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A combined molecular dynamic simulation and Urea 14N NMR relaxation study of the Urea - lysozyme system
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
2010 (Engelska)Ingår i: Spectrochimica Acta Part A - Molecular and Biomolecular Spectroscopy, ISSN 1386-1425, E-ISSN 1873-3557, Vol. 75, nr 3, s. 953-9Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Urea in the lysozyme solvation shell has been studied by utilizing a combination of urea , water NMR relaxation experiments and a molecular dynamics simulation of the urea–lysozyme system. Samples with lysozyme in the native fold in water as well as in 3 M urea have been studied, as well as denatured lysozyme in a 8.5 M urea solvent. The spin relaxation rates of the samples with folded protein show a clear field dependence, which is consistent with a few urea molecules having long residence times on the protein surface and preferentially located in pockets and grooves on the protein. By combining the 3 M urea NMR relaxation data and data from the MD simulation, a full parameter set of the relaxation model is found which can successfully predict the experimental relaxation rates of the 3 M urea sample. However, in the parameter fitting it is evident that the rotational dynamics of urea in the MD simulation is slightly too fast to be consistent with the NMR relaxation rates, perhaps a result of the fast dynamics of the TIP3P water model. The relaxation rates of urea in the proximity of the unfolded lysozyme lack field dependence, which can be interpreted as a loss of pockets and grooves on the denatured protein. The extracted model parameters from the 3 M sample are adjusted and tested on a simple model of the unfolded protein sample and are seen to be in agreement with the relaxation rates. It is shown that the combination of NMR relaxation and MD simulations can be used to create a microscopic picture of the solvent at the protein interface, which can be used for example in the study of chemical denaturation.

Ort, förlag, år, upplaga, sidor
Elsevier , 2010. Vol. 75, nr 3, s. 953-9
Nyckelord [en]
14N-urea NMR-relaxation, Molecular dynamics simulation, Urea–lysozyme system
Identifikatorer
URN: urn:nbn:se:umu:diva-30184DOI: 10.1016/j.saa.2009.11.054ISI: 000275584000002PubMedID: 20061179OAI: oai:DiVA.org:umu-30184DiVA, id: diva2:280454
Tillgänglig från: 2009-12-10 Skapad: 2009-12-10 Senast uppdaterad: 2018-06-08Bibliografiskt granskad
Ingår i avhandling
1. On the mechanism of Urea-induced protein denaturation
Öppna denna publikation i ny flik eller fönster >>On the mechanism of Urea-induced protein denaturation
2010 (Engelska)Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
Abstract [en]

It is well known that folded proteins in water are destabilized by the addition of urea. When a protein loses its ability to perform its biological activity due to a change in its structure, it is said to denaturate. The mechanism by which urea denatures proteins has been thoroughly studied in the past but no proposed mechanism has yet been widely accepted. The topic of this thesis is the study of the mechanism of urea-induced protein denaturation, by means of Molecular Dynamics (MD) computer simulations and Nuclear Magnetic Resonance (NMR) spectroscopy.

Paper I takes a thermodynamic approach to the analysis of protein – urea solution MD simulations. It is shown that the protein – solvent interaction energies decrease significantly upon the addition of urea. This is the result of a decrease in the Lennard-Jones energies, which is the MD simulation equivalent to van der Waals interactions. This effect will favor the unfolded protein state due to its higher number of protein - solvent contacts. In Paper II, we show that a combination of NMR spin relaxation experiments and MD simulations can successfully be used to study urea in the protein solvation shell. The urea molecule was found to be dynamic, which indicates that no specific binding sites exist. In contrast to the thermodynamic approach in Paper I, in Paper III we utilize MD simulations to analyze the affect of urea on the kinetics of local processes in proteins. Urea is found to passively unfold proteins by decreasing the refolding rate of local parts of the protein that have unfolded by thermal fluctuations.

Based upon the results of Paper I – III and previous studies in the field, I propose a mechanism in which urea denatures proteins mainly by an enthalpic driving force due to attractive van der Waals interactions. Urea interacts favorably with all the different parts of the protein. The greater solvent accessibility of the unfolded protein is ultimately the factor that causes unfolded protein structures to be favored in concentrated urea solutions.

Ort, förlag, år, upplaga, sidor
Umeå: Department of Chemistry, Umeå university, 2010. s. 52
Nyckelord
Chemical denaturation, Protein unfolding, urea, MD simulations, NMR spectroscopy
Nationell ämneskategori
Fysikalisk kemi
Forskningsämne
fysikalisk kemi
Identifikatorer
urn:nbn:se:umu:diva-33151 (URN)978-91-7264-997-2 (ISBN)
Disputation
2010-05-07, KBC huset, KB3A9, Umeå Universitet, Umeå, 13:00 (Engelska)
Opponent
Handledare
Tillgänglig från: 2010-04-16 Skapad: 2010-04-13 Senast uppdaterad: 2018-06-08Bibliografiskt granskad

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Lindgren, MatteusSparrman, TobiasWestlund, Per-Olof

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