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Nguyen H, Pérez A, Bermeo S, Simmerling C. Refinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and Their Complexes with Proteins. J Chem Theory Comput 2015; 11:3714-28. [PMID: 26574454 PMCID: PMC4805114 DOI: 10.1021/acs.jctc.5b00271] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Generalized Born (GB) implicit solvent model has undergone significant improvements in accuracy for modeling of proteins and small molecules. However, GB still remains a less widely explored option for nucleic acid simulations, in part because fast GB models are often unable to maintain stable nucleic acid structures or they introduce structural bias in proteins, leading to difficulty in application of GB models in simulations of protein-nucleic acid complexes. Recently, GB-neck2 was developed to improve the behavior of protein simulations. In an effort to create a more accurate model for nucleic acids, a similar procedure to the development of GB-neck2 is described here for nucleic acids. The resulting parameter set significantly reduces absolute and relative energy error relative to Poisson-Boltzmann for both nucleic acids and nucleic acid-protein complexes, when compared to its predecessor GB-neck model. This improvement in solvation energy calculation translates to increased structural stability for simulations of DNA and RNA duplexes, quadruplexes, and protein-nucleic acid complexes. The GB-neck2 model also enables successful folding of small DNA and RNA hairpins to near native structures as determined from comparison with experiment. The functional form and all required parameters are provided here and also implemented in the AMBER software.
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Affiliation(s)
- Hai Nguyen
- Department of Chemistry, ‡Laufer Center for Physical and Quantitative Biology, and §Department of Biochemistry, Stony Brook University , Stony Brook, New York 11794, USA
| | - Alberto Pérez
- Department of Chemistry, ‡Laufer Center for Physical and Quantitative Biology, and §Department of Biochemistry, Stony Brook University , Stony Brook, New York 11794, USA
| | - Sherry Bermeo
- Department of Chemistry, ‡Laufer Center for Physical and Quantitative Biology, and §Department of Biochemistry, Stony Brook University , Stony Brook, New York 11794, USA
| | - Carlos Simmerling
- Department of Chemistry, ‡Laufer Center for Physical and Quantitative Biology, and §Department of Biochemistry, Stony Brook University , Stony Brook, New York 11794, USA
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2
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Caruso M, Gatto E, Placidi E, Ballano G, Formaggio F, Toniolo C, Zanuy D, Alemán C, Venanzi M. A single-residue substitution inhibits fibrillization of Ala-based pentapeptides. A spectroscopic and molecular dynamics investigation. SOFT MATTER 2014; 10:2508-2519. [PMID: 24647758 DOI: 10.1039/c3sm52831f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The aggregation properties of two Ala-based pentapeptides were investigated by spectroscopic techniques and molecular dynamics (MD) simulations. The two peptides, both functionalized at the N-terminus with a pyrenyl group, differ in the insertion of an α-aminoisobutyric acid residue at position 4. We showed that this single modification of the homo-peptide sequence inhibits the aggregation of the pentapeptide in aqueous solutions. Atomic force microscopy imaging revealed that the two peptides form mesoscopic aggregates of very different morphologies when deposited on mica. MD experiments showed that the two peptides have a very different propensity to form β-pleated sheet structures, as confirmed by our spectroscopic measurements. The implications of these findings for our understanding of the mechanism leading to the formation of amyloid structures, primary responsible for numerous neurodegenerative diseases, are also discussed.
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Affiliation(s)
- Mario Caruso
- Department of Chemical Sciences and Technologies, University of Rome "Tor Vergata", 00133 Rome, Italy.
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3
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Naserian-Nik AM, Tahani M, Karttunen M. Pulling of double-stranded DNA by atomic force microscopy: a simulation in atomistic details. RSC Adv 2013. [DOI: 10.1039/c3ra23213a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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4
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Printz M, Richert C. Pyrenylmethyldeoxyadenosine: A 3′-Cap for Universal DNA Hybridization Probes. Chemistry 2009; 15:3390-402. [DOI: 10.1002/chem.200801587] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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5
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Réblová K, Fadrná E, Sarzynska J, Kulinski T, Kulhánek P, Ennifar E, Koca J, Sponer J. Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics. Biophys J 2007; 93:3932-49. [PMID: 17704156 PMCID: PMC2099213 DOI: 10.1529/biophysj.107.110056] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Explicit solvent molecular dynamics simulations (in total almost 800 ns including locally enhanced sampling runs) were applied with different ion conditions and with two force fields (AMBER and CHARMM) to characterize typical geometries adopted by the flanking bases in the RNA kissing-loop complexes. We focus on flanking base positions in multiple x-ray and NMR structures of HIV-1 DIS kissing complexes and kissing complex from the large ribosomal subunit of Haloarcula marismortui. An initial x-ray open conformation of bulged-out bases in HIV-1 DIS complexes, affected by crystal packing, tends to convert to a closed conformation formed by consecutive stretch of four stacked purine bases. This is in agreement with those recent crystals where the packing is essentially avoided. We also observed variants of the closed conformation with three stacked bases, while nonnegligible populations of stacked geometries with bulged-in bases were detected, too. The simulation results reconcile differences in positions of the flanking bases observed in x-ray and NMR studies. Our results suggest that bulged-out geometries are somewhat more preferred, which is in accord with recent experiments showing that they may mediate tertiary contacts in biomolecular assemblies or allow binding of aminoglycoside antibiotics.
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Affiliation(s)
- Kamila Réblová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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6
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7
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Zuo X, Cui G, Merz KM, Zhang L, Lewis FD, Tiede DM. X-ray diffraction "fingerprinting" of DNA structure in solution for quantitative evaluation of molecular dynamics simulation. Proc Natl Acad Sci U S A 2006; 103:3534-9. [PMID: 16505363 PMCID: PMC1383498 DOI: 10.1073/pnas.0600022103] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Solution state x-ray diffraction fingerprinting is demonstrated as a method for experimentally assessing the accuracy of molecular dynamics (MD) simulations. Fourier transforms of coordinate data from MD simulations are used to produce reciprocal space "fingerprints" of atomic pair distance correlations that are characteristic of the ensemble and are the direct numerical analogues of experimental solution x-ray diffraction (SXD). SXD experiments and MD simulations were carried out to test the ability of experiment and simulation to resolve sequence-dependent modifications in helix conformation for B-form DNA. SXD experiments demonstrated that solution-state poly(AT) and poly(A)-poly(T) duplex DNA sequences exist in ensembles close to canonical B-form and B'-form structures, respectively. In contrast, MD simulations analyzed in terms of SXD fingerprints are shown to deviate from experiment, most significantly for poly(A)-poly(T) duplex DNA. Compared with experiment, MD simulation shortcomings were found to include both mismatches in simulated conformer structures and number population within the ensembles. This work demonstrates an experimental approach for quantitatively evaluating MD simulations and other coordinate models to simulate biopolymer structure in solution and suggests opportunities to use solution diffraction data as experimental benchmarks for developing supramolecular force fields optimized for a range of in situ applications.
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Affiliation(s)
- Xiaobing Zuo
- *Chemistry Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439
| | - Guanglei Cui
- Department of Chemistry, University of Florida, 2328 New Physics Building, Gainesville, FL 32611-8435; and
| | - Kenneth M. Merz
- Department of Chemistry, University of Florida, 2328 New Physics Building, Gainesville, FL 32611-8435; and
| | - Ligang Zhang
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208
| | - Frederick D. Lewis
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208
| | - David M. Tiede
- *Chemistry Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439
- To whom correspondence should be addressed. E-mail:
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8
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Cheng X, Kelso C, Hornak V, de los Santos C, Grollman AP, Simmerling C. Dynamic behavior of DNA base pairs containing 8-oxoguanine. J Am Chem Soc 2005; 127:13906-18. [PMID: 16201812 PMCID: PMC8295720 DOI: 10.1021/ja052542s] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The process by which DNA repair enzymes recognize and selectively excise damaged bases in duplex DNA is fundamental to our mechanistic understanding of these critical biological reactions. 8-Oxoguanine (8-oxoG) is the most common form of oxidative DNA damage; unrepaired, this lesion generates a G:C-->T:A mutation. Central to the recognition and repair of DNA damage is base extrusion, a process in which the damaged base lesion or, in some cases, its partner disengages from the helix and is bound to the enzyme's active site where base excision takes place. The conformation adopted by 8-oxoG in duplex DNA is affected by the base positioned opposite this lesion; conformational changes may also take place when the damaged base binds to its cognate repair enzyme. We performed unrestrained molecular dynamics simulations for several 13-mer DNA duplexes. Oligomers containing G:C and 8oxoG:C pairs adopted Watson-Crick geometries in stable B-form duplexes; 8oxoG showed increased local and global flexibility and a reduced barrier to base extrusion. Duplexes containing the G:A mismatch showed much larger structural fluctuations and failed to adopt a well-defined structure. For the 8oxoG:A mismatch that is recognized by the DNA glycosylase MutY, the damaged nucleoside underwent spontaneous and reproducible anti-->syn transitions. The syn conformation is thermodynamically preferred. Steric hindrance and unfavorable electrostatics associated with the 8oxoG O8 atom in the anti conformation were the major driving forces for this transition. Transition events follow two qualitatively different pathways. The overall anti-->syn transition rate and relative probability of the two transition paths were dependent on local sequence context. These simulations indicate that both the dynamic and equilibrium behavior of the duplex change as a result of oxidation; these differences may provide valuable new insight into the selective action of enzymes on damaged DNA.
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Affiliation(s)
- Xiaolin Cheng
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400
| | - Catherine Kelso
- Ward Melville High School, East Setauket, NY 11733
- Center for Structural Biology, Stony Brook University, Stony Brook, NY 11794-3400
| | - Viktor Hornak
- Center for Structural Biology, Stony Brook University, Stony Brook, NY 11794-3400
| | - Carlos de los Santos
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-3400
| | - Arthur P. Grollman
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-3400
| | - Carlos Simmerling
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400
- Center for Structural Biology, Stony Brook University, Stony Brook, NY 11794-3400
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9
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Cheng X, Cui G, Hornak V, Simmerling C. Modified replica exchange simulation methods for local structure refinement. J Phys Chem B 2005; 109:8220-30. [PMID: 16851961 PMCID: PMC4805125 DOI: 10.1021/jp045437y] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Parallel tempering, also known as replica exchange molecular dynamics (REMD), has recently been successfully used to study the structure and thermodynamic properties of biomolecules such as peptides and small proteins. For large systems, however, applying REMD can be costly since the number of replicas needed increases as the square root of the number of degrees of freedom in the system. Often, enhanced sampling is only needed for a subset of atoms, such as a loop region of a large protein or a small ligand binding to a receptor. In such applications, it is often reasonable to assume a weak dependence of the structure of the larger region on the instantaneous conformation of the smaller region of interest. For these cases, we derived two variant replica exchange methods, partial replica exchange molecular dynamics (PREMD) and local replica exchange molecular dynamics (LREMD). The Hamiltonian for the system is separated, with replica exchange carried out only for terms involving the subsystem of interest while the remainder of the system is maintained at a single temperature. The number of replicas required for efficient exchange thus depends on the number of degrees of freedom in the fragment needing refinement rather than on the size of the full system. The method can be applied to much larger systems than was previously practical. This also provides a means to preserve the integrity of the structure outside the refinement region without introduction of restraints. LREMD takes this weak coupling approximation a step further, employing only a single representation of the large fragment that simultaneously interacts with all of the replicas of the subsystem of interest. This is obtained by combining replica exchange with the locally enhanced sampling approximation (LES), reducing the computational expense of replica exchange simulations to near that of a single standard molecular dynamics (MD) simulation. Use of LREMD also permits the use of LES without requiring the specification of a single temperature, a known difficulty for standard LES simulations. We tested these two methods on the loop region of an RNA hairpin model system and find significant advantages over standard MD and REMD simulations.
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Affiliation(s)
- Xiaolin Cheng
- Department of Chemistry and Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794-3400, USA
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10
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Fadrná E, Spacková N, Stefl R, Koca J, Cheatham TE, Sponer J. Molecular dynamics simulations of Guanine quadruplex loops: advances and force field limitations. Biophys J 2005; 87:227-42. [PMID: 15240460 PMCID: PMC1304345 DOI: 10.1529/biophysj.103.034751] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A computational analysis of d(GGGGTTTTGGGG)(2) guanine quadruplexes containing either lateral or diagonal four-thymidine loops was carried out using molecular dynamics (MD) simulations in explicit solvent, locally enhanced sampling (LES) simulations, systematic conformational search, and free energy molecular-mechanics, Poisson Boltzmann, surface area (MM-PBSA) calculations with explicit inclusion of structural monovalent cations. The study provides, within the approximations of the applied all-atom additive force field, a qualitatively complete analysis of the available loop conformational space. The results are independent of the starting structures. Major conformational transitions not seen in conventional MD simulations are observed when LES is applied. The favored LES structures consistently provide lower free energies (as estimated by molecular-mechanics, Poisson Boltzmann, surface area) than other structures. Unfortunately, the predicted optimal structure for the diagonal loop arrangement differs substantially from the atomic resolution experiments. This result is attributed to force field deficiencies, such as the potential misbalance between solute-cation and solvent-cation terms. The MD simulations are unable to maintain the stable coordination of the monovalent cations inside the diagonal loops as reported in a recent x-ray study. The optimal diagonal and lateral loop arrangements appear to be close in energy although a proper inclusion of the loop monovalent cations could stabilize the diagonal architecture.
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Affiliation(s)
- Eva Fadrná
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
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11
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Chapter 6 Molecular Modeling and Atomistic Simulation of Nucleic Acids. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/s1574-1400(05)01006-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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12
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Kawai K, Yoshida H, Takada T, Tojo S, Majima T. Formation of Pyrene Dimer Radical Cation at the Internal Site of Oligodeoxynucleotides. J Phys Chem B 2004. [DOI: 10.1021/jp049543b] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Hiroko Yoshida
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Tadao Takada
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Sachiko Tojo
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Tetsuro Majima
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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13
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García-Cruz I, Martínez-Magadán JM, Bofill JM, Illas F. Theoretical Prediction of Benzyne-Like Species in Pyrene Diradicals. J Phys Chem A 2004. [DOI: 10.1021/jp037795r] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- I. García-Cruz
- Programa de Ingenieria Molecular, Instituto Mexicano del Petróleo, Eje Central Lázaro Cárdenas 152, Colonia San Bartolo Atepehuacán, México D. F., 07730, México, Departament de Química Orgànica i Centre especial de Recerca en Química Teòrica, Universitat de Barcelona i Parc Científic de Barcelona, C/Martí i Franquès 1, 08028 Barcelona, Spain, and Departament de Química Física i Centre especial de Recerca en Química Teòrica, Universitat de Barcelona i Parc Científic de Barcelona, C/Martí i Franquès 1,
| | - J. M. Martínez-Magadán
- Programa de Ingenieria Molecular, Instituto Mexicano del Petróleo, Eje Central Lázaro Cárdenas 152, Colonia San Bartolo Atepehuacán, México D. F., 07730, México, Departament de Química Orgànica i Centre especial de Recerca en Química Teòrica, Universitat de Barcelona i Parc Científic de Barcelona, C/Martí i Franquès 1, 08028 Barcelona, Spain, and Departament de Química Física i Centre especial de Recerca en Química Teòrica, Universitat de Barcelona i Parc Científic de Barcelona, C/Martí i Franquès 1,
| | - J. M. Bofill
- Programa de Ingenieria Molecular, Instituto Mexicano del Petróleo, Eje Central Lázaro Cárdenas 152, Colonia San Bartolo Atepehuacán, México D. F., 07730, México, Departament de Química Orgànica i Centre especial de Recerca en Química Teòrica, Universitat de Barcelona i Parc Científic de Barcelona, C/Martí i Franquès 1, 08028 Barcelona, Spain, and Departament de Química Física i Centre especial de Recerca en Química Teòrica, Universitat de Barcelona i Parc Científic de Barcelona, C/Martí i Franquès 1,
| | - F. Illas
- Programa de Ingenieria Molecular, Instituto Mexicano del Petróleo, Eje Central Lázaro Cárdenas 152, Colonia San Bartolo Atepehuacán, México D. F., 07730, México, Departament de Química Orgànica i Centre especial de Recerca en Química Teòrica, Universitat de Barcelona i Parc Científic de Barcelona, C/Martí i Franquès 1, 08028 Barcelona, Spain, and Departament de Química Física i Centre especial de Recerca en Química Teòrica, Universitat de Barcelona i Parc Científic de Barcelona, C/Martí i Franquès 1,
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14
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Somoza MM, Andreatta D, Murphy CJ, Coleman RS, Berg MA. Effect of lesions on the dynamics of DNA on the picosecond and nanosecond timescales using a polarity sensitive probe. Nucleic Acids Res 2004; 32:2494-507. [PMID: 15131253 PMCID: PMC419465 DOI: 10.1093/nar/gkh577] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2004] [Revised: 04/12/2004] [Accepted: 04/12/2004] [Indexed: 01/12/2023] Open
Abstract
This paper explores the effects of structural modifications on the fast dynamics of DNA and the ability of time-resolved Stokes shift spectroscopy to measure those changes. The time-resolved Stokes shift of a synthetic coumarin base-pair replacement within an oligomer is measured between 40 ps and 40 ns. Comparisons are made between 17mers without modification, with a deleted base near the coumarin and with the coumarin placed near the end of the oligomer. The deletion of a next-to-nearest-neighbor base pair does not change the subnanosecond dynamics, but does cause an additional motion with a time constant of approximately 20 ns. A candidate for this motion is the flipping of the abasic sugar out of the helix and the concomitant intrusion of water into the interior of the helix. A nearby chain end causes little change in the dynamics after 1 ns but leads to a reduction in the amplitude of the dynamics between 40 ps and 1 ns. We suggest that at the chain end, where DNA on one side of the probe has been replaced by water, the charge- stabilizing dynamics have the same overall amplitude, but that much of the relaxation occurs before the start of the measurement time window.
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Affiliation(s)
- Mark M Somoza
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
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15
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Pan Y, MacKerell AD. Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening. Nucleic Acids Res 2004; 31:7131-40. [PMID: 14654688 PMCID: PMC291876 DOI: 10.1093/nar/gkg941] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
DNA and RNA are known to have different structural properties. In the present study, molecular dynamics (MD) simulations on a series of RNA and DNA duplexes indicate differential structural flexibility for the two classes of oligonucleotides. In duplex RNA, multiple base pairs experienced local opening events into the major groove on the nanosecond time scale, while such events were not observed in the DNA simulations. Three factors are indicated to be responsible for the base opening events in RNA: solvent-base interactions, 2'OH(n)-O4'(n+1) intra-strand hydrogen bonding, and enhanced rigid body motion of RNA at the nucleoside level. Water molecules in the major groove of RNA contribute to initiation of base pair opening. Stabilization of the base pair open state is due to a 'conformational switch' comprised of 2'OH(n)-O4'(n+1) hydrogen bonding and a rigid body motion of the nucleoside moiety in RNA. This rigid body motion is associated with decreased flexibility of the glycosyl linkage and sugar moieties in A-form structures. The observed opening rates in RNA are consistent with the imino proton exchange experiments for AU base pairs, although not for GC base pairs, while structural and flexibility changes associated with the proposed conformational switch are consistent with survey data of RNA and DNA crystal structures. The possible relevance of base pair opening events in RNA to its many biological functions is discussed.
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Affiliation(s)
- Yongping Pan
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
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16
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Cheng X, Hornak V, Simmerling C. Improved Conformational Sampling through an Efficient Combination of Mean-Field Simulation Approaches. J Phys Chem B 2003. [DOI: 10.1021/jp034505y] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiaolin Cheng
- Department of Chemistry and Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794-3400
| | - Viktor Hornak
- Department of Chemistry and Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794-3400
| | - Carlos Simmerling
- Department of Chemistry and Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794-3400
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17
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Réblová K, Spacková N, Stefl R, Csaszar K, Koca J, Leontis NB, Sponer J. Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E. Biophys J 2003; 84:3564-82. [PMID: 12770867 PMCID: PMC1302943 DOI: 10.1016/s0006-3495(03)75089-9] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Explicit solvent and counterion molecular dynamics simulations have been carried out for a total of >80 ns on the bacterial and spinach chloroplast 5S rRNA Loop E motifs. The Loop E sequences form unique duplex architectures composed of seven consecutive non-Watson-Crick basepairs. The starting structure of spinach chloroplast Loop E was modeled using isostericity principles, and the simulations refined the geometries of the three non-Watson-Crick basepairs that differ from the consensus bacterial sequence. The deep groove of Loop E motifs provides unique sites for cation binding. Binding of Mg(2+) rigidifies Loop E and stabilizes its major groove at an intermediate width. In the absence of Mg(2+), the Loop E motifs show an unprecedented degree of inner-shell binding of monovalent cations that, in contrast to Mg(2+), penetrate into the most negative regions inside the deep groove. The spinach chloroplast Loop E shows a marked tendency to compress its deep groove compared with the bacterial consensus. Structures with a narrow deep groove essentially collapse around a string of Na(+) cations with long coordination times. The Loop E non-Watson-Crick basepairing is complemented by highly specific hydration sites ranging from water bridges to hydration pockets hosting 2 to 3 long-residing waters. The ordered hydration is intimately connected with RNA local conformational variations.
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Affiliation(s)
- Kamila Réblová
- National Center for Biomolecular Research, Brno, Czech Republic
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