1
|
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.
Collapse
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
| |
Collapse
|
2
|
Oprzeska-Zingrebe EA, Smiatek J. Basket-type G-quadruplex with two tetrads in the presence of TMAO and urea: A molecular dynamics study. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
3
|
Kim H, Pak Y. Improving All-Atom Force Field to Accurately Describe DNA G-Quadruplex Loops. J Phys Chem B 2022; 126:6199-6209. [PMID: 35951994 DOI: 10.1021/acs.jpcb.2c04256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The DNA G-quadruplex (GQ) displays structural polymorphisms, and interactions between its loops and flanking sequences critically determine which of the diverse GQ conformers is adopted. All-atom molecular dynamics (MD) simulations of GQs are computationally challenging due to slow folding times and force field (ff) artifacts. In an earlier study, a direct folding simulation of the simplest DNA GQ (TBA15) was first reported using a modified version of the AMBER bsc1 ff (bsc1_vdW ff). Despite this successful folding simulation, it was later found that the bsc1_vdW ff is somewhat limited in terms of describing loop structures of GQs, which is problematic because GQ loop regions play key roles in ligand binding to modulate GQ activities. In this study, we further modified the bsc1_vdW ff to enhance the GQ loop prediction by fine-tuning a limited number of van der Waals (vdW) parameters of the standard AMBER bsc1 ff to improve the GQ loop distribution of a target GQ system (three-layered antiparallel GQ; mHtel21). Test simulations of this newly generated ff (bsc1_vdWL ff) on DNA GQs with diverse topologies (hybrid1, hybrid2, and parallel propeller) revealed that loop structures were predicted more accurately than by the bsc1_vdW ff. We consider that enhanced sampling MD simulation methods in combination with bsc1_vdWL provide useful simulation protocols for resolving outstanding issues of DNA GQ folding and GQ/ligand binding at the all-atom level.
Collapse
Affiliation(s)
- Hyeonjun Kim
- Department of Chemistry and Institute of Functional Materials, Pusan National University, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 46241, S. Korea
| | - Youngshang Pak
- Department of Chemistry and Institute of Functional Materials, Pusan National University, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 46241, S. Korea
| |
Collapse
|
4
|
Yoon HJ, Jeong J, Kim G, Lee HH, Jang S. The point mutation of the cholesterol trafficking membrane protein NPC1 may affect its proper function in more than a single step: Molecular dynamics simulation study. Comput Biol Chem 2022; 99:107725. [PMID: 35850050 DOI: 10.1016/j.compbiolchem.2022.107725] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 06/29/2022] [Accepted: 07/04/2022] [Indexed: 11/16/2022]
Abstract
The Niemann-Pick type C1 (NPC1) protein is one of the key players of cholesterol trafficking from the lysosome and its function is closely coupled with the Niemann-Pick type C2 (NPC2) protein. The dysfunction of one of these proteins can cause problems in the overall cholesterol homeostasis and leads to a disease, which is called the Niemann-Pick type C (NPC) disease. The parts of the cholesterol transport mechanism by NPC1 have begun to recently emerge, especially after the full-length NPC1 structure was determined from a cryo-EM study. However, many details about the overall cholesterol trafficking process by NPC1 still remain to be elucidated. Notably, the NPC1 could act as one of the target proteins for the control of infectious diseases due to its role as the virus entry point into the cells as well as for cancer treatment due to the inhibitory effect of tumor growth. A mutation of NPC1 can leads to dysfunctions and understanding this process can provide valuable insights into the mechanisms of the corresponding protein and the therapeutic strategies against the disease that are caused by the mutation. It has been found that patients with the point mutation R518W (or R518Q) on the NPC1 show the accumulation of lipids within the lysosomal lumen. In this paper, we report how the corresponding mutation can affect the cholesterol transport process by NPC1 in the different stages by the molecular dynamics simulations. The simulation results show that the point mutation intervenes at least at two different steps during the cholesterol transport by NPC1 and NPC2 in combination, which includes the association step of NPC2 with the NPC1, the cholesterol transfer step from NPC2 to NPC1-NTD while the cholesterol passage within the NPC1 via a channel is relatively unaffected by R518W mutation. The detailed analysis of the resulting simulation trajectories reveals the important structural features that are essential for the proper functioning of the NPC1 for the cholesterol transport, and it shows how the overall structure, which thereby includes the function, can be affected by a single mutation.
Collapse
Affiliation(s)
- Hye-Jin Yoon
- Department of Chemistry, Seoul National University, Seoul, the Republic of Korea
| | - Jian Jeong
- Department of Chemistry, Sejong University, Seoul, the Republic of Korea
| | - Guun Kim
- Department of Physics, Sejong University, Seoul, the Republic of Korea
| | - Hyung Ho Lee
- Department of Chemistry, Seoul National University, Seoul, the Republic of Korea.
| | - Soonmin Jang
- Department of Chemistry, Sejong University, Seoul, the Republic of Korea.
| |
Collapse
|
5
|
Kim H, Pak Y. Computational study of the
pK
a
values of a modified G·C base pair in duplex
DNA. B KOREAN CHEM SOC 2021. [DOI: 10.1002/bkcs.12461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Hyeonjun Kim
- Department of Chemistry and Institute of Functional Materials Pusan National University Busan South Korea
| | - Youngshang Pak
- Department of Chemistry and Institute of Functional Materials Pusan National University Busan South Korea
| |
Collapse
|
6
|
Laouer K, Schmid M, Wien F, Changenet P, Hache F. Folding Dynamics of DNA G-Quadruplexes Probed by Millisecond Temperature Jump Circular Dichroism. J Phys Chem B 2021; 125:8088-8098. [PMID: 34279936 DOI: 10.1021/acs.jpcb.1c01993] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
G-quadruplexes play important roles in cellular regulatory functions, but despite significant experimental and theoretical efforts, their folding mechanisms remain poorly understood. In this context, we developed a T-jump experiment to access the thermal denaturation and renaturation dynamics of short intramolecular G-quadruplexes in vitro, on the time scale of a few hundred milliseconds. With this new setup, we compared the thermal denaturation and renaturation kinetics of three antiparallel topologies made of the human telomeric sequences d[(5'-GGG(TTAGGG)3-3']/Na+ and d[5'-AGGG(TTAGGG)3-3']/Na+ and the thrombin-binding aptamer sequence d[5'-GGTTGGTGTGGTTGG-3']/K+, with those of the parallel topology made of the human CEB25 minisatellite d[5'-AAGGGTGGGTGTAAGTGTGGGTGGGT-3']/Na+. In all cases, exponential kinetics of the order of several hundred milliseconds were observed. Measurements performed for different initial temperatures revealed distinct denaturation and renaturation dynamics, ruling out a simple two-state mechanism. The parallel topology, in which all guanines adopt an anti conformation, displays much slower dynamics than antiparallel topologies associated with very low activation barriers. This behavior can be explained by the constrained conformational space due to the presence of the single-base propeller loops that likely hinders the movement of the coiled DNA strand and reduces the contribution of the entropy during the renaturation process at high temperatures.
Collapse
Affiliation(s)
- K Laouer
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS -INSERM, Institut Polytechnique de Paris, 91128 Cedex Palaiseau, France
| | - M Schmid
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS -INSERM, Institut Polytechnique de Paris, 91128 Cedex Palaiseau, France
| | - F Wien
- L'orme des merisiers, Synchrotron SOLEIL, 91192 Gif sur Yvette, France
| | - P Changenet
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS -INSERM, Institut Polytechnique de Paris, 91128 Cedex Palaiseau, France
| | - F Hache
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS -INSERM, Institut Polytechnique de Paris, 91128 Cedex Palaiseau, France
| |
Collapse
|
7
|
Wu J, Wang S, Li X, Zhang Q, Yang J, Ma Y, Guan Z, Yang Z. Selective Anti-melanoma Effect of Phosphothioated Aptamer Encapsulated by Neutral Cytidinyl/Cationic Lipids. Front Cell Dev Biol 2021; 9:660233. [PMID: 34262898 PMCID: PMC8273494 DOI: 10.3389/fcell.2021.660233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 06/01/2021] [Indexed: 12/11/2022] Open
Abstract
BC15-31 is a DNA aptamer that targets heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1), which plays a crucial role in the process of pre-RNA maturation and is also essential for the rapid proliferation of tumor cells. In this research, we modified BC15-31 with a phosphorothioate (PS) backbone, LNA, and 2-O-MOE to enhance its stability and target affinity. In addition, a neutral cytidinyl lipid (DNCA) and a cationic lipid (CLD) were mixed to encapsulate modified aptamers with the aim of improving their cell permeability with low toxicity. Under the DNCA/CLD package, aptamers are mainly distributed in the nucleus. A modified sequence WW-24 showed an excellent selective anti-melanoma (A375 cells, ∼25 nM, 80%) activity, targeted to both hnRNP A1 and hnRNP A2/B1 found by the BLI experiment, and induced more early and late apoptosis in vitro, which also showed stronger antitumor effect and longer accumulation time in vivo. These results provide a new strategy for further clinical applications.
Collapse
Affiliation(s)
- Jing Wu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Shuhe Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Xiang Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Qi Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Jie Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Yuan Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Zhu Guan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| |
Collapse
|
8
|
Kim H, Yang C, Pak Y. Free-Energy Landscape of a pH-Modulated G·C Base Pair Transition from Watson-Crick to Hoogsteen State in Duplex DNA. J Chem Theory Comput 2021; 17:2556-2565. [PMID: 33689343 DOI: 10.1021/acs.jctc.0c01330] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In double-helical DNAs, the most stable Watson-Crick (WC) base pair (bp) can be in thermal equilibrium with much less abundant Hoogsteen (HG) bp by the spontaneous rotation of the glycosidic angle in purine bases. Previous experimental studies showed that in the case of a G·C bp, the population of the transient HG is enhanced as a protonated form (HG+) through the protonation of the cytosine base under weakly acidic conditions. Hence, pH is a key factor that can modulate this transition event from the WC to HG+ bp. In this study, to computationally probe the overall free-energy landscapes of this pH-modulated G·C HG breathing, a comprehensive classical molecular dynamics (MD) simulation protocol is proposed using an enhanced sampling MD in conjunction with the standard thermodynamic integration method. From this MD protocol proposed, the free-energy surfaces of the G·C bp transition from the WC to HG bp were constructed successfully at any pH range, producing pH-dependent free-energy quantities in close agreement with previously reported experimental results. The simulation protocol is expected to provide valuable atomistic insight into the DNA bp transition events coupled with protonation or tautomeric shift in a target bp.
Collapse
Affiliation(s)
- Hyeonjun Kim
- Department of Chemistry and Institute of Functional Materials, Pusan National University, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 46241, South Korea
| | - Changwon Yang
- Department of Chemistry, Sejong University, 209, Neungdong-ro, Gwangjin-gu, Seoul 05006, South Korea
| | - Youngshang Pak
- Department of Chemistry and Institute of Functional Materials, Pusan National University, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 46241, South Korea
| |
Collapse
|
9
|
Oprzeska-Zingrebe EA, Smiatek J. Interactions of a DNA G-quadruplex with TMAO and urea: a molecular dynamics study on co-solute compensation mechanisms. Phys Chem Chem Phys 2021; 23:1254-1264. [PMID: 33355575 DOI: 10.1039/d0cp05356b] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We study the individual and combined influence of TMAO and urea on a basket-type DNA G-quadruplex by means of atomistic molecular dynamics (MD) simulations. In combination with the Kirkwood-Buff theory of solutions, we propose a simple mechanism to elucidate the impact of TMAO and urea on the G-quadruplex. Our results reveal the importance of the molecular accumulation around the DNA in terms of stabilizing or destabilizing effects. The results for mixtures show only a weak interaction between both co-solutes, which highlights the additivity of contributions. Despite the fact, that TMAO can to some extent compensate the adverse impact of urea on the G-quadruplex structure, the destabilizing influence is not completely eliminated. This observation opens the door for further research on selective stabilization of DNA G-quadruplexes by modulating the concentrations of TMAO and urea in solution.
Collapse
Affiliation(s)
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, D-70569 Stuttgart, Germany.
| |
Collapse
|
10
|
Ray D, Andricioaei I. Free Energy Landscape and Conformational Kinetics of Hoogsteen Base Pairing in DNA vs. RNA. Biophys J 2020; 119:1568-1579. [PMID: 32946766 DOI: 10.1016/j.bpj.2020.08.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 05/10/2020] [Accepted: 08/25/2020] [Indexed: 10/23/2022] Open
Abstract
Genetic information is encoded in the DNA double helix, which, in its physiological milieu, is characterized by the iconical Watson-Crick nucleo-base pairing. Recent NMR relaxation experiments revealed the transient presence of an alternative, Hoogsteen (HG) base pairing pattern in naked DNA duplexes, and estimated its relative stability and lifetime. In contrast with DNA, such structures were not observed in RNA duplexes. Understanding HG base pairing is important because the underlying "breathing" motion between the two conformations can significantly modulate protein binding. However, a detailed mechanistic insight into the transition pathways and kinetics is still missing. We performed enhanced sampling simulation (with combined metadynamics and adaptive force-bias method) and Markov state modeling to obtain accurate free energy, kinetics, and the intermediates in the transition pathway between Watson-Crick and HG base pairs for both naked B-DNA and A-RNA duplexes. The Markov state model constructed from our unbiased MD simulation data revealed previously unknown complex extrahelical intermediates in the seemingly simple process of base flipping in B-DNA. Extending our calculation to A-RNA, for which HG base pairing is not observed experimentally, resulted in relatively unstable, single-hydrogen-bonded, distorted Hoogsteen-like bases. Unlike B-DNA, the transition pathway primarily involved base paired and intrahelical intermediates with transition timescales much longer than that of B-DNA. The seemingly obvious flip-over reaction coordinate (i.e., the glycosidic torsion angle) is unable to resolve the intermediates. Instead, a multidimensional picture involving backbone dihedral angles and distance between hydrogen bond donor and acceptor atoms is required to gain insight into the molecular mechanism.
Collapse
Affiliation(s)
| | - Ioan Andricioaei
- Department of Chemistry; Department of Physics and Astronomy, University of California Irvine, Irvine, California.
| |
Collapse
|
11
|
Yoon HJ, Jeong H, Lee HH, Jang S. Molecular dynamics study with mutation shows that N-terminal domain structural re-orientation in Niemann-Pick type C1 is required for proper alignment of cholesterol transport. J Neurochem 2020; 156:967-978. [PMID: 32880929 PMCID: PMC7461377 DOI: 10.1111/jnc.15150] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/30/2020] [Accepted: 07/30/2020] [Indexed: 11/27/2022]
Abstract
The lysosomal membrane protein Niemann‐Pick type C1 (NPC1) and Niemann‐Pick type C2 (NPC2) are main players of cholesterol control in the lysosome and it is known that the mutation on these proteins leads to the cholesterol trafficking‐related neurodegenerative disease, which is called the NPC disease. The mutation R518W or R518Q on the NPC1 is one of the type of disease‐related mutation that causes cholesterol transports to be cut in half, which results in the accumulation of cholesterol and lipids in the late endosomal/lysosomal compartment of the cell. Even though there has been significant progress with understanding the cholesterol transport by NPC1 in combination with NPC2, especially after the structural determination of the full‐length NPC1 in 2016, many details such as the interaction of the full‐length NPC1 with the NPC2, the molecular motions responsible for the cholesterol transport during and after this interaction, and the structure and the function relations of many mutations are still not well understood. In this study, we report the extensive molecular dynamics simulations in order to gain insight into the structure and the dynamics of NPC1 lumenal domain for the cholesterol transport and the disease behind the mutation (R518W). It was found that the mutation induces a structural shift of the N‐terminal domain, toward the loop region in the middle lumenal domain, which is believed to play a central role in the interaction with NPC2 protein, so the interaction with the NPC2 protein might be less favorable compared to the wild NPC1. Also, the simulation indicates the possible re‐orientation of the N‐terminal domain with both the wild and the R518W‐mutated NPC1 after receiving the cholesterol from the NPC2 that align to form an internal tunnel, which is a possible pose for further action in cholesterol trafficking. We believe the current study can provide a better understanding of the cholesterol transport by NPC1 especially the role of NTD of NPC1 in combination with NPC2 interactions.
Collapse
Affiliation(s)
- Hye-Jin Yoon
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Hyunah Jeong
- Department of Chemistry, Sejong University, Seoul, Republic of Korea
| | - Hyung Ho Lee
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Soonmin Jang
- Department of Chemistry, Sejong University, Seoul, Republic of Korea
| |
Collapse
|
12
|
Structure-switching fluorescence aptasensor for sensitive detection of chloramphenicol. Mikrochim Acta 2020; 187:505. [PMID: 32815083 DOI: 10.1007/s00604-020-04471-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 08/02/2020] [Indexed: 01/09/2023]
Abstract
The performance of chloramphenicol aptamer, including binding thermodynamics, structure switching, and binding domain, was investigated by isothermal titration calorimetry, circular dichroism, and molecular docking. Then, a new fluorescence aptasensor was developed with signal amplification mediated by exonuclease I-catalyzed reaction and hybridization chain reaction (HCR) for chloramphenicol detection. In this system, the aptamer-binding domain is blocked by the initiator of HCR, the aptamer undergoes structure switching in the presence of chloramphenicol, and DNA dissociation occurs. The released aptamer is subsequently recognized and cleaved by Exo I to set free chloramphenicol. With the Exo I-assisted chloramphenicol recycling, an increasing number of initiators were exposed from the digestion of the initiator-aptamer complex. Then, the chain-like assembly of FAM labeled H1 and H2 through HCR was triggered by the initiator, generating a long DNA polymer. Under optimum conditions, the aptasensor exhibited a log-linear range from 0.001 to 100 nM of chloramphenicol and a detection limit of 0.3 pM. Additionally, the designed biosensing platform was applied to determine chloramphenicol in milk and lake water with high accuracy. The current approach provides a new avenue to develop sensitive aptasensors with the assistance of binding mechanism between aptamer and target compounds. Graphical abstract.
Collapse
|
13
|
Kim H, Pak Y. Balancing All‐Atom Force Field for
DNA
Simulations Using Osmotic Pressure Data. B KOREAN CHEM SOC 2020. [DOI: 10.1002/bkcs.12065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Hyeonjun Kim
- Department of Chemistry and Institute of Functional MaterialsPusan National University Busan 46241 South Korea
| | - Youngshang Pak
- Department of Chemistry and Institute of Functional MaterialsPusan National University Busan 46241 South Korea
| |
Collapse
|
14
|
Khoshbin Z, Housaindokht MR, Izadyar M, Bozorgmehr MR, Verdian A. Temperature and molecular crowding effects on the sensitivity of T30695 aptamer toward Pb2+ion: a joint molecular dynamics simulation and experimental study. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1751842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Zahra Khoshbin
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Mohammad Izadyar
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Asma Verdian
- Department of Food Safety and Quality Control, Research Institute of Food Science and Technology (RIFST), Mashhad, Iran
| |
Collapse
|
15
|
Zhang H, Gong Q, Zhang H, Chen C. FSATOOL: A useful tool to do the conformational sampling and trajectory analysis work for biomolecules. J Comput Chem 2020; 41:156-164. [PMID: 31603251 DOI: 10.1002/jcc.26083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/10/2019] [Accepted: 09/12/2019] [Indexed: 12/27/2022]
Abstract
Reliable conformational sampling and trajectory analysis are always important to the study of the folding or binding mechanisms of biomolecules. Generally, one has to prepare many complicated parameters and follow a lot of steps to obtain the final data. The whole process is too complicated to new users. In this article, we provide a convenient and user-friendly tool that is compatible to AMBER, called fast sampling and analysis tool (FSATOOL). FSATOOL has some useful features. First and the most important, the whole work is extremely simplified into two steps, one is the fast sampling procedure and the other is the trajectory analysis procedure. Second, it contains several powerful sampling methods for the simulation on graphics process unit, including our previous mixing replica exchange molecular dynamics method. The method combines the advantages of the biased and unbiased simulations. Finally, it extracts the dominant transition pathways automatically from the folding network by Markov state model. Users do not need to do the tedious intermediate steps by hand. To illustrate the usage of FSATOOL in practice, we perform one simulation for a RNA hairpin in explicit solvent. All the results are presented. © 2019 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Haomiao Zhang
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Qiankun Gong
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Haozhe Zhang
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Changjun Chen
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| |
Collapse
|
16
|
Molecular dynamics simulations of G-quadruplexes: The basic principles and their application to folding and ligand binding. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2020. [DOI: 10.1016/bs.armc.2020.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
Revealing conformational dynamics of 2'-O-methyl-RNA guanine modified G-quadruplex by replica exchange molecular dynamics. Biochem Biophys Res Commun 2019; 520:14-19. [PMID: 31564415 DOI: 10.1016/j.bbrc.2019.09.065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/08/2019] [Accepted: 09/16/2019] [Indexed: 12/12/2022]
Abstract
Thrombin-binding DNA aptamer (TBA) can fold into an antiparallel unimolecular G-quadruplex (G4) structure. Different types of modifications lead to various effects on the structure and stability of the G4 structure. Previous study has shown that a modified TBA (mTBA) that 2'-deoxy guanine (dG) at positions 10 and 11 in the TBA sequence were replaced by 2'-O-methyl-RNA guanine (2'OMe-G) can't fold into a well-defined G4 structure. In order to investigate the detailed structural information and probe the instability factors, we successfully employed the replica exchange molecular dynamics (REMD) to characterize the large conformational variations of the mTBA and systemically describe the influences of the 2'OMe-G on the mTBA in terms of conformation variations and the probability distributions of Hoogsteen hydrogen bonds, dihedral, sugar pucker and glycosyl torsion angle. Replacing position 10 with the 2'OMe-G (2'OMe-G10) induced a strong destabilization of the aptamer, while the 2'OMe-G at position 11(2'OMe-G11) was less destabilizing. More importantly, the glycosyl torsion angle and sugar pucker of 2'OMe-G10 were the most critical destabilization factors. These results were in good agreement with the theoretical and experimental results. Moreover, the structure information can be used as guidelines for the further design of modifications on G4 structure.
Collapse
|
19
|
Seelam Prabhakar P, A Manderville R, D Wetmore S. Impact of the Position of the Chemically Modified 5-Furyl-2'-Deoxyuridine Nucleoside on the Thrombin DNA Aptamer-Protein Complex: Structural Insights into Aptamer Response from MD Simulations. Molecules 2019; 24:molecules24162908. [PMID: 31405145 PMCID: PMC6720718 DOI: 10.3390/molecules24162908] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/06/2019] [Accepted: 08/07/2019] [Indexed: 02/07/2023] Open
Abstract
Aptamers are functional nucleic acids that bind to a range of targets (small molecules, proteins or cells) with a high affinity and specificity. Chemically-modified aptamers are of interest because the incorporation of novel nucleobase components can enhance aptamer binding to target proteins, while fluorescent base analogues permit the design of functional aptasensors that signal target binding. However, since optimally modified nucleoside designs have yet to be identified, information about how to fine tune aptamer stability and target binding affinity is required. The present work uses molecular dynamics (MD) simulations to investigate modifications to the prototypical thrombin-binding aptamer (TBA), which is a 15-mer DNA sequence that folds into a G-quadruplex structure connected by two TT loops and one TGT loop. Specifically, we modeled a previously synthesized thymine (T) analog, namely 5-furyl-2′-deoxyuridine (5FurU), into each of the six aptamer locations occupied by a thymine base in the TT or TGT loops of unbound and thrombin bound TBA. This modification and aptamer combination were chosen as a proof-of-principle because previous experimental studies have shown that TBA displays emissive sensitivity to target binding based on the local environment polarity at different 5FurU modification sites. Our simulations reveal that the chemically-modified base imparts noticeable structural changes to the aptamer without affecting the global conformation. Depending on the modification site, 5FurU performance is altered due to changes in the local environment, including the modification site structural dynamics, degree of solvent exposure, stacking with neighboring bases, and interactions with thrombin. Most importantly, these changes directly correlate with the experimentally-observed differences in the stability, binding affinity and emissive response of the modified aptamers. Therefore, the computational protocols implemented in the present work can be used in subsequent studies in a predictive way to aid the fine tuning of aptamer target recognition for use as biosensors (aptasensors) and/or therapeutics.
Collapse
Affiliation(s)
- Preethi Seelam Prabhakar
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AL T1K 3M4, Canada
| | - Richard A Manderville
- Department of Chemistry and Toxicology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AL T1K 3M4, Canada.
| |
Collapse
|
20
|
Metadynamics to Enhance Sampling in Biomolecular Simulations. Methods Mol Biol 2019. [PMID: 31396904 DOI: 10.1007/978-1-4939-9608-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Molecular dynamics is a powerful simulation method to provide detailed atomic-scale insight into a range of biological processes including protein folding, biochemical reactions, ligand binding, and many others. Over the last several decades, enhanced sampling methods have been developed to address the large separation in time scales between a molecular dynamics simulation (usually microseconds or shorter) and the time scales of biological processes (often orders of magnitude longer). This chapter specifically focuses on the metadynamics family of methods, which achieves enhanced sampling through the introduction of a history-dependent bias potential that is based on one or more slow degrees of freedom, called collective variables. We introduce the method and its recent variants related to biomolecular studies and then discuss frontier areas of the method. A large part of this chapter is devoted to helping new users of the method understand how to choose metadynamics parameters properly and apply the method to their system of interest.
Collapse
|
21
|
Kührová P, Mlýnský V, Zgarbová M, Krepl M, Bussi G, Best RB, Otyepka M, Šponer J, Banáš P. Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions. J Chem Theory Comput 2019; 15:3288-3305. [PMID: 30896943 PMCID: PMC7491206 DOI: 10.1021/acs.jctc.8b00955] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Molecular dynamics (MD) simulations became a leading tool for investigation of structural dynamics of nucleic acids. Despite recent efforts to improve the empirical potentials (force fields, ffs), RNA ffs have persisting deficiencies, which hamper their utilization in quantitatively accurate simulations. Previous studies have shown that at least two salient problems contribute to difficulties in the description of free-energy landscapes of small RNA motifs: (i) excessive stabilization of the unfolded single-stranded RNA ensemble by intramolecular base-phosphate and sugar-phosphate interactions and (ii) destabilization of the native folded state by underestimation of stability of base pairing. Here, we introduce a general ff term (gHBfix) that can selectively fine-tune nonbonding interaction terms in RNA ffs, in particular, the H bonds. The gHBfix potential affects the pairwise interactions between all possible pairs of the specific atom types, while all other interactions remain intact; i.e., it is not a structure-based model. In order to probe the ability of the gHBfix potential to refine the ff nonbonded terms, we performed an extensive set of folding simulations of RNA tetranucleotides and tetraloops. On the basis of these data, we propose particular gHBfix parameters to modify the AMBER RNA ff. The suggested parametrization significantly improves the agreement between experimental data and the simulation conformational ensembles, although our current ff version still remains far from being flawless. While attempts to tune the RNA ffs by conventional reparametrizations of dihedral potentials or nonbonded terms can lead to major undesired side effects, as we demonstrate for some recently published ffs, gHBfix has a clear promising potential to improve the ff performance while avoiding introduction of major new imbalances.
Collapse
Affiliation(s)
- 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
| | - Vojtěch Mlýnský
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Marie Zgarbová
- 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
| | - Miroslav Krepl
- 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
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, SISSA, via Bonomea 265, 34136 Trieste, Italy
| | - Robert B. Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| | - 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
- 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
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, 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
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| |
Collapse
|
22
|
Mo M, Kong D, Ji H, Lin D, Tang X, Yang Z, He Y, Wu L. Reversible Photocontrol of Thrombin Activity by Replacing Loops of Thrombin Binding Aptamer using Azobenzene Derivatives. Bioconjug Chem 2019; 30:231-241. [PMID: 30582682 DOI: 10.1021/acs.bioconjchem.8b00848] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The photoisomerization of azobenzenes provides a general means for the photocontrol of many important biomolecular structures and organismal functions. For temporal and spatial control activity of thrombin binding aptamer (TBA) by light, azobenzene derivatives were carefully selected as light-triggered molecular switches to replace TT loops and the TGT loop of TBA to reversibly control enzyme activity. These molecules interconverted between the trans and cis states under alternate UV and visible light irradiation, which consequently triggered reversible formation of G-quadruplex morphology. In addition, we investigated the impact of three azobenzene derivatives on stability, thrombin binding ability, and anticoagulant properties. The result showed that 4,4'-bis(hydroxymethyl)azobenzene at the TGT loop position significantly photoregulated affinity to thrombin and blood clotting in human plasma, which provided a successful strategy to control blood clotting in human plasma and a further evidence for design of TBA analogues with pivotal positions of modifications.
Collapse
Affiliation(s)
- Mengwu Mo
- School of Chemical Sciences , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Dejia Kong
- School of Chemical Sciences , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Heming Ji
- School of Chemical Sciences , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Dao Lin
- School of Chemical Sciences , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China
| | - Yujian He
- School of Chemical Sciences , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Li Wu
- School of Chemical Sciences , University of Chinese Academy of Sciences , Beijing 100049 , China.,State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China
| |
Collapse
|
23
|
Dans PD, Gallego D, Balaceanu A, Darré L, Gómez H, Orozco M. Modeling, Simulations, and Bioinformatics at the Service of RNA Structure. Chem 2019. [DOI: 10.1016/j.chempr.2018.09.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
24
|
Yang C, Kim E, Lim M, Pak Y. Computational Probing of Watson-Crick/Hoogsteen Breathing in a DNA Duplex Containing N1-Methylated Adenine. J Chem Theory Comput 2018; 15:751-761. [PMID: 30501194 DOI: 10.1021/acs.jctc.8b00936] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
DNA breathing is a local conformational fluctuation spontaneously occurring in double-stranded DNAs. In particular, the possibility of individual base pairs (bps) in duplex DNA to flip between alternate bp modes, i.e., Watson-Crick (WC)-like and Hoogsteen (HG)-like, at relevant time scales has impacted DNA research fields for many years. In this study, to computationally probe effects of chemical modification on the DNA breathing, we present a free energy landscape of spontaneous thermal transitions between WC and HG bps in a free DNA duplex containing N1-methylated adenine (m1A). For the current free energy computation, a variant of well-tempered metadynamics simulation was extensively performed for a total of 40 μs to produce free energy surfaces. The free energy profile indicated that, upon the chemical modification of adenine, the HG bp (m1A·T) was located in the most favorable conformation (96.7%); however, the canonical WC bp (m1A·T) was distorted into two WC-like bps of WC* (2.8%) and WC** (0.5%). The conformational exchange between these two minor WC-like bps occurs with the first hundred nanoseconds. The transition between WC-like and HG bp features multiple transition pathways displaying various extents of base flipping in combination with glycosidic rotation. Analysis of the simulated ensemble showed that the m1A-induced changes of the backbone and sugar pucker were in a reasonable agreement with previous results inferred from NMR experiments. Also, this study revealed that the formation of the stable HG bp upon the mutation alters the characteristics of dynamic fluctuations of the neighboring WC residues of m1A. We expect this simulation approach to be a robust computational scheme to complement and guide future high-resolution experiments on many outstanding issues of duplex DNA breathing.
Collapse
Affiliation(s)
- Changwon Yang
- Department of Chemistry and Institute of Functional Materials , Pusan National University , Busan 46241 , South Korea
| | - Eunae Kim
- College of Pharmacy , Chosun University , Gwangju 61452 , South Korea
| | - Manho Lim
- Department of Chemistry and Institute of Functional Materials , Pusan National University , Busan 46241 , South Korea
| | - Youngshang Pak
- Department of Chemistry and Institute of Functional Materials , Pusan National University , Busan 46241 , South Korea
| |
Collapse
|
25
|
Si MK, Pramanik SK, Ganguly B. Tuning the ring strain effect in acridine derivatives on binding affinity with G-quadruplex-DNA: A computational and experimental study. Int J Biol Macromol 2018; 124:1177-1185. [PMID: 30521912 DOI: 10.1016/j.ijbiomac.2018.12.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 12/01/2018] [Accepted: 12/01/2018] [Indexed: 12/22/2022]
Abstract
Search for inhibitors to stabilize the telomeric G-quadruplex in order to deter telomerase activity is an active area of research. Inhibitors play an important role to initiate the tumor cell mortalization process. This work reports for the first time of acridine derivative with four membered ammonium rings at the side chain to surpass the binding ability against BRACO-19 with G-quadruplex-DNA. It is known in the literature that acridine based molecule BRACO-19 can effectively bind with G-quadruplex-DNA. The computational study performed in this study revealed that the binding ability of acridine based molecule can be augmented with subtle variation in the molecular structure of the drug like candidates. Steered molecular dynamics (SMD) performed with the acridine derivatives and G-quadruplex DNA showed the importance of ring strain to the side chain of those ligand molecules. The rupture force analysis, hydrogen bonding interactions and the calculated free energies in MM-PBSA method suggest that ligand 3 is superior than that of BRACO-19. The synthesized ligand 3 and BRACO-19 showed the binding constants obtained from ITC measurements are 4 × 106 mol-1 and 2.6 × 106, which corroborates the computational findings.
Collapse
Affiliation(s)
- Mrinal Kanti Si
- Computation and Simulation Unit (Analytical and Environmental Science Division and Centralized Instrument Facility), CSIR-Central Salt & Marine Chemicals Research Institute, India; Academy of Scientific and Innovative Research, CSIR-CSMCRI, Bhavnagar, Gujarat 364 002, India
| | - Sumit Kumar Pramanik
- Computation and Simulation Unit (Analytical and Environmental Science Division and Centralized Instrument Facility), CSIR-Central Salt & Marine Chemicals Research Institute, India
| | - Bishwajit Ganguly
- Computation and Simulation Unit (Analytical and Environmental Science Division and Centralized Instrument Facility), CSIR-Central Salt & Marine Chemicals Research Institute, India; Academy of Scientific and Innovative Research, CSIR-CSMCRI, Bhavnagar, Gujarat 364 002, India.
| |
Collapse
|
26
|
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.
Collapse
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.
| |
Collapse
|
27
|
Havrila M, Stadlbauer P, Kührová P, Banáš P, Mergny JL, Otyepka M, Šponer J. Structural dynamics of propeller loop: towards folding of RNA G-quadruplex. Nucleic Acids Res 2018; 46:8754-8771. [PMID: 30165550 PMCID: PMC6158699 DOI: 10.1093/nar/gky712] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 07/03/2018] [Accepted: 07/27/2018] [Indexed: 02/04/2023] Open
Abstract
We have carried out an extended set of standard and enhanced-sampling MD simulations (for a cumulative simulation time of 620 μs) with the aim to study folding landscapes of the rGGGUUAGGG and rGGGAGGG parallel G-hairpins (PH) with propeller loop. We identify folding and unfolding pathways of the PH, which is bridged with the unfolded state via an ensemble of cross-like structures (CS) possessing mutually tilted or perpendicular G-strands interacting via guanine-guanine H-bonding. The oligonucleotides reach the PH conformation from the unfolded state via a conformational diffusion through the folding landscape, i.e. as a series of rearrangements of the H-bond interactions starting from compacted anti-parallel hairpin-like structures. Although isolated PHs do not appear to be thermodynamically stable we suggest that CS and PH-types of structures are sufficiently populated during RNA guanine quadruplex (GQ) folding within the context of complete GQ-forming sequences. These structures may participate in compact coil-like ensembles that involve all four G-strands and already some bound ions. Such ensembles can then rearrange into the fully folded parallel GQs via conformational diffusion. We propose that the basic atomistic folding mechanism of propeller loops suggested in this work may be common for their formation in RNA and DNA GQs.
Collapse
Affiliation(s)
- Marek Havrila
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Petra Kührová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Jean-Louis Mergny
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- Université de Bordeaux, INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, Pessac, France
| | - Michal Otyepka
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| |
Collapse
|
28
|
Islam B, Stadlbauer P, Krepl M, Havrila M, Haider S, Sponer J. Structural Dynamics of Lateral and Diagonal Loops of Human Telomeric G-Quadruplexes in Extended MD Simulations. J Chem Theory Comput 2018; 14:5011-5026. [DOI: 10.1021/acs.jctc.8b00543] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Barira Islam
- Institute of Biophysics
of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Petr Stadlbauer
- Institute of Biophysics
of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Miroslav Krepl
- Institute of Biophysics
of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Marek Havrila
- Institute of Biophysics
of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Shozeb Haider
- UCL School of
Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, U.K
| | - Jiri Sponer
- Institute of Biophysics
of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| |
Collapse
|
29
|
Kulkarni M, Yang C, Pak Y. Refined Alkali Metal Ion Parameters for the OPC Water Model. B KOREAN CHEM SOC 2018. [DOI: 10.1002/bkcs.11527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mandar Kulkarni
- Department of Chemistry and Institute of Functional Materials; Pusan National University; Busan 609-735 South Korea
| | - Changwon Yang
- Department of Chemistry and Institute of Functional Materials; Pusan National University; Busan 609-735 South Korea
| | - Youngshang Pak
- Department of Chemistry and Institute of Functional Materials; Pusan National University; Busan 609-735 South Korea
| |
Collapse
|
30
|
Gutiérrez I, Garavís M, de Lorenzo S, Villasante A, González C, Arias-Gonzalez JR. Single-Stranded Condensation Stochastically Blocks G-Quadruplex Assembly in Human Telomeric RNA. J Phys Chem Lett 2018; 9:2498-2503. [PMID: 29688724 DOI: 10.1021/acs.jpclett.8b00722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
TERRA is an RNA molecule transcribed from human subtelomeric regions toward chromosome ends potentially involved in regulation of heterochromatin stability, semiconservative replication, and telomerase inhibition, among others. TERRA contains tandem repeats of the sequence GGGUUA, with a strong tendency to fold into a four-stranded arrangement known as a parallel G-quadruplex. Here, we demonstrate by using single-molecule force spectroscopy that this potential is limited by the inherent capacity of RNA to self-associate randomly and further condense into entropically more favorable structures. We stretched RNA constructions with more than four and less than eight hexanucleotide repeats, thus unable to form several G-quadruplexes in tandem, flanked by non-G-rich overhangs of random sequence by optical tweezers on a one by one basis. We found that condensed RNA stochastically blocks G-quadruplex folding pathways with a near 20% probability, a behavior that is not found in DNA analogous molecules.
Collapse
Affiliation(s)
- Irene Gutiérrez
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia) , Cantoblanco, 28049 Madrid , Spain
| | - Miguel Garavís
- Instituto de Química Física Rocasolano, CSIC , C/Serrano 119 , 28006 Madrid , Spain
| | - Sara de Lorenzo
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia) , Cantoblanco, 28049 Madrid , Spain
| | - Alfredo Villasante
- Centro de Biología Molecular "Severo Ochoa" CSIC-UAM , C/Nicolás Cabrera 1 , 28049 Madrid , Spain
| | - Carlos González
- Instituto de Química Física Rocasolano, CSIC , C/Serrano 119 , 28006 Madrid , Spain
| | - 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" , Cantoblanco, 28049 Madrid , Spain
| |
Collapse
|
31
|
Šponer J, Bussi G, Krepl M, Banáš P, Bottaro S, Cunha RA, Gil-Ley A, Pinamonti G, Poblete S, Jurečka P, Walter NG, Otyepka M. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chem Rev 2018; 118:4177-4338. [PMID: 29297679 PMCID: PMC5920944 DOI: 10.1021/acs.chemrev.7b00427] [Citation(s) in RCA: 327] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Indexed: 12/14/2022]
Abstract
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.
Collapse
Affiliation(s)
- Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Sandro Bottaro
- Structural Biology and NMR Laboratory, Department of Biology , University of Copenhagen , Copenhagen 2200 , Denmark
| | - Richard A Cunha
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Alejandro Gil-Ley
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Giovanni Pinamonti
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Simón Poblete
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| |
Collapse
|