1
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Mousivand M, Bagherzadeh K, Anfossi L, Javan-Nikkhah M. Key criteria for engineering mycotoxin binding aptamers via computational simulations: Aflatoxin B1 as a case study. Biotechnol J 2021; 17:e2100280. [PMID: 34800084 DOI: 10.1002/biot.202100280] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 11/16/2021] [Accepted: 11/16/2021] [Indexed: 12/30/2022]
Abstract
Due to the difficulties in monoclonal antibody production specific to mycotoxins, aptameric probes have been considered as suitable alternatives. The low efficiency of the SELEX procedure in screening high affinity aptamers for binding mycotoxins as small molecules can be significantly improved through computational techniques. Previously, we designed five new aptamers to aflatoxin B1 (AFB1) based on a known aptamer sequence (Patent: PCT/CA2010/001 292, Apt1) through a genetic algorithm-based in silico maturation strategy and experimentally measured their affinity to the target toxin. Here, integrated molecular dynamic simulation (MDs) studies with molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) analysis to clarify the binding modes, critical interacting nucleic bases and energy component contributions in the six AFB1-binding aptamers. The aptamer F20, which was selected in the first work, showed the best free binding energy and complex stability compared to other aptamers. The trajectory analysis revealed that AFB1 recognized F20 through the groove binding mode along with precise shape complementarity. The MD simulation results revealed that dynamic water intermediate interactions also play a key role in promoting complex stability. According to the MM-PBSA calculations, van der Waals contacts were identified as dominant energy components in all complexes. Interestingly, a high consistency is observed between the experimentally obtained binding affinities of the six aptamers with their free energy solvation. The computational findings, confirmed via previous experiments, highlighted the binding modes, the dynamic hydration of complex components and the total free interacting energy as the crucial criteria in discovering high functional aptameric probes.
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Affiliation(s)
- Maryam Mousivand
- Microbial Biotechnology Department, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization, Department of Plant Protection, College of Agricultural Sciences and Engineering, University of Tehran, Karaj, Iran
| | - Kowsar Bagherzadeh
- Stem Cell and Regenerative Medicine Research Center, Iran University of Medical Sciences, Eye Research Center, the Five Senses Health Institute, Rassoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Laura Anfossi
- Department of Chemistry, University of Turin, Department of Plant Protection, College of Agricultural Sciences and Engineering, University of Tehran, Turin, Italy
| | - Mohammad Javan-Nikkhah
- Microbial Biotechnology Department, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization, Department of Plant Protection, College of Agricultural Sciences and Engineering, University of Tehran, Karaj, Iran
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2
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Du C, Wang Y, Gong S. Regulation of the ThiM riboswitch is facilitated by the trapped structure formed during transcription of the wild-type sequence. FEBS Lett 2021; 595:2816-2828. [PMID: 34644399 DOI: 10.1002/1873-3468.14202] [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: 06/18/2021] [Revised: 09/17/2021] [Accepted: 09/20/2021] [Indexed: 11/09/2022]
Abstract
The ThiM riboswitch from Escherichia coli is a typical mRNA device that modulates downstream gene expression by sensing TPP. The helix-based RNA folding theory is used to investigate its detailed regulatory behaviors in cells. This RNA molecule is transcriptionally trapped in a state with the unstructured SD sequence in the absence of TPP, which induces downstream gene expression. As a key step to turn on gene expression, formation of this trapped state (the genetic ON state) highly depends on the co-transcriptional folding of its wild-type sequence. Instead of stabilities of the genetic ON and OFF states, the transcription rate, pause, and ligand levels are combined to affect the ThiM riboswitch-mediated gene regulation, which is consistent with a kinetic control model.
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Affiliation(s)
- Chengyi Du
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, China
| | - Yujie Wang
- Department of Physics and Telecommunication Engineering, Zhoukou Normal University, China
| | - Sha Gong
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, China
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3
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Omar SI, Zhao M, Sekar RV, Moghadam SA, Tuszynski JA, Woodside MT. Modeling the structure of the frameshift-stimulatory pseudoknot in SARS-CoV-2 reveals multiple possible conformers. PLoS Comput Biol 2021; 17:e1008603. [PMID: 33465066 PMCID: PMC7845960 DOI: 10.1371/journal.pcbi.1008603] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 01/29/2021] [Accepted: 12/02/2020] [Indexed: 01/26/2023] Open
Abstract
The coronavirus causing the COVID-19 pandemic, SARS-CoV-2, uses -1 programmed ribosomal frameshifting (-1 PRF) to control the relative expression of viral proteins. As modulating -1 PRF can inhibit viral replication, the RNA pseudoknot stimulating -1 PRF may be a fruitful target for therapeutics treating COVID-19. We modeled the unusual 3-stem structure of the stimulatory pseudoknot of SARS-CoV-2 computationally, using multiple blind structural prediction tools followed by μs-long molecular dynamics simulations. The results were compared for consistency with nuclease-protection assays and single-molecule force spectroscopy measurements of the SARS-CoV-1 pseudoknot, to determine the most likely conformations. We found several possible conformations for the SARS-CoV-2 pseudoknot, all having an extended stem 3 but with different packing of stems 1 and 2. Several conformations featured rarely-seen threading of a single strand through junctions formed between two helices. These structural models may help interpret future experiments and support efforts to discover ligands inhibiting -1 PRF in SARS-CoV-2.
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Affiliation(s)
- Sara Ibrahim Omar
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Meng Zhao
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | | | | | - Jack A. Tuszynski
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
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4
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Duan Q, Tao P, Wang J, Xiao Y. Molecular dynamics study of ways of RNA base-pair formation. Phys Rev E 2020; 102:032403. [PMID: 33076020 DOI: 10.1103/physreve.102.032403] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 08/21/2020] [Indexed: 06/11/2023]
Abstract
Base pairing is a fundamental phenomenon in RNA structure and function. However, although there have been considerable recent advances, some important aspects of base-pair formation are still unknown, including the ways of base-pair formation and detailed roles of metal ions. Here we show that base pairs can form through four different ways: stabilizing, bridging, rotating, and shifting. Among them the stabilizing and bridging ways involve direct binding of metal ions while the rotating and shifting ways do not in most cases. Furthermore, we find that the formations of base pairs in different positions of the hairpin stem may adopt different ways.
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Affiliation(s)
- Qiangqiang Duan
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Peng Tao
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Jun Wang
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Yi Xiao
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
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5
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Chakraborty D, Wales DJ. Dynamics of an adenine-adenine RNA conformational switch from discrete path sampling. J Chem Phys 2019; 150:125101. [DOI: 10.1063/1.5070152] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, USA
| | - David J. Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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6
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Yang L, Zhong Z, Tong C, Jia H, Liu Y, Chen G. Single-Molecule Mechanical Folding and Unfolding of RNA Hairpins: Effects of Single A-U to A·C Pair Substitutions and Single Proton Binding and Implications for mRNA Structure-Induced -1 Ribosomal Frameshifting. J Am Chem Soc 2018; 140:8172-8184. [PMID: 29884019 DOI: 10.1021/jacs.8b02970] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A wobble A·C pair can be protonated at near physiological pH to form a more stable wobble A+·C pair. Here, we constructed an RNA hairpin (rHP) and three mutants with one A-U base pair substituted with an A·C mismatch on the top (near the loop, U22C), middle (U25C), and bottom (U29C) positions of the stem, respectively. Our results on single-molecule mechanical (un)folding using optical tweezers reveal the destabilization effect of A-U to A·C pair substitution and protonation-dependent enhancement of mechanical stability facilitated through an increased folding rate, or decreased unfolding rate, or both. Our data show that protonation may occur rapidly upon the formation of an apparent mechanical folding transition state. Furthermore, we measured the bulk -1 ribosomal frameshifting efficiencies of the hairpins by a cell-free translation assay. For the mRNA hairpins studied, -1 frameshifting efficiency correlates with mechanical unfolding force at equilibrium and folding rate at around 15 pN. U29C has a frameshifting efficiency similar to that of rHP (∼2%). Accordingly, the bottom 2-4 base pairs of U29C may not form under a stretching force at pH 7.3, which is consistent with the fact that the bottom base pairs of the hairpins may be disrupted by ribosome at the slippery site. U22C and U25C have a similar frameshifting efficiency (∼1%), indicating that both unfolding and folding rates of an mRNA hairpin in a crowded environment may affect frameshifting. Our data indicate that mechanical (un)folding of RNA hairpins may mimic how mRNAs unfold and fold in the presence of translating ribosomes.
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Affiliation(s)
- Lixia Yang
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Zhensheng Zhong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371.,School of Physics, and State Key Laboratory of Optoelectronic Materials and Technologies , Sun Yat-sen University , Guangzhou 510275 , People's Republic of China
| | - Cailing Tong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Huan Jia
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Yiran Liu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
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7
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Q Nguyen KK, Gomez YK, Bakhom M, Radcliffe A, La P, Rochelle D, Lee JW, Sorin EJ. Ensemble simulations: folding, unfolding and misfolding of a high-efficiency frameshifting RNA pseudoknot. Nucleic Acids Res 2017; 45:4893-4904. [PMID: 28115636 PMCID: PMC5416846 DOI: 10.1093/nar/gkx012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 01/11/2017] [Indexed: 12/11/2022] Open
Abstract
Massive all-atom molecular dynamics simulations were conducted across a distributed computing network to study the folding, unfolding, misfolding and conformational plasticity of the high-efficiency frameshifting double mutant of the 26 nt potato leaf roll virus RNA pseudoknot. Our robust sampling, which included over 40 starting structures spanning the spectrum from the extended unfolded state to the native fold, yielded nearly 120 μs of cumulative sampling time. Conformational microstate transitions on the 1.0 ns to 10.0 μs timescales were observed, with post-equilibration sampling providing detailed representations of the conformational free energy landscape and the complex folding mechanism inherent to the pseudoknot motif. Herein, we identify and characterize two alternative native structures, three intermediate states, and numerous misfolded states, the latter of which have not previously been characterized via atomistic simulation techniques. While in line with previous thermodynamics-based models of a general RNA folding mechanism, our observations indicate that stem-strand-sequence-separation may serve as an alternative predictor of the order of stem formation during pseudoknot folding. Our results contradict a model of frameshifting based on structural rigidity and resistance to mechanical unfolding, and instead strongly support more recent studies in which conformational plasticity is identified as a determining factor in frameshifting efficiency.
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Affiliation(s)
- Khai K Q Nguyen
- Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA 90840, USA.,Department of Computer Engineering & Computer Science, California State University Long Beach, Long Beach, CA 90840, USA
| | - Yessica K Gomez
- Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA 90840, USA.,Department of Physics & Astronomy, California State University Long Beach, Long Beach, CA 90840, USA
| | - Mona Bakhom
- Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA 90840, USA
| | - Amethyst Radcliffe
- Department of Physics & Astronomy, California State University Long Beach, Long Beach, CA 90840, USA
| | - Phuc La
- Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA 90840, USA
| | - Dakota Rochelle
- Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA 90840, USA
| | - Ji Won Lee
- Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA 90840, USA
| | - Eric J Sorin
- Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA 90840, USA
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8
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Suresh G, Srinivasan H, Nanda S, Priyakumar UD. Ligand-Induced Stabilization of a Duplex-like Architecture Is Crucial for the Switching Mechanism of the SAM-III Riboswitch. Biochemistry 2016; 55:3349-60. [PMID: 27249101 DOI: 10.1021/acs.biochem.5b00973] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Riboswitches are structured RNA motifs that control gene expression by sensing the concentrations of specific metabolites and make up a promising new class of antibiotic targets. S-Adenosylmethionine (SAM)-III riboswitch, mainly found in lactic acid bacteria, is involved in regulating methionine and SAM biosynthetic pathways. SAM-III riboswitch regulates the gene expression by switching the translation process on and off with respect to the absence and presence of the SAM ligand, respectively. In this study, an attempt is made to understand the key conformational transitions involved in ligand binding using atomistic molecular dynamics (MD) simulations performed in an explicit solvent environment. G26 is found to recognize the SAM ligand by forming hydrogen bonds, whereas the absence of the ligand leads to opening of the binding pocket. Consistent with experimental results, the absence of the SAM ligand weakens the base pairing interactions between the nucleobases that are part of the Shine-Dalgarno (SD) and anti-Shine-Dalgarno (aSD) sequences, which in turn facilitates recognition of the SD sequence by ribosomes. Detailed analysis reveals that a duplex-like structure formed by nucleotides from different parts of the RNA and the adenine base of the ligand is crucial for the stability of the completely folded state in the presence of the ligand. Previous experimental studies have shown that the SAM-III riboswitch exists in equilibrium between the unfolded and partially folded states in the absence of the ligand, which completely folds upon binding of the ligand. Comparison of the results presented here to the available experimental data indicates the structures obtained using the MD simulations resemble the partially folded state. Thus, this study provides a detailed understanding of the fully and partially folded structures of the SAM-III riboswitch in the presence and absence of the ligand, respectively. This study hypothesizes a dual role for the SAM ligand, which facilitates conformational switching between partially and fully folded states by forming a stable duplex-like structure and strengthening the interactions between SD and aSD nucleotides.
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Affiliation(s)
- Gorle Suresh
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology , Hyderabad 500 032, India
| | - Harini Srinivasan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology , Hyderabad 500 032, India
| | - Shivani Nanda
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology , Hyderabad 500 032, India
| | - U Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology , Hyderabad 500 032, India
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9
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Santamaría-Holek I, López-Alamilla NJ, Hidalgo-Soria M, Pérez-Madrid A. Nonlinear irreversible thermodynamics of single-molecule experiments. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:062714. [PMID: 26172743 DOI: 10.1103/physreve.91.062714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Indexed: 06/04/2023]
Abstract
Irreversible thermodynamics of single-molecule experiments subject to external constraining forces of a mechanical nature is presented. Extending Onsager's formalism to the nonlinear case of systems under nonequilibrium external constraints, we are able to calculate the entropy production and the general nonlinear kinetic equations for the variables involved. In particular, we analyze the case of RNA stretching protocols obtaining critical oscillations between different configurational states when forced by external means to remain in the unstable region of its free-energy landscape, as observed in experiments. We also calculate the entropy produced during these hopping events and show how resonant phenomena in stretching experiments of single RNA macromolecules may arise. We also calculate the hopping rates using Kramer's approach obtaining a good comparison with experiments.
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Affiliation(s)
- I Santamaría-Holek
- UMDI-Facultad de Ciencias, Universidad Nacional Autónoma de México Campus Juriquilla, Querétaro 76230, México
| | - N J López-Alamilla
- UMDI-Facultad de Ciencias, Universidad Nacional Autónoma de México Campus Juriquilla, Querétaro 76230, México
| | - M Hidalgo-Soria
- UMDI-Facultad de Ciencias, Universidad Nacional Autónoma de México Campus Juriquilla, Querétaro 76230, México
| | - A Pérez-Madrid
- Departament de Física Fonamental, Facultat de Física, Universitat de Barcelona, Marti i Franques, 08028 Barcelona, Spain
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10
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Chakraborty D, Collepardo-Guevara R, Wales DJ. Energy Landscapes, Folding Mechanisms, and Kinetics of RNA Tetraloop Hairpins. J Am Chem Soc 2014; 136:18052-61. [DOI: 10.1021/ja5100756] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Debayan Chakraborty
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | | | - David J. Wales
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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11
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Abstract
Folding may be described conceptually in terms of trajectories over a landscape of free energies corresponding to different molecular configurations. In practice, energy landscapes can be difficult to measure. Single-molecule force spectroscopy (SMFS), whereby structural changes are monitored in molecules subjected to controlled forces, has emerged as a powerful tool for probing energy landscapes. We summarize methods for reconstructing landscapes from force spectroscopy measurements under both equilibrium and nonequilibrium conditions. Other complementary, but technically less demanding, methods provide a model-dependent characterization of key features of the landscape. Once reconstructed, energy landscapes can be used to study critical folding parameters, such as the characteristic transition times required for structural changes and the effective diffusion coefficient setting the timescale for motions over the landscape. We also discuss issues that complicate measurement and interpretation, including the possibility of multiple states or pathways and the effects of projecting multiple dimensions onto a single coordinate.
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Affiliation(s)
- Michael T Woodside
- Department of Physics, University of Alberta, Edmonton, Alberta T6G2E1, Canada;
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12
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Chen J, Gong S, Wang Y, Zhang W. Kinetic partitioning mechanism of HDV ribozyme folding. J Chem Phys 2014; 140:025102. [DOI: 10.1063/1.4861037] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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13
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Lin JC, Hyeon C, Thirumalai D. Sequence-dependent folding landscapes of adenine riboswitch aptamers. Phys Chem Chem Phys 2013; 16:6376-82. [PMID: 24366448 DOI: 10.1039/c3cp53932f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Expression of a large fraction of genes in bacteria is controlled by riboswitches, which are found in the untranslated region of mRNA. Structurally riboswitches have a conserved aptamer domain to which a metabolite binds, resulting in a conformational change in the downstream expression platform. Prediction of the functions of riboswitches requires a quantitative description of the folding landscape so that the barriers and time scales for the conformational change in the switching region in the aptamer can be estimated. Using a combination of all atom molecular dynamics (MD) and coarse-grained model simulations we studied the response of adenine (A) binding add and pbuE A-riboswitches to mechanical force. The two riboswitches contain a structurally similar three-way junction formed by three paired helices, P1, P2, and P3, but carry out different functions. Using pulling simulations, with structures generated in MD simulations, we show that after P1 rips the dominant unfolding pathway in the add A-riboswitch is the rupture of P2 followed by unraveling of P3. In the pbuE A-riboswitch, after P1 unfolds P3 ruptures ahead of P2. The order of unfolding of the helices, which is in accord with single molecule pulling experiments, is determined by the relative stabilities of the individual helices. Our results show that the stability of isolated helices determines the order of assembly and response to force in these non-coding regions. We use the simulated free energy profile for the pbuE A-riboswitch to estimate the time scale for allosteric switching, which shows that this riboswitch is under kinetic control lending additional support to the conclusion based on single molecule pulling experiments. A consequence of the stability hypothesis is that a single point mutation (U28C) in the P2 helix of the add A-riboswitch, which increases the stability of P2, would make the folding landscapes of the two riboswitches similar. This prediction can be tested in single molecule pulling experiments.
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Affiliation(s)
- Jong-Chin Lin
- Department of Chemistry and Biochemistry, Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA.
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14
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Liu K, Zheng X, Samuel AZ, Ramkumar SG, Ghosh S, Tan X, Wang D, Shuai Z, Ramakrishnan S, Liu D, Zhang X. Stretching single polymer chains of donor-acceptor foldamers: toward the quantitative study on the extent of folding. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:14438-14443. [PMID: 24168699 DOI: 10.1021/la403709u] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Single-molecule force spectroscopy has proven to be an efficient tool for the quantitative characterization of flexible foldamers on the single-molecule level in this study. The extent of folding has been estimated quantitatively for the first time to the best of our knowledge, which is crucial for a better understanding of the "folding-process" on single-molecule level. Therefore, this study may provide a guidance to regulate folding for realizing rational control over the functions of bulk materials.
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Affiliation(s)
- Kai Liu
- Key Lab of Organic Optoelectronics & Molecular Engineering Department of Chemistry, Tsinghua University , Beijing 100084, People's Republic of China
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15
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Di Palma F, Colizzi F, Bussi G. Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch. RNA (NEW YORK, N.Y.) 2013; 19:1517-1524. [PMID: 24051105 PMCID: PMC3851719 DOI: 10.1261/rna.040493.113] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 08/02/2013] [Indexed: 05/28/2023]
Abstract
Riboswitches are structured mRNA elements that modulate gene expression. They undergo conformational changes triggered by highly specific interactions with sensed metabolites. Among the structural rearrangements engaged by riboswitches, the forming and melting of the aptamer terminal helix, the so-called P1 stem, is essential for genetic control. The structural mechanisms by which this conformational change is modulated upon ligand binding mostly remain to be elucidated. Here, we used pulling molecular dynamics simulations to study the thermodynamics of the P1 stem in the add adenine riboswitch. The P1 ligand-dependent stabilization was quantified in terms of free energy and compared with thermodynamic data. This comparison suggests a model for the aptamer folding in which direct P1-ligand interactions play a minor role on the conformational switch when compared with those related to the ligand-induced aptamer preorganization.
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16
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Lin JC, Thirumalai D. Kinetics of allosteric transitions in S-adenosylmethionine riboswitch are accurately predicted from the folding landscape. J Am Chem Soc 2013; 135:16641-50. [PMID: 24087850 DOI: 10.1021/ja408595e] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Riboswitches are RNA elements that allosterically regulate gene expression by binding cellular metabolites. The SAM-III riboswitch, one of several classes that binds S-adenosylmethionine (SAM), represses translation upon binding SAM (OFF state) by encrypting the ribosome binding sequence. We have carried out simulations of the RNA by applying mechanical force (f) to the ends of SAM-III, with and without SAM, to get quantitative insights into the f-dependent structural changes. Force-extension (z) curves (FECs) for the apo (ON) state, obtained in simulations in which f is increased at a constant loading rate, show three intermediates, with the first one being the rupture of SAM binding region, which is greatly stabilized in the OFF state. Force-dependent free energy profiles, G(z,f), as a function of z, obtained in equilibrium constant force simulations, reveal the intermediates observed in FECs. The predicted stability difference between the ON and OFF states using G(z,f) is in excellent agreement with experiments. Remarkably, using G(z,f)s and estimate of an effective diffusion constant at a single value of f allows us to predict the f-dependent transition rates using theory of first passage times for both the apo and holo states. To resolve the kinetics of assembly of SAM-III riboswitch in structural terms, we use force stretch-quench pulse sequences in which the force on RNA is maintained at a low (fq) value starting from a high value for a time period tq. Variation of tq over a wide range results in resolution of elusive states involved in the SAM binding pocket and leads to accurate determination of folding times down to fq = 0. Quantitative measure of the folding kinetics, obtained from the folding landscape, allows us to propose that, in contrast to riboswitches regulating transcription, SAM-III functions under thermodynamic control provided the basal concentration of SAM exceeds a small critical value. All of the predictions are amenable to tests in single molecule pulling experiments.
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Affiliation(s)
- Jong-Chin Lin
- Department of Chemistry and Biochemistry, Biophysics Program, Institute for Physical Sciences and Technology, University of Maryland , College Park, Maryland 20742, United States
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