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Cachau RE, Gussio R, Beutler JA, Chmurny GN, Hilton BD, Muschik GM, Erickson JW. Solution Structure of Taxol Determined Using a Novel Feedback-Scaling Procedure for Noe-Restrained Molecular Dynamics. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/109434209400800104] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The increasing availability of high-performance com puters makes it possible to treat larger systems in shorter computing times. However, a more challeng ing aspect of the availability of larger and faster com puters is the exploration of alternative algorithms. This is especially important in view of new computer archi tectures. In this work we describe a novel technique for feedback-scaling individual NOE distance restraints during molecular-dynamics-simulated annealing ex periments.
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Affiliation(s)
- Raul E. Cachau
- NATIONAL CANCER INSTITUTE FREDERICK CANCER RESEARCH
AND DEVELOPMENT CENTER FREDERICK, MARYLAND 21702
| | - Rick Gussio
- NATIONAL CANCER INSTITUTE FREDERICK CANCER RESEARCH
AND DEVELOPMENT CENTER FREDERICK, MARYLAND 21702
| | - John A. Beutler
- NATIONAL CANCER INSTITUTE FREDERICK CANCER RESEARCH
AND DEVELOPMENT CENTER FREDERICK, MARYLAND 21702
| | - Gwendolyn N. Chmurny
- NATIONAL CANCER INSTITUTE FREDERICK CANCER RESEARCH
AND DEVELOPMENT CENTER FREDERICK, MARYLAND 21702
| | - Bruce D. Hilton
- NATIONAL CANCER INSTITUTE FREDERICK CANCER RESEARCH
AND DEVELOPMENT CENTER FREDERICK, MARYLAND 21702
| | - Gary M. Muschik
- NATIONAL CANCER INSTITUTE FREDERICK CANCER RESEARCH
AND DEVELOPMENT CENTER FREDERICK, MARYLAND 21702
| | - John W. Erickson
- NATIONAL CANCER INSTITUTE FREDERICK CANCER RESEARCH
AND DEVELOPMENT CENTER FREDERICK, MARYLAND 21702
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2
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Palazzesi F, Barducci A, Tollinger M, Parrinello M. The allosteric communication pathways in KIX domain of CBP. Proc Natl Acad Sci U S A 2013; 110:14237-42. [PMID: 23940332 PMCID: PMC3761601 DOI: 10.1073/pnas.1313548110] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Allosteric regulation plays an important role in a myriad of biomacromolecular processes. Specifically, in a protein, the process of allostery refers to the transmission of a local perturbation, such as ligand binding, to a distant site. Decades after the discovery of this phenomenon, models built on static images of proteins are being reconsidered with the knowledge that protein dynamics plays an important role in its function. Molecular dynamics simulations are a valuable tool for studying complex biomolecular systems, providing an atomistic description of their structure and dynamics. Unfortunately, their predictive power has been limited by the complexity of the biomolecule free-energy surface and by the length of the allosteric timescale (in the order of milliseconds). In this work, we are able to probe the origins of the allosteric changes that transcription factor mixed lineage leukemia (MLL) causes to the interactions of KIX domain of CREB-binding protein (CBP) with phosphorylated kinase inducible domain (pKID), by combing all-atom molecular dynamics with enhanced sampling methods recently developed in our group. We discuss our results in relation to previous NMR studies. We also develop a general simulations protocol to study allosteric phenomena and many other biological processes that occur in the micro/milliseconds timescale.
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Affiliation(s)
- Ferruccio Palazzesi
- Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich, CH-8093 Zurich, Switzerland
- Facoltà di Informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, 6900 Lugano, Switzerland
| | - Alessandro Barducci
- Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich, CH-8093 Zurich, Switzerland
- Facoltà di Informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, 6900 Lugano, Switzerland
- Laboratoire de Biophysique Statistique, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland; and
| | - Martin Tollinger
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
| | - Michele Parrinello
- Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich, CH-8093 Zurich, Switzerland
- Facoltà di Informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, 6900 Lugano, Switzerland
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3
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Kahn TR, Fong KK, Jordan B, Lek JC, Levitan R, Mitchell PS, Wood C, Hatcher ME. An FTIR investigation of flanking sequence effects on the structure and flexibility of DNA binding sites. Biochemistry 2009; 48:1315-21. [PMID: 19166330 DOI: 10.1021/bi8015235] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fourier transform infrared (FTIR) spectroscopy and a library of FTIR marker bands have been used to examine the structure and relative flexibilities conferred by different flanking sequences on the EcoRI binding site. This approach allowed us to examine unique peaks and subtle changes in the spectra of d(AAAGAATTCTTT)(2), d(TTCGAATTCGAA)(2), and d(CGCGAATTCGCG)(2) and thereby identify local changes in base pairing, base stacking, backbone conformation, glycosidic bond rotation, and sugar puckering in the studied sequences. The changes in flanking sequences induce differences in the sugar puckers, glycosidic bond rotation, and backbone conformations. Varying levels of local flexibility are observed within the sequences in agreement with previous biological activity assays. The results also provide supporting evidence for the presence of a splay in the G(4)-C(9) base pair of the EcoRI binding site and a potential pocket of flexibility at the G(4) cleavage site that have been proposed in the literature. In sum, we have demonstrated that FTIR is a powerful methodology for studying the effect of flanking sequences on DNA structure and flexibility, for it can provide information about the local structure of the nucleic acid and the overall relative flexibilities conferred by different flanking sequences.
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Affiliation(s)
- Talia R Kahn
- Joint Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, USA
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4
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Narayana N, Weiss MA. Crystallographic analysis of a sex-specific enhancer element: sequence-dependent DNA structure, hydration, and dynamics. J Mol Biol 2008; 385:469-90. [PMID: 18992257 DOI: 10.1016/j.jmb.2008.10.041] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2008] [Revised: 10/02/2008] [Accepted: 10/06/2008] [Indexed: 11/29/2022]
Abstract
The crystal structure of a sex-specific enhancer element is described at a resolution of 1.6 A. This 16-bp site, designated Dsx(A), functions in the regulation of a genetic switch between male and female patterns of gene expression in Drosophila melanogaster. Related sites are broadly conserved in metazoans, including in the human genome. This enhancer element is unusually rich in general regulatory sequences related to DNA recognition by multiple classes of eukaryotic transcription factors, including the DM motifs, homeodomain, and high mobility group box. Whereas free DNA is often crystallized as an A-form double helix, Dsx(A) was crystallized as B-DNA and thus provides a model for the prebound conformation of diverse regulatory DNA complexes. Sequence-dependent conformational properties that extend features of shorter B-DNA fragments with respect to double helical parameters, groove widths, hydration, and binding of divalent metal ions are observed. The structure also exhibits a sequence-dependent pattern of isotropic thermal B-factors, suggesting possible variation in the local flexibility of the DNA backbone. Such fluctuations are in accord with structural variability observed in prior B-DNA structures. We speculate that sites of intrinsic flexibility within a DNA control element provide hinges for its protein-directed reorganization in a transcriptional preinitiation complex.
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Affiliation(s)
- Narendra Narayana
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
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5
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Beckman RA, Moreland D, Louise-May S, Humblet C. RNA unrestrained molecular dynamics ensemble improves agreement with experimental NMR data compared to single static structure: a test case. J Comput Aided Mol Des 2006; 20:263-79. [PMID: 17006738 DOI: 10.1007/s10822-006-9049-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2005] [Accepted: 05/05/2006] [Indexed: 11/30/2022]
Abstract
Nuclear magnetic resonance (NMR) provides structural and dynamic information reflecting an average, often non-linear, of multiple solution-state conformations. Therefore, a single optimized structure derived from NMR refinement may be misleading if the NMR data actually result from averaging of distinct conformers. It is hypothesized that a conformational ensemble generated by a valid molecular dynamics (MD) simulation should be able to improve agreement with the NMR data set compared with the single optimized starting structure. Using a model system consisting of two sequence-related self-complementary ribonucleotide octamers for which NMR data was available, 0.3 ns particle mesh Ewald MD simulations were performed in the AMBER force field in the presence of explicit water and counterions. Agreement of the averaged properties of the molecular dynamics ensembles with NMR data such as homonuclear proton nuclear Overhauser effect (NOE)-based distance constraints, homonuclear proton and heteronuclear (1)H-(31)P coupling constant (J) data, and qualitative NMR information on hydrogen bond occupancy, was systematically assessed. Despite the short length of the simulation, the ensemble generated from it agreed with the NMR experimental constraints more completely than the single optimized NMR structure. This suggests that short unrestrained MD simulations may be of utility in interpreting NMR results. As expected, a 0.5 ns simulation utilizing a distance dependent dielectric did not improve agreement with the NMR data, consistent with its inferior exploration of conformational space as assessed by 2-D RMSD plots. Thus, ability to rapidly improve agreement with NMR constraints may be a sensitive diagnostic of the MD methods themselves.
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Affiliation(s)
- Robert A Beckman
- Discovery Research Informatics, Computer-Assisted Drug Design, Pfizer Global Research and Development, Ann Arbor, MI 48105, USA.
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6
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Zagrovic B, van Gunsteren WF. Comparing atomistic simulation data with the NMR experiment: how much can NOEs actually tell us? Proteins 2006; 63:210-8. [PMID: 16425239 DOI: 10.1002/prot.20872] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Simulated molecular dynamics trajectories of proteins and nucleic acids are often compared with nuclear magnetic resonance (NMR) data for the purposes of assessing the quality of the force field used or, equally important, trying to interpret ambiguous experimental data. In particular, nuclear Overhauser enhancement (NOE) intensities or atom-atom distances derived from them are frequently calculated from the simulated ensembles because the distance restraints derived from NOEs are the key ingredient in NMR-based protein structure determination. In this study, we ask how diverse and nonnative-like an ensemble of structures can be and still match the experimental NOE distance upper bounds well. We present two examples in which simulated ensembles of highly nonnative polypeptide structures (an unfolded state ensemble of the villin headpiece and a high-temperature denatured ensemble of lysozyme) are shown to match fairly well the experimental NOE distance upper bounds from which the corresponding native structures were derived. For example, the unfolded ensemble of villin headpiece, which is on average 0.90 +/- 0.13 nm root-mean-square deviation away from the native NMR structure, deviates from the experimental restraints by only 0.027 nm on average. However, this artificially good agreement is largely a consequence of 1) the highly nonlinear effects of r(-6) (or r(-3)) averaging and 2) focusing only on the experimentally observed set of NOE bounds. Namely, in addition to the experimentally observed NOEs, both simulated ensembles (especially the villin ensemble) also predict a large number of NOEs, which are not seen in the experiment. If these are taken into account, the agreement between simulation and experiment gets markedly worse, as it should, given the nonnative nature of the underlying simulated ensembles. In light of the examples given, we conclude that comparing experimental NOE distance restraints with large simulated ensembles provides just by itself only limited information about the quality of simulation.
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Affiliation(s)
- Bojan Zagrovic
- Department of Chemistry and Applied Biosciences, ETH Hönggerberg, Zürich, Switzerland
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7
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Otting G, Billeter M, Wüthrich K, Roth HJ, Leumann C, Eschenmoser A. Warum Pentose- und nicht Hexose-Nucleinsäuren?? Teil VI. ‘Homo-DNS’:1H-,13C-,31P- und15N-NMR-spektroskopische Untersuchung von ddGlc(A-A-A-A-A-T-T-T-T-T) in wässriger Lösung. Helv Chim Acta 2004. [DOI: 10.1002/hlca.19930760802] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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8
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Winger RH, Liedl KR, Pichler A, Hallbrucker A, Mayer E. Helix morphology changes in B-DNA induced by spontaneous B(I)<==>B(II) substrate interconversion. J Biomol Struct Dyn 1999; 17:223-35. [PMID: 10563572 DOI: 10.1080/07391102.1999.10508355] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Investigations of spontaneous, i.e. not forced, B-DNA's B(I)<==>B(II) substate transitions are carried out on the d(CGCGAATTCGCG)2 EcoRI dodecamer sequence using Molecular Dynamics Simulations. Analysis of the resulting transition processes with respect to the backbone angles reveals concerted changes not only for backbone angles epsilon, zeta, and beta, but also for the 5'-delta and 5'-chi angles. For alpha and delta inside the interconverting base step, a change is seen in short lived B(II) conformers. With respect to base morphology distinct changes are observed for buckle, propeller twist, shift, roll and twist, as well as x-displacement and tip. The base mainly involved in the changes is identified as the base preceding the interconverting phosphate. Altogether single B(I)<==>B(II) interconversions result only in local distortions represented by the larger spread of most parameters. Comparison of the atomic positional fluctuations derived from the simulation with those obtained from the static X-ray structure results in striking similarities.
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Affiliation(s)
- R H Winger
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Austria
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9
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Schneider TR, Brünger AT, Nilges M. Influence of internal dynamics on accuracy of protein NMR structures: derivation of realistic model distance data from a long molecular dynamics trajectory. J Mol Biol 1999; 285:727-40. [PMID: 9878440 DOI: 10.1006/jmbi.1998.2323] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In order to study the effect of internal dynamics on the accuracy of NMR structures in detail, we generated NOE distance data from a long molecular dynamics trajectory of BPTI. Cross-relaxation rates were calculated from the trajectory by analysis of the appropriate proton-proton vector autocorrelation functions. A criterion for the convergence of correlation functions was developed, and the analysis was restricted to those correlation functions that had converged within the simulation time. Effective distances were determined from the calculated cross-relaxation rates. Internal dynamics affected the derived distances in a realistic way, since they were subject both to radial averaging (which increases the cross-relaxation rate) and angular averaging (which decreases the cross-relaxation rate). The comparison of the effective distances with average distance between the protons during the trajectory showed that for most the effects of angular and distance averaging essentially cancel out. For these distances, the effective distance derived from an NOE is therefore a very good estimate of the average distance, or the distance in the average structure. However, for about 10% of the distances, the effective distance was more than 10% larger than the average distance, while for about 5%, it was more than 10% smaller, in some cases by more than 2 A. Little correlation is observed between the effects on cross-relaxation rates to different protons of the same residue. The results of this analysis have implications for the way structures are calculated from NOE distance data. For many distances, the assumption of a rigid structure is valid, and large error bounds would result in the loss of too much information content. On the other hand, the error bounds very often employed are not wide enough for some of the effects seen in our study.
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Affiliation(s)
- T R Schneider
- Universität Göttingen Institut für Anorganische Chemie, Tammannstr. 4, Göttingen, D-37077, Germany
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10
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Hatcher ME, Mattiello DL, Meints GA, Orban J, Drobny GP. A Solid-State Deuterium NMR Study of the Localized Dynamics at the C9pG10 Step in the DNA Dodecamer [d(CGCGAATTCGCG)]2. J Am Chem Soc 1998. [DOI: 10.1021/ja971266h] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mary E. Hatcher
- Contribution from the Department of Chemistry, University of Washington, Seattle, Washington 98195, and Center for Advanced Research in Biotechnology, University of Maryland, Biotechnology Institute, Rockville, Maryland 20850
| | - Debra L. Mattiello
- Contribution from the Department of Chemistry, University of Washington, Seattle, Washington 98195, and Center for Advanced Research in Biotechnology, University of Maryland, Biotechnology Institute, Rockville, Maryland 20850
| | - Gary A. Meints
- Contribution from the Department of Chemistry, University of Washington, Seattle, Washington 98195, and Center for Advanced Research in Biotechnology, University of Maryland, Biotechnology Institute, Rockville, Maryland 20850
| | - John Orban
- Contribution from the Department of Chemistry, University of Washington, Seattle, Washington 98195, and Center for Advanced Research in Biotechnology, University of Maryland, Biotechnology Institute, Rockville, Maryland 20850
| | - Gary P. Drobny
- Contribution from the Department of Chemistry, University of Washington, Seattle, Washington 98195, and Center for Advanced Research in Biotechnology, University of Maryland, Biotechnology Institute, Rockville, Maryland 20850
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11
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Jeltsch A. Flexibility of DNA in complex with proteins deduced from the distribution of bending angles observed by scanning force microscopy. Biophys Chem 1998; 74:53-7. [PMID: 17029732 DOI: 10.1016/s0301-4622(98)00163-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/1998] [Revised: 03/30/1998] [Accepted: 04/30/1998] [Indexed: 11/30/2022]
Abstract
Flexibility and dynamics of DNA are important for DNA-binding and recognition by proteins. Here the flexibility of DNA is calculated from the distribution of DNA-bending angles of single DNA molecules as observed by scanning force microscopy by applying an equation that links the force constant of DNA-bending (f) to the variance of the distribution of bending angles (sigma): f=RT/sigma(2). Using published data, f is calculated to be 3-5 J/degree(2) for free DNA. Thus, bending DNA by 20 degrees requires approx. 0.5-1 kJ/mol. This result shows that DNA is very flexible and readily can be bent by thermal motion. DNA-flexibility is not altered in some protein-DNA complexes (HhaI methyltransferase, EcoRV restriction endonuclease). In contrast, DNA-binding by EcoRI endonuclease increases DNA-flexibility and binding by EcoRI methyltransferase restricts the flexibility of DNA. During the transition of the RNA polymerase-sigma(54)-DNA complex from the closed to the open form and of cro repressor from a non-specific to a specific binding mode the flexibility of the DNA is strongly reduced.
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Affiliation(s)
- A Jeltsch
- Institut für Biochemie, Fachbereich Biologie, Heinrich-Buff-Ring 58, 35392 Giessen, Germany.
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12
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Beger RD, Arthanari HB, Basu S, Bolton PH. Interresidue quiet NOEs for DNA structural studies. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 1998; 132:34-40. [PMID: 9615411 DOI: 10.1006/jmre.1998.1403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The potential utility of long-range NOEs in DNA has not been exploited since the observed signals have contributions both from the direct magnetization route and from multiple diffusion pathways. The Quiet NOE approach can be used to select for the direct magnetization transfer pathway by suppressing spin diffusion. A single-band Quiet NOE, which allows detection of the direct NOEs between protons in a selected chemical shift window, has been demonstrated on two duplex DNAs, and the NOEs observed can contain important structural information.
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Affiliation(s)
- R D Beger
- Chemistry Department, Wesleyan University, Middletown, Connecticut 06459, USA
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13
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Young MA, Ravishanker G, Beveridge DL. A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation. Biophys J 1997; 73:2313-36. [PMID: 9370428 PMCID: PMC1181136 DOI: 10.1016/s0006-3495(97)78263-8] [Citation(s) in RCA: 271] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We report the results of four new molecular dynamics (MD) simulations on the DNA duplex of sequence d(CGCGAATTCGCG)2, including explicit consideration of solvent water, and a sufficient number of Na+ counterions to provide electroneutrality to the system. Our simulations are configured particularly to characterize the latest MD models of DNA, and to provide a basis for examining the sensitivity of MD results to the treatment of boundary conditions, electrostatics, initial placement of solvent, and run lengths. The trajectories employ the AMBER 4.1 force field. The simulations use particle mesh Ewald summation for boundary conditions, and range in length from 500 ps to 5.0 ns. Analysis of the results is carried out by means of time series for conformationalm, helicoidal parameters, newly developed indices of DNA axis bending, and groove widths. The results support a dynamically stable model of B-DNA for d(CGCGAATTCGCG)2 over the entire length of the trajectory. The MD results are compared with corresponding crystallographic and NMR studies on the d(CGCGAATTCGCG)2 duplex, and placed in the context of observed behavior of B-DNA by comparisons with the complete crystallographic data base of B-form structures. The calculated distributions of mobile solvent molecules, both water and counterions, are displayed. The calculated solvent structure of the primary solvation shell is compared with the location of ordered solvent positions in the corresponding crystal structure. The results indicate that ordered solvent positions in crystals are roughly twice as structured as bulk water. Detailed analysis of the solvent dynamics reveals evidence of the incorporation of ions in the primary solvation of the minor groove B-form DNA. The idea of localized complexation of otherwise mobile counterions in electronegative pockets in the grooves of DNA helices introduces an additional source of sequence-dependent effects on local conformational, helicoidal, and morphological structure, and may have important implications for understanding the functional energetics and specificity of the interactions of DNA and RNA with regulatory proteins, pharmaceutical agents, and other ligands.
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Affiliation(s)
- M A Young
- Chemistry Department, Wesleyan University, Middletown, Connecticut 06459, USA
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14
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Duan Y, Wilkosz P, Crowley M, Rosenberg JM. Molecular dynamics simulation study of DNA dodecamer d(CGCGAATTCGCG) in solution: conformation and hydration. J Mol Biol 1997; 272:553-72. [PMID: 9325112 DOI: 10.1006/jmbi.1997.1247] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A molecular dynamics simulation of the dodecamer duplex d(CGCGAATTCGCG) using the particle mesh Ewald sum assumed a B-conformation remarkably close to the observed X-ray structure. The Ewald summation method effectively eliminates the usual "cut-off" of long-range interactions and allowed us to evaluate the full effect of the electrostatic forces. This simulation showed remarkable agreement with the Dickerson X-ray structure in both average structure and B-factors; within the EcoRI site itself, the rms deviation between the average theoretical and observed structures was 1.1 A. The width of the minor groove fluctuated between a wide and narrow configuration with the latter corresponding closely to the X-ray structure. The simulation also suggested a strong sequence-dependent signature on the minor groove width in both wide and narrow conformers. Hydration shells in both the major and minor grooves were observed. The "spine of hydration" in the minor groove was clear. In the major groove the first hydration shell appears to be a ribbon-like structure that reproduces the principal features of observed X-ray structures; subtle variations of this hydration pattern suggest sequence dependencies. Sequence-dependent features were also examined for helical and other geometric parameters. The successful reproduction of many experimentally observed fine structural features shows that the Ewald summation significantly improves the fidelity of the calculations.
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Affiliation(s)
- Y Duan
- Department of Biological Sciences and W. M. Keck Center for Advanced Training in Computational Biology Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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15
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Tapia O, Velázquez I. Molecular Dynamics Simulations of DNA with Protein's Consistent GROMOS Force Field and the Role of Counterions' Symmetry. J Am Chem Soc 1997. [DOI: 10.1021/ja9641665] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- O. Tapia
- Contribution from the Department of Physical Chemistry, Uppsala University, Box 532, 75121, UPPSALA, Sweden
| | - I. Velázquez
- Contribution from the Department of Physical Chemistry, Uppsala University, Box 532, 75121, UPPSALA, Sweden
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16
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Robinson BH, Mailer C, Drobny G. Site-specific dynamics in DNA: experiments. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 1997; 26:629-58. [PMID: 9241432 DOI: 10.1146/annurev.biophys.26.1.629] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
This chapter reviews the dynamics information obtained from experimental magnetic resonance studies of site-specifically labeled duplex DNA. A previous review (43) discusses the dynamics of duplex DNA; it develops a theory that shows how magnetic resonance experiments are used to detect those dynamics. The methods for obtaining information about dynamics as well as a summary of what is now known about the site-specific dynamics of DNA are presented. This review contains two methods sections which present results using electron paramagnetic resonance and nuclear magnetic resonance active probes.
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Affiliation(s)
- B H Robinson
- Department of Chemistry, University of Washington, Seattle 98195, USA
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17
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Norberg J, Nilsson L. Constant pressure molecular dynamics simulations of the dodecamers: d(GCGCGCGCGCGC)2 and r(GCGCGCGCGCGC)2. J Chem Phys 1996. [DOI: 10.1063/1.471341] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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18
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Schellman JA, Harvey SC. Static contributions to the persistence length of DNA and dynamic contributions to DNA curvature. Biophys Chem 1995; 55:95-114. [PMID: 7632879 DOI: 10.1016/0301-4622(94)00144-9] [Citation(s) in RCA: 108] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Long molecules of DNA have the statistical properties of a worm-like coil. Deviations from linearity occur both because of small dynamic bends induced by thermal motion and from a random distribution of static bends. The latter originate in the different conformations of each of the possible base pair sequences. In this paper a statistical theory of the persistence length of DNA is developed which includes both static and dynamic effects for each base pair sequence, as well as the sequence-dependent correlations of bending angles. The result applies to a generic DNA, i.e., the average over an ensemble of all possible sequences. The theory is also applied to the generation of the average properties of curved DNAs by an analytic method that includes dynamic averaging as well as correlated bends. These results provide information which supplements that obtained by others using Monte Carlo methods. The additivity relation 1/P = 1/P(S) + 1/P(d) proposed by Trifonov et al., where P is the persistence length and P(S) and P(d) are the persistence lengths arising from purely static and dynamic effects, respectively, has been verified to be accurate to better than 0.5%. This is true for both a simplified model and one that includes a complete set of static bends at all base pair sequences.
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Affiliation(s)
- J A Schellman
- Institute for Molecular Biology, University of Oregon, Eugene, USA
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19
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Lee H, Darden TA, Pedersen LG. Molecular dynamics simulation studies of a high resolution Z‐DNA crystal. J Chem Phys 1995. [DOI: 10.1063/1.468564] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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20
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Gaudin F, Paquet F, Chanteloup L, Beau JM, Nguyen TT, Lancelot G. Selectively 13C-enriched DNA: dynamics of the C1'-H1' vector in d(CGCAAATTTGCG)2. JOURNAL OF BIOMOLECULAR NMR 1995; 5:49-58. [PMID: 7881272 DOI: 10.1007/bf00227469] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
In order to examine the internal dynamic processes of the dodecamer d(CGCAAATTTGCG)2, the 13C-enriched oligonucleotide has been synthesized. The three central thymines were selectively 13C-labeled at the C1' position and their spin-lattice relaxation parameters R(CZ), R(CX,Y), R(HZ-->CZ), R(2HZCZ), R(2HZCX,Y) and R(HZC) were measured. Density functions were computed for two models of internal motions. Comparisons of the experimental data were made with spin-lattice relaxation rates rather than with the density functions, whose values were altered by accumulation of the uncertainties of each relaxation rate measurement. The spin-lattice relaxation rates were computed with respect to the motions of the sugar around the C1'-N1 bond. A two-state jump model between the anti- and syn-conformations with P(anti)/P(syn) = 91/9 or a restricted rotation model with delta chi = 28 degrees and an internal diffusion coefficient of 30 x 10(7) s-1 gave a good fit with the experimental data. Twist, tilt or roll base motions have little effect on 13C1' NMR relaxation. Simulation of spin-relaxation rates with the data obtained at several temperatures between 7 and 32 degrees C, where the dodecamer is double stranded, shows that the internal motion amplitude is independent of the temperature within this range, as expected for internal motion. Using the strong correlation which exists in a B-DNA structure between the chi and delta angle, we suggest that the change in the glycosidic angle value should be indicative of a sugar puckering between the C1'-exo and C2'-endo conformations.
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Affiliation(s)
- F Gaudin
- Centre de Biophysique Moléculaire, CNRS, Orléans, France
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21
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Agris PF, Brown SC. Systems for the NMR study of modified nucleoside-dependent, metal-ion induced conformational changes in nucleic acids. Methods Enzymol 1995; 261:270-99. [PMID: 8569499 DOI: 10.1016/s0076-6879(95)61014-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- P F Agris
- Department of Biochemistry, North Carolina State University, Raleigh 27695, USA
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22
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Radha PK, Nibedita R, Kumar RA, Hosur RV. Distance geometry in NMR determination of solution conformation of nucleic acids: application of d-ACCGTTAACGGT. Methods Enzymol 1995; 261:73-89. [PMID: 8569514 DOI: 10.1016/s0076-6879(95)61005-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- P K Radha
- Chemical Physics Group, Tata Institute of Fundamental Research, Bombay, India
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23
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Affiliation(s)
- B A Luxon
- Department of Human Biological Chemistry and Genetics, University of Texas Medical Branch, Galveston 77555, USA
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24
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Young MA, Srinivasan J, Goljer I, Kumar S, Beveridge DL, Bolton PH. Structure determination and analysis of local bending in an A-tract DNA duplex: comparison of results from crystallography, nuclear magnetic resonance, and molecular dynamics simulation on d(CGCAAAAATGCG). Methods Enzymol 1995; 261:121-44. [PMID: 8569492 DOI: 10.1016/s0076-6879(95)61007-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We have presented a detailed analysis for structure determinations for the DNA duplex d(CGCAAAAATGCG) obtained from X-ray crystallography, nuclear magnetic resonance, and molecular dynamics simulation. Each of the structures for the duplex deviates from the structure of the canonical form of B-DNA in a number of observable characteristics. Specifically, the three determinations all contain DNA axis deflections at the junctions of the A-tract with the flanking sequences. The analysis provided shows that the general characteristics of the structures obtained for d(CGCAAAAATGCG) from X-ray, NMR, and MD methods turn out to be quite similar. The extent to which this result can be generalized remains to be established by consideration of similar cross-comparisons on diverse oligonucleotide structures.
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Affiliation(s)
- M A Young
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459-0280, USA
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25
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Kumar S, Duan Y, Kollman PA, Rosenberg JM. Molecular dynamics simulations suggest that the Eco RI kink is an example of molecular strain. J Biomol Struct Dyn 1994; 12:487-525. [PMID: 7727057 DOI: 10.1080/07391102.1994.10508757] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The energy surface in the vicinity of the "Eco RI kink" was investigated by conducting both in vacuo molecular dynamics simulations as well as a simulation with explicit solvent. The in vacuo simulations used the "all atom" AMBER 3.0 force field with a distant dependent dielectric function and "hydrated" counter ions while the simulation with explicit solvent used the AMBER 4.0 force field, fully charged phosphates and counter ions and a dielectric constant of 1.0. The thrust of the simulations was to discriminate between two models of the energy surface of the deformed DNA as found in the recognition complex with Eco RI endonuclease. In the intrinsic model, the kinked DNA is a local minimum of the energy surface intrinsic to the DNA itself while in the strained model there is no significant energy barrier separating kinked and regular B-DNA. The two models have significant implications for theories of indirect recognition of DNA based on sequence-dependent deformability. The simulations suggest that the Eco RI-kinked structure is an example of molecular strain because it is not near a minimum of any of the potential energy functions examined. The simulations leave the question of an energy barrier somewhat open and raise the possibility that the Eco RI kink is at (or near) a point of dynamic instability of the energy surface (either a true maximum or a saddle point).
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Affiliation(s)
- S Kumar
- Dept. of Biological Sciences, W.M. Keck Center for Advanced Training in Computational Biology, University of Pittsburgh, PA 15260, USA
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26
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Vincent SJF, Zwahlen C, Bodenhausen G. Selektive Messung der Zeitabhängigkeit des transienten Overhauser-Effekts in NMR-Spektren; Anwendung auf Oligonucleotide. Angew Chem Int Ed Engl 1994. [DOI: 10.1002/ange.19941060319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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27
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Mierke DF, Kessler H. Improved molecular dynamics simulations for the determination of peptide structures. Biopolymers 1993; 33:1003-17. [PMID: 8343582 DOI: 10.1002/bip.360330703] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In this article a few methods or modifications proven to be useful in the conformational examination of peptides and related molecules by molecular dynamics are illustrated. The first is the explicit use of organic solvents in the simulations. For many cases such solvents are appropriate since the nmr measurements (or other experimental observations) were carried out in the same solvent. Here, the use of dimethylsulfoxide and chloroform in molecular dynamics is described, with some advantages of the use of these solvents high-lighted. A constant allowing for the scaling of the nonbonded interactions of the force field, an idea previously employed in distance geometry and simulated annealing, has been implemented. The usefulness of this method is that when the nonbonded term is turned to zero, atoms can pass through each other, while the connectivity of the molecule is maintained. It will be shown that such simulations, if a sufficient driving force is present (i.e., nuclear Overhauser effects restraints), can produce the correct stereoconfiguration (i.e., chiral center) as well as configurational isomer (i.e., cis/trans isomers). Lastly, a penalty term for coupling constants directly related to the Karplus curve has been implemented into the potential energy force field. The advantages of this method over the commonly used dihedral angle restraining are discussed. In particular, it is shown that with more than one coupling constant about a dihedral angle a great reduction of the allowed conformational space is obtained.
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Affiliation(s)
- D F Mierke
- Organisch Chemisches Institut, Technische Universität München, Garching, Germany
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28
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Walters KJ, Russu IM. Sequence dependence of purine C8H exchange kinetics in the dodecamer 5'-d(CGCGAATTCGCG)-3'. Biopolymers 1993; 33:943-51. [PMID: 8318667 DOI: 10.1002/bip.360330610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Proton nmr spectroscopy is used to measure the deuterium exchange rates of C8 protons in individual purines of the dodecamer 5'-d(CGCGAATTCGCG)-3' and their temperature dependence. In perfect agreement with results from tritium labeling and laser Raman spectroscopy, we find that the DNA secondary structure retards the rates of purine C8H exchange. The largest effects are observed for the C8 protons of adenines whose rates of exchange at 40 degrees C are 3- to 4-fold lower than that in 5'-adenosine monophosphate. Moreover, the retardation of exchange at the central adenine is greater than that at its 5'-neighbor. For the guanines, the exchange rates are up to 2-fold lower than that in 5'-guanosine monophosphate, and the largest retardation is observed for the bases at positions 10 and 12. A dependence on base sequence is also observed for the activation energy for exchange. The activation energy is largest for the adenines and its value is 4 kcal/mol higher than that in 5'-adenosine monophosphate. The lowest activation energy is observed for the guanine in position 4 and the value is the same as in 5'-guanosine monophosphate. These results demonstrate the sensitivity of the purine C8H exchange kinetics to sequence-dependent conformational features of B-DNA in solution state.
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Affiliation(s)
- K J Walters
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06459
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29
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Prévost C, Louise-May S, Ravishanker G, Lavery R, Beveridge DL. Persistence analysis of the static and dynamical helix deformations of DNA oligonucleotides: application to the crystal structure and molecular dynamics simulation of d(CGCGAATTCGCG)2. Biopolymers 1993; 33:335-50. [PMID: 8461448 DOI: 10.1002/bip.360330303] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A theory and graphical presentation for the analysis of helix structure and deformations in oligonucleotides is presented. The parameters "persistence" and "flexibility" as defined in the configurational statistics of polymers of infinite length are reformulated at the oligonucleotide level in an extension of J. A. Schellman's method [(1974) Biopolymers, Vol. 17, pp. 217-226], and used as a basis for a systematic "Persistence Analysis" of the helix deformation properties for all possible subsequences in the structure. The basis for the analysis is a set of link vectors referenced to individual base pairs, and is limited to sequences exhibiting only perturbed rod-like behavior, i.e., below the threshold for supercoiling. The present application of the method is concerned with a physical model for the angular component of bending, so the link vectors are defined as the unit components of a global helix axis obtained by the procedure "Curves" of R. Lavery and H. Sklenar [(1988) J. Biomol. Struct. Dynam., Vol. 6, pp. 63-91; (1989) ibid., Vol. 6, pp. 655-667]. A discussion of the relationship between global bending and relative orientation of base pairs is provided. Our approach is illustrated by analysis of some model oligonucleotide structures with intrinsic kinks, the crystal structure of the dodecamer d(CGCGAATTCGCG)2, and the results of two molecular dynamics simulations on this dodecamer using two variations of the GROMOS force field. The results indicate that essentially all aspects of curvature in short oligonucleotides can be determined, such as the position and orientation of each bend, the sharpness or smoothness, and the location and linearity of subsequences. In the case of molecular dynamics simulations, where a Boltzmann ensemble of structures is analyzed, the spatial extent of the deformations (flexibility) is also considered.
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Affiliation(s)
- C Prévost
- Centre de Biophysique Moléculaire, Orléans, France
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30
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Brünger AT, Nilges M. Computational challenges for macromolecular structure determination by X-ray crystallography and solution NMR-spectroscopy. Q Rev Biophys 1993; 26:49-125. [PMID: 8210313 DOI: 10.1017/s0033583500003966] [Citation(s) in RCA: 135] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Macromolecular structure determination by X-ray crystallography and solution NMR spectroscopy has experienced unprecedented growth during the past decade.
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Affiliation(s)
- A T Brünger
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06511
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31
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An indexed bibliography of antisense literature, 1992. ANTISENSE RESEARCH AND DEVELOPMENT 1993; 3:95-153. [PMID: 8495109 DOI: 10.1089/ard.1993.3.95] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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32
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Khare D, Orban J. Synthesis of backbone deuterium labelled [r(CGCGAAUUCGCG)]2 and HPLC purification of synthetic RNA. Nucleic Acids Res 1992; 20:5131-6. [PMID: 1383940 PMCID: PMC334295 DOI: 10.1093/nar/20.19.5131] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The chemical synthesis of backbone deuterium labelled [r(CGCGAAU*U*CGCG)]2 (U* = [5'-2H]U) is described. An efficient purification procedure was developed using a polymeric reverse phase (PRP) HPLC column at 60 degrees C. This procedure provided pure RNA dodecamer in the multi-milligram quantities (39% overall yield) necessary for dynamics studies using solid-state deuterium NMR. The purification method has been effectively applied to other RNA sequences and will assist biophysical studies which require relatively large quantities of RNA oligomers.
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Affiliation(s)
- D Khare
- Maryland Biotechnology Institute, University of Maryland, Rockville 20850
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33
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Mauffret O, Hartmann B, Convert O, Lavery R, Fermandjian S. The fine structure of two DNA dodecamers containing the cAMP responsive element sequence and its inverse. Nuclear magnetic resonance and molecular simulation studies. J Mol Biol 1992; 227:852-75. [PMID: 1328653 DOI: 10.1016/0022-2836(92)90227-b] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
1H and 31P n.m.r. (nuclear magnetic resonance) spectroscopy have been used in conjunction with molecular simulation to determine the structure of two DNA dodecamers. The first of these, CATGACGTCATG, contains the octameric sequence CRE (cAMP responsive element), while the second is the reversed sequence, GTACTGCAGTAC. Structure determination was based on both NOESY (nuclear Overhauser spectroscopy) derived distances and COSY (correlated spectroscopy) dihedral angle data. Access to the 31P spectra also allowed the epsilon backbone angles to be determined. Considerable care was taken in deriving structural parameters from the n.m.r. data and an excellent level of agreement is obtained with the simulated conformations. Both dodecamers are found to belong to the B-DNA family; however, there is a striking difference between the CRE sequence and its inverse, the former conformation alone showing a strong structural heterogeneity.
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Affiliation(s)
- O Mauffret
- Pharmacologie Moléculaire (Inserm U 140, CNRS URA 158), Institut Gustave Roussy, Villejuif, France
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