Hydrodynamic properties of nitrogenase — the MoFe protein from Azotobacter vinelandii studied by dynamic light scattering and hydrodynamic modelling

Hellweg, Thomas; Eimer, Wolfgang; Krahn, Eugen; Schneider, Klaus; Müller, Achim

doi:10.1016/s0167-4838(96)00179-3

Cited by 21 publications

(18 citation statements)

References 25 publications

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“…When taking the hydrodynamic interactions into account, the choice of a hydrodynamic radius, a, is a crucial element in the model. This value agrees with earlier estimates by de la Torre et al, 45,48 Antosiewicz and Porschke, 46 Hellweg et al, 47 and Banachowicz et al 49 However, since the distance between the successive C ␣ atoms along the protein backbone is 3.8 Å, some of the beads representing amino acids overlap. Figure 1 shows the dependence of DЈ = D / D 0 on the hydrodynamic radius.…”

Section: ͑2͒supporting

confidence: 91%

Proteins in a shear flow

Szymczak

Cieplak

2007

The Journal of Chemical Physics

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The conformational dynamics of a single protein molecule in a shear flow is investigated using Brownian dynamics simulations. A structure-based coarse grained model of a protein is used. We consider two proteins, ubiquitin and integrin, and find that at moderate shear rates they unfold through a sequence of metastable states-a pattern which is distinct from a smooth unraveling found in homopolymers. Full unfolding occurs only at very large shear rates. Furthermore, the hydrodynamic interactions between the amino acids are shown to hinder the shear flow unfolding. The characteristics of the unfolding process depend on whether a protein is anchored or not, and if it is, on the choice of an anchoring point.

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Section: ͑2͒supporting

confidence: 91%

Proteins in a shear flow

Szymczak

Cieplak

2007

The Journal of Chemical Physics

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“…A clear advantage of BPR models is that the number of elements in the model is much smaller than in bead-peratom (BPA) models (see below), and therefore they can be applied to large molecules, such as some high-molecularweight proteins (Hellweg et al, 1997). As a disadvantage, we mention the fact of bead overlapping in most versions of this method.…”

Section: Bead Per Residue Modelsmentioning

confidence: 99%

Calculation of Hydrodynamic Properties of Globular Proteins from Their Atomic-Level Structure

Torre

Huertas

Carrasco

2000

Biophysical Journal

994

904

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The solution properties, including hydrodynamic quantities and the radius of gyration, of globular proteins are calculated from their detailed, atomic-level structure, using bead-modeling methodologies described in our previous article (, Biophys. J. 76:3044-3057). We review how this goal has been pursued by other authors in the past. Our procedure starts from a list of atomic coordinates, from which we build a primary hydrodynamic model by replacing nonhydrogen atoms with spherical elements of some fixed radius. The resulting particle, consisting of overlapping spheres, is in turn represented by a shell model treated as described in our previous work. We have applied this procedure to a set of 13 proteins. For each protein, the atomic element radius is adjusted, to fit all of the hydrodynamic properties, taking values close to 3 A, with deviations that fall within the error of experimental data. Some differences are found in the atomic element radius found for each protein, which can be explained in terms of protein hydration. A computational shortcut makes the procedure feasible, even in personal computers. All of the model-building and calculations are carried out with a HYDROPRO public-domain computer program.

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“…1B). The frictional ratio was calculated as 0.92, indicating that M.HpyAVIB is more or less spherical in structure (an ideal spherical protein would give a value of 1.0) [21].…”

Section: Resultsmentioning

confidence: 99%

Mutations in hpyAVIBM, C⁵ cytosine DNA methyltransferase from Helicobacter pylori result in relaxed specificity

et al. 2012

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The genome of Helicobacter pylori is rich in restriction-modification (RM) systems. Approximately 4% of the genome codes for components of RM systems. hpyAVIBM, which codes for a phase-variable C 5 cytosine methyltransferase (MTase) from H. pylori, lacks a cognate restriction enzyme. Over-expression of M.HpyAVIB in Escherichia coli enhances the rate of mutations. However, when the catalytically inactive F9N or C82W mutants of M.HpyAVIB were expressed in E. coli, mutations were not observed. The M.HpyAVIB gene itself was mutated to give rise to different variants of the MTase. M.HpyAVIB variants were purified and differences in kinetic properties and specificity were observed. Intriguingly, purified MTase variants showed relaxed substrate specificity. Homologues of hpyA-VIBM homologues amplified and sequenced from different clinical isolates showed similar variations in sequence. Thus, hpyAVIBM presents an interesting example of allelic variations in H. pylori where changes in the nucleotide sequence result in proteins with new properties.

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Hydrodynamic properties of nitrogenase — the MoFe protein from Azotobacter vinelandii studied by dynamic light scattering and hydrodynamic modelling

Cited by 21 publications

References 25 publications

Proteins in a shear flow

Proteins in a shear flow

Calculation of Hydrodynamic Properties of Globular Proteins from Their Atomic-Level Structure

Mutations in hpyAVIBM, C⁵ cytosine DNA methyltransferase from Helicobacter pylori result in relaxed specificity

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Hydrodynamic properties of nitrogenase — the MoFe protein from Azotobacter vinelandii studied by dynamic light scattering and hydrodynamic modelling

Cited by 21 publications

References 25 publications

Proteins in a shear flow

Proteins in a shear flow

Calculation of Hydrodynamic Properties of Globular Proteins from Their Atomic-Level Structure

Mutations in hpyAVIBM, C5 cytosine DNA methyltransferase from Helicobacter pylori result in relaxed specificity

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Product

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Mutations in hpyAVIBM, C⁵ cytosine DNA methyltransferase from Helicobacter pylori result in relaxed specificity