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The water R1(ω) NMRD profiles of a hydrated protein from molecular dynamics simulation
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
2013 (Engelska)Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, nr 33, s. 14089-14097Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

 The hydration of a protein, peroxiredoxin 5, is obtained from a molecular dynamics simulation and compared with the picture of hydration which is obtained by analysing the water proton R1 NMRD profiles using a generally accepted relaxation model [K. Venu, V.P. Denisov and B. Halle, J. Am. Chem. Soc. 119,3122(1997)]. The discrepancy between the hydration pictures derived from the water R1 0)-NMRD profiles and MD is relevant in a discussion of the factors behind the stretched NMRD profile, the distribution of orientationalorder parameters and residence times of buried water used in the NMRD model.

Ort, förlag, år, upplaga, sidor
RSC Publishing, 2013. Vol. 15, nr 33, s. 14089-14097
Nationell ämneskategori
Kemi
Identifikatorer
URN: urn:nbn:se:umu:diva-73724DOI: 10.1039/C3CP51147BISI: 000322517800041OAI: oai:DiVA.org:umu-73724DiVA, id: diva2:633460
Tillgänglig från: 2013-06-27 Skapad: 2013-06-27 Senast uppdaterad: 2018-06-08Bibliografiskt granskad
Ingår i avhandling
1. Analysis of NMR Spin-lattice Relaxation Dispersion on Complex Systems
Öppna denna publikation i ny flik eller fönster >>Analysis of NMR Spin-lattice Relaxation Dispersion on Complex Systems
2015 (Engelska)Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
Abstract [en]

This thesis focus on the analysis of spin-lattice NMRD relaxation profilesmeasured in various complex systems such as proteins, zeolites and ionicliquids. Proton, deuterium and fluoride T1-NMRD relaxation profiles wereobtained from a fast-field cycling (FFC) instrument. It is found that alsopossible to obtain NMRD profiles from the molecular dynamics (MD)simulation trajectories. NMRD Profiles were analyzed by using differentrelaxation models, such as the Solomon-Bloembergen-Morgan (SBM) theoryand the Stochastic Liouville (SL) theory.

Paper I described the hydration of protein PrxV obtained from a MDsimulation, and compared with the picture emerges from an analysis byusing a generally accepted relaxation model [appendix C]. The result showsthat the information from NMRD analysis is an averaged picture of watermolecules with similar relaxation times; and the MD simulations containsinformation of all types of interested water molecules with differentresidence times.

In paper II NMRD profiles have been used to characterize the hydration ofthe oxygen-evolving complex in state S1 of photosystem II. NMRDexperiments were performed on both intact protein samples and Mndepletedsamples, and characteristic dispersion difference were foundbetween 0.03 MHz to 1 MHz; approximately. Both the SBM theory and theSL theory have been used to explain this dispersion difference, and it isfound that this is due to a paramagnetic enhancement of 1-2 water moleculesnearby ~10 Å from the spin center of the Mn4CaO5 cluster. The result showsthe reorientation of the molecular cluster is in μs time interval. Whencompare these two theories, the SL theory presented a better interpretationbecause parameters obtained from the SBM theory shows they didn’t fulfilthe presupposed perturbation criterion (the Kubo term).

Paper III deals with the water dynamics in the restricted/confined spaces inthe zeolite samples (H-ZSM-5 and NH4-ZSM-5) and obtained by proton anddeuterium spin-lattice NMRD profiles. The results show that the spin-latticeNMRD can be used to characterize various zeolites. The temperature has aweak effect on the relaxation rate R1, but the change of different counter ionsmay change the hydration and the translational diffusion pores and givedifferent R1.

Proton and fluoride NMRD profiles and MD simulations were both used tostudy the dynamics of BMIM[PF6] in paper IV. Results indicate the reorientation of the molecules are in the ns time regime, and the effectivecorrelation time obtained from 1H and 19F are the same. From the MDsimulation it is found the reorientation of [PF6]- ions is much faster (in ps)compare with BMIM+ ion which moves in the ns time range.

With previous results, the FFC NMRD profiles are indeed very informativetools to study the molecular dynamics of complex systems. The MDsimulation can be used as a complementary method to obtain detailedinformation. By combine these two methods, it provide a more colorfulpicture in the study of protein hydration and liquid molecular dynamics.

Ort, förlag, år, upplaga, sidor
Umeå: Umeå university, 2015. s. 56
Nyckelord
NMRD, relaxation theory, hydration, MD, FFC, PrxV, OEC complex, ZSM-5, BMIM [PF6, ]
Nationell ämneskategori
Teoretisk kemi
Forskningsämne
fysikalisk kemi
Identifikatorer
urn:nbn:se:umu:diva-110721 (URN)978-91-7601-382-3 (ISBN)
Disputation
2015-11-26, KBC-huset, sal KB3B1, Umeå Universitet, Umeå, 10:00 (Engelska)
Opponent
Handledare
Tillgänglig från: 2015-11-05 Skapad: 2015-10-26 Senast uppdaterad: 2018-06-07Bibliografiskt granskad

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