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A comparative study of the second-order hydrophobic moments for globular proteins: the consensus scale of hydrophobicity and the CHARMM partial atomic charges.

ABSTRACT: In this paper, the second-order hydrophobic moment for fifteen globular proteins in 150 nonhomologous protein chains was performed in a comparative study involving two sets of hydrophobicity: one selected from the consensus scale and the other derived from the CHARMM partial atomic charges. These proteins were divided into three groups, based on their number of residues (N) and the asphericity (?). Proteins in Group I were spherical and those in Groups II and III were prolate. The size of the proteins is represented by the mean radius of gyration (R(g) ), which follows the Flory scaling law, R(g) ? N(?). The mean value of v was 0.35, which is similar to a polymer chain in a poor solvent. The spatial distributions of the second-order moment for each of the proteins, obtained from the two sets of hydrophobicity, were compared using the Pearson correlation coefficient; the results reveal that there is a strong correlation between the two data sets for each protein structure when the CHARMM partial atomic charges, |q(i)| ? 0.3, assigned for polar atoms, are used. The locations at which these distributions vanish and approach a negative value are at approximately 50% of the percentage of solvent accessibility, indicating that there is a transition point from hydrophobic interior to hydrophilic exterior in the proteins. This may suggest that there is a position for the proteins to determine the residues at exposed sites beyond this range.

SUBMITTER: Tsai CF

PROVIDER: S-EPMC3257080 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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A comparative study of the second-order hydrophobic moments for globular proteins: the consensus scale of hydrophobicity and the CHARMM partial atomic charges.

Tsai Cheng-Fang CF Lee Kuei-Jen KJ

International journal of molecular sciences 20111129 12

In this paper, the second-order hydrophobic moment for fifteen globular proteins in 150 nonhomologous protein chains was performed in a comparative study involving two sets of hydrophobicity: one selected from the consensus scale and the other derived from the CHARMM partial atomic charges. These proteins were divided into three groups, based on their number of residues (N) and the asphericity (δ). Proteins in Group I were spherical and those in Groups II and III were prolate. The size of the pr ...[more]

PMID: 22272083

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Project description:Recent studies have highlighted a group of 4-repeat (4R) tauopathies that are characterised neuropathologically by widespread, globular glial inclusions (GGIs). Tau immunohistochemistry reveals 4R immunoreactive globular oligodendroglial and astrocytic inclusions and the latter are predominantly negative for Gallyas silver staining. These cases are associated with a range of clinical presentations, which correlate with the severity and distribution of underlying tau pathology and neurodegeneration. Their heterogeneous clinicopathological features combined with their rarity and under-recognition have led to cases characterised by GGIs being described in the literature using various and redundant terminologies. In this report, a group of neuropathologists form a consensus on the terminology and classification of cases with GGIs. After studying microscopic images from previously reported cases with suspected GGIs (n = 22), this panel of neuropathologists with extensive experience in the diagnosis of neurodegenerative diseases and a documented record of previous experience with at least one case with GGIs, agreed that (1) GGIs were present in all the cases reviewed; (2) the morphology of globular astrocytic inclusions was different to tufted astrocytes and finally that (3) the cases represented a number of different neuropathological subtypes. They also agreed that the different morphological subtypes are likely to be part of a spectrum of a distinct disease entity, for which they recommend that the overarching term globular glial tauopathy (GGT) should be used. Type I cases typically present with frontotemporal dementia, which correlates with the fronto-temporal distribution of pathology. Type II cases are characterised by pyramidal features reflecting motor cortex involvement and corticospinal tract degeneration. Type III cases can present with a combination of frontotemporal dementia and motor neuron disease with fronto-temporal cortex, motor cortex and corticospinal tract being severely affected. Extrapyramidal features can be present in Type II and III cases and significant degeneration of the white matter is a feature of all GGT subtypes. Improved detection and classification will be necessary for the establishment of neuropathological and clinical diagnostic research criteria in the future.

Dataset Information

A comparative study of the second-order hydrophobic moments for globular proteins: the consensus scale of hydrophobicity and the CHARMM partial atomic charges.

Publications

A comparative study of the second-order hydrophobic moments for globular proteins: the consensus scale of hydrophobicity and the CHARMM partial atomic charges.

Similar Datasets

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