1
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Joshi A, Avni A, Walimbe A, Rai SK, Sarkar S, Mukhopadhyay S. Hydrogen-Bonded Network of Water in Phase-Separated Biomolecular Condensates. J Phys Chem Lett 2024; 15:7724-7734. [PMID: 39042834 DOI: 10.1021/acs.jpclett.4c01153] [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: 07/25/2024]
Abstract
Biomolecular condensates formed via phase separation of intrinsically disordered proteins/regions (IDPs/IDRs) and nucleic acids are associated with cell physiology and disease. Water makes up for ∼60-70% of the condensate volume and is thought to influence the complex interplay of chain-chain and chain-solvent interactions, modulating the mesoscale properties of condensates. The behavior of water in condensates and the key roles of protein hydration water in driving the phase separation remain elusive. Here, we employ single-droplet vibrational Raman spectroscopy to illuminate the structural redistribution within protein hydration water during the phase separation of neuronal IDPs. Our Raman measurements reveal the changes in the water hydrogen bonding network during homotypic and heterotypic phase separation governed by various molecular drivers. Such single-droplet water Raman measurements offer a potent generic tool to unmask the intriguing interplay of sequence-encoded chain-chain and chain-solvent interactions governing macromolecular phase separation into membraneless organelles, synthetic condensates, and protocells.
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2
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Marshall LK, Fahrenbach AC, Thordarson P. RNA-Binding Peptides Inspired by the RNA Recognition Motif. ACS Chem Biol 2024; 19:243-248. [PMID: 38314708 DOI: 10.1021/acschembio.3c00694] [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: 02/07/2024]
Abstract
β-Hairpin peptides with RNA-binding sequences mimicking the central two β-strands of the RNA recognition motif (RRM) protein domain have been observed to bind in a 2:1 fashion to a series of RNA homooligonucleotides in aqueous solution (PBS buffer, pH 7.40) with binding energies (-27 to -35 kJ mol-1) similar to those of full-size protein RRMs. The peptides display mild selectivities with respect to the binding of the different homooligomers. Binding studies in 500 mM magnesium chloride suggest that the complex formation is not predominantly driven by Coulombic attraction. These peptides represent a starting point for further studies of non-Coulombic binding of RNA by peptides and proteins, which is important in the context of contemporary biology, potential therapeutic applications, and prebiotic peptide-RNA interactions.
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3
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Zhao Y, Wang J, Chang F, Gong W, Liu Y, Li C. Identification of metal ion-binding sites in RNA structures using deep learning method. Brief Bioinform 2023; 24:7034467. [PMID: 36772993 DOI: 10.1093/bib/bbad049] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/21/2022] [Accepted: 01/24/2023] [Indexed: 02/12/2023] Open
Abstract
Metal ion is an indispensable factor for the proper folding, structural stability and functioning of RNA molecules. However, it is very difficult for experimental methods to detect them in RNAs. With the increase of experimentally resolved RNA structures, it becomes possible to identify the metal ion-binding sites in RNA structures through in-silico methods. Here, we propose an approach called Metal3DRNA to identify the binding sites of the most common metal ions (Mg2+, Na+ and K+) in RNA structures by using a three-dimensional convolutional neural network model. The negative samples, screened out based on the analysis for binding surroundings of metal ions, are more like positive ones than the randomly selected ones, which are beneficial to a powerful predictor construction. The microenvironments of the spatial distributions of C, O, N and P atoms around a sample are extracted as features. Metal3DRNA shows a promising prediction power, generally surpassing the state-of-the-art methods FEATURE and MetalionRNA. Finally, utilizing the visualization method, we inspect the contributions of nucleotide atoms to the classification in several cases, which provides a visualization that helps to comprehend the model. The method will be helpful for RNA structure prediction and dynamics simulation study. Availability and implementation: The source code is available at https://github.com/ChunhuaLiLab/Metal3DRNA.
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Affiliation(s)
- Yanpeng Zhao
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Jingjing Wang
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Fubin Chang
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Weikang Gong
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Yang Liu
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Chunhua Li
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
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4
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McGregor LA, Zhu B, Goetz AM, Sczepanski JT. Thymine DNA Glycosylase is an RNA-Binding Protein with High Selectivity for G-Rich Sequences. J Biol Chem 2023; 299:104590. [PMID: 36889585 PMCID: PMC10124917 DOI: 10.1016/j.jbc.2023.104590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/17/2023] [Accepted: 02/27/2023] [Indexed: 03/08/2023] Open
Abstract
Thymine DNA glycosylase (TDG) is a multifaceted enzyme involved in several critical biological pathways, including transcriptional activation, DNA demethylation, and DNA repair. Recent studies have established regulatory relationships between TDG and RNA, but the molecular interactions underlying these relationships is poorly understood. Herein, we now demonstrate that TDG binds directly to RNA with nanomolar affinity. Using synthetic oligonucleotides of defined length and sequence, we show that TDG has a strong preference for binding G-rich sequences in single-stranded RNA but binds weakly to single-stranded DNA and duplex RNA. TDG also binds tightly to endogenous RNA sequences. Studies with truncated proteins indicate that TDG binds RNA primarily through its structured catalytic domain and that its disordered C-terminal domain plays a key role in regulating TDG's affinity and selectivity for RNA. Finally, we show that RNA competes with DNA for binding to TDG, resulting in inhibition of TDG-mediated excision in the presence of RNA. Together, this work provides support for and insights into a mechanism wherein TDG-mediated processes (e.g., DNA demethylation) are regulated through the direct interactions of TDG with RNA.
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Affiliation(s)
- Lauren A McGregor
- Department of Chemistry, Texas A&M University, College Station, Texas, 77843, USA
| | - Baiyu Zhu
- Department of Chemistry, Texas A&M University, College Station, Texas, 77843, USA
| | - Allison M Goetz
- Department of Chemistry, Texas A&M University, College Station, Texas, 77843, USA
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5
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Cole CC, Misiura M, Hulgan SAH, Peterson CM, Williams JW, Kolomeisky AB, Hartgerink JD. Cation-π Interactions and Their Role in Assembling Collagen Triple Helices. Biomacromolecules 2022; 23:4645-4654. [PMID: 36239387 DOI: 10.1021/acs.biomac.2c00856] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cation-π interactions play a significant role in the stabilization of globular proteins. However, their role in collagen triple helices is less well understood and they have rarely been used in de novo designed collagen mimetic systems. In this study, we analyze the stabilizing and destabilizing effects in pairwise amino acid interactions between cationic and aromatic residues in both axial and lateral sequential relationships. Thermal unfolding experiments demonstrated that only axial pairs are stabilizing, while the lateral pairs are uniformly destabilizing. Molecular dynamics simulations show that pairs with an axial relationship can achieve a near-ideal interaction distance, but pairs in a lateral relationship do not. Arginine-π systems were found to be more stabilizing than lysine-π and histidine-π. Arginine-π interactions were then studied in more chemically diverse ABC-type heterotrimeric helices, where arginine-tyrosine pairs were found to form the best helix. This work helps elucidate the role of cation-π interactions in triple helices and illustrates their utility in designing collagen mimetic peptides.
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Affiliation(s)
- Carson C Cole
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Mikita Misiura
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Sarah A H Hulgan
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Caroline M Peterson
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Joseph W Williams
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Anatoly B Kolomeisky
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Jeffrey D Hartgerink
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States.,Department of Bioengineering, Rice University, 6100 Main Street, Houston, Texas 77005, United States
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6
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Michieletto D, Marenda M. Rheology and Viscoelasticity of Proteins and Nucleic Acids Condensates. JACS AU 2022; 2:1506-1521. [PMID: 35911447 PMCID: PMC9326828 DOI: 10.1021/jacsau.2c00055] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Phase separation is as familiar as watching vinegar separating from oil in vinaigrette. The observation that phase separation of proteins and nucleic acids is widespread in living cells has opened an entire field of research into the biological significance and the biophysical mechanisms of phase separation and protein condensation in biology. Recent evidence indicates that certain proteins and nucleic acids condensates are not simple liquids and instead display both viscous and elastic behaviors, which in turn may have biological significance. The aim of this Perspective is to review the state-of-the-art of this quickly emerging field focusing on the material and rheological properties of protein condensates. Finally, we discuss the different techniques that can be employed to quantify the viscoelasticity of condensates and highlight potential future directions and opportunities for interdisciplinary cross-talk between chemists, physicists, and biologists.
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Affiliation(s)
- Davide Michieletto
- School
of Physics and Astronomy, University of
Edinburgh, Peter Guthrie
Tait Road, Edinburgh EH9
3FD, U.K.
- MRC
Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, U.K.
| | - Mattia Marenda
- School
of Physics and Astronomy, University of
Edinburgh, Peter Guthrie
Tait Road, Edinburgh EH9
3FD, U.K.
- MRC
Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, U.K.
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7
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Mitra D, Das Mohapatra PK. In silico comparative structural and compositional analysis of glycoproteins of RSV to study the nature of stability and transmissibility of RSV A. SYSTEMS MICROBIOLOGY AND BIOMANUFACTURING 2022; 3:312-327. [PMID: 38013803 PMCID: PMC9135598 DOI: 10.1007/s43393-022-00110-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/07/2022] [Accepted: 05/08/2022] [Indexed: 11/29/2022]
Abstract
The current scenario of COVID-19 makes us to think about the devastating diseases that kill so many people every year. Analysis of viral proteins contributes many things that are utterly useful in the evolution of therapeutic drugs and vaccines. In this study, sequence and structure of fusion glycoproteins and major surface glycoproteins of respiratory syncytial virus (RSV) were analysed to reveal the stability and transmission rate. RSV A has the highest abundance of aromatic residues. The Kyte-Doolittle scale indicates the hydrophilic nature of RSV A protein which leads to the higher transmission rate of this virus. Intra-protein interactions such as carbonyl interactions, cation-pi, and salt bridges were shown to be greater in RSV A compared to RSV B, which might lead to improved stability. This study discovered the presence of a network aromatic-sulphur interaction in viral proteins. Analysis of ligand binding pocket of RSV proteins indicated that drugs are performing better on RSV B than RSV A. It was also shown that increasing the number of tunnels in RSV A proteins boosts catalytic activity. This study will be helpful in drug discovery and vaccine development.
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Affiliation(s)
- Debanjan Mitra
- Department of Microbiology, Raiganj University, Raiganj, WB India
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8
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Lichtinger SM, Garaizar A, Collepardo-Guevara R, Reinhardt A. Targeted modulation of protein liquid-liquid phase separation by evolution of amino-acid sequence. PLoS Comput Biol 2021; 17:e1009328. [PMID: 34428231 PMCID: PMC8415608 DOI: 10.1371/journal.pcbi.1009328] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 09/03/2021] [Accepted: 08/07/2021] [Indexed: 12/27/2022] Open
Abstract
Rationally and efficiently modifying the amino-acid sequence of proteins to control their ability to undergo liquid-liquid phase separation (LLPS) on demand is not only highly desirable, but can also help to elucidate which protein features are important for LLPS. Here, we propose a computational method that couples a genetic algorithm to a sequence-dependent coarse-grained protein model to evolve the amino-acid sequences of phase-separating intrinsically disordered protein regions (IDRs), and purposely enhance or inhibit their capacity to phase-separate. We validate the predicted critical solution temperatures of the mutated sequences with ABSINTH, a more accurate all-atom model. We apply the algorithm to the phase-separating IDRs of three naturally occurring proteins, namely FUS, hnRNPA1 and LAF1, as prototypes of regions that exist in cells and undergo homotypic LLPS driven by different types of intermolecular interaction, and we find that the evolution of amino-acid sequences towards enhanced LLPS is driven in these three cases, among other factors, by an increase in the average size of the amino acids. However, the direction of change in the molecular driving forces that enhance LLPS (such as hydrophobicity, aromaticity and charge) depends on the initial amino-acid sequence. Finally, we show that the evolution of amino-acid sequences to modulate LLPS is strongly coupled to the make-up of the medium (e.g. the presence or absence of RNA), which may have significant implications for our understanding of phase separation within the many-component mixtures of biological systems.
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Affiliation(s)
- Simon M. Lichtinger
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Adiran Garaizar
- Department of Physics, Cavendish Laboratory, Maxwell Centre, University of Cambridge, Cambridge, United Kingdom
| | - Rosana Collepardo-Guevara
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Physics, Cavendish Laboratory, Maxwell Centre, University of Cambridge, Cambridge, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Aleks Reinhardt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
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9
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Alshareedah I, Kaur T, Ngo J, Seppala H, Kounatse LAD, Wang W, Moosa MM, Banerjee PR. Interplay between Short-Range Attraction and Long-Range Repulsion Controls Reentrant Liquid Condensation of Ribonucleoprotein-RNA Complexes. J Am Chem Soc 2019; 141:14593-14602. [PMID: 31437398 DOI: 10.1021/jacs.9b03689] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In eukaryotic cells, ribonucleoproteins (RNPs) form mesoscale condensates by liquid-liquid phase separation that play essential roles in subcellular dynamic compartmentalization. The formation and dissolution of many RNP condensates are finely dependent on the RNA-to-RNP ratio, giving rise to a windowlike phase separation behavior. This is commonly referred to as reentrant liquid condensation (RLC). Here, using ribonucleoprotein-inspired polypeptides with low-complexity RNA-binding sequences as well as an archetypal disordered RNP, fused in sarcoma, as model systems, we investigate the molecular driving forces underlying this nonmonotonous phase transition. We show that an interplay between short-range cation-π attractions and long-range electrostatic forces governs the heterotypic RLC behavior of RNP-RNA complexes. Short-range attractions, which can be encoded by both polypeptide chain primary sequence and nucleic acid base sequence, control the two-phase coexistence regime, regulate material properties of polypeptide-RNA condensates, and oppose condensate reentrant dissolution. In the presence of excess RNA, a competition between short-range attraction and long-range electrostatic repulsion drives the formation of a colloidlike cluster phase. With increasing short-range attraction, the fluid dynamics of the cluster phase is arrested, leading to the formation of a colloidal gel. Our results reveal that phase behavior, supramolecular organization, and material states of RNP-RNA assemblies are controlled by a dynamic interplay between molecular interactions at different length scales.
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Affiliation(s)
- Ibraheem Alshareedah
- Department of Physics , University at Buffalo , Buffalo , New York 14260 , United States
| | - Taranpreet Kaur
- Department of Physics , University at Buffalo , Buffalo , New York 14260 , United States
| | - Jason Ngo
- Department of Physics , University at Buffalo , Buffalo , New York 14260 , United States
| | - Hannah Seppala
- Department of Physics , University at Buffalo , Buffalo , New York 14260 , United States
| | | | - Wei Wang
- Department of Physics , University at Buffalo , Buffalo , New York 14260 , United States
| | - Mahdi Muhammad Moosa
- Department of Physics , University at Buffalo , Buffalo , New York 14260 , United States
| | - Priya R Banerjee
- Department of Physics , University at Buffalo , Buffalo , New York 14260 , United States
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10
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Hosseini M, Roy P, Sissler M, Zirbel CL, Westhof E, Leontis N. How to fold and protect mitochondrial ribosomal RNA with fewer guanines. Nucleic Acids Res 2019; 46:10946-10968. [PMID: 30215760 PMCID: PMC6237812 DOI: 10.1093/nar/gky762] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 09/06/2018] [Indexed: 01/25/2023] Open
Abstract
Mammalian mitochondrial ribosomes evolved from bacterial ribosomes by reduction of ribosomal RNAs, increase of ribosomal protein content, and loss of guanine nucleotides. Guanine is the base most sensitive to oxidative damage. By systematically comparing high-quality, small ribosomal subunit RNA sequence alignments and solved 3D ribosome structures from mammalian mitochondria and bacteria, we deduce rules for folding a complex RNA with the remaining guanines shielded from solvent. Almost all conserved guanines in both bacterial and mammalian mitochondrial ribosomal RNA form guanine-specific, local or long-range, RNA–RNA or RNA–protein interactions. Many solvent-exposed guanines conserved in bacteria are replaced in mammalian mitochondria by bases less sensitive to oxidation. New guanines, conserved only in the mitochondrial alignment, are strategically positioned at solvent inaccessible sites to stabilize the ribosomal RNA structure. New mitochondrial proteins substitute for truncated RNA helices, maintain mutual spatial orientations of helices, compensate for lost RNA–RNA interactions, reduce solvent accessibility of bases, and replace guanines conserved in bacteria by forming specific amino acid–RNA interactions.
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Affiliation(s)
- Maryam Hosseini
- Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Poorna Roy
- Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Marie Sissler
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg France
| | - Craig L Zirbel
- Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Eric Westhof
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg France
| | - Neocles Leontis
- Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA
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11
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Retureau R, Oguey C, Mauffret O, Hartmann B. Structural Explorations of NCp7-Nucleic Acid Complexes Give Keys to Decipher the Binding Process. J Mol Biol 2019; 431:1966-1980. [PMID: 30876916 DOI: 10.1016/j.jmb.2019.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/25/2019] [Accepted: 03/02/2019] [Indexed: 02/06/2023]
Abstract
A comprehensive view of all the structural aspects related to NCp7 is essential to understand how this protein, crucial in many steps of the HIV-1 cycle, binds and anneals nucleic acids (NAs), mainly thanks to two zinc fingers, ZF1 and ZF2. Here, we inspected the structural properties of the available experimental models of NCp7 bound to either DNA or RNA molecules, or free of ligand. Our analyses included the characterization of the relative positioning of ZF1 and ZF2, accessibility measurements and the exhaustive, quantitative mapping of the contacts between amino acids and nucleotides by a recent tessellation method, VLDM. This approach unveiled the intimate connection between NA binding process and the conformations explored by the free protein. It also provided new insights into the functional specializations of ZF1 and ZF2. The larger accessibility of ZF2 in free NCp7 and the consistency of the ZF2/NA interface in different models and conditions give ZF2 the lead of the binding process. ZF1 contributes to stabilize the complexes through various organizations of the ZF1/NA interface. This work outcome is a global binding scheme of NCp7 to DNA and RNA, and an example of how protein-NA complexes are stabilized.
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Affiliation(s)
- Romain Retureau
- LBPA, UMR 8113, ENS Paris-Saclay-CNRS, 61 avenue du Président Wilson, 94235 Cachan cedex, France
| | - Christophe Oguey
- LPTM, CNRS UMR 8089, Université de Cergy-Pontoise, 2 avenue Adolphe Chauvin, 95031 Cergy-Pontoise, France
| | - Olivier Mauffret
- LBPA, UMR 8113, ENS Paris-Saclay-CNRS, 61 avenue du Président Wilson, 94235 Cachan cedex, France.
| | - Brigitte Hartmann
- LBPA, UMR 8113, ENS Paris-Saclay-CNRS, 61 avenue du Président Wilson, 94235 Cachan cedex, France.
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12
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Zhao YY, Mao MW, Zhang WJ, Wang J, Li HT, Yang Y, Wang Z, Wu JW. Expanding RNA binding specificity and affinity of engineered PUF domains. Nucleic Acids Res 2018; 46:4771-4782. [PMID: 29490074 PMCID: PMC5961129 DOI: 10.1093/nar/gky134] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 02/08/2018] [Accepted: 02/16/2018] [Indexed: 12/26/2022] Open
Abstract
Specific manipulation of RNA is necessary for the research in biotechnology and medicine. The RNA-binding domains of Pumilio/fem-3 mRNA binding factors (PUF domains) are programmable RNA binding scaffolds used to engineer artificial proteins that specifically modulate RNAs. However, the native PUF domains generally recognize 8-nt RNAs, limiting their applications. Here, we modify the PUF domain of human Pumilio1 to engineer PUFs that recognize RNA targets of different length. The engineered PUFs bind to their RNA targets specifically and PUFs with more repeats have higher binding affinity than the canonical eight-repeat domains; however, the binding affinity reaches the peak at those with 9 and 10 repeats. Structural analysis on PUF with nine repeats reveals a higher degree of curvature, and the RNA binding unexpectedly and dramatically opens the curved structure. Investigation of the residues positioned in between two RNA bases demonstrates that tyrosine and arginine have favored stacking interactions. Further tests on the availability of the engineered PUFs in vitro and in splicing function assays indicate that our engineered PUFs bind RNA targets with high affinity in a programmable way.
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Affiliation(s)
- Yang-Yang Zhao
- Center for Life Sciences, Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Miao-Wei Mao
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biological Science, Shanghai 200031, China
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Wen-Jing Zhang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning 116044, China
| | - Jue Wang
- Institute of Molecular Enzymology, Soochow University, Suzhou, Jiangsu 215123, China
| | - Hai-Tao Li
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yi Yang
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zefeng Wang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biological Science, Shanghai 200031, China
- Enzerna Biosciences, Inc., 125 South Road, 925B Kenan Labs, CB#3266, Chapel Hill, NC 27599, USA
| | - Jia-Wei Wu
- Center for Life Sciences, Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute of Molecular Enzymology, Soochow University, Suzhou, Jiangsu 215123, China
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13
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Reiss CW, Strobel SA. Structural basis for ligand binding to the guanidine-II riboswitch. RNA (NEW YORK, N.Y.) 2017; 23:1338-1343. [PMID: 28600356 PMCID: PMC5558903 DOI: 10.1261/rna.061804.117] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 05/22/2017] [Indexed: 05/04/2023]
Abstract
The guanidine-II riboswitch, also known as mini-ykkC, is a conserved mRNA element with more than 800 examples in bacteria. It consists of two stem-loops capped by identical, conserved tetraloops that are separated by a linker region of variable length and sequence. Like the guanidine-I riboswitch, it controls the expression of guanidine carboxylases and SugE-like genes. The guanidine-II riboswitch specifically binds free guanidinium cations and functions as a translationally controlled on-switch. Here we report the structure of a P2 stem-loop from the Pseudomonas aeruginosa guanidine-II riboswitch aptamer bound to guanidine at 1.57 Å resolution. The hairpins dimerize via the conserved tetraloop, which also contains the binding pocket. Two guanidinium molecules bind near the dimerization interface, one in each tetraloop. The guanidinium cation is engaged in extensive hydrogen bonding to the RNA. Contacts include the Hoogsteen face of a guanine base and three nonbridging phosphate oxygens. Cation-π interactions and ionic interactions also stabilize ligand binding. The guanidine-II riboswitch utilizes the same recognition strategies as the guanidine-I riboswitch while adopting an entirely different and much smaller RNA fold.
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Affiliation(s)
- Caroline W Reiss
- Department of Molecular Biophysics and Biochemistry, Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Scott A Strobel
- Department of Molecular Biophysics and Biochemistry, Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, USA
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14
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Frankel EA, Strulson CA, Keating CD, Bevilacqua PC. Cooperative Interactions in the Hammerhead Ribozyme Drive pK a Shifting of G12 and Its Stacked Base C17. Biochemistry 2017; 56:2537-2548. [PMID: 28485924 DOI: 10.1021/acs.biochem.7b00174] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
General acid-base catalysis is a key mechanistic strategy in protein and RNA enzymes. Ribozymes use hydrated metal ions, nucleobases, and organic cofactors to carry this out. In most small ribozymes, a guanosine is positioned to participate in proton transfer with the nucleophilic 2'-OH. The unshifted pKa values for nucleobases and solvated metal ions are far from neutrality, however, and thus nonideal for general acid-base catalysis. Herein, evidence is provided for cooperative interaction in the hammerhead ribozyme among the guanine that interacts with the nucleophilic 2'-OH, G12, the -1 nucleobase C17, and Mg2+ ions. We introduce global fitting for analyzing ribozyme rate-pH data parametric in Mg2+ concentration and benchmark this method on data from the hepatitis delta virus ribozyme. We then apply global fitting to new rate-pH data for the hammerhead ribozyme using a minimal three-dimensional, four-channel cooperative model. The value for the pKa of G12 that we obtain is channel-dependent and varies from 8.1 to 9.9, shifting closest toward neutrality in the presence of two cationic species: C17H+ and a Mg2+ ion. The value for the pKa of the -1 nucleotide, C17, is increased a remarkable 3.5-5 pKa units toward neutrality. Shifting of the pKa of C17 appears to be driven by an electrostatic sandwich of C17 between carbonyl groups of the 5'-neighboring U and of G12 and involves cation-π interactions. Rate-pH profiles reveal that the major reactive channel under biological Mg2+ and pH involves a cationic C17 rather than a second metal ion. Substitution of a cationic base for a metal underscores the versatility of RNA.
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Affiliation(s)
- Erica A Frankel
- Department of Chemistry, Pennsylvania State University , University Park, Pennsylvania 16802, United States.,Center for RNA Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Christopher A Strulson
- Department of Chemistry, Pennsylvania State University , University Park, Pennsylvania 16802, United States.,Center for RNA Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Christine D Keating
- Department of Chemistry, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Philip C Bevilacqua
- Department of Chemistry, Pennsylvania State University , University Park, Pennsylvania 16802, United States.,Center for RNA Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States.,Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States
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Reiss CW, Xiong Y, Strobel SA. Structural Basis for Ligand Binding to the Guanidine-I Riboswitch. Structure 2016; 25:195-202. [PMID: 28017522 DOI: 10.1016/j.str.2016.11.020] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/11/2016] [Accepted: 11/28/2016] [Indexed: 12/15/2022]
Abstract
The guanidine-I riboswitch is a conserved RNA element with approximately 2,000 known examples across four phyla of bacteria. It exists upstream of nitrogen metabolism and multidrug resistance transporter genes and alters expression through the specific recognition of a free guanidinium cation. Here we report the structure of a guanidine riboswitch aptamer from Sulfobacillus acidophilus at 2.7 Å resolution. Helices P1, P1a, P1b, and P2 form a coaxial stack that acts as a scaffold for ligand binding. A previously unidentified P3 helix docks into P1a to form the guanidinium binding pocket, which is completely enclosed. Every functional group of the ligand is recognized through hydrogen bonding to guanine bases and phosphate oxygens. Guanidinium binding is further stabilized through cation-π interactions with guanine bases. This allows the riboswitch to recognize guanidinium while excluding other bacterial metabolites with a guanidino group, including the amino acid arginine.
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Affiliation(s)
- Caroline W Reiss
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Yong Xiong
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Scott A Strobel
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA.
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