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Zhang Z, Mlýnský V, Krepl M, Šponer J, Stadlbauer P. Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations. J Chem Inf Model 2024; 64:3896-3911. [PMID: 38630447 PMCID: PMC11094737 DOI: 10.1021/acs.jcim.4c00227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 05/14/2024]
Abstract
Guanine quadruplex (GQ) is a noncanonical nucleic acid structure formed by guanine-rich DNA and RNA sequences. Folding of GQs is a complex process, where several aspects remain elusive, despite being important for understanding structure formation and biological functions of GQs. Pulling experiments are a common tool for acquiring insights into the folding landscape of GQs. Herein, we applied a computational pulling strategy─steered molecular dynamics (SMD) simulations─in combination with standard molecular dynamics (MD) simulations to explore the unfolding landscapes of tetrameric parallel GQs. We identified anisotropic properties of elastic conformational changes, unfolding transitions, and GQ mechanical stabilities. Using a special set of structural parameters, we found that the vertical component of pulling force (perpendicular to the average G-quartet plane) plays a significant role in disrupting GQ structures and weakening their mechanical stabilities. We demonstrated that the magnitude of the vertical force component depends on the pulling anchor positions and the number of G-quartets. Typical unfolding transitions for tetrameric parallel GQs involve base unzipping, opening of the G-stem, strand slippage, and rotation to cross-like structures. The unzipping was detected as the first and dominant unfolding event, and it usually started at the 3'-end. Furthermore, results from both SMD and standard MD simulations indicate that partial spiral conformations serve as a transient ensemble during the (un)folding of GQs.
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Affiliation(s)
- Zhengyue Zhang
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
- CEITEC−Central
European Institute of Technology, Masaryk
University, Kamenice
5, Brno 625 00, Czech Republic
- National
Center for Biomolecular Research,
Faculty of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Vojtěch Mlýnský
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
| | - Miroslav Krepl
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
| | - Jiří Šponer
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
| | - Petr Stadlbauer
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
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Stadlbauer P, Mlýnský V, Krepl M, Šponer J. Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations. J Chem Inf Model 2023; 63:4716-4731. [PMID: 37458574 PMCID: PMC10428220 DOI: 10.1021/acs.jcim.3c00171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Indexed: 08/15/2023]
Abstract
Guanine quadruplexes (GQs) are non-canonical nucleic acid structures involved in many biological processes. GQs formed in single-stranded regions often need to be unwound by cellular machinery, so their mechanochemical properties are important. Here, we performed steered molecular dynamics simulations of human telomeric GQs to study their unfolding. We examined four pulling regimes, including a very slow setup with pulling velocity and force load accessible to high-speed atomic force microscopy. We identified multiple factors affecting the unfolding mechanism, i.e.,: (i) the more the direction of force was perpendicular to the GQ channel axis (determined by GQ topology), the more the base unzipping mechanism happened, (ii) the more parallel the direction of force was, GQ opening and cross-like GQs were more likely to occur, (iii) strand slippage mechanism was possible for GQs with an all-anti pattern in a strand, and (iv) slower pulling velocity led to richer structural dynamics with sampling of more intermediates and partial refolding events. We also identified that a GQ may eventually unfold after a force drop under forces smaller than those that the GQ withstood before the drop. Finally, we found out that different unfolding intermediates could have very similar chain end-to-end distances, which reveals some limitations of structural interpretations of single-molecule spectroscopic data.
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Affiliation(s)
- Petr Stadlbauer
- Institute of Biophysics of the Czech
Academy of Sciences, Královopolská 135, Brno 612 00, Czech Republic
| | - Vojtěch Mlýnský
- Institute of Biophysics of the Czech
Academy of Sciences, Královopolská 135, Brno 612 00, Czech Republic
| | - Miroslav Krepl
- Institute of Biophysics of the Czech
Academy of Sciences, Královopolská 135, Brno 612 00, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech
Academy of Sciences, Královopolská 135, Brno 612 00, Czech Republic
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3
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Stadlbauer P, Kührová P, Vicherek L, Banáš P, Otyepka M, Trantírek L, Šponer J. Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes. Nucleic Acids Res 2019; 47:7276-7293. [PMID: 31318975 PMCID: PMC6698752 DOI: 10.1093/nar/gkz610] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 06/26/2019] [Accepted: 07/03/2019] [Indexed: 12/29/2022] Open
Abstract
Guanine quadruplexes (G4s) are non-canonical nucleic acids structures common in important genomic regions. Parallel-stranded G4 folds are the most abundant, but their folding mechanism is not fully understood. Recent research highlighted that G4 DNA molecules fold via kinetic partitioning mechanism dominated by competition amongst diverse long-living G4 folds. The role of other intermediate species such as parallel G-triplexes and G-hairpins in the folding process has been a matter of debate. Here, we use standard and enhanced-sampling molecular dynamics simulations (total length of ∼0.9 ms) to study these potential folding intermediates. We suggest that parallel G-triplex per se is rather an unstable species that is in local equilibrium with a broad ensemble of triplex-like structures. The equilibrium is shifted to well-structured G-triplex by stacked aromatic ligand and to a lesser extent by flanking duplexes or nucleotides. Next, we study propeller loop formation in GGGAGGGAGGG, GGGAGGG and GGGTTAGGG sequences. We identify multiple folding pathways from different unfolded and misfolded structures leading towards an ensemble of intermediates called cross-like structures (cross-hairpins), thus providing atomistic level of description of the single-molecule folding events. In summary, the parallel G-triplex is a possible, but not mandatory short-living (transitory) intermediate in the folding of parallel-stranded G4.
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Affiliation(s)
- Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences, v. v. i., Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Šlechtitelů 27, 771 46 Olomouc, Czech Republic
| | - Petra Kührová
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Šlechtitelů 27, 771 46 Olomouc, Czech Republic.,Department of Physical Chemistry, Faculty of Science, Palacky University, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Lukáš Vicherek
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Pavel Banáš
- Institute of Biophysics of the Czech Academy of Sciences, v. v. i., Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Šlechtitelů 27, 771 46 Olomouc, Czech Republic.,Department of Physical Chemistry, Faculty of Science, Palacky University, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Michal Otyepka
- Institute of Biophysics of the Czech Academy of Sciences, v. v. i., Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Šlechtitelů 27, 771 46 Olomouc, Czech Republic.,Department of Physical Chemistry, Faculty of Science, Palacky University, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Lukáš Trantírek
- Institute of Biophysics of the Czech Academy of Sciences, v. v. i., Královopolská 135, 612 65 Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, v. v. i., Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Šlechtitelů 27, 771 46 Olomouc, Czech Republic.,Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
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4
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Kim HW, Rhee YM, Shin SK. Charge-dipole interactions in G-quadruplex thrombin-binding aptamer. Phys Chem Chem Phys 2019; 20:21068-21074. [PMID: 30074033 DOI: 10.1039/c8cp03050b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
DNAs form various structures through hydrogen-bonding, base-stacking and electrostatic interactions. Although these noncovalent interactions are known to be cooperative in stabilizing a G-quadruplex (G4) structure of DNA, we find from all-atom molecular dynamics simulations that the electrostatic charge-dipole interaction is competitive with both hydrogen-bonding and base-stacking interactions. For the thrombin-binding aptamer (TBA) forming a chair-type antiparallel G4 structure, we have examined effects of an intercalating metal ion [K+, Sr2+, Mn+: an ion having a charge of n+ (n = 1-4) with the ionic radius of K+] on structural properties and noncovalent interactions. When K+ in the TBA·K+ complex is replaced with Sr2+, guanine dipoles in the two G-tetrads are realigned toward the central metal ion, thereby distorting the planar G4 geometry. Replacing K+ with Sr2+ significantly enhances the charge-dipole interaction but substantially reduces the number of hydrogen bonds in the G-tetrads. In the case of TBA·Mn+ complexes, as the charge n increases, the charge-dipole interaction increases but both of the hydrogen-bonding and base-stacking interactions decrease. These results suggest that the charge-dipole interaction realigning guanine dipoles in the G-tetrads is not cooperative but competitive with both hydrogen-bonding and base-stacking interactions favoring the planar G-tetrad geometry. Obviously, the charge state of an intercalating metal ion is as important as the ionic radius in forming a stable G4 structure. Thus, a delicate balance between these competing noncovalent interactions makes the chair-type antiparallel G4 structure of TBA selective for intercalating metal ions.
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Affiliation(s)
- Hyun Woo Kim
- Center for Molecular Modeling and Simulation, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea
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5
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Pal S, Paul S. Conformational deviation of Thrombin binding G-quadruplex aptamer (TBA) in presence of divalent cation Sr 2+: A classical molecular dynamics simulation study. Int J Biol Macromol 2018; 121:350-363. [PMID: 30308284 DOI: 10.1016/j.ijbiomac.2018.09.102] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 08/27/2018] [Accepted: 09/17/2018] [Indexed: 11/28/2022]
Abstract
Thrombin binding TBA-G-quadruplex aptamer (TBA) plays a major role in blood coagulation cascade. The 15-mer TBA sequence tends to form four-stranded TBA-G-quadruplex structure. In this research work, a series of explicit solvent classical MD simulations of the TBA is carried out using different salt (SrCl2) concentrations (0, 50, 100 and 200 mM). Here we have also testified the effect of salt concentration of divalent cation Sr2+ on the conformational change of quadruplex DNA. The structural deviations, fluctuations, torsional angles and the affinity of the ion are explored at different salt concentrations. It is found that the conformation of TBA-G-quadruplex at 0 mM and 50 mM salt concentrations, is very much different than the other salt concentrations (100 mM and 200 mM). Also observed are as follows: (i) no exchange of Sr2+ ion between inside and outside of the channel, (ii) an enhancement in the Sr2+ ion density around the phosphate region of the loop residues as salt concentration increases and (iii) the stacking of T3 and T4 residues of loop-1 that appears up to 50 mM concentration, vanishes as the salt concentration is increased further.
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Affiliation(s)
- Saikat Pal
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India.
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Abstract
Genomes contain rare guanine-rich sequences capable of assembling into four-stranded helical structures, termed G-quadruplexes, with potential roles in gene regulation and chromosome stability. Their mechanical unfolding has only been reported to date by all-atom simulations, which cannot dissect the major physical interactions responsible for their cohesion. Here, we propose a mesoscopic model to describe both the mechanical and thermal stability of DNA G-quadruplexes, where each nucleotide of the structure, as well as each central cation located at the inner channel, is mapped onto a single bead. In this framework we are able to simulate loading rates similar to the experimental ones, which are not reachable in simulations with atomistic resolution. In this regard, we present single-molecule force-induced unfolding experiments by a high-resolution optical tweezers on a DNA telomeric sequence capable of adopting a G-quadruplex conformation. Fitting the parameters of the model to the experiments we find a correct prediction of the rupture-force kinetics and a good agreement with previous near equilibrium measurements. Since G-quadruplex unfolding dynamics is halfway in complexity between secondary nucleic acids and tertiary protein structures, our model entails a nanoscale paradigm for non-equilibrium processes in the cell.
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Šponer J, Bussi G, Stadlbauer P, Kührová P, Banáš P, Islam B, Haider S, Neidle S, Otyepka M. Folding of guanine quadruplex molecules-funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies. Biochim Biophys Acta Gen Subj 2016; 1861:1246-1263. [PMID: 27979677 DOI: 10.1016/j.bbagen.2016.12.008] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 12/04/2016] [Accepted: 12/11/2016] [Indexed: 01/18/2023]
Abstract
BACKGROUND Guanine quadruplexes (GQs) play vital roles in many cellular processes and are of much interest as drug targets. In contrast to the availability of many structural studies, there is still limited knowledge on GQ folding. SCOPE OF REVIEW We review recent molecular dynamics (MD) simulation studies of the folding of GQs, with an emphasis paid to the human telomeric DNA GQ. We explain the basic principles and limitations of all types of MD methods used to study unfolding and folding in a way accessible to non-specialists. We discuss the potential role of G-hairpin, G-triplex and alternative GQ intermediates in the folding process. We argue that, in general, folding of GQs is fundamentally different from funneled folding of small fast-folding proteins, and can be best described by a kinetic partitioning (KP) mechanism. KP is a competition between at least two (but often many) well-separated and structurally different conformational ensembles. MAJOR CONCLUSIONS The KP mechanism is the only plausible way to explain experiments reporting long time-scales of GQ folding and the existence of long-lived sub-states. A significant part of the natural partitioning of the free energy landscape of GQs comes from the ability of the GQ-forming sequences to populate a large number of syn-anti patterns in their G-tracts. The extreme complexity of the KP of GQs typically prevents an appropriate description of the folding landscape using just a few order parameters or collective variables. GENERAL SIGNIFICANCE We reconcile available computational and experimental studies of GQ folding and formulate basic principles characterizing GQ folding landscapes. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
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Affiliation(s)
- Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic; Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic.
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, 34136 Trieste, Italy
| | - Petr Stadlbauer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic; Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Petra Kührová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Barira Islam
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Shozeb Haider
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Stephen Neidle
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
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Stadlbauer P, Mazzanti L, Cragnolini T, Wales DJ, Derreumaux P, Pasquali S, Šponer J. Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes. J Chem Theory Comput 2016; 12:6077-6097. [DOI: 10.1021/acs.jctc.6b00667] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Petr Stadlbauer
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
- Regional
Centre of Advanced Technologies and Materials, Departments of Physical
Chemistry, Faculty of Science, Palacký University, 17. listopadu
1192/12, 771 46 Olomouc, Czech Republic
| | - Liuba Mazzanti
- Laboratoire
de Biochimie Théorique, IBPC, CNRS UPR9080, Université Sorbonne Paris Cite, Paris Diderot, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Tristan Cragnolini
- Department
of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K
| | - David J. Wales
- Department
of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Philippe Derreumaux
- Laboratoire
de Biochimie Théorique, IBPC, CNRS UPR9080, Université Sorbonne Paris Cite, Paris Diderot, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Samuela Pasquali
- Laboratoire
de Biochimie Théorique, IBPC, CNRS UPR9080, Université Sorbonne Paris Cite, Paris Diderot, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Jiří Šponer
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
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Zeng X, Zhang L, Xiao X, Jiang Y, Guo Y, Yu X, Pu X, Li M. Unfolding mechanism of thrombin-binding aptamer revealed by molecular dynamics simulation and Markov State Model. Sci Rep 2016; 6:24065. [PMID: 27045335 PMCID: PMC4820715 DOI: 10.1038/srep24065] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 03/16/2016] [Indexed: 12/27/2022] Open
Abstract
Thrombin-binding aptamer (TBA) with the sequence 5′GGTTGGTGTGGTTGG3′ could fold into G-quadruplex, which correlates with functionally important genomic regionsis. However, unfolding mechanism involved in the structural stability of G-quadruplex has not been satisfactorily elucidated on experiments so far. Herein, we studied the unfolding pathway of TBA by a combination of molecular dynamics simulation (MD) and Markov State Model (MSM). Our results revealed that the unfolding of TBA is not a simple two-state process but proceeds along multiple pathways with multistate intermediates. One high flux confirms some observations from NMR experiment. Another high flux exhibits a different and simpler unfolding pathway with less intermediates. Two important intermediate states were identified. One is similar to the G-triplex reported in the folding of G-quadruplex, but lack of H-bonding between guanines in the upper plane. More importantly, another intermediate state acting as a connector to link the folding region and the unfolding one, was the first time identified, which exhibits higher population and stability than the G-triplex-like intermediate. These results will provide valuable information for extending our understanding the folding landscape of G-quadruplex formation.
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Affiliation(s)
- Xiaojun Zeng
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
| | - Liyun Zhang
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
| | - Xiuchan Xiao
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
| | - Yuanyuan Jiang
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
| | - Yanzhi Guo
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
| | - Xinyan Yu
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
| | - Xuemei Pu
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
| | - Menglong Li
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
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10
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Stadlbauer P, Kührová P, Banáš P, Koča J, Bussi G, Trantírek L, Otyepka M, Šponer J. Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations. Nucleic Acids Res 2015; 43:9626-44. [PMID: 26433223 PMCID: PMC4787745 DOI: 10.1093/nar/gkv994] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 09/22/2015] [Indexed: 11/13/2022] Open
Abstract
DNA G-hairpins are potential key structures participating in folding of human telomeric guanine quadruplexes (GQ). We examined their properties by standard MD simulations starting from the folded state and long T-REMD starting from the unfolded state, accumulating ∼130 μs of atomistic simulations. Antiparallel G-hairpins should spontaneously form in all stages of the folding to support lateral and diagonal loops, with sub-μs scale rearrangements between them. We found no clear predisposition for direct folding into specific GQ topologies with specific syn/anti patterns. Our key prediction stemming from the T-REMD is that an ideal unfolded ensemble of the full GQ sequence populates all 4096 syn/anti combinations of its four G-stretches. The simulations can propose idealized folding pathways but we explain that such few-state pathways may be misleading. In the context of the available experimental data, the simulations strongly suggest that the GQ folding could be best understood by the kinetic partitioning mechanism with a set of deep competing minima on the folding landscape, with only a small fraction of molecules directly folding to the native fold. The landscape should further include non-specific collapse processes where the molecules move via diffusion and consecutive random rare transitions, which could, e.g. structure the propeller loops.
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Affiliation(s)
- Petr Stadlbauer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Petra Kührová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Jaroslav Koča
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic National Center for Biomolecular Research, Faculty of Science, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, 34136 Trieste, Italy
| | - Lukáš Trantírek
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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11
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Bergues-Pupo AE, Arias-Gonzalez JR, Morón MC, Fiasconaro A, Falo F. Role of the central cations in the mechanical unfolding of DNA and RNA G-quadruplexes. Nucleic Acids Res 2015; 43:7638-47. [PMID: 26170233 PMCID: PMC4551928 DOI: 10.1093/nar/gkv690] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 06/23/2015] [Indexed: 12/20/2022] Open
Abstract
Cations are known to mediate diverse interactions in nucleic acids duplexes but they are critical in the arrangement of four-stranded structures. Here, we use all-atom molecular dynamics simulations with explicit solvent to analyse the mechanical unfolding of representative intramolecular G-quadruplex structures: a parallel, a hybrid and an antiparallel DNA and a parallel RNA, in the presence of stabilising cations. We confirm the stability of these conformations in the presence of \documentclass[12pt]{minimal}
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}{}$\rm {K}^+$\end{document} central ions and observe distortions from the tetrad topology in their absence. Force-induced unfolding dynamics is then investigated. We show that the unfolding events in the force-extension curves are concomitant to the loss of coordination between the central ions and the guanines of the G-quadruplex. We found lower ruptures forces for the parallel configuration with respect to the antiparallel one, while the behaviour of the force pattern of the parallel RNA appears similar to the parallel DNA. We anticipate that our results will be essential to interpret the fine structure rupture profiles in stretching assays at high resolution and will shed light on the mechanochemical activity of G-quadruplex-binding machinery.
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Affiliation(s)
- Ana Elisa Bergues-Pupo
- Departamento de Física de la Materia Condensada, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Mariano Esquillor, 50018 Zaragoza, Spain Departamento de Física, Universidad de Oriente, 90500 Santiago de Cuba, Cuba
| | - J Ricardo Arias-Gonzalez
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia), Cantoblanco, 28049 Madrid, Spain CNB-CSIC-IMDEA Nanociencia Associated Unit 'Unidad de Nanobiotecnología, Madrid, Spain'
| | - María Carmen Morón
- Departamento de Física de la Materia Condensada, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain Instituto de Ciencia de Materiales de Aragón (ICMA), Consejo Superior de Investigaciones Científicas, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Alessandro Fiasconaro
- School of Mathematical Sciences, Queen Mary University of London - Mile End Road, London E1 4NS, UK
| | - Fernando Falo
- Departamento de Física de la Materia Condensada, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Mariano Esquillor, 50018 Zaragoza, Spain
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12
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Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations. Biochimie 2014; 105:22-35. [DOI: 10.1016/j.biochi.2014.07.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Accepted: 07/01/2014] [Indexed: 11/23/2022]
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13
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Stadlbauer P, Krepl M, Cheatham TE, Koča J, Šponer J. Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations. Nucleic Acids Res 2013; 41:7128-43. [PMID: 23700306 PMCID: PMC3737530 DOI: 10.1093/nar/gkt412] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 04/18/2013] [Accepted: 04/24/2013] [Indexed: 12/31/2022] Open
Abstract
Explicit solvent molecular dynamics simulations have been used to complement preceding experimental and computational studies of folding of guanine quadruplexes (G-DNA). We initiate early stages of unfolding of several G-DNAs by simulating them under no-salt conditions and then try to fold them back using standard excess salt simulations. There is a significant difference between G-DNAs with all-anti parallel stranded stems and those with stems containing mixtures of syn and anti guanosines. The most natural rearrangement for all-anti stems is a vertical mutual slippage of the strands. This leads to stems with reduced numbers of tetrads during unfolding and a reduction of strand slippage during refolding. The presence of syn nucleotides prevents mutual strand slippage; therefore, the antiparallel and hybrid quadruplexes initiate unfolding via separation of the individual strands. The simulations confirm the capability of G-DNA molecules to adopt numerous stable locally and globally misfolded structures. The key point for a proper individual folding attempt appears to be correct prior distribution of syn and anti nucleotides in all four G-strands. The results suggest that at the level of individual molecules, G-DNA folding is an extremely multi-pathway process that is slowed by numerous misfolding arrangements stabilized on highly variable timescales.
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Affiliation(s)
- Petr Stadlbauer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT 84124, USA and CEITEC – Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Miroslav Krepl
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT 84124, USA and CEITEC – Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Thomas E. Cheatham
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT 84124, USA and CEITEC – Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jaroslav Koča
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT 84124, USA and CEITEC – Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT 84124, USA and CEITEC – Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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14
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Kim E, Yang C, Pak Y. Free-Energy Landscape of a Thrombin-Binding DNA Aptamer in Aqueous Environment. J Chem Theory Comput 2012; 8:4845-51. [DOI: 10.1021/ct300714u] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Eunae Kim
- BK-21 Project
Team, College of Pharmacy, Chosun University, Gwangju 501-759, Republic of Korea
- Supercomputing Center, Korea Institute of Science and Technology Information, Daejeon 305-806, Republic of
Korea
| | - Changwon Yang
- Department of Chemistry
and Institute
of Functional Materials, Pusan National University, Busan 609-735, Republic of Korea
| | - Youngshang Pak
- Department of Chemistry
and Institute
of Functional Materials, Pusan National University, Busan 609-735, Republic of Korea
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15
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šponer J, Cang X, Cheatham TE. Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures. Methods 2012; 57:25-39. [PMID: 22525788 PMCID: PMC3775459 DOI: 10.1016/j.ymeth.2012.04.005] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Revised: 04/04/2012] [Accepted: 04/06/2012] [Indexed: 11/29/2022] Open
Abstract
The article reviews the application of biomolecular simulation methods to understand the structure, dynamics and interactions of nucleic acids with a focus on explicit solvent molecular dynamics simulations of guanine quadruplex (G-DNA and G-RNA) molecules. While primarily dealing with these exciting and highly relevant four-stranded systems, where recent and past simulations have provided several interesting results and novel insight into G-DNA structure, the review provides some general perspectives on the applicability of the simulation techniques to nucleic acids.
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Affiliation(s)
- Jiří šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
- CEITEC – Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Xiaohui Cang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Thomas E. Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, Skaggs Hall 201, 2000 East 30 South, University of Utah, Salt Lake City, UT 84112, United States
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