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Hydrophobic, hydrophilic, and charged amino acid networks within protein.

ABSTRACT: The native three-dimensional structure of a single protein is determined by the physicochemical nature of its constituent amino acids. The 20 different types of amino acids, depending on their physicochemical properties, can be grouped into three major classes: hydrophobic, hydrophilic, and charged. The anatomy of the weighted and unweighted networks of hydrophobic, hydrophilic, and charged residues separately for a large number of proteins were studied. Results showed that the average degree of the hydrophobic networks has a significantly larger value than that of hydrophilic and charged networks. The average degree of the hydrophilic networks is slightly higher than that of the charged networks. The average strength of the nodes of hydrophobic networks is nearly equal to that of the charged network, whereas that of hydrophilic networks has a smaller value than that of hydrophobic and charged networks. The average strength for each of the three types of networks varies with its degree. The average strength of a node in a charged network increases more sharply than that of the hydrophobic and hydrophilic networks. Each of the three types of networks exhibits the "small-world" property. Our results further indicate that the all-amino-acids networks and hydrophobic networks are of assortative type. Although most of the hydrophilic and charged networks are of the assortative type, few others have the characteristics of disassortative mixing of the nodes. We have further observed that all-amino-acids networks and hydrophobic networks bear the signature of hierarchy, whereas the hydrophilic and charged networks do not have any hierarchical signature.

SUBMITTER: Aftabuddin M

PROVIDER: S-EPMC1914426 | biostudies-literature | 2007 Jul

REPOSITORIES: biostudies-literature

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Hydrophobic, hydrophilic, and charged amino acid networks within protein.

Aftabuddin Md M Kundu S S

Biophysical journal 20061215 1

The native three-dimensional structure of a single protein is determined by the physicochemical nature of its constituent amino acids. The 20 different types of amino acids, depending on their physicochemical properties, can be grouped into three major classes: hydrophobic, hydrophilic, and charged. The anatomy of the weighted and unweighted networks of hydrophobic, hydrophilic, and charged residues separately for a large number of proteins were studied. Results showed that the average degree of ...[more]

PMID: 17172302

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Project description:BackgroundAutism spectrum disorder (ASD) is often accompanied by intellectual disability (ID). Despite extensive studies, however, the genetic basis for this comorbidity is still not clear. In this study, we tried to develop an analyzing pipeline for de novo mutations and possible pathways related to ID phenotype in ASD. Whole-exome sequencing (WES) was performed to screen de novo mutations and candidate genes in 79 ASD children together with their parents (trios). The de novo altering genes and relative pathways which were associated with ID phenotype were analyzed. The connection nodes (genes) of above pathways were selected, and the diagnostic value of these selected genes for ID phenotype in the study population was also evaluated.ResultsWe identified 89 de novo mutant genes, of which 34 genes were previously reported to be associated with ASD, including double hits in the EGF repeats of NOTCH1 gene (p.V999M and p.S1027L). Interestingly, of these 34 genes, 22 may directly affect intelligence quotient (IQ). Further analyses revealed that these IQ-related genes were enriched in protein synthesis, energy metabolism, and amino acid metabolism, and at least 9 genes (CACNA1A, ALG9, PALM2, MGAT4A, PCK2, PLEKHA1, PSME3, ADI1, and TLE3) were involved in all these three pathways. Seven patients who harbored these gene mutations showed a high prevalence of a low IQ score (< 70), a non-verbal language, and an early diagnostic age (< 4 years). Furthermore, our panel of these 9 genes reached a 10.2% diagnostic rate (5/49) in early diagnostic patients with a low IQ score and also reached a 10% diagnostic yield in those with both a low IQ score and non-verbal language (4/40).ConclusionWe found some new genetic disposition for ASD accompanied with intellectual disability in this study. Our results may be helpful for etiologic research and early diagnoses of intellectual disability in ASD. Larger population studies and further mechanism studies are warranted.

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Hydrophobic, hydrophilic, and charged amino acid networks within protein.

Publications

Hydrophobic, hydrophilic, and charged amino acid networks within protein.

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