Accurate ab initio prediction of NMR chemical shifts of nucleic acids and nucleic acids/protein complexes.

Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE

Publication: 1992- : Oxford : Oxford University Press
Original Publication: London, Information Retrieval ltd.

DNA/*chemistry ; DNA-Binding Proteins/*chemistry ; Nuclear Magnetic Resonance, Biomolecular/*methods; Antiviral Agents/chemistry ; Cidofovir ; Cytosine/analogs & derivatives ; Cytosine/chemistry ; DNA/metabolism ; DNA-Binding Proteins/metabolism ; G-Quadruplexes ; Lac Repressors/chemistry ; Lac Repressors/metabolism ; Models, Molecular ; Operator Regions, Genetic ; Organophosphonates/chemistry ; Promoter Regions, Genetic ; Protein Binding ; Protons

NMR chemical shift predictions based on empirical methods are nowadays indispensable tools during resonance assignment and 3D structure calculation of proteins. However, owing to the very limited statistical data basis, such methods are still in their infancy in the field of nucleic acids, especially when non-canonical structures and nucleic acid complexes are considered. Here, we present an ab initio approach for predicting proton chemical shifts of arbitrary nucleic acid structures based on state-of-the-art fragment-based quantum chemical calculations. We tested our prediction method on a diverse set of nucleic acid structures including double-stranded DNA, hairpins, DNA/protein complexes and chemically-modified DNA. Overall, our quantum chemical calculations yield highly/very accurate predictions with mean absolute deviations of 0.3-0.6 ppm and correlation coefficients (r(2)) usually above 0.9. This will allow for identifying misassignments and validating 3D structures. Furthermore, our calculations reveal that chemical shifts of protons involved in hydrogen bonding are predicted significantly less accurately. This is in part caused by insufficient inclusion of solvation effects. However, it also points toward shortcomings of current force fields used for structure determination of nucleic acids. Our quantum chemical calculations could therefore provide input for force field optimization.
(© The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W713-7. (PMID: 17517771)
EMBO J. 2002 Jun 17;21(12):2866-76. (PMID: 12065400)
Proteins. 2008 May 1;71(2):641-54. (PMID: 17975838)
J Chem Theory Comput. 2012 Apr 10;8(4):1480-92. (PMID: 26596758)
RNA. 2005 Jul;11(7):1012-6. (PMID: 15987812)
J Phys Chem B. 2013 Feb 21;117(7):1989-98. (PMID: 23398371)
J Chem Phys. 2008 Feb 7;128(5):052201. (PMID: 18266406)
J Am Chem Soc. 2004 Apr 14;126(14):4726-34. (PMID: 15070392)
Nucleic Acids Res. 2009 Oct;37(19):6625-34. (PMID: 19717545)
J Phys Chem B. 2007 Mar 15;111(10):2658-67. (PMID: 17315915)
FEBS J. 2010 Mar;277(5):1107-17. (PMID: 19951353)
J Chem Phys. 2006 Nov 21;125(19):194104. (PMID: 17129086)
J Am Chem Soc. 2010 Sep 8;132(35):12331-42. (PMID: 20704263)
Biochemistry. 2011 May 17;50(19):3903-12. (PMID: 21443203)
J Biomol NMR. 2011 May;50(1):43-57. (PMID: 21448735)
J Biomol NMR. 2001 Dec;21(4):321-33. (PMID: 11824752)
J Biomol NMR. 2001 Sep;21(1):11-29. (PMID: 11693565)
J Biomol NMR. 2010 Sep;48(1):13-22. (PMID: 20628786)
Proteins. 2011 Jul;79(7):2189-202. (PMID: 21557322)
J Phys Chem B. 2009 Jul 30;113(30):10380-8. (PMID: 19575540)
J Phys Chem B. 2013 Oct 31;117(43):13497-506. (PMID: 24033307)
J Biomol NMR. 1999 Mar;13(3):199-211. (PMID: 10212983)
J Biomol NMR. 1997 Dec;10(4):329-36. (PMID: 9460240)
J Biomol NMR. 2003 May;26(1):25-37. (PMID: 12766400)
Nat Methods. 2014 Apr;11(4):413-6. (PMID: 24584194)
J Biomol NMR. 2008 Jun;41(2):77-88. (PMID: 18484179)
J Biomol NMR. 2007 Jul;38(3):255-66. (PMID: 17562185)
J Biomol NMR. 2007 Jul;38(3):221-35. (PMID: 17558470)
J Biomol NMR. 2002 Sep;24(1):1-14. (PMID: 12449414)
J Magn Reson. 2001 Jul;151(1):1-8. (PMID: 11444931)
J Biomol Struct Dyn. 1984 Aug;2(1):233-48. (PMID: 6400932)
J Phys Chem A. 2007 Jun 14;111(23):5111-5. (PMID: 17511438)
Proc Natl Acad Sci U S A. 2008 Sep 23;105(38):14389-94. (PMID: 18787110)
J Biomol Struct Dyn. 1986 Aug;4(1):99-110. (PMID: 3271436)
J Am Chem Soc. 2001 May 2;123(17):4014-22. (PMID: 11457152)
Chemistry. 2012 Sep 24;18(39):12372-87. (PMID: 22899588)
J Biomol NMR. 2003 Jul;26(3):215-40. (PMID: 12766419)
J Am Chem Soc. 2010 Dec 8;132(48):17139-48. (PMID: 21073198)
J Phys Chem B. 2013 Feb 21;117(7):2045-52. (PMID: 23320790)
J Biomol Struct Dyn. 1985 Aug;3(1):145-60. (PMID: 3917012)
J Biomol NMR. 2011 Nov;51(3):303-12. (PMID: 21866436)
Annu Rev Phys Chem. 2002;53:349-78. (PMID: 11972012)
J Chem Theory Comput. 2013 Mar 12;9(3):1641-56. (PMID: 26587625)
J Biomol NMR. 2011 May;50(1):19-33. (PMID: 21305337)
J Chem Theory Comput. 2013 Aug 13;9(8):3806-15. (PMID: 26584127)
J Biomol Struct Dyn. 1998 Dec;16(3):619-29. (PMID: 10052618)
J Phys Chem B. 2007 Jun 14;111(23):6577-85. (PMID: 17516673)
Proc Natl Acad Sci U S A. 2008 Feb 12;105(6):1891-6. (PMID: 18250334)
J Biomol NMR. 2007 Aug;38(4):289-302. (PMID: 17610132)
Chem Soc Rev. 2010 Feb;39(2):578-90. (PMID: 20111782)
J Biomol NMR. 2009 Nov;45(3):245-53. (PMID: 19644655)
Curr Opin Chem Biol. 2009 Jun;13(3):345-53. (PMID: 19515602)
J Chem Theory Comput. 2012 Nov 13;8(11):4818-27. (PMID: 26605634)
J Chem Theory Comput. 2013 Apr 9;9(4):2104-14. (PMID: 26583557)
J Am Chem Soc. 2011 Feb 23;133(7):2264-74. (PMID: 21280608)
Proc Natl Acad Sci U S A. 2009 Oct 6;106(40):16972-7. (PMID: 19805131)
Phys Chem Chem Phys. 2012 Jun 7;14(21):7837-45. (PMID: 22314755)
Biopolymers. 2002 Dec 15;65(6):408-23. (PMID: 12434429)
J Biomol NMR. 1995 Dec;6(4):341-6. (PMID: 8563464)
J Phys Chem B. 2008 Mar 20;112(11):3470-8. (PMID: 18298109)
J Chem Phys. 2013 Jul 21;139(3):034101. (PMID: 23883004)

PDB 1AHD; 1KR8; 1L1M; 2KKM; 2KZD; 2KZE; 2L8P; 2LAR

0 (Antiviral Agents)
0 (DNA-Binding Proteins)
0 (Lac Repressors)
0 (Organophosphonates)
0 (Protons)
8J337D1HZY (Cytosine)
9007-49-2 (DNA)
JIL713Q00N (Cidofovir)

Date Created: 20141119 Date Completed: 20150512 Latest Revision: 20181202

20221213

PMC4267612

10.1093/nar/gku1006

25404135