Top Buy Now Summary References
Home
>
Section
>
Chapter

The Ad-MD method to calculate NMR shift including effects due to conformational dynamics: the 31 P NMR shift in DNA

Fukal, J.ří; Buděšínský, M.š; Páv, O.ře.; Jurečka, P.; Zgarbová, M.; Šebera, J.; Sychrovský, V.ír.

Journal of Computational Chemistry 43(2): 132-143

2022

ISSN/ISBN: 1096-987X
PMID: 34729803
Accession: 080374277

Full-Text Article emailed within 1 workday
Payments are secure & encrypted
Powered by Stripe
Powered by PayPal

Summary
A method for averaging of NMR parameters by molecular dynamics (MD) has been derived from the method of statistical averaging in MD snapshots, benchmarked and applied to structurally dynamic interpretation of the 31 P NMR shift (δ31P ) in DNA phosphates. The method employs adiabatic dependence of an NMR parameter on selected geometric parameter(s) that is weighted by MD-calculated probability distribution(s) for the geometric parameter(s) (Ad-MD method). The usage of Ad-MD for polymers is computationally convenient when one pre-calculated structural dependence of an NMR parameter is employed for all chemically equivalent units differing only in dynamic behavior. The Ad-MD method is benchmarked against the statistical averaging method for δ31P in the model phosphates featuring distinctively different structures and dynamic behavior. The applicability of Ad-MD is illustrated by calculating 31 P NMR spectra in the Dickerson-Drew DNA dodecamer. δ31P was calculated with the B3LYP/IGLO-III/PCM(water) and the probability distributions for the torsion angles adjacent to the phosphorus atoms in the DNA phosphates were calculated using the OL15 force field.

References

Smith; Silverman; Heckert; Brodke; Hayes; Silverman; Mattimore 1997: Shift-related Differeces in Industrial Injuries: Application of a new Research Method in Fixed-shift and Rotating-shift Systems International Journal of Occupational and Environmental Health 3(Suppl 2: S46-S52
Traiphol, R.; Charoenthai, N. 2008: Effects of conformational change and segmental aggregation on photoemission of illuminophores in conjugated polymer MEH-PPV : Blue shift versus red shift Synthetic Metals 158(3-4): 135-142
Quaegebeur, J.P.; Yasukawa, T. 1982: Application of lanthanide nuclear magnetic resonance shift reagents in conformational analysis of flexible chain molecules. a pseudocontact-shift and relaxation investigation The Journal of Physical Chemistry 86(2): 204-216
Reinberg, A.; Chaumont, A.J. Laporte, A.; Chambon, P.; Vincendon, G.; Skoulios, G.; Bochart, M.; Nicolai, A.; Abulker, C. 1973: Changes in circadian temporal structure including sleep of 20 shift workers 8 hour shift weekly rotation a field study with auto rhythmometry International Journal of Chronobiology 1(4): 352-353
Herman, L. Ammon; Paul, H. Mazzocchi; Elena, J. Colicelli 1978: An investigation of the utility of using n.m.r. lanthanide shift reagents for 13C assignments in selected aromatic ethers and ketones. A detailed description of the lanthanide induced shift ratio method for lanthanide shift reagentsubstrate geometry analysis Magnetic Resonance in Chemistry 11(1): 1-8
Corrêa, R.J.; Mota, C.J.A. 2002: A fast and easy computational method to calculate the (13)C NMR chemical shift of organic species adsorbed on the zeolite surface Journal of the American Chemical Society 124(14): 3484-3485
Jinle, Z.H.A.N.G.; Biao, M.A.; Zehn, M. 2010: Study on shift dynamics and shift quality of dual clutch transmissions International Journal of Vehicle Systems Modelling and Testing 5(2-3): 103-123
Ekman, J.; Quartey, P.; Ussif, A.M.; Ricklund, N.; Egbenya, D.L.; Wiafe, G.A.; Tsegah, K.M.; Karikari, A.; Löfstedt, H.åk.; Djankpa, F.T. 2023: Dynamics of pre-shift and post-shift lung function parameters among wood workers in Ghana Annals of Occupational and Environmental Medicine 35: E39
Aykut, A.O.; Atilgan, A.R.; Atilgan, C. 2013: Designing molecular dynamics simulations to shift populations of the conformational states of calmodulin Plos Computational Biology 9(12): E1003366
Erren, T.C. 2013: Shift work and cancer research: can chronotype predict susceptibility in night-shift and rotating-shift workers? Occupational and Environmental Medicine 70(4): 283-284
Shan, F.K.; Liu, G.X.; Lee, W.J.; Shin, B.C. 2006: Stokes shift, blue shift and red shift of ZnO-based thin films deposited by pulsed-laser deposition Journal of Crystal Growth 291(2): 328-333
Greives, N.; Zhou, H-Xiang. 2014: Both protein dynamics and ligand concentration can shift the binding mechanism between conformational selection and induced fit Proceedings of the National Academy of Sciences of the United States of America 111(28): 10197-10202
Dračínský, M.; Möller, H.M.; Exner, T.E. 2013: Conformational Sampling by Ab Initio Molecular Dynamics Simulations Improves NMR Chemical Shift Predictions Journal of Chemical Theory and Computation 9(8): 3806-3815
Chan, S. 2024: AMERICANS' REACTION TO CHINA'S RISE: Power Shift, Problem Shift and Policy Shift Routledge Handbook on Global China: 67-77
Mauss, D.; Litaker, D.; Jarczok, M.N.; Li, J.; Bosch, J.A.; Fischer, J.E. 2013: Anti-clockwise rotating shift work and health: would you prefer 3-shift or 4-shift operation? American Journal of Industrial Medicine 56(5): 599-608
Epsztajn, J.; Bieniek, A.; Brzezinski, J.Z.; Kalinowski, H.O. 1986: The conformational analysis of benzocycloalkanones using the lanthanide induced shift method Tetrahedron (Oxford. Print) 42(13): 3559-3568
Kantermann, T; Haubruge, D; Skene, D J. 2013: The Shift-Work Accident Rate is More Related to the Shift Type than to Shift Rotation Human and Ecological Risk Assessment An International Journal 19(6): 1586-1594
Hughes, R.; Stone, P. 2004: The perils of shift work: evening shift, night shift, and rotating shifts: are they for you? American Journal of Nursing 104(9): 60-63
Xu, X.; Ishima, R.; Ames, J.B. 2011: Conformational dynamics of recoverin's Ca2+-myristoyl switch probed by 15N NMR relaxation dispersion and chemical shift analysis Proteins 79(6): 1910-1922
Mao, W.; Suprapto, undefined; Hung, C.W.; Chien, Y. 2016: Unambiguous galileo acquisition using binary phase-shift keying-like parallel shift-and-combine method ICIC Express Letters, Part B: Applications 7(5): 1013-1022