Nucleic acid helix structure determination from NMR proton chemical shifts
We present a method for de novo derivation of the three-dimensional helix structure of nucleic acids using non-exchangeable proton chemical shifts as sole source of experimental restraints. The method is called che mical shift de nov o structure derivation p rotocol employing s ingular value decompo...
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| Published in | Journal of biomolecular NMR Vol. 56; no. 2; pp. 95 - 112 |
|---|---|
| Main Authors | , , |
| Format | Journal Article |
| Language | English |
| Published |
Dordrecht
Springer Netherlands
01.06.2013
Springer Nature B.V |
| Subjects | |
| Online Access | Get full text |
| ISSN | 0925-2738 1573-5001 1573-5001 |
| DOI | 10.1007/s10858-013-9725-y |
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| Abstract | We present a method for
de novo
derivation of the three-dimensional helix structure of nucleic acids using non-exchangeable proton chemical shifts as sole source of experimental restraints. The method is called
che
mical shift de nov
o
structure derivation
p
rotocol employing
s
ingular value decomposition (CHEOPS) and uses iterative singular value decomposition to optimize the structure in helix parameter space. The correct performance of CHEOPS and its range of application are established via an extensive set of structure derivations using either simulated or experimental chemical shifts as input. The simulated input data are used to assess in a defined manner the effect of errors or limitations in the input data on the derived structures. We find that the RNA helix parameters can be determined with high accuracy. We finally demonstrate via three deposited RNA structures that experimental proton chemical shifts suffice to derive RNA helix structures with high precision and accuracy. CHEOPS provides, subject to further development, new directions for high-resolution NMR structure determination of nucleic acids. |
|---|---|
| AbstractList | We present a method for de novo derivation of the three-dimensional helix structure of nucleic acids using non-exchangeable proton chemical shifts as sole source of experimental restraints. The method is called chemical shift de novo structure derivation protocol employing singular value decomposition (CHEOPS) and uses iterative singular value decomposition to optimize the structure in helix parameter space. The correct performance of CHEOPS and its range of application are established via an extensive set of structure derivations using either simulated or experimental chemical shifts as input. The simulated input data are used to assess in a defined manner the effect of errors or limitations in the input data on the derived structures. We find that the RNA helix parameters can be determined with high accuracy. We finally demonstrate via three deposited RNA structures that experimental proton chemical shifts suffice to derive RNA helix structures with high precision and accuracy. CHEOPS provides, subject to further development, new directions for high-resolution NMR structure determination of nucleic acids. We present a method for de novo derivation of the three-dimensional helix structure of nucleic acids using non-exchangeable proton chemical shifts as sole source of experimental restraints. The method is called chemical shift de novo structure derivation protocol employing singular value decomposition (CHEOPS) and uses iterative singular value decomposition to optimize the structure in helix parameter space. The correct performance of CHEOPS and its range of application are established via an extensive set of structure derivations using either simulated or experimental chemical shifts as input. The simulated input data are used to assess in a defined manner the effect of errors or limitations in the input data on the derived structures. We find that the RNA helix parameters can be determined with high accuracy. We finally demonstrate via three deposited RNA structures that experimental proton chemical shifts suffice to derive RNA helix structures with high precision and accuracy. CHEOPS provides, subject to further development, new directions for high-resolution NMR structure determination of nucleic acids.We present a method for de novo derivation of the three-dimensional helix structure of nucleic acids using non-exchangeable proton chemical shifts as sole source of experimental restraints. The method is called chemical shift de novo structure derivation protocol employing singular value decomposition (CHEOPS) and uses iterative singular value decomposition to optimize the structure in helix parameter space. The correct performance of CHEOPS and its range of application are established via an extensive set of structure derivations using either simulated or experimental chemical shifts as input. The simulated input data are used to assess in a defined manner the effect of errors or limitations in the input data on the derived structures. We find that the RNA helix parameters can be determined with high accuracy. We finally demonstrate via three deposited RNA structures that experimental proton chemical shifts suffice to derive RNA helix structures with high precision and accuracy. CHEOPS provides, subject to further development, new directions for high-resolution NMR structure determination of nucleic acids. We present a method for de novo derivation of the three-dimensional helix structure of nucleic acids using non-exchangeable proton chemical shifts as sole source of experimental restraints. The method is called chemical shift de novo structure derivation protocol employing singular value decomposition (CHEOPS) and uses iterative singular value decomposition to optimize the structure in helix parameter space. The correct performance of CHEOPS and its range of application are established via an extensive set of structure derivations using either simulated or experimental chemical shifts as input. The simulated input data are used to assess in a defined manner the effect of errors or limitations in the input data on the derived structures. We find that the RNA helix parameters can be determined with high accuracy. We finally demonstrate via three deposited RNA structures that experimental proton chemical shifts suffice to derive RNA helix structures with high precision and accuracy. CHEOPS provides, subject to further development, new directions for high-resolution NMR structure determination of nucleic acids.[PUBLICATION ABSTRACT] We present a method for de novo derivation of the three-dimensional helix structure of nucleic acids using non-exchangeable proton chemical shifts as sole source of experimental restraints. The method is called che mical shift de nov o structure derivation p rotocol employing s ingular value decomposition (CHEOPS) and uses iterative singular value decomposition to optimize the structure in helix parameter space. The correct performance of CHEOPS and its range of application are established via an extensive set of structure derivations using either simulated or experimental chemical shifts as input. The simulated input data are used to assess in a defined manner the effect of errors or limitations in the input data on the derived structures. We find that the RNA helix parameters can be determined with high accuracy. We finally demonstrate via three deposited RNA structures that experimental proton chemical shifts suffice to derive RNA helix structures with high precision and accuracy. CHEOPS provides, subject to further development, new directions for high-resolution NMR structure determination of nucleic acids. |
| Author | van der Werf, Ramon M. Tessari, Marco Wijmenga, Sybren S. |
| Author_xml | – sequence: 1 givenname: Ramon M. surname: van der Werf fullname: van der Werf, Ramon M. organization: Department of Biophysical Chemistry, Institute of Molecules and Materials, Radboud University Nijmegen – sequence: 2 givenname: Marco surname: Tessari fullname: Tessari, Marco organization: Department of Biophysical Chemistry, Institute of Molecules and Materials, Radboud University Nijmegen – sequence: 3 givenname: Sybren S. surname: Wijmenga fullname: Wijmenga, Sybren S. email: S.Wijmenga@science.ru.nl organization: Department of Biophysical Chemistry, Institute of Molecules and Materials, Radboud University Nijmegen |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/23564038$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.1073/pnas.0800256105 10.1016/j.pnmrs.2010.01.002 10.1093/nar/gkm774 10.1080/07391102.1989.10507726 10.1126/science.1202692 10.1016/0166-1280(81)85115-9 10.1093/nar/gkg680 10.1128/AAC.00817-09 10.1016/0022-2836(73)90182-4 10.1021/ja010033u 10.1007/BF00227472 10.1021/bi9607214 10.1007/s10858-006-9087-9 10.1016/j.jmb.2011.01.049 10.1007/s10858-010-9424-x 10.1038/nsmb.1790 10.1016/S0006-3495(92)81649-1 10.1002/bip.20650 10.1073/pnas.1007988107 10.1006/jmrb.1994.1021 10.1021/bi970122c 10.1073/pnas.0610313104 10.1093/nar/gki704 10.1006/jmbi.2001.4987 10.1021/bi00440a039 10.1021/ja9902221 10.1073/pnas.85.23.8785 10.1006/jmbi.1996.0855 10.1002/(SICI)1097-458X(200002)38:2<95::AID-MRC592>3.0.CO;2-M 10.1007/BF00197633 10.1021/bi00189a037 10.1186/1471-2105-11-231 10.1017/S0033583500004169 10.1007/s10858-008-9288-5 10.1093/nar/gkn305 10.1038/nprot.2007.221 10.1016/S0959-440X(00)00087-7 10.1016/j.sbi.2009.07.015 10.1093/nar/gkg654 10.1021/bi00023a002 10.1021/ja9528846 10.1016/j.jmb.2007.08.033 10.1021/ja011646+ 10.1016/S0079-6565(97)00023-X 10.1023/A:1018348123074 10.1093/nar/gkl582 10.1073/pnas.1003995107 10.1016/j.ymeth.2008.12.003 10.1016/j.pnmrs.2008.06.002 10.1016/S1074-5521(02)00153-9 10.1126/science.1194294 10.1023/A:1011914132531 10.1038/nsmb986 10.1016/0079-6565(96)01028-X |
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| References | Jenner, Demeshkina, Yusupova, Yusupov (CR25) 2010; 17 Staple, Butcher (CR49) 2003; 31 Flodell, Petersen, Girard, Zdunek, Kidd-Ljunggren, Schleucher, Wijmenga (CR18) 2006; 34 Lam, Chi (CR29) 2010; 56 Dickerson (CR14) 1989; 6 Gurel, Blaha, Steitz, Moore (CR23) 2009; 53 Olson, Bansal, Burley, Dickerson, Gerstein, Harvey, Heinemann, Lu, Neidle, Shakked, Sklenar, Suzuki, Tung, Westhof, Wolberger, Berman (CR37) 2001; 313 Jin, Kelley, Loakes, Ramakrishnan (CR26) 2010; 107 Shajani, Varani (CR45) 2007; 86 Dunkle, Wang, Feldman, Pulk, Chen, Kapral, Noeske, Richardson, Blanchard, Cate (CR16) 2011; 332 Cavalli, Salvatella, Dobson, Vendruscolo (CR10) 2007; 104 Petzold, Duchardt, Flodell, Larsson, Kidd-Ljunggren, Wijmenga, Schleucher (CR40) 2007; 35 Tolbert, Miyazaki, Barton, Kinde, Starck, Singh, Bax, Case, Summers (CR50) 2010; 47 Ramesh, Wakeman, Winkler (CR43) 2011; 407 Grzesiek, Sass (CR22) 2009; 19 Lu, Olson (CR30) 2003; 31 Gelbin, Schneider, Clowney, Hsieh, Olson, Berman (CR19) 1996; 118 Cornilescu, Hu, Bax (CR11) 1999; 121 Allain, Varani (CR1) 1997; 267 Dunkle, Xiong, Mankin, Cate (CR15) 2010; 107 Tukalo, Yaremchuk, Fukunaga, Yokoyama, Cusack (CR51) 2005; 12 Brunger (CR8) 1992 Kuszewski, Schwieters, Clore (CR28) 2001; 123 Pardi, Hare, Wang (CR39) 1988; 85 Gronenborn, Clore (CR21) 1989; 28 Mooren, Pulleyblank, Wijmenga, Vandeven, Hilbers (CR35) 1994; 33 Dejaegere, Bryce, Case, Facelli, de Dios (CR13) 1999 Altona, Faber, Hoekzema (CR2) 2000; 38 Musselman, Pitt, Gulati, Foster, Andricioaei, Al-Hashimi (CR36) 2006; 36 Ribas-Prado, Giessner-Prettre (CR44) 1981; 76 Portmann, Usman, Egli (CR42) 1995; 34 Ben-Shem, Jenner, Yusupova, Yusupov (CR5) 2010; 330 Arnott, Hukins (CR3) 1973; 81 Sibille, Pardi, Simorre, Blackledge (CR48) 2001; 123 Egli, Portmann, Usman (CR17) 1996; 35 Cromsigt, Hilbers, Wijmenga (CR12) 2001; 21 Berman, Olson, Beveridge, Westbrook, Gelbin, Demeny, Hsieh, Srinivasan, Schneider (CR6) 1992; 63 Marcheschi, Staple, Butcher (CR31) 2007; 373 Mielke, Krishnan (CR33) 2009; 54 Wijmenga, Heus, Leeuw, Hoppe, van der Graaf, Hilbers (CR56) 1995; 5 Olson, Esguerra, Xin, Lu (CR38) 2009; 47 Vicens, Westhof (CR53) 2002; 9 Wijmenga, van Buuren (CR54) 1998; 32 Case (CR9) 1995; 6 Mollova, Pardi (CR34) 2000; 10 Shen, Lange, Delagio, Rossi, Aramini, Liu, Eletsky, Wu, Singarapu, Lemak, Ignatchenko, Arrowsmith, Szyperski, Montelione, Baker, Bax (CR46) 2008; 105 Wishart, Arndt, Berjanskii, Tang, Zhou, Lin (CR58) 2008; 36 Borgias, James (CR7) 1990; 87 Popenda, Szachniuk, Blazewicz, Wasik, Burke, Blazewicz, Adamiak (CR41) 2010; 11 Wijmenga, Kruithof, Hilbers (CR57) 1997; 10 Keepers, James (CR27) 1984; 57 Haeberli, Berger, Pallan, Egli (CR24) 2005; 33 Wijmenga, Heus, Werten, Vandermarel, Vanboom, Hilbers (CR55) 1994; 103 Bailor, Musselman, Hansen, Gulati, Patel, Al-Hashimi (CR4) 2007; 2 Varani, Aboul-ela, Allain (CR52) 1996; 29 Shen, Vernon, Baker, Bax (CR47) 2009; 43 Giessner-Prettre, Pullman (CR20) 1987; 20 McDowell, He, Chen, Turner (CR32) 1997; 36 C Musselman (9725_CR36) 2006; 36 JW Keepers (9725_CR27) 1984; 57 S Portmann (9725_CR42) 1995; 34 Y Shen (9725_CR47) 2009; 43 SS Wijmenga (9725_CR54) 1998; 32 E Mollova (9725_CR34) 2000; 10 C Altona (9725_CR2) 2000; 38 AM Gronenborn (9725_CR21) 1989; 28 A Dejaegere (9725_CR13) 1999 P Haeberli (9725_CR24) 2005; 33 G Gurel (9725_CR23) 2009; 53 SP Mielke (9725_CR33) 2009; 54 DS Wishart (9725_CR58) 2008; 36 R Ribas-Prado (9725_CR44) 1981; 76 FHT Allain (9725_CR1) 1997; 267 K Petzold (9725_CR40) 2007; 35 LB Jenner (9725_CR25) 2010; 17 MH Bailor (9725_CR4) 2007; 2 C Giessner-Prettre (9725_CR20) 1987; 20 WK Olson (9725_CR38) 2009; 47 M Tukalo (9725_CR51) 2005; 12 A Ramesh (9725_CR43) 2011; 407 BS Tolbert (9725_CR50) 2010; 47 RJ Marcheschi (9725_CR31) 2007; 373 JA McDowell (9725_CR32) 1997; 36 HM Berman (9725_CR6) 1992; 63 Z Shajani (9725_CR45) 2007; 86 G Varani (9725_CR52) 1996; 29 MMW Mooren (9725_CR35) 1994; 33 S Arnott (9725_CR3) 1973; 81 SS Wijmenga (9725_CR55) 1994; 103 S Flodell (9725_CR18) 2006; 34 JAMTC Cromsigt (9725_CR12) 2001; 21 JA Dunkle (9725_CR15) 2010; 107 A Cavalli (9725_CR10) 2007; 104 Q Vicens (9725_CR53) 2002; 9 DA Case (9725_CR9) 1995; 6 M Egli (9725_CR17) 1996; 35 SS Wijmenga (9725_CR56) 1995; 5 N Sibille (9725_CR48) 2001; 123 A Ben-Shem (9725_CR5) 2010; 330 S Grzesiek (9725_CR22) 2009; 19 J Kuszewski (9725_CR28) 2001; 123 WK Olson (9725_CR37) 2001; 313 XJ Lu (9725_CR30) 2003; 31 Y Shen (9725_CR46) 2008; 105 G Cornilescu (9725_CR11) 1999; 121 H Jin (9725_CR26) 2010; 107 RE Dickerson (9725_CR14) 1989; 6 SL Lam (9725_CR29) 2010; 56 JA Dunkle (9725_CR16) 2011; 332 A Pardi (9725_CR39) 1988; 85 A Gelbin (9725_CR19) 1996; 118 DW Staple (9725_CR49) 2003; 31 SS Wijmenga (9725_CR57) 1997; 10 M Popenda (9725_CR41) 2010; 11 BA Borgias (9725_CR7) 1990; 87 AT Brunger (9725_CR8) 1992 20859781 - J Biomol NMR. 1997 Dec;10(4):337-50 19738021 - Antimicrob Agents Chemother. 2009 Dec;53(12):5010-4 12888491 - Nucleic Acids Res. 2003 Aug 1;31(15):4326-31 19716691 - Curr Opin Struct Biol. 2009 Oct;19(5):585-95 20400952 - Nat Struct Mol Biol. 2010 May;17(5):555-60 9096230 - J Mol Biol. 1997 Mar 28;267(2):338-51 18515350 - Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W496-502 11734011 - J Am Chem Soc. 2001 Dec 12;123(49):12135-46 18326625 - Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4685-90 20421507 - Proc Natl Acad Sci U S A. 2010 May 11;107(19):8593-8 21109664 - Science. 2010 Nov 26;330(6008):1203-9 3194389 - Proc Natl Acad Sci U S A. 1988 Dec;85(23):8785-9 16945960 - Nucleic Acids Res. 2006;34(16):4449-57 20459631 - BMC Bioinformatics. 2010 May 06;11:231 12930962 - Nucleic Acids Res. 2003 Sep 1;31(17):5108-21 3327086 - Q Rev Biophys. 1987 Nov;20(3-4):113-72 17571061 - Nat Protoc. 2007;2(6):1536-46 8003496 - Biochemistry. 1994 Jun 14;33(23):7315-25 20633356 - Prog Nucl Magn Reson Spectrosc. 2010 Apr;56(3):289-310 16027443 - Nucleic Acids Res. 2005 Jul 18;33(13):3965-75 10851189 - Curr Opin Struct Biol. 2000 Jun;10(3):298-302 9201950 - Biochemistry. 1997 Jul 1;36(26):8030-8 17154290 - Biopolymers. 2007 Aug 5-15;86(5-6):348-59 21596992 - Science. 2011 May 20;332(6032):981-4 8563464 - J Biomol NMR. 1995 Dec;6(4):341-6 17077936 - J Biomol NMR. 2006 Dec;36(4):235-49 16155583 - Nat Struct Mol Biol. 2005 Oct;12(10):923-30 20549304 - J Biomol NMR. 2010 Jul;47(3):205-19 4777309 - J Mol Biol. 1973 Dec 5;81(2):93-105 19034676 - J Biomol NMR. 2009 Feb;43(2):63-78 12079787 - Chem Biol. 2002 Jun;9(6):747-55 20876128 - Proc Natl Acad Sci U S A. 2010 Oct 5;107(40):17152-7 11601858 - J Mol Biol. 2001 Oct 12;313(1):229-37 20160946 - Prog Nucl Magn Reson Spectrosc. 2009 Apr 5;54(3-4):141-165 7511032 - J Magn Reson B. 1994 Feb;103(2):134-41 11457140 - J Am Chem Soc. 2001 May 2;123(17):3903-18 2550066 - Biochemistry. 1989 Jul 11;28(14):5978-84 8679609 - Biochemistry. 1996 Jul 2;35(26):8489-94 2619931 - J Biomol Struct Dyn. 1989 Feb;6(4):627-34 17868691 - J Mol Biol. 2007 Oct 26;373(3):652-63 17535901 - Proc Natl Acad Sci U S A. 2007 Jun 5;104(23):9615-20 21315082 - J Mol Biol. 2011 Apr 8;407(4):556-70 19150407 - Methods. 2009 Mar;47(3):177-86 7779802 - Biochemistry. 1995 Jun 13;34(23 ):7569-75 7533569 - J Biomol NMR. 1995 Jan;5(1):82-6 17933777 - Nucleic Acids Res. 2007;35(20):6854-61 11693565 - J Biomol NMR. 2001 Sep;21(1):11-29 1384741 - Biophys J. 1992 Sep;63(3):751-9 |
| References_xml | – volume: 105 start-page: 4685 year: 2008 end-page: 4690 ident: CR46 article-title: Consistent blind protein structure generation from NMR chemical shift data publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.0800256105 – volume: 56 start-page: 289 year: 2010 end-page: 310 ident: CR29 article-title: Use of chemical shifts for structural studies of nucleic acids publication-title: Prog Nucl Magn Reson Spectrosc doi: 10.1016/j.pnmrs.2010.01.002 – volume: 35 start-page: 6854 year: 2007 end-page: 6861 ident: CR40 article-title: Conserved nucleotides in an RNA essential for hepatitis B virus replication show distinct mobility patterns publication-title: Nucleic Acids Res doi: 10.1093/nar/gkm774 – volume: 6 start-page: 627 year: 1989 end-page: 634 ident: CR14 article-title: Definitions and nomenclature of nucleic acid structure parameters publication-title: J Biomol Struct Dyn doi: 10.1080/07391102.1989.10507726 – volume: 332 start-page: 981 year: 2011 end-page: 984 ident: CR16 article-title: Structures of the bacterial ribosome in classical and hybrid states of tRNA binding publication-title: Science doi: 10.1126/science.1202692 – volume: 76 start-page: 81 year: 1981 end-page: 92 ident: CR44 article-title: Parameters for the calculation of the ring current and atomic magnetic anisotropy contributions to magnetic shielding constants: nucleic acid bases and intercalating agents publication-title: J Mol Struct THEOCHEM doi: 10.1016/0166-1280(81)85115-9 – volume: 31 start-page: 5108 year: 2003 end-page: 5121 ident: CR30 article-title: 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures publication-title: Nucleic Acids Res doi: 10.1093/nar/gkg680 – year: 1992 ident: CR8 publication-title: X-PLOR version 3.1 a system for X-ray crystallography and NMR – volume: 53 start-page: 5010 year: 2009 end-page: 5014 ident: CR23 article-title: Structures of triacetyloleandomycin and mycalamide A bind to the large ribosomal subunit of Haloarcula marismortui publication-title: Antimicrob Agents Chemother doi: 10.1128/AAC.00817-09 – volume: 81 start-page: 93 year: 1973 end-page: 105 ident: CR3 article-title: Refinement of the structure of B-DNA and implications for the analysis of X-ray diffraction data from fibers of biopolymers publication-title: J Mol Biol doi: 10.1016/0022-2836(73)90182-4 – volume: 123 start-page: 3903 year: 2001 end-page: 3918 ident: CR28 article-title: Improving the accuracy of NMR structures of DNA by means of a database potential of mean force describing base–base positional interactions publication-title: J Am Chem Soc doi: 10.1021/ja010033u – volume: 5 start-page: 82 year: 1995 end-page: 86 ident: CR56 article-title: Sequential backbone assignment of uniformly C13-labeled RNAs by a 2-dimensional P(CC)H-TOCSY triple-resonance NMR experiment publication-title: J Biomol NMR doi: 10.1007/BF00227472 – volume: 35 start-page: 8489 year: 1996 end-page: 8494 ident: CR17 article-title: RNA hydration: a detailed look publication-title: Biochemistry doi: 10.1021/bi9607214 – volume: 36 start-page: 235 year: 2006 end-page: 249 ident: CR36 article-title: Impact of static and dynamic A-form heterogeneity on the determination of RNA global structure dynamics using NMR residual dipolar couplings publication-title: J Biomol NMR doi: 10.1007/s10858-006-9087-9 – volume: 57 start-page: 404 year: 1984 end-page: 426 ident: CR27 article-title: A theoretical studie of distance determinations from NMR. Two-dimensional nuclear overhauser effect spectra publication-title: J Magn Reson – volume: 407 start-page: 556 year: 2011 end-page: 570 ident: CR43 article-title: Insights into metalloregulation by M-box riboswitch RNAs via structural analysis of manganese-bound complexes publication-title: J Mol Biol doi: 10.1016/j.jmb.2011.01.049 – volume: 47 start-page: 205 year: 2010 end-page: 219 ident: CR50 article-title: Major groove width variations in RNA structures determined by NMR and impact of 13C residual chemical shift anisotropy and 1H–13C residual dipolar coupling on refinement publication-title: J Biomol NMR doi: 10.1007/s10858-010-9424-x – volume: 17 start-page: 555 year: 2010 end-page: 560 ident: CR25 article-title: Structural aspects of messenger RNA reading frame maintenance by the ribosome publication-title: Nat Struct Mol Biol doi: 10.1038/nsmb.1790 – volume: 63 start-page: 751 year: 1992 end-page: 759 ident: CR6 article-title: The nucleic acid database: a comprehensive relational database of three-dimensional structures of nucleic acids publication-title: Biophys J doi: 10.1016/S0006-3495(92)81649-1 – volume: 86 start-page: 348 year: 2007 end-page: 359 ident: CR45 article-title: NMR studies of dynamics in RNA and DNA by C-13 relaxation publication-title: Biopolymers doi: 10.1002/bip.20650 – volume: 107 start-page: 17152 year: 2010 end-page: 17157 ident: CR15 article-title: Structures of the ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.1007988107 – volume: 103 start-page: 134 year: 1994 end-page: 141 ident: CR55 article-title: Assignment strategies and analysis of cross-peak patterns and intensities in the 3-dimensional homonuclear TOCSY-NOESY of RNA publication-title: J Magn Reson Ser B doi: 10.1006/jmrb.1994.1021 – volume: 36 start-page: 8030 year: 1997 end-page: 8038 ident: CR32 article-title: Investigation of the structural basis for thermodynamic stabilities of tandem GU wobble pairs: NMR structures of (rGGAGUUCC)(2) and (rGGAUGUCC)(2) publication-title: Biochemistry doi: 10.1021/bi970122c – volume: 104 start-page: 9615 year: 2007 end-page: 9620 ident: CR10 article-title: Protein structure determination from NMR chemical shifts publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.0610313104 – volume: 33 start-page: 3965 year: 2005 end-page: 3975 ident: CR24 article-title: Syntheses of 4’-thioribonucleosides and thermodynamic stability and crystal structure of RNA oligomers with incorporated 4’-thiocytosine publication-title: Nucleic Acids Res doi: 10.1093/nar/gki704 – volume: 313 start-page: 229 year: 2001 end-page: 237 ident: CR37 article-title: A standard reference frame for the description of nucleic acid base-pair geometry publication-title: J Mol Biol doi: 10.1006/jmbi.2001.4987 – volume: 28 start-page: 5978 year: 1989 end-page: 5984 ident: CR21 article-title: Analysis of the relative contributions of the nuclear overhauser interproton distance restraints and the empirical energy function in the calculation of oligonucleotide structures using restrained molecular dynamics publication-title: Biochemistry doi: 10.1021/bi00440a039 – year: 1999 ident: CR13 article-title: An empirical analysis of proton chemical shifts in nucleic acids publication-title: Modeling NMR chemical shifts. Gaining insight into structure and environment – volume: 121 start-page: 2949 year: 1999 end-page: 2950 ident: CR11 article-title: Identification of the hydrogen bonding network in a protein by scalar couplings publication-title: J Am Chem Soc doi: 10.1021/ja9902221 – volume: 85 start-page: 8785 year: 1988 end-page: 8789 ident: CR39 article-title: Determination of DNA structures by NMR and distance geometry techniques: a computer simulation publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.85.23.8785 – volume: 267 start-page: 338 year: 1997 end-page: 351 ident: CR1 article-title: How accurately and precisely can RNA structure be determined by NMR? publication-title: J Mol Biol doi: 10.1006/jmbi.1996.0855 – volume: 38 start-page: 95 year: 2000 end-page: 107 ident: CR2 article-title: Double-helical DNA H chemical shifts: an accurate and balanced predictive empirical scheme publication-title: Magn Reson Chem doi: 10.1002/(SICI)1097-458X(200002)38:2<95::AID-MRC592>3.0.CO;2-M – volume: 6 start-page: 341 year: 1995 end-page: 346 ident: CR9 article-title: Calibration of ring-current effects in proteins and nucleic acids publication-title: J Biomol NMR doi: 10.1007/BF00197633 – volume: 33 start-page: 7315 year: 1994 end-page: 7325 ident: CR35 article-title: The solution structure of the hairpin formed by d(TCTCTC-TTT-GAGAGA) publication-title: Biochemistry doi: 10.1021/bi00189a037 – volume: 11 start-page: 231 year: 2010 end-page: 237 ident: CR41 article-title: RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-11-231 – volume: 20 start-page: 113 year: 1987 end-page: 172 ident: CR20 article-title: Quantum mechanical calculations of NMR chemical shifts in nucleic acids publication-title: Q Rev Biophys doi: 10.1017/S0033583500004169 – volume: 43 start-page: 63 year: 2009 end-page: 78 ident: CR47 article-title: De novo protein structure generation from incomplete chemical shift assignments publication-title: J Biomol NMR doi: 10.1007/s10858-008-9288-5 – volume: 36 start-page: W496 year: 2008 end-page: W502 ident: CR58 article-title: CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data publication-title: Nucleic Acids Res doi: 10.1093/nar/gkn305 – volume: 87 start-page: 475 year: 1990 end-page: 487 ident: CR7 article-title: Mardigras—a procedure for matrix analysis of relaxation for discerning geometry of an aqueous structure publication-title: J Magn Reson – volume: 2 start-page: 1536 year: 2007 end-page: 1546 ident: CR4 article-title: Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings publication-title: Nat Protoc doi: 10.1038/nprot.2007.221 – volume: 10 start-page: 298 year: 2000 end-page: 302 ident: CR34 article-title: NMR Solution structure determination of RNAs publication-title: Curr Opin Struct Biol doi: 10.1016/S0959-440X(00)00087-7 – volume: 19 start-page: 585 year: 2009 end-page: 595 ident: CR22 article-title: From biomolecular structure to functional understanding: new NMR developments narrow the gap publication-title: Curr Opin Struct Biol doi: 10.1016/j.sbi.2009.07.015 – volume: 31 start-page: 4326 year: 2003 end-page: 4331 ident: CR49 article-title: Solution structure of the HIV-1 frameshift inducing stem-loop RNA publication-title: Nucleic Acids Res doi: 10.1093/nar/gkg654 – volume: 34 start-page: 7569 year: 1995 end-page: 7575 ident: CR42 article-title: The crystal-structure of R(Ccccgggg) in 2 distinct lattices publication-title: Biochemistry doi: 10.1021/bi00023a002 – volume: 118 start-page: 519 year: 1996 end-page: 529 ident: CR19 article-title: Geometric parameters in nucleic acids: sugar and phosphate constituents publication-title: J Am Chem Soc doi: 10.1021/ja9528846 – volume: 373 start-page: 652 year: 2007 end-page: 663 ident: CR31 article-title: Programmed ribosomal frameshifting in SIV is induced by a highly STRUCTURED RNA stem–loop publication-title: J Mol Biol doi: 10.1016/j.jmb.2007.08.033 – volume: 123 start-page: 12135 year: 2001 end-page: 12146 ident: CR48 article-title: Refinement of local and long-range structural order in theophylline-binding RNA using C-13-H-1 residual dipolar couplings and restrained molecular dynamics publication-title: J Am Chem Soc doi: 10.1021/ja011646+ – volume: 32 start-page: 287 year: 1998 end-page: 387 ident: CR54 article-title: The use of NMR methods for conformational studies of nucleic acids publication-title: Prog Nucl Magn Reson Spectrosc doi: 10.1016/S0079-6565(97)00023-X – volume: 10 start-page: 337 year: 1997 end-page: 350 ident: CR57 article-title: Analysis of H-1 chemical shifts in DNA: assessment of the reliability of H-1 chemical shift calculations for use in structure refinement publication-title: J Biomol NMR doi: 10.1023/A:1018348123074 – volume: 34 start-page: 4449 year: 2006 end-page: 4457 ident: CR18 article-title: Solution structure of the apical stem-loop of the human hepatitis B virus encapsidation signal publication-title: Nucleic Acids Res doi: 10.1093/nar/gkl582 – volume: 107 start-page: 8593 year: 2010 end-page: 8598 ident: CR26 article-title: Structure of the 70S ribosome bound to release factor 2 and a substrate analog provides insights into catalysis of peptide release publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.1003995107 – volume: 47 start-page: 177 year: 2009 end-page: 186 ident: CR38 article-title: New information content in RNA base pairing deduced from quantitative analysis of high-resolution structures publication-title: Methods doi: 10.1016/j.ymeth.2008.12.003 – volume: 54 start-page: 141 year: 2009 end-page: 165 ident: CR33 article-title: Characterization of protein secondary structure from NMR chemical shifts publication-title: Prog Nucl Magn Reson Spectrosc doi: 10.1016/j.pnmrs.2008.06.002 – volume: 9 start-page: 747 year: 2002 end-page: 755 ident: CR53 article-title: Crystal structure of a complex between the aminoglycoside tobramycin and an oligonucleotide containing the ribosomal decoding A site publication-title: Chem Biol doi: 10.1016/S1074-5521(02)00153-9 – volume: 330 start-page: 1203 year: 2010 end-page: 1209 ident: CR5 article-title: Crystal structure of the eukaryotic ribosome publication-title: Science doi: 10.1126/science.1194294 – volume: 21 start-page: 11 year: 2001 end-page: 29 ident: CR12 article-title: Prediction of proton chemical shifts in RNA—their use in structure refinement and validation publication-title: J Biomol NMR doi: 10.1023/A:1011914132531 – volume: 12 start-page: 923 year: 2005 end-page: 930 ident: CR51 article-title: The crystal structure of leucyl-tRNA synthetase complexed with tRNA(Leu) in the post-transfer- editing conformation publication-title: Nat Struct Mol Biol doi: 10.1038/nsmb986 – volume: 29 start-page: 51 year: 1996 end-page: 127 ident: CR52 article-title: NMR investigation of RNA structure publication-title: Prog Nucl Magn Reson Spectrosc doi: 10.1016/0079-6565(96)01028-X – volume: 330 start-page: 1203 year: 2010 ident: 9725_CR5 publication-title: Science doi: 10.1126/science.1194294 – volume: 121 start-page: 2949 year: 1999 ident: 9725_CR11 publication-title: J Am Chem Soc doi: 10.1021/ja9902221 – volume: 10 start-page: 337 year: 1997 ident: 9725_CR57 publication-title: J Biomol NMR doi: 10.1023/A:1018348123074 – volume: 36 start-page: W496 year: 2008 ident: 9725_CR58 publication-title: Nucleic Acids Res doi: 10.1093/nar/gkn305 – volume: 31 start-page: 5108 year: 2003 ident: 9725_CR30 publication-title: Nucleic Acids Res doi: 10.1093/nar/gkg680 – volume: 17 start-page: 555 year: 2010 ident: 9725_CR25 publication-title: Nat Struct Mol Biol doi: 10.1038/nsmb.1790 – volume: 407 start-page: 556 year: 2011 ident: 9725_CR43 publication-title: J Mol Biol doi: 10.1016/j.jmb.2011.01.049 – volume: 6 start-page: 627 year: 1989 ident: 9725_CR14 publication-title: J Biomol Struct Dyn doi: 10.1080/07391102.1989.10507726 – volume: 107 start-page: 8593 year: 2010 ident: 9725_CR26 publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.1003995107 – volume: 36 start-page: 235 year: 2006 ident: 9725_CR36 publication-title: J Biomol NMR doi: 10.1007/s10858-006-9087-9 – volume: 33 start-page: 3965 year: 2005 ident: 9725_CR24 publication-title: Nucleic Acids Res doi: 10.1093/nar/gki704 – volume: 63 start-page: 751 year: 1992 ident: 9725_CR6 publication-title: Biophys J doi: 10.1016/S0006-3495(92)81649-1 – volume: 103 start-page: 134 year: 1994 ident: 9725_CR55 publication-title: J Magn Reson Ser B doi: 10.1006/jmrb.1994.1021 – volume: 5 start-page: 82 year: 1995 ident: 9725_CR56 publication-title: J Biomol NMR doi: 10.1007/BF00227472 – volume: 56 start-page: 289 year: 2010 ident: 9725_CR29 publication-title: Prog Nucl Magn Reson Spectrosc doi: 10.1016/j.pnmrs.2010.01.002 – volume: 12 start-page: 923 year: 2005 ident: 9725_CR51 publication-title: Nat Struct Mol Biol doi: 10.1038/nsmb986 – volume: 10 start-page: 298 year: 2000 ident: 9725_CR34 publication-title: Curr Opin Struct Biol doi: 10.1016/S0959-440X(00)00087-7 – volume: 54 start-page: 141 year: 2009 ident: 9725_CR33 publication-title: Prog Nucl Magn Reson Spectrosc doi: 10.1016/j.pnmrs.2008.06.002 – volume: 47 start-page: 177 year: 2009 ident: 9725_CR38 publication-title: Methods doi: 10.1016/j.ymeth.2008.12.003 – volume: 313 start-page: 229 year: 2001 ident: 9725_CR37 publication-title: J Mol Biol doi: 10.1006/jmbi.2001.4987 – volume: 36 start-page: 8030 year: 1997 ident: 9725_CR32 publication-title: Biochemistry doi: 10.1021/bi970122c – volume: 38 start-page: 95 year: 2000 ident: 9725_CR2 publication-title: Magn Reson Chem doi: 10.1002/(SICI)1097-458X(200002)38:2<95::AID-MRC592>3.0.CO;2-M – volume: 105 start-page: 4685 year: 2008 ident: 9725_CR46 publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.0800256105 – volume: 118 start-page: 519 year: 1996 ident: 9725_CR19 publication-title: J Am Chem Soc doi: 10.1021/ja9528846 – volume: 43 start-page: 63 year: 2009 ident: 9725_CR47 publication-title: J Biomol NMR doi: 10.1007/s10858-008-9288-5 – volume: 81 start-page: 93 year: 1973 ident: 9725_CR3 publication-title: J Mol Biol doi: 10.1016/0022-2836(73)90182-4 – volume: 33 start-page: 7315 year: 1994 ident: 9725_CR35 publication-title: Biochemistry doi: 10.1021/bi00189a037 – volume: 2 start-page: 1536 year: 2007 ident: 9725_CR4 publication-title: Nat Protoc doi: 10.1038/nprot.2007.221 – volume: 9 start-page: 747 year: 2002 ident: 9725_CR53 publication-title: Chem Biol doi: 10.1016/S1074-5521(02)00153-9 – volume: 104 start-page: 9615 year: 2007 ident: 9725_CR10 publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.0610313104 – volume: 267 start-page: 338 year: 1997 ident: 9725_CR1 publication-title: J Mol Biol doi: 10.1006/jmbi.1996.0855 – volume: 86 start-page: 348 year: 2007 ident: 9725_CR45 publication-title: Biopolymers doi: 10.1002/bip.20650 – volume: 87 start-page: 475 year: 1990 ident: 9725_CR7 publication-title: J Magn Reson – volume: 29 start-page: 51 year: 1996 ident: 9725_CR52 publication-title: Prog Nucl Magn Reson Spectrosc doi: 10.1016/0079-6565(96)01028-X – volume-title: Modeling NMR chemical shifts. Gaining insight into structure and environment year: 1999 ident: 9725_CR13 – volume: 6 start-page: 341 year: 1995 ident: 9725_CR9 publication-title: J Biomol NMR – volume: 373 start-page: 652 year: 2007 ident: 9725_CR31 publication-title: J Mol Biol doi: 10.1016/j.jmb.2007.08.033 – volume: 107 start-page: 17152 year: 2010 ident: 9725_CR15 publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.1007988107 – volume: 31 start-page: 4326 year: 2003 ident: 9725_CR49 publication-title: Nucleic Acids Res doi: 10.1093/nar/gkg654 – volume: 28 start-page: 5978 year: 1989 ident: 9725_CR21 publication-title: Biochemistry doi: 10.1021/bi00440a039 – volume: 35 start-page: 6854 year: 2007 ident: 9725_CR40 publication-title: Nucleic Acids Res doi: 10.1093/nar/gkm774 – volume: 47 start-page: 205 year: 2010 ident: 9725_CR50 publication-title: J Biomol NMR doi: 10.1007/s10858-010-9424-x – volume: 332 start-page: 981 year: 2011 ident: 9725_CR16 publication-title: Science doi: 10.1126/science.1202692 – volume: 19 start-page: 585 year: 2009 ident: 9725_CR22 publication-title: Curr Opin Struct Biol doi: 10.1016/j.sbi.2009.07.015 – volume: 32 start-page: 287 year: 1998 ident: 9725_CR54 publication-title: Prog Nucl Magn Reson Spectrosc doi: 10.1016/S0079-6565(97)00023-X – volume: 35 start-page: 8489 year: 1996 ident: 9725_CR17 publication-title: Biochemistry doi: 10.1021/bi9607214 – volume: 123 start-page: 3903 year: 2001 ident: 9725_CR28 publication-title: J Am Chem Soc doi: 10.1021/ja010033u – volume: 34 start-page: 4449 year: 2006 ident: 9725_CR18 publication-title: Nucleic Acids Res doi: 10.1093/nar/gkl582 – volume: 85 start-page: 8785 year: 1988 ident: 9725_CR39 publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.85.23.8785 – volume: 53 start-page: 5010 year: 2009 ident: 9725_CR23 publication-title: Antimicrob Agents Chemother doi: 10.1128/AAC.00817-09 – volume: 34 start-page: 7569 year: 1995 ident: 9725_CR42 publication-title: Biochemistry doi: 10.1021/bi00023a002 – volume-title: X-PLOR version 3.1 a system for X-ray crystallography and NMR year: 1992 ident: 9725_CR8 – volume: 57 start-page: 404 year: 1984 ident: 9725_CR27 publication-title: J Magn Reson – volume: 11 start-page: 231 year: 2010 ident: 9725_CR41 publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-11-231 – volume: 76 start-page: 81 year: 1981 ident: 9725_CR44 publication-title: J Mol Struct THEOCHEM doi: 10.1016/0166-1280(81)85115-9 – volume: 20 start-page: 113 year: 1987 ident: 9725_CR20 publication-title: Q Rev Biophys doi: 10.1017/S0033583500004169 – volume: 123 start-page: 12135 year: 2001 ident: 9725_CR48 publication-title: J Am Chem Soc doi: 10.1021/ja011646+ – volume: 21 start-page: 11 year: 2001 ident: 9725_CR12 publication-title: J Biomol NMR doi: 10.1023/A:1011914132531 – reference: 16027443 - Nucleic Acids Res. 2005 Jul 18;33(13):3965-75 – reference: 20876128 - Proc Natl Acad Sci U S A. 2010 Oct 5;107(40):17152-7 – reference: 18515350 - Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W496-502 – reference: 12079787 - Chem Biol. 2002 Jun;9(6):747-55 – reference: 7533569 - J Biomol NMR. 1995 Jan;5(1):82-6 – reference: 9096230 - J Mol Biol. 1997 Mar 28;267(2):338-51 – reference: 4777309 - J Mol Biol. 1973 Dec 5;81(2):93-105 – reference: 9201950 - Biochemistry. 1997 Jul 1;36(26):8030-8 – reference: 16945960 - Nucleic Acids Res. 2006;34(16):4449-57 – reference: 11601858 - J Mol Biol. 2001 Oct 12;313(1):229-37 – reference: 20421507 - Proc Natl Acad Sci U S A. 2010 May 11;107(19):8593-8 – reference: 19716691 - Curr Opin Struct Biol. 2009 Oct;19(5):585-95 – reference: 19150407 - Methods. 2009 Mar;47(3):177-86 – reference: 8003496 - Biochemistry. 1994 Jun 14;33(23):7315-25 – reference: 3327086 - Q Rev Biophys. 1987 Nov;20(3-4):113-72 – reference: 11693565 - J Biomol NMR. 2001 Sep;21(1):11-29 – reference: 21315082 - J Mol Biol. 2011 Apr 8;407(4):556-70 – reference: 19034676 - J Biomol NMR. 2009 Feb;43(2):63-78 – reference: 19738021 - Antimicrob Agents Chemother. 2009 Dec;53(12):5010-4 – reference: 17535901 - Proc Natl Acad Sci U S A. 2007 Jun 5;104(23):9615-20 – reference: 7511032 - J Magn Reson B. 1994 Feb;103(2):134-41 – reference: 11457140 - J Am Chem Soc. 2001 May 2;123(17):3903-18 – reference: 17571061 - Nat Protoc. 2007;2(6):1536-46 – reference: 21109664 - Science. 2010 Nov 26;330(6008):1203-9 – reference: 20160946 - Prog Nucl Magn Reson Spectrosc. 2009 Apr 5;54(3-4):141-165 – reference: 20549304 - J Biomol NMR. 2010 Jul;47(3):205-19 – reference: 11734011 - J Am Chem Soc. 2001 Dec 12;123(49):12135-46 – reference: 18326625 - Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4685-90 – reference: 17154290 - Biopolymers. 2007 Aug 5-15;86(5-6):348-59 – reference: 17868691 - J Mol Biol. 2007 Oct 26;373(3):652-63 – reference: 20633356 - Prog Nucl Magn Reson Spectrosc. 2010 Apr;56(3):289-310 – reference: 21596992 - Science. 2011 May 20;332(6032):981-4 – reference: 3194389 - Proc Natl Acad Sci U S A. 1988 Dec;85(23):8785-9 – reference: 7779802 - Biochemistry. 1995 Jun 13;34(23 ):7569-75 – reference: 20459631 - BMC Bioinformatics. 2010 May 06;11:231 – reference: 2619931 - J Biomol Struct Dyn. 1989 Feb;6(4):627-34 – reference: 17933777 - Nucleic Acids Res. 2007;35(20):6854-61 – reference: 12888491 - Nucleic Acids Res. 2003 Aug 1;31(15):4326-31 – reference: 20859781 - J Biomol NMR. 1997 Dec;10(4):337-50 – reference: 16155583 - Nat Struct Mol Biol. 2005 Oct;12(10):923-30 – reference: 10851189 - Curr Opin Struct Biol. 2000 Jun;10(3):298-302 – reference: 20400952 - Nat Struct Mol Biol. 2010 May;17(5):555-60 – reference: 8679609 - Biochemistry. 1996 Jul 2;35(26):8489-94 – reference: 8563464 - J Biomol NMR. 1995 Dec;6(4):341-6 – reference: 1384741 - Biophys J. 1992 Sep;63(3):751-9 – reference: 2550066 - Biochemistry. 1989 Jul 11;28(14):5978-84 – reference: 17077936 - J Biomol NMR. 2006 Dec;36(4):235-49 – reference: 12930962 - Nucleic Acids Res. 2003 Sep 1;31(17):5108-21 |
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| Snippet | We present a method for
de novo
derivation of the three-dimensional helix structure of nucleic acids using non-exchangeable proton chemical shifts as sole... We present a method for de novo derivation of the three-dimensional helix structure of nucleic acids using non-exchangeable proton chemical shifts as sole... |
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| SubjectTerms | Biochemistry Biological and Medical Physics Biophysics Decomposition Nuclear Magnetic Resonance, Biomolecular - methods Nucleic Acid Conformation Nucleic acids Nucleic Acids - chemistry Physics Physics and Astronomy Protons RNA - chemistry Spectroscopy/Spectrometry |
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| Title | Nucleic acid helix structure determination from NMR proton chemical shifts |
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