Quantum Chemical Calculations of NMR Chemical Shifts in Phosphorylated Intrinsically Disordered Proteins

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14740%2F19%3A00107747" target="_blank" >RIV/00216224:14740/19:00107747 - isvavai.cz</a>

Alternative codes found

RIV/00216208:11160/19:10400946

Result on the web

<a href="https://pubs.acs.org/doi/10.1021/acs.jctc.8b00257" target="_blank" >https://pubs.acs.org/doi/10.1021/acs.jctc.8b00257</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1021/acs.jctc.8b00257" target="_blank" >10.1021/acs.jctc.8b00257</a>

Result language

angličtina

Original language name

Quantum Chemical Calculations of NMR Chemical Shifts in Phosphorylated Intrinsically Disordered Proteins

Original language description

Quantum mechanics (QM) calculations are applied to examine H-1, C-13, N-15, and P-31 chemical shifts of two phosphorylation sites in an intrinsically disordered protein region. The QM calculations employ a combination of (1) structural ensembles generated by molecular dynamics, (2) a fragmentation technique based on the adjustable density matrix assembler, and (3) density functional methods. The combined computational approach is used to obtain chemical shifts (i) in the S19 and S40 residues of the non-phosphorylated and (ii) in the pS19 and pS40 residues of the doubly phosphorylated human tyrosine hydroxylase 1 as the system of interest. We study the effects of conformational averaging and explicit solvent sampling as well as the effects of phosphorylation on the computed chemical shifts. Good to great quantitative agreement with the experiment is achieved for all nuclei, provided that the systematic error cancellation is optimized by the choice of a suitable NMR standard. The effect of the standard reference on the computed N-15 and P-31 chemical shifts is demonstrated by employing three different referencing methods. Error bars associated with the statistical averaging of the computed P-31 chemical shifts are larger than the difference between the P-31 chemical shift of pS19 and pS40. The sequence trend of P-31 shifts therefore could not be reliably reproduced. On the contrary, the calculations correctly predict the change of the C-13 chemical shift for CB induced by the phosphorylation of the serine residues. The present work demonstrates that QM calculations coupled with molecular dynamics simulations and fragmentation techniques can be used as an alternative to empirical prediction tools in the structure characterization of intrinsically disordered proteins.

Czech name

—

Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

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OECD FORD branch

10403 - Physical chemistry

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2019

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Journal of Chemical Theory and Computation

ISSN

1549-9618

e-ISSN

—

Volume of the periodical

15

Issue of the periodical within the volume

10

Country of publishing house

US - UNITED STATES

Number of pages

17

Pages from-to

5642-5658

UT code for WoS article

000489678700041

EID of the result in the Scopus database

2-s2.0-85072993684