modulate replication and repair activities in the cell10,11.
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Affiliation(s)
- Ariel Afek
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, NC, USA
| | - Atul Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Harshit Sahay
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC, USA
- Program in Computational Biology and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Alon Senitzki
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Suela Xhani
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - Mimi Fang
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
| | - Raul Salinas
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Zachery Mielko
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC, USA
- Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC, USA
| | - Miles A Pufall
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Tali E Haran
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Maria A Schumacher
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Hashim M Al-Hashimi
- Department of Chemistry, Duke University, Durham, NC, USA.
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.
| | - Raluca Gordân
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC, USA.
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA.
- Department of Computer Science, Duke University, Durham, NC, USA.
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
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10
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Manafzadeh AR, Gatesy SM. A coordinate-system-independent method for comparing joint rotational mobilities. J Exp Biol 2020; 223:jeb227108. [PMID: 32747453 DOI: 10.1242/jeb.227108] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/29/2020] [Indexed: 08/26/2023]
Abstract
Three-dimensional studies of range of motion currently plot joint poses in a 'Euler space' whose axes are angles measured in the joint's three rotational degrees of freedom. Researchers then compute the volume of a pose cloud to measure rotational mobility. However, pairs of poses that are equally different from one another in orientation are not always plotted equally far apart in Euler space. This distortion causes a single joint's mobility to change when measured based on different joint coordinate systems and precludes fair comparison among joints. Here, we present two alternative spaces inspired by a 16th century map projection - cosine-corrected and sine-corrected Euler spaces - that allow coordinate-system-independent comparison of joint rotational mobility. When tested with data from a bird hip joint, cosine-corrected Euler space demonstrated a 10-fold reduction in variation among mobilities measured from three joint coordinate systems. This new quantitative framework enables previously intractable, comparative studies of articular function.
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Affiliation(s)
- Armita R Manafzadeh
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
| | - Stephen M Gatesy
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
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11
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Girard N, Dagenais P, Lacroix-Labonté J, Legault P. A multi-axial RNA joint with a large range of motion promotes sampling of an active ribozyme conformation. Nucleic Acids Res 2019; 47:3739-3751. [PMID: 30993347 PMCID: PMC6468304 DOI: 10.1093/nar/gkz098] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 01/17/2019] [Accepted: 02/12/2019] [Indexed: 12/21/2022] Open
Abstract
Investigating the dynamics of structural elements in functional RNAs is important to better understand their mechanism and for engineering RNAs with novel functions. Previously, we performed rational engineering studies with the Varkud satellite (VS) ribozyme and switched its specificity toward non-natural hairpin substrates through modification of a critical kissing-loop interaction (KLI). We identified functional VS ribozyme variants with surrogate KLIs (ribosomal RNA L88/L22 and human immunodeficiency virus-1 TAR/TAR*), but they displayed ∼100-fold lower cleavage activity. Here, we characterized the dynamics of KLIs to correlate dynamic properties with function and improve the activity of designer ribozymes. Using temperature replica exchange molecular dynamics, we determined that the natural KLI in the VS ribozyme supports conformational sampling of its closed and active state, whereas the surrogate KLIs display more restricted motions. Based on in vitro selection, the cleavage activity of a VS ribozyme variant with the TAR/TAR* KLI could be markedly improved by partly destabilizing the KLI but increasing conformation sampling. We formulated a mechanistic model for substrate binding in which the KLI dynamics contribute to formation of the active site. Our model supports the modular nature of RNA in which subdomain structure and dynamics contribute to define the thermodynamics and kinetics relevant to RNA function.
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Affiliation(s)
- Nicolas Girard
- Département de biochimie et médecine moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, H3C 3J7, Canada
| | - Pierre Dagenais
- Département de biochimie et médecine moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, H3C 3J7, Canada
| | - Julie Lacroix-Labonté
- Département de biochimie et médecine moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, H3C 3J7, Canada
| | - Pascale Legault
- Département de biochimie et médecine moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, H3C 3J7, Canada
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12
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Rangadurai A, Szymaski ES, Kimsey IJ, Shi H, Al-Hashimi HM. Characterizing micro-to-millisecond chemical exchange in nucleic acids using off-resonance R 1ρ relaxation dispersion. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 112-113:55-102. [PMID: 31481159 PMCID: PMC6727989 DOI: 10.1016/j.pnmrs.2019.05.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 05/10/2023]
Abstract
This review describes off-resonance R1ρ relaxation dispersion NMR methods for characterizing microsecond-to-millisecond chemical exchange in uniformly 13C/15N labeled nucleic acids in solution. The review opens with a historical account of key developments that formed the basis for modern R1ρ techniques used to study chemical exchange in biomolecules. A vector model is then used to describe the R1ρ relaxation dispersion experiment, and how the exchange contribution to relaxation varies with the amplitude and frequency offset of an applied spin-locking field, as well as the population, exchange rate, and differences in chemical shifts of two exchanging species. Mathematical treatment of chemical exchange based on the Bloch-McConnell equations is then presented and used to examine relaxation dispersion profiles for more complex exchange scenarios including three-state exchange. Pulse sequences that employ selective Hartmann-Hahn cross-polarization transfers to excite individual 13C or 15N spins are then described for measuring off-resonance R1ρ(13C) and R1ρ(15N) in uniformly 13C/15N labeled DNA and RNA samples prepared using commercially available 13C/15N labeled nucleotide triphosphates. Approaches for analyzing R1ρ data measured at a single static magnetic field to extract a full set of exchange parameters are then presented that rely on numerical integration of the Bloch-McConnell equations or the use of algebraic expressions. Methods for determining structures of nucleic acid excited states are then reviewed that rely on mutations and chemical modifications to bias conformational equilibria, as well as structure-based approaches to calculate chemical shifts. Applications of the methodology to the study of DNA and RNA conformational dynamics are reviewed and the biological significance of the exchange processes is briefly discussed.
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Affiliation(s)
- Atul Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Eric S Szymaski
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Isaac J Kimsey
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA; Nymirum, 4324 S. Alston Avenue, Durham, NC 27713, USA(1)
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, NC 27710, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA; Department of Chemistry, Duke University, Durham, NC 27710, USA.
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13
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Yang C, Kim E, Lim M, Pak Y. Computational Probing of Watson-Crick/Hoogsteen Breathing in a DNA Duplex Containing N1-Methylated Adenine. J Chem Theory Comput 2018; 15:751-761. [PMID: 30501194 DOI: 10.1021/acs.jctc.8b00936] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
DNA breathing is a local conformational fluctuation spontaneously occurring in double-stranded DNAs. In particular, the possibility of individual base pairs (bps) in duplex DNA to flip between alternate bp modes, i.e., Watson-Crick (WC)-like and Hoogsteen (HG)-like, at relevant time scales has impacted DNA research fields for many years. In this study, to computationally probe effects of chemical modification on the DNA breathing, we present a free energy landscape of spontaneous thermal transitions between WC and HG bps in a free DNA duplex containing N1-methylated adenine (m1A). For the current free energy computation, a variant of well-tempered metadynamics simulation was extensively performed for a total of 40 μs to produce free energy surfaces. The free energy profile indicated that, upon the chemical modification of adenine, the HG bp (m1A·T) was located in the most favorable conformation (96.7%); however, the canonical WC bp (m1A·T) was distorted into two WC-like bps of WC* (2.8%) and WC** (0.5%). The conformational exchange between these two minor WC-like bps occurs with the first hundred nanoseconds. The transition between WC-like and HG bp features multiple transition pathways displaying various extents of base flipping in combination with glycosidic rotation. Analysis of the simulated ensemble showed that the m1A-induced changes of the backbone and sugar pucker were in a reasonable agreement with previous results inferred from NMR experiments. Also, this study revealed that the formation of the stable HG bp upon the mutation alters the characteristics of dynamic fluctuations of the neighboring WC residues of m1A. We expect this simulation approach to be a robust computational scheme to complement and guide future high-resolution experiments on many outstanding issues of duplex DNA breathing.
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Affiliation(s)
- Changwon Yang
- Department of Chemistry and Institute of Functional Materials , Pusan National University , Busan 46241 , South Korea
| | - Eunae Kim
- College of Pharmacy , Chosun University , Gwangju 61452 , South Korea
| | - Manho Lim
- Department of Chemistry and Institute of Functional Materials , Pusan National University , Busan 46241 , South Korea
| | - Youngshang Pak
- Department of Chemistry and Institute of Functional Materials , Pusan National University , Busan 46241 , South Korea
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14
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Merriman DK, Yuan J, Shi H, Majumdar A, Herschlag D, Al-Hashimi HM. Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics. RNA (NEW YORK, N.Y.) 2018; 24:1363-1376. [PMID: 30012568 PMCID: PMC6140463 DOI: 10.1261/rna.066258.118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 07/05/2018] [Indexed: 05/03/2023]
Abstract
Helical elements separated by bulges frequently undergo transitions between unstacked and coaxially stacked conformations during the folding and function of noncoding RNAs. Here, we examine the dynamic properties of poly-pyrimidine bulges of varying length (n = 1-4, 7) across a range of Mg2+ concentrations using HIV-1 TAR RNA as a model system and solution NMR spectroscopy. In the absence of Mg2+, helices linked by bulges with n ≥ 3 residues adopt predominantly unstacked conformations (stacked population <15%), whereas one-bulge and two-bulge motifs adopt predominantly stacked conformations (stacked population >74%). In the presence of 3 mM Mg2+, the helices predominantly coaxially stack (stacked population >84%), regardless of bulge length, and the midpoint for the Mg2+-dependent stacking transition is within threefold regardless of bulge length. In the absence of Mg2+, the difference between free energy of interhelical coaxial stacking across the bulge variants is estimated to be ∼2.9 kcal/mol, based on an NMR chemical shift mapping with stacking being more energetically disfavored for the longer bulges. This difference decreases to ∼0.4 kcal/mol in the presence of Mg2+ NMR RDCs and resonance intensity data show increased dynamics in the stacked state with increasing bulge length in the presence of Mg2+ We propose that Mg2+ helps to neutralize the growing electrostatic repulsion in the stacked state with increasing bulge length thereby increasing the number of coaxial conformations that are sampled. Energetically compensated interhelical stacking dynamics may help to maximize the conformational adaptability of RNA and allow a wide range of conformations to be optimally stabilized by proteins and ligands.
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Affiliation(s)
- Dawn K Merriman
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Jiayi Yuan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Ananya Majumdar
- Biomolecular NMR Facility, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
| | - Hashim M Al-Hashimi
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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15
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Ganser LR, Lee J, Rangadurai A, Merriman DK, Kelly ML, Kansal AD, Sathyamoorthy B, Al-Hashimi HM. High-performance virtual screening by targeting a high-resolution RNA dynamic ensemble. Nat Struct Mol Biol 2018; 25:425-434. [PMID: 29728655 PMCID: PMC5942591 DOI: 10.1038/s41594-018-0062-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 03/27/2018] [Indexed: 12/22/2022]
Abstract
Dynamic ensembles hold great promise in advancing RNA-targeted drug discovery. Here we subjected the transactivation response element (TAR) RNA from human immunodeficiency virus type-1 to experimental high-throughput screening against ~100,000 drug-like small molecules. Results were augmented with 170 known TAR-binding molecules and used to generate sublibraries optimized for evaluating enrichment when virtually screening a dynamic ensemble of TAR determined by combining NMR spectroscopy data and molecular dynamics simulations. Ensemble-based virtual screening scores molecules with an area under the receiver operator characteristic curve of ~0.85-0.94 and with ~40-75% of all hits falling within the top 2% of scored molecules. The enrichment decreased significantly for ensembles generated from the same molecular dynamics simulations without input NMR data and for other control ensembles. The results demonstrate that experimentally determined RNA ensembles can significantly enrich libraries with true hits and that the degree of enrichment is dependent on the accuracy of the ensemble.
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Affiliation(s)
- Laura R Ganser
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Janghyun Lee
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Atul Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | | | - Megan L Kelly
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Aman D Kansal
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | | | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.
- Department of Chemistry, Duke University, Durham, NC, USA.
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16
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Grytz CM, Kazemi S, Marko A, Cekan P, Güntert P, Sigurdsson ST, Prisner TF. Determination of helix orientations in a flexible DNA by multi-frequency EPR spectroscopy. Phys Chem Chem Phys 2018; 19:29801-29811. [PMID: 29090294 DOI: 10.1039/c7cp04997h] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Distance measurements are performed between a pair of spin labels attached to nucleic acids using Pulsed Electron-Electron Double Resonance (PELDOR, also called DEER) spectroscopy which is a complementary tool to other structure determination methods in structural biology. The rigid spin label Ç, when incorporated pairwise into two helical parts of a nucleic acid molecule, allows the determination of both the mutual orientation and the distance between those labels, since Ç moves rigidly with the helix to which it is attached. We have developed a two-step protocol to investigate the conformational flexibility of flexible nucleic acid molecules by multi-frequency PELDOR. In the first step, a library with a broad collection of conformers, which are in agreement with topological constraints, NMR restraints and distances derived from PELDOR, was created. In the second step, a weighted structural ensemble of these conformers was chosen, such that it fits the multi-frequency PELDOR time traces of all doubly Ç-labelled samples simultaneously. This ensemble reflects the global structure and the conformational flexibility of the two-way DNA junction. We demonstrate this approach on a flexible bent DNA molecule, consisting of two short helical parts with a five adenine bulge at the center. The kink and twist motions between both helical parts were quantitatively determined and showed high flexibility, in agreement with a Förster Resonance Energy Transfer (FRET) study on a similar bent DNA motif. The approach presented here should be useful to describe the relative orientation of helical motifs and the conformational flexibility of nucleic acid structures, both alone and in complexes with proteins and other molecules.
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Affiliation(s)
- C M Grytz
- Institute of Physical and Theoretical Chemistry, Goethe University, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany.
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17
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Sathyamoorthy B, Shi H, Zhou H, Xue Y, Rangadurai A, Merriman DK, Al-Hashimi HM. Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A. Nucleic Acids Res 2017; 45:5586-5601. [PMID: 28369571 PMCID: PMC5435913 DOI: 10.1093/nar/gkx186] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/06/2017] [Accepted: 03/17/2017] [Indexed: 12/18/2022] Open
Abstract
In the canonical DNA double helix, Watson-Crick (WC) base pairs (bps) exist in dynamic equilibrium with sparsely populated (∼0.02-0.4%) and short-lived (lifetimes ∼0.2-2.5 ms) Hoogsteen (HG) bps. To gain insights into transient HG bps, we used solution-state nuclear magnetic resonance spectroscopy, including measurements of residual dipolar couplings and molecular dynamics simulations, to examine how a single HG bp trapped using the N1-methylated adenine (m1A) lesion affects the structural and dynamic properties of two duplexes. The solution structure and dynamic ensembles of the duplexes reveals that in both cases, m1A forms a m1A•T HG bp, which is accompanied by local and global structural and dynamic perturbations in the double helix. These include a bias toward the BI backbone conformation; sugar repuckering, major-groove directed kinking (∼9°); and local melting of neighboring WC bps. These results provide atomic insights into WC/HG breathing dynamics in unmodified DNA duplexes as well as identify structural and dynamic signatures that could play roles in m1A recognition and repair.
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Affiliation(s)
- Bharathwaj Sathyamoorthy
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Chemistry, Duke University, Durham, NC 27710, USA
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, NC 27710, USA
| | - Huiqing Zhou
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yi Xue
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Chemistry, Duke University, Durham, NC 27710, USA
| | - Atul Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | | | - Hashim M. Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Chemistry, Duke University, Durham, NC 27710, USA
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18
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Andrałojć W, Ravera E, Salmon L, Parigi G, Al-Hashimi HM, Luchinat C. Inter-helical conformational preferences of HIV-1 TAR-RNA from maximum occurrence analysis of NMR data and molecular dynamics simulations. Phys Chem Chem Phys 2017; 18:5743-52. [PMID: 26360616 DOI: 10.1039/c5cp03993b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Detecting conformational heterogeneity in biological macromolecules is a key for the understanding of their biological function. We here provide a comparison between two independent approaches to assess conformational heterogeneity: molecular dynamics simulations, performed without inclusion of any experimental data, and maximum occurrence (MaxOcc) distribution over the topologically available conformational space. The latter only reflects the extent of the averaging and identifies regions which are most compliant with the experimentally measured NMR Residual Dipolar Couplings (RDCs). The analysis was performed for the HIV-1 TAR RNA, consisting of two helical domains connected by a flexible bulge junction, for which four sets of RDCs were available as well as an 8.2 μs all-atom molecular dynamics simulation. A sample and select approach was previously applied to extract from the molecular dynamics trajectory conformational ensembles in agreement with the four sets of RDCs. The MaxOcc analysis performed here identifies the most likely sampled region in the conformational space of the system which, strikingly, overlaps well with the structures independently sampled in the molecular dynamics calculations and even better with the RDC selected ensemble.
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Affiliation(s)
- Witold Andrałojć
- Magnetic Resonance Center "CERM", University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy.
| | - Enrico Ravera
- Magnetic Resonance Center "CERM", University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy. and Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Loïc Salmon
- Department of Molecular, Cellular and Developmental Biology and Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Giacomo Parigi
- Magnetic Resonance Center "CERM", University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy. and Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Department of Chemistry, Duke University School of Medicine, 307 Research Drive, Durham, North Carolina 27710, USA
| | - Claudio Luchinat
- Magnetic Resonance Center "CERM", University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy. and Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
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19
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Schreck JS, Ouldridge TE, Romano F, Louis AA, Doye JPK. Characterizing the bending and flexibility induced by bulges in DNA duplexes. J Chem Phys 2016; 142:165101. [PMID: 25933790 DOI: 10.1063/1.4917199] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Advances in DNA nanotechnology have stimulated the search for simple motifs that can be used to control the properties of DNA nanostructures. One such motif, which has been used extensively in structures such as polyhedral cages, two-dimensional arrays, and ribbons, is a bulged duplex, that is, two helical segments that connect at a bulge loop. We use a coarse-grained model of DNA to characterize such bulged duplexes. We find that this motif can adopt structures belonging to two main classes: one where the stacking of the helices at the center of the system is preserved, the geometry is roughly straight, and the bulge is on one side of the duplex and the other where the stacking at the center is broken, thus allowing this junction to act as a hinge and increasing flexibility. Small loops favor states where stacking at the center of the duplex is preserved, with loop bases either flipped out or incorporated into the duplex. Duplexes with longer loops show more of a tendency to unstack at the bulge and adopt an open structure. The unstacking probability, however, is highest for loops of intermediate lengths, when the rigidity of single-stranded DNA is significant and the loop resists compression. The properties of this basic structural motif clearly correlate with the structural behavior of certain nano-scale objects, where the enhanced flexibility associated with larger bulges has been used to tune the self-assembly product as well as the detailed geometry of the resulting nanostructures. We further demonstrate the role of bulges in determining the structure of a "Z-tile," a basic building block for nanostructures.
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Affiliation(s)
- John S Schreck
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Thomas E Ouldridge
- Rudolph Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
| | - Flavio Romano
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Ard A Louis
- Rudolph Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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20
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Ren A, Xue Y, Peselis A, Serganov A, Al-Hashimi HM, Patel DJ. Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch. Cell Rep 2015; 13:1800-13. [PMID: 26655897 DOI: 10.1016/j.celrep.2015.10.062] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 08/17/2015] [Accepted: 10/20/2015] [Indexed: 12/24/2022] Open
Abstract
Naturally occurring L-glutamine riboswitches occur in cyanobacteria and marine metagenomes, where they reside upstream of genes involved in nitrogen metabolism. By combining X-ray, NMR, and MD, we characterized an L-glutamine-dependent conformational transition in the Synechococcus elongatus glutamine riboswitch from tuning fork to L-shaped alignment of stem segments. This transition generates an open ligand-binding pocket with L-glutamine selectivity enforced by Mg(2+)-mediated intermolecular interactions. The transition also stabilizes the P1 helix through a long-range "linchpin" Watson-Crick G-C pair-capping interaction, while melting a short helix below P1 potentially capable of modulating downstream readout. NMR data establish that the ligand-free glutamine riboswitch in Mg(2+) solution exists in a slow equilibrium between flexible tuning fork and a minor conformation, similar, but not identical, to the L-shaped bound conformation. We propose that an open ligand-binding pocket combined with a high conformational penalty for forming the ligand-bound state provide mechanisms for reducing binding affinity while retaining high selectivity.
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Affiliation(s)
- Aiming Ren
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Yi Xue
- Department of Biochemistry and Chemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Alla Peselis
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Alexander Serganov
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Chemistry, Duke University Medical Center, Durham, NC 27710, USA.
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
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21
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Mustoe AM, Al-Hashimi HM, Brooks CL. Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme. Nucleic Acids Res 2015; 44:402-12. [PMID: 26481360 PMCID: PMC4705646 DOI: 10.1093/nar/gkv1055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Accepted: 10/03/2015] [Indexed: 12/20/2022] Open
Abstract
A requirement for specific RNA folding is that the free-energy landscape discriminate against non-native folds. While tertiary interactions are critical for stabilizing the native fold, they are relatively non-specific, suggesting additional mechanisms contribute to tertiary folding specificity. In this study, we use coarse-grained molecular dynamics simulations to explore how secondary structure shapes the tertiary free-energy landscape of the Azoarcus ribozyme. We show that steric and connectivity constraints posed by secondary structure strongly limit the accessible conformational space of the ribozyme, and that these so-called topological constraints in turn pose strong free-energy penalties on forming different tertiary contacts. Notably, native A-minor and base-triple interactions form with low conformational free energy, while non-native tetraloop/tetraloop–receptor interactions are penalized by high conformational free energies. Topological constraints also give rise to strong cooperativity between distal tertiary interactions, quantitatively matching prior experimental measurements. The specificity of the folding landscape is further enhanced as tertiary contacts place additional constraints on the conformational space, progressively funneling the molecule to the native state. These results indicate that secondary structure assists the ribozyme in navigating the otherwise rugged tertiary folding landscape, and further emphasize topological constraints as a key force in RNA folding.
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Affiliation(s)
- Anthony M Mustoe
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Chemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Charles L Brooks
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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22
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Yang S, Al-Hashimi HM. Unveiling Inherent Degeneracies in Determining Population-Weighted Ensembles of Interdomain Orientational Distributions Using NMR Residual Dipolar Couplings: Application to RNA Helix Junction Helix Motifs. J Phys Chem B 2015; 119:9614-26. [PMID: 26131693 DOI: 10.1021/acs.jpcb.5b03859] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A growing number of studies employ time-averaged experimental data to determine dynamic ensembles of biomolecules. While it is well-known that different ensembles can satisfy experimental data to within error, the extent and nature of these degeneracies, and their impact on the accuracy of the ensemble determination remains poorly understood. Here, we use simulations and a recently introduced metric for assessing ensemble similarity to explore degeneracies in determining ensembles using NMR residual dipolar couplings (RDCs) with specific application to A-form helices in RNA. Various target ensembles were constructed representing different domain-domain orientational distributions that are confined to a topologically restricted (<10%) conformational space. Five independent sets of ensemble averaged RDCs were then computed for each target ensemble and a "sample and select" scheme used to identify degenerate ensembles that satisfy RDCs to within experimental uncertainty. We find that ensembles with different ensemble sizes and that can differ significantly from the target ensemble (by as much as ∑Ω ∼ 0.4 where ∑Ω varies between 0 and 1 for maximum and minimum ensemble similarity, respectively) can satisfy the ensemble averaged RDCs. These deviations increase with the number of unique conformers and breadth of the target distribution, and result in significant uncertainty in determining conformational entropy (as large as 5 kcal/mol at T = 298 K). Nevertheless, the RDC-degenerate ensembles are biased toward populated regions of the target ensemble, and capture other essential features of the distribution, including the shape. Our results identify ensemble size as a major source of uncertainty in determining ensembles and suggest that NMR interactions such as RDCs and spin relaxation, on their own, do not carry the necessary information needed to determine conformational entropy at a useful level of precision. The framework introduced here provides a general approach for exploring degeneracies in ensemble determination for different types of experimental data.
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Affiliation(s)
- Shan Yang
- †Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Stanford, California 94305, United States
| | - Hashim M Al-Hashimi
- ‡Department of Biochemistry and Chemistry, Duke University Medical Center, Durham, North Carolina 27705, United States
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23
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Frank AT, Zhang Q, Al-Hashimi HM, Andricioaei I. Slowdown of Interhelical Motions Induces a Glass Transition in RNA. Biophys J 2015; 108:2876-85. [PMID: 26083927 PMCID: PMC4472199 DOI: 10.1016/j.bpj.2015.04.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 03/21/2015] [Accepted: 04/21/2015] [Indexed: 12/29/2022] Open
Abstract
RNA function depends crucially on the details of its dynamics. The simplest RNA dynamical unit is a two-way interhelical junction. Here, for such a unit--the transactivation response RNA element--we present evidence from molecular dynamics simulations, supported by nuclear magnetic resonance relaxation experiments, for a dynamical transition near 230 K. This glass transition arises from the freezing out of collective interhelical motional modes. The motions, resolved with site-specificity, are dynamically heterogeneous and exhibit non-Arrhenius relaxation. The microscopic origin of the glass transition is a low-dimensional, slow manifold consisting largely of the Euler angles describing interhelical reorientation. Principal component analysis over a range of temperatures covering the glass transition shows that the abrupt slowdown of motion finds its explanation in a localization transition that traps probability density into several disconnected conformational pools over the low-dimensional energy landscape. Upon temperature increase, the probability density pools then flood a larger basin, akin to a lakes-to-sea transition. Simulations on transactivation response RNA are also used to backcalculate inelastic neutron scattering data that match previous inelastic neutron scattering measurements on larger and more complex RNA structures and which, upon normalization, give temperature-dependent fluctuation profiles that overlap onto a glass transition curve that is quasi-universal over a range of systems and techniques.
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Affiliation(s)
- Aaron T Frank
- Department of Chemistry, University of California at Irvine, Irvine, California
| | - Qi Zhang
- The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina
| | - Ioan Andricioaei
- Department of Chemistry, University of California at Irvine, Irvine, California.
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24
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Kerpedjiev P, Höner Zu Siederdissen C, Hofacker IL. Predicting RNA 3D structure using a coarse-grain helix-centered model. RNA (NEW YORK, N.Y.) 2015; 21:1110-1121. [PMID: 25904133 PMCID: PMC4436664 DOI: 10.1261/rna.047522.114] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 02/13/2015] [Indexed: 06/04/2023]
Abstract
A 3D model of RNA structure can provide information about its function and regulation that is not possible with just the sequence or secondary structure. Current models suffer from low accuracy and long running times and either neglect or presume knowledge of the long-range interactions which stabilize the tertiary structure. Our coarse-grained, helix-based, tertiary structure model operates with only a few degrees of freedom compared with all-atom models while preserving the ability to sample tertiary structures given a secondary structure. It strikes a balance between the precision of an all-atom tertiary structure model and the simplicity and effectiveness of a secondary structure representation. It provides a simplified tool for exploring global arrangements of helices and loops within RNA structures. We provide an example of a novel energy function relying only on the positions of stems and loops. We show that coupling our model to this energy function produces predictions as good as or better than the current state of the art tools. We propose that given the wide range of conformational space that needs to be explored, a coarse-grain approach can explore more conformations in less iterations than an all-atom model coupled to a fine-grain energy function. Finally, we emphasize the overarching theme of providing an ensemble of predicted structures, something which our tool excels at, rather than providing a handful of the lowest energy structures.
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Affiliation(s)
| | - Christian Höner Zu Siederdissen
- Institute for Theoretical Chemistry, A-1090 Vienna, Austria Bioinformatics Group, Department of Computer Science, Universität Leipzig, D-04107 Leipzig, Germany Interdisciplinary Center for Bioinformatics, Universität Leipzig, D-04107 Leipzig, Germany
| | - Ivo L Hofacker
- Institute for Theoretical Chemistry, A-1090 Vienna, Austria Research Group Bioinformatics and Computational Biology, University of Vienna, A-1090 Vienna, Austria Center for non-coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Science, University of Copenhagen, DK-1870 Frederiksberg, Denmark
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25
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Zhou H, Hintze BJ, Kimsey IJ, Sathyamoorthy B, Yang S, Richardson JS, Al-Hashimi HM. New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey. Nucleic Acids Res 2015; 43:3420-33. [PMID: 25813047 PMCID: PMC4402545 DOI: 10.1093/nar/gkv241] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 03/01/2015] [Indexed: 11/14/2022] Open
Abstract
Hoogsteen (HG) base pairs (bps) provide an alternative pairing geometry to Watson-Crick (WC) bps and can play unique functional roles in duplex DNA. Here, we use structural features unique to HG bps (syn purine base, HG hydrogen bonds and constricted C1'-C1' distance across the bp) to search for HG bps in X-ray structures of DNA duplexes in the Protein Data Bank. The survey identifies 106 A•T and 34 G•C HG bps in DNA duplexes, many of which are undocumented in the literature. It also uncovers HG-like bps with syn purines lacking HG hydrogen bonds or constricted C1'-C1' distances that are analogous to conformations that have been proposed to populate the WC-to-HG transition pathway. The survey reveals HG preferences similar to those observed for transient HG bps in solution by nuclear magnetic resonance, including stronger preferences for A•T versus G•C bps, TA versus GG steps, and also suggests enrichment at terminal ends with a preference for 5'-purine. HG bps induce small local perturbations in neighboring bps and, surprisingly, a small but significant degree of DNA bending (∼14°) directed toward the major groove. The survey provides insights into the preferences and structural consequences of HG bps in duplex DNA.
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Affiliation(s)
- Huiqing Zhou
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Bradley J Hintze
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Isaac J Kimsey
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | | | - Shan Yang
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | | | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University, Durham, NC 27710, USA Department of Chemistry, Duke University, Durham, NC 27708, USA
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26
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Mustoe AM, Liu X, Lin PJ, Al-Hashimi HM, Fierke CA, Brooks CL. Noncanonical secondary structure stabilizes mitochondrial tRNA(Ser(UCN)) by reducing the entropic cost of tertiary folding. J Am Chem Soc 2015; 137:3592-9. [PMID: 25705930 PMCID: PMC4399864 DOI: 10.1021/ja5130308] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Mammalian mitochondrial tRNA(Ser(UCN)) (mt-tRNA(Ser)) and pyrrolysine tRNA (tRNA(Pyl)) fold to near-canonical three-dimensional structures despite having noncanonical secondary structures with shortened interhelical loops that disrupt the conserved tRNA tertiary interaction network. How these noncanonical tRNAs compensate for their loss of tertiary interactions remains unclear. Furthermore, in human mt-tRNA(Ser), lengthening the variable loop by the 7472insC mutation reduces mt-tRNA(Ser) concentration in vivo through poorly understood mechanisms and is strongly associated with diseases such as deafness and epilepsy. Using simulations of the TOPRNA coarse-grained model, we show that increased topological constraints encoded by the unique secondary structure of wild-type mt-tRNA(Ser) decrease the entropic cost of folding by ∼2.5 kcal/mol compared to canonical tRNA, offsetting its loss of tertiary interactions. Further simulations show that the pathogenic 7472insC mutation disrupts topological constraints and hence destabilizes the mutant mt-tRNA(Ser) by ∼0.6 kcal/mol relative to wild-type. UV melting experiments confirm that insertion mutations lower mt-tRNA(Ser) melting temperature by 6-9 °C and increase the folding free energy by 0.8-1.7 kcal/mol in a largely sequence- and salt-independent manner, in quantitative agreement with our simulation predictions. Our results show that topological constraints provide a quantitative framework for describing key aspects of RNA folding behavior and also provide the first evidence of a pathogenic mutation that is due to disruption of topological constraints.
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Affiliation(s)
- Anthony M. Mustoe
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Xin Liu
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Paul J. Lin
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Hashim M. Al-Hashimi
- Departments of Biochemistry and Chemistry, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Carol A. Fierke
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Charles L. Brooks
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
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27
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Herschlag D, Allred BE, Gowrishankar S. From static to dynamic: the need for structural ensembles and a predictive model of RNA folding and function. Curr Opin Struct Biol 2015; 30:125-133. [PMID: 25744941 DOI: 10.1016/j.sbi.2015.02.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/11/2015] [Accepted: 02/11/2015] [Indexed: 12/18/2022]
Abstract
To understand RNA, it is necessary to move beyond a descriptive categorization towards quantitative predictions of its molecular conformations and functional behavior. An incisive approach to understanding the function and folding of biological RNA systems involves characterizing small, simple components that are largely responsible for the behavior of complex systems including helix-junction-helix elements and tertiary motifs. State-of-the-art methods have permitted unprecedented insight into the conformational ensembles of these elements revealing, for example, that conformations of helix-junction-helix elements are confined to a small region of the ensemble, that this region is highly dependent on the junction's topology, and that the correct alignment of tertiary motifs may be a rare conformation on the overall folding landscape. Further characterization of RNA components and continued development of experimental and computational methods with the goal of quantitatively predicting RNA folding and functional behavior will be critical to understanding biological RNA systems.
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Affiliation(s)
- Daniel Herschlag
- Department of Biochemistry, Beckman Center, B400, 279 W. Campus Dr. MC: 5307, Stanford University, Stanford, CA 94305, USA; Department of Chemistry, 333 Campus Drive, Mudd Building, Room 121, Stanford University, Stanford, CA 94305, USA; Department of Chemical Engineering, 443 Via Ortega, Room 129, Stanford University, Stanford, CA 94305, USA.
| | - Benjamin E Allred
- Department of Biochemistry, Beckman Center, B400, 279 W. Campus Dr. MC: 5307, Stanford University, Stanford, CA 94305, USA
| | - Seshadri Gowrishankar
- Department of Chemical Engineering, 443 Via Ortega, Room 129, Stanford University, Stanford, CA 94305, USA
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28
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Dickson A, Mustoe AM, Salmon L, Brooks CL. Efficient in silico exploration of RNA interhelical conformations using Euler angles and WExplore. Nucleic Acids Res 2014; 42:12126-37. [PMID: 25294827 PMCID: PMC4231733 DOI: 10.1093/nar/gku799] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 08/04/2014] [Accepted: 08/25/2014] [Indexed: 12/20/2022] Open
Abstract
HIV-1 TAR RNA is a two-helix bulge motif that plays a critical role in HIV viral replication and is an important drug target. However, efforts at designing TAR inhibitors have been challenged by its high degree of structural flexibility, which includes slow large-amplitude reorientations of its helices with respect to one another. Here, we use the recently introduced algorithm WExplore in combination with Euler angles to achieve unprecedented sampling of the TAR conformational ensemble. Our ensemble achieves similar agreement with experimental NMR data when compared with previous TAR computational studies, and is generated at a fraction of the computational cost. It clearly emerges from configuration space network analysis that the intermittent formation of the A22-U40 base pair acts as a reversible switch that enables sampling of interhelical conformations that would otherwise be topologically disallowed. We find that most previously determined ligand-bound structures are found in similar location in the network, and we use a sample-and-select approach to guide the construction of a set of novel conformations which can serve as the basis for future drug development efforts. Collectively, our findings demonstrate the utility of WExplore in combination with suitable order parameters as a method for exploring RNA conformational space.
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Affiliation(s)
- Alex Dickson
- Department of Chemistry, University of Michigan, 930 N University, Ann Arbor, MI 48109, USA
| | - Anthony M Mustoe
- Department of Biophysics, University of Michigan, 930 N University, Ann Arbor, MI 48109, USA
| | - Loïc Salmon
- Department of Biophysics, University of Michigan, 930 N University, Ann Arbor, MI 48109, USA
| | - Charles L Brooks
- Department of Chemistry, University of Michigan, 930 N University, Ann Arbor, MI 48109, USA Department of Biophysics, University of Michigan, 930 N University, Ann Arbor, MI 48109, USA
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29
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Ravera E, Salmon L, Fragai M, Parigi G, Al-Hashimi H, Luchinat C. Insights into domain-domain motions in proteins and RNA from solution NMR. Acc Chem Res 2014; 47:3118-26. [PMID: 25148413 PMCID: PMC4204921 DOI: 10.1021/ar5002318] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Many multidomain proteins and ribonucleic acids consist of domains
that autonomously fold and that are linked together by flexible junctions.
This architectural design allows domains to sample a wide range of
positions with respect to one another, yet do so in a way that retains
structural specificity, since the number of sampled conformations
remains extremely small compared to the total conformations that would
be sampled if the domains were connected by an infinitely long linker.
This “tuned” flexibility in interdomain conformation
is in turn used in many biochemical processes. There is great
interest in characterizing the dynamic properties
of multidomain systems, and moving beyond conventional descriptions
in terms of static structures, toward the characterization of population-weighted
ensembles describing a distribution of many conformations sampled
in solution. There is also great interest in understanding the design
principles and underlying physical and chemical interactions that
specify the nature of interdomain flexibility. NMR spectroscopy is
one of the most powerful techniques for characterizing motions in
complex biomolecules and has contributed greatly toward our basic
understanding of dynamics in proteins and nucleic acids and its role
in folding, recognition, and signaling. Here, we review methods
that have been developed in our laboratories
to address these challenges. Our approaches are based on the ability
of one domain of the molecule to self-align in a magnetic field, or
to dominate the overall orientation of the molecule, so that the conformational
freedom of other domains can be assessed by their degree of alignment
induced by the aligned part. In turn, this self-alignment ability
can be intrinsic or can be caused by tagging appropriate constructs
to the molecule of interest. In general, self-alignment is due to
magnetic susceptibility anisotropy. Nucleic acids with elongated helices
have this feature, as well as several paramagnetic metal centers that
can be found in, or attached to, a protein domain.
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Affiliation(s)
- Enrico Ravera
- CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry “U. Schiff”, University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Loïc Salmon
- Department
of Biophysics, University of Michigan, 830 N. University, Ann Arbor, Michigan 48109, United States
| | - Marco Fragai
- CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry “U. Schiff”, University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Giacomo Parigi
- CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry “U. Schiff”, University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Hashim Al-Hashimi
- Department
of Biochemistry and Department of Chemistry, Duke University School of Medicine, 307 Research Drive, Durham, North Carolina 27710, United States
| | - Claudio Luchinat
- CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry “U. Schiff”, University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
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30
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Barros SA, Chenoweth DM. Recognition of nucleic acid junctions using triptycene-based molecules. Angew Chem Int Ed Engl 2014; 53:13746-50. [PMID: 25257803 DOI: 10.1002/anie.201407061] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 10/09/2014] [Indexed: 12/24/2022]
Abstract
The modulation of nucleic acids by small molecules is an essential process across the kingdoms of life. Targeting nucleic acids with small molecules represents a significant challenge at the forefront of chemical biology. Nucleic acid junctions are ubiquitous structural motifs in nature and in designed materials. Herein, we describe a new class of structure-specific nucleic acid junction stabilizers based on a triptycene scaffold. Triptycenes provide significant stabilization of DNA and RNA three-way junctions, providing a new scaffold for the development of nucleic acid junction binders with enhanced recognition properties. Additionally, we report cytotoxicity and cell uptake data in two human ovarian carcinoma cell lines.
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Affiliation(s)
- Stephanie A Barros
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104 (USA)
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31
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Barros SA, Chenoweth DM. Recognition of Nucleic Acid Junctions Using Triptycene-Based Molecules. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201407061] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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32
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Mustoe AM, Brooks CL, Al-Hashimi HM. Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity. Nucleic Acids Res 2014; 42:11792-804. [PMID: 25217593 PMCID: PMC4191394 DOI: 10.1093/nar/gku807] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Recent studies have shown that basic steric and connectivity constraints encoded at the secondary structure level are key determinants of 3D structure and dynamics in simple two-way RNA junctions. However, the role of these topological constraints in higher order RNA junctions remains poorly understood. Here, we use a specialized coarse-grained molecular dynamics model to directly probe the thermodynamic contributions of topological constraints in defining the 3D architecture and dynamics of transfer RNA (tRNA). Topological constraints alone restrict tRNA's allowed conformational space by over an order of magnitude and strongly discriminate against formation of non-native tertiary contacts, providing a sequence independent source of folding specificity. Topological constraints also give rise to long-range correlations between the relative orientation of tRNA's helices, which in turn provides a mechanism for encoding thermodynamic cooperativity between distinct tertiary interactions. These aspects of topological constraints make it such that only several tertiary interactions are needed to confine tRNA to its native global structure and specify functionally important 3D dynamics. We further show that topological constraints are conserved across tRNA's different naturally occurring secondary structures. Taken together, our results emphasize the central role of secondary-structure-encoded topological constraints in defining RNA 3D structure, dynamics and folding.
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Affiliation(s)
- Anthony M Mustoe
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Charles L Brooks
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Chemistry, Duke University School of Medicine, Durham, NC 27710, USA
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33
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Eichhorn CD, Al-Hashimi HM. Structural dynamics of a single-stranded RNA-helix junction using NMR. RNA (NEW YORK, N.Y.) 2014; 20:782-91. [PMID: 24742933 PMCID: PMC4024633 DOI: 10.1261/rna.043711.113] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Many regulatory RNAs contain long single strands (ssRNA) that adjoin secondary structural elements. Here, we use NMR spectroscopy to study the dynamic properties of a 12-nucleotide (nt) ssRNA tail derived from the prequeuosine riboswitch linked to the 3' end of a 48-nt hairpin. Analysis of chemical shifts, NOE connectivity, (13)C spin relaxation, and residual dipolar coupling data suggests that the first two residues (A25 and U26) in the ssRNA tail stack onto the adjacent helix and assume an ordered conformation. The following U26-A27 step marks the beginning of an A6-tract and forms an acute pivot point for substantial motions within the tail, which increase toward the terminal end. Despite substantial internal motions, the ssRNA tail adopts, on average, an A-form helical conformation that is coaxial with the helix. Our results reveal a surprising degree of structural and dynamic complexity at the ssRNA-helix junction, which involves a fine balance between order and disorder that may facilitate efficient pseudoknot formation on ligand recognition.
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Affiliation(s)
- Catherine D. Eichhorn
- Chemical Biology Doctoral Program, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Hashim M. Al-Hashimi
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
- Corresponding authorE-mail
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34
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Yang S, Salmon L, Al-Hashimi HM. Measuring similarity between dynamic ensembles of biomolecules. Nat Methods 2014; 11:552-4. [PMID: 24705474 PMCID: PMC4041546 DOI: 10.1038/nmeth.2921] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 03/04/2014] [Indexed: 12/31/2022]
Abstract
We present a simple and general approach termed REsemble for quantifying population overlap and structural similarity between ensembles. This approach captures improvements in the quality of ensembles determined using increasing input experimental data--improvements that go undetected when conventional methods for comparing ensembles are used--and reveals unexpected similarities between RNA ensembles determined using NMR and molecular dynamics simulations.
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Affiliation(s)
- Shan Yang
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Loïc Salmon
- Biophysics, University of Michigan, Ann Arbor, Michigan, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Chemistry, Duke University School of Medicine, Durham, North Carolina, USA
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35
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From a structural average to the conformational ensemble of a DNA bulge. Proc Natl Acad Sci U S A 2014; 111:E1473-80. [PMID: 24706812 DOI: 10.1073/pnas.1317032111] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Direct experimental measurements of conformational ensembles are critical for understanding macromolecular function, but traditional biophysical methods do not directly report the solution ensemble of a macromolecule. Small-angle X-ray scattering interferometry has the potential to overcome this limitation by providing the instantaneous distance distribution between pairs of gold-nanocrystal probes conjugated to a macromolecule in solution. Our X-ray interferometry experiments reveal an increasing bend angle of DNA duplexes with bulges of one, three, and five adenosine residues, consistent with previous FRET measurements, and further reveal an increasingly broad conformational ensemble with increasing bulge length. The distance distributions for the AAA bulge duplex (3A-DNA) with six different Au-Au pairs provide strong evidence against a simple elastic model in which fluctuations occur about a single conformational state. Instead, the measured distance distributions suggest a 3A-DNA ensemble with multiple conformational states predominantly across a region of conformational space with bend angles between 24 and 85 degrees and characteristic bend directions and helical twists and displacements. Additional X-ray interferometry experiments revealed perturbations to the ensemble from changes in ionic conditions and the bulge sequence, effects that can be understood in terms of electrostatic and stacking contributions to the ensemble and that demonstrate the sensitivity of X-ray interferometry. Combining X-ray interferometry ensemble data with molecular dynamics simulations gave atomic-level models of representative conformational states and of the molecular interactions that may shape the ensemble, and fluorescence measurements with 2-aminopurine-substituted 3A-DNA provided initial tests of these atomistic models. More generally, X-ray interferometry will provide powerful benchmarks for testing and developing computational methods.
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36
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Mustoe AM, Al-Hashimi HM, Brooks CL. Coarse grained models reveal essential contributions of topological constraints to the conformational free energy of RNA bulges. J Phys Chem B 2014; 118:2615-27. [PMID: 24547945 PMCID: PMC3983386 DOI: 10.1021/jp411478x] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
![]()
Recent studies have shown that simple
stereochemical constraints
encoded at the RNA secondary structure level significantly restrict
the orientation of RNA helices across two-way junctions and yield
physically reasonable distributions of RNA 3D conformations. Here
we develop a new coarse-grain model, TOPRNA, that is optimized for
exploring detailed aspects of these topological constraints in complex
RNA systems. Unlike prior models, TOPRNA effectively treats RNAs as
collections of semirigid helices linked by freely rotatable single
strands, allowing us to isolate the effects of secondary structure
connectivity and sterics on 3D structure. Simulations of bulge junctions
show that TOPRNA captures new aspects of topological constraints,
including variations arising from deviations in local A-form structure,
translational displacements of the helices, and stereochemical constraints
imposed by bulge-linker nucleotides. Notably, these aspects of topological
constraints define free energy landscapes that coincide with the distribution
of bulge conformations in the PDB. Our simulations also quantitatively
reproduce NMR RDC measurements made on HIV-1 TAR at low salt concentrations,
although not for different TAR mutants or at high salt concentrations.
Our results confirm that topological constraints are an important
determinant of bulge conformation and dynamics and demonstrate the
utility of TOPRNA for studying the topological constraints of complex
RNAs.
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Affiliation(s)
- Anthony M Mustoe
- Departments of Biophysics and ‡Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109, United States
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37
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Graph-based sampling for approximating global helical topologies of RNA. Proc Natl Acad Sci U S A 2014; 111:4079-84. [PMID: 24591615 DOI: 10.1073/pnas.1318893111] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A current challenge in RNA structure prediction is the description of global helical arrangements compatible with a given secondary structure. Here we address this problem by developing a hierarchical graph sampling/data mining approach to reduce conformational space and accelerate global sampling of candidate topologies. Starting from a 2D structure, we construct an initial graph from size measures deduced from solved RNAs and junction topologies predicted by our data-mining algorithm RNAJAG trained on known RNAs. We sample these graphs in 3D space guided by knowledge-based statistical potentials derived from bending and torsion measures of internal loops as well as radii of gyration for known RNAs. Graph sampling results for 30 representative RNAs are analyzed and compared with reference graphs from both solved structures and predicted structures by available programs. This comparison indicates promise for our graph-based sampling approach for characterizing global helical arrangements in large RNAs: graph rmsds range from 2.52 to 28.24 Å for RNAs of size 25-158 nucleotides, and more than half of our graph predictions improve upon other programs. The efficiency in graph sampling, however, implies an additional step of translating candidate graphs into atomic models. Such models can be built with the same idea of graph partitioning and build-up procedures we used for RNA design.
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38
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Dickson A, Brooks CL. WExplore: hierarchical exploration of high-dimensional spaces using the weighted ensemble algorithm. J Phys Chem B 2014; 118:3532-42. [PMID: 24490961 DOI: 10.1021/jp411479c] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
As most relevant motions in biomolecular systems are inaccessible to conventional molecular dynamics simulations, algorithms that enhance sampling of rare events are indispensable. Increasing interest in intrinsically disordered systems and the desire to target ensembles of protein conformations (rather than single structures) in drug development motivate the need for enhanced sampling algorithms that are not limited to "two-basin" problems, and can efficiently determine structural ensembles. For systems that are not well-studied, this must often be done with little or no information about the dynamics of interest. Here we present a novel strategy to determine structural ensembles that uses dynamically defined sampling regions that are organized in a hierarchical framework. It is based on the weighted ensemble algorithm, where an ensemble of copies of the system ("replicas") is directed to new regions of configuration space through merging and cloning operations. The sampling hierarchy allows for a large number of regions to be defined, while using only a small number of replicas that can be balanced over multiple length scales. We demonstrate this algorithm on two model systems that are analytically solvable and examine the 10-residue peptide chignolin in explicit solvent. The latter system is analyzed using a configuration space network, and novel hydrogen bonds are found that facilitate folding.
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Affiliation(s)
- Alex Dickson
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan, United States
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39
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Borkar AN, De Simone A, Montalvao RW, Vendruscolo M. A method of determining RNA conformational ensembles using structure-based calculations of residual dipolar couplings. J Chem Phys 2014; 138:215103. [PMID: 23758399 DOI: 10.1063/1.4804301] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
We describe a method of determining the conformational fluctuations of RNA based on the incorporation of nuclear magnetic resonance (NMR) residual dipolar couplings (RDCs) as replica-averaged structural restraints in molecular dynamics simulations. In this approach, the alignment tensor required to calculate the RDCs corresponding to a given conformation is estimated from its shape, and multiple replicas of the RNA molecule are simulated simultaneously to reproduce in silico the ensemble-averaging procedure performed in the NMR measurements. We provide initial evidence that with this approach it is possible to determine accurately structural ensembles representing the conformational fluctuations of RNA by applying the reference ensemble test to the trans-activation response element of the human immunodeficiency virus type 1.
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Affiliation(s)
- Aditi N Borkar
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
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40
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Abstract
Conformational changes in nucleic acids play a key role in the way genetic information is stored, transferred, and processed in living cells. Here, we describe new approaches that employ a broad range of experimental data, including NMR-derived chemical shifts and residual dipolar couplings, small-angle X-ray scattering, and computational approaches such as molecular dynamics simulations to determine ensembles of DNA and RNA at atomic resolution. We review the complementary information that can be obtained from diverse sets of data and the various methods that have been developed to combine these data with computational methods to construct ensembles and assess their uncertainty. We conclude by surveying RNA and DNA ensembles determined using these methods, highlighting the unique physical and functional insights obtained so far.
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Affiliation(s)
- Loïc Salmon
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109;
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41
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Kim N, Petingi L, Schlick T. Network Theory Tools for RNA Modeling. WSEAS TRANSACTIONS ON MATHEMATICS 2013; 9:941-955. [PMID: 25414570 PMCID: PMC4235620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
An introduction into the usage of graph or network theory tools for the study of RNA molecules is presented. By using vertices and edges to define RNA secondary structures as tree and dual graphs, we can enumerate, predict, and design RNA topologies. Graph connectivity and associated Laplacian eigenvalues relate to biological properties of RNA and help understand RNA motifs as well as build, by computational design, various RNA target structures. Importantly, graph theoretical representations of RNAs reduce drastically the conformational space size and therefore simplify modeling and prediction tasks. Ongoing challenges remain regarding general RNA design, representation of RNA pseudoknots, and tertiary structure prediction. Thus, developments in network theory may help advance RNA biology.
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Affiliation(s)
- Namhee Kim
- New York University Department of Chemistry Courant Institute of Mathematical Sciences 251 Mercer Street New York, NY 10012, USA
| | - Louis Petingi
- College of Staten Island City University of New York Department of Computer Science 2800 Victory Boulevard Staten Island, NY 10314, USA
| | - Tamar Schlick
- New York University Department of Chemistry Courant Institute of Mathematical Sciences 251 Mercer Street New York, NY 10012, USA
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Salmon L, Bascom G, Andricioaei I, Al-Hashimi HM. A general method for constructing atomic-resolution RNA ensembles using NMR residual dipolar couplings: the basis for interhelical motions revealed. J Am Chem Soc 2013; 135:5457-66. [PMID: 23473378 DOI: 10.1021/ja400920w] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ability to modulate alignment and measure multiple independent sets of NMR residual dipolar couplings (RDCs) has made it possible to characterize internal motions in proteins at atomic resolution and with time scale sensitivity ranging from picoseconds up to milliseconds. The application of such methods to the study of RNA dynamics, however, remains fundamentally limited by the inability to modulate alignment and by strong couplings between internal and overall motions that complicate the quantitative interpretation of RDCs. Here, we address this problem by showing that RNA alignment can be generally modulated, in a controlled manner, by variable elongation of A-form helices and that the information contained within the measured RDCs can be extracted even in the presence of strong couplings between motions and overall alignment via structure-based prediction of alignment. Using this approach, four RDC data sets, and a broad conformational pool obtained from a 8.2 μs molecular dynamics simulation, we successfully construct and validate an atomic resolution ensemble of human immunodeficiency virus type I transactivation response element RNA. This ensemble reveals local motions in and around the bulge involving changes in stacking and hydrogen-bonding interactions, which are undetectable by traditional spin relaxation and drive global changes in interhelical orientation. This new approach broadens the scope of using RDCs in characterizing the dynamics of nucleic acids.
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Affiliation(s)
- Loïc Salmon
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109, USA
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Mustoe AM, Bailor MH, Teixeira RM, Brooks CL, Al-Hashimi HM. New insights into the fundamental role of topological constraints as a determinant of two-way junction conformation. Nucleic Acids Res 2011; 40:892-904. [PMID: 21937512 PMCID: PMC3258142 DOI: 10.1093/nar/gkr751] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Recent studies have shown that topological constraints encoded at the RNA secondary structure level involving basic steric and stereochemical forces can significantly restrict the orientations sampled by helices across two-way RNA junctions. Here, we formulate these topological constraints in greater quantitative detail and use this topological framework to rationalize long-standing but poorly understood observations regarding the basic behavior of RNA two-way junctions. Notably, we show that the asymmetric nature of the A-form helix and the finite length of a bulge provide a physical basis for the experimentally observed directionality and bulge-length amplitude dependence of bulge induced inter-helical bends. We also find that the topologically allowed space can be modulated by variations in sequence, particularly with the addition of non-canonical GU base pairs at the junction, and, surprisingly, by the length of the 5′ and 3′ helices. A survey of two-way RNA junctions in the protein data bank confirms that junction residues have a strong preference to adopt looped-in, non-canonically base-paired conformations, providing a route for extending our bulge-directed framework to internal loop motifs and implying a simplified link between secondary and tertiary structure. Finally, our results uncover a new simple mechanism for coupling junction-induced topological constraints with tertiary interactions.
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Affiliation(s)
- Anthony M Mustoe
- Departments of Chemistry & Biophysics, The University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109-1055, USA
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