Related ArticlesThe electric dipole moment of DNA-binding HU protein calculated by the use of an NMR database.
Biophys Chem. 1999 Aug 30;80(3):153-63
Authors: Takashima S, Yamaoka K
Electric birefringence measurements indicated the presence of a large permanent dipole moment in HU protein-DNA complex. In order to substantiate this observation, numerical computation of the dipole moment of HU protein homodimer was carried out by using NMR protein databases. The dipole moments of globular proteins have hitherto been calculated with X-ray databases and NMR data have never been used before. The advantages of NMR databases are: (a) NMR data are obtained, unlike X-ray databases, using protein solutions. Accordingly, this method eliminates the bothersome question as to the possible alteration of the protein structure due to the transition from the crystalline state to the solution state. This question is particularly important for proteins such as HU protein which has some degree of internal flexibility; (b) the three-dimensional coordinates of hydrogen atoms in protein molecules can be determined with a sufficient resolution and this enables the N-H as well as C = O bond moments to be calculated. Since the NMR database of HU protein from Bacillus stearothermophilus consists of 25 models, the surface charge as well as the core dipole moments were computed for each of these structures. The results of these calculations show that the net permanent dipole moments of HU protein homodimer is approximately 500-530 D (1 D = 3.33 x 10(-30) Cm) at pH 7.5 and 600-630 D at the isoelectric point (pH 10.5). These permanent dipole moments are unusually large for a small protein of the size of 19.5 kDa. Nevertheless, the result of numerical calculations is compatible with the electro-optical observation, confirming a very large dipole moment in this protein.
Local protein backbone folds determined by calculated NMR chemical shifts.
Local protein backbone folds determined by calculated NMR chemical shifts.
Local protein backbone folds determined by calculated NMR chemical shifts.
J Comput Chem. 2011 Sep 9;
Authors: Czajlik A, Hudáky I, Perczel A
Abstract
NMR chemical shifts (CSs: ?N(NH) , ?C(?) , ?C(?) , ?C', ?H(NH) , and ?H(?) ) were computed for the amino acid backbone conformers (?(L) , ?(L) , ?(L) , ?(L) , ?(L) , ?(D) , ?(D) , ?(D) , and ?(D) ) modeled by oligoalanine structures. Topological differences of the extended fold were investigated on single ?-strands,...
High-resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations
High-resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations
Abstract We present a novel structure determination approach that exploits the global orientational restraints from RDCs to resolve ambiguous NOE assignments. Unlike traditional approaches that bootstrap the initial fold from ambiguous NOE assignments, we start by using RDCs to compute accurate secondary structure element (SSE) backbones at the beginning of structure calculation. Our structure determination package, called rdc-Panda (RDC-based SSE PAcking with...
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[NMR paper] Principal components analysis of protein structure ensembles calculated using NMR dat
Principal components analysis of protein structure ensembles calculated using NMR data.
Related Articles Principal components analysis of protein structure ensembles calculated using NMR data.
J Biomol NMR. 2001 May;20(1):61-70
Authors: Howe PW
One important problem when calculating structures of biomolecules from NMR data is distinguishing converged structures from outlier structures. This paper describes how Principal Components Analysis (PCA) has the potential to classify calculated structures automatically, according to correlated...
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[NMR paper] The structure and dipole moment of globular proteins in solution and crystalline stat
The structure and dipole moment of globular proteins in solution and crystalline states: use of NMR and X-ray databases for the numerical calculation of dipole moment.
Related Articles The structure and dipole moment of globular proteins in solution and crystalline states: use of NMR and X-ray databases for the numerical calculation of dipole moment.
Biopolymers. 2001 Apr 5;58(4):398-409
Authors: Takashima S
The large dipole moment of globular proteins has been well known because of the detailed studies using dielectric relaxation and...
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[NMR paper] Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemica
Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-custom-pnas_full_free.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an...
The electric dipole moment of DNA-binding HU protein calculated by the use of an NMR
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