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ScanMoment: a web server for combinatorial analysis of basic residues in nucleic acid binding sites.

Massey SE - Bioinformation (2009)

Bottom Line: A sliding window is used to generate a plot displaying regions of the protein sequence that possesses a high Basic Moment and hus likely to possess a BFAH motif.The user may vary the periodicity from that of an alpha-helix (100 degrees ), to those of other secondary structures such as beta sheets and 3(10) helices.The procedure has been used to characterize the presence of BFAHs in the N-terminal extensions of the eukaryotic aminoacyl-tRNA synthetases and to indicate the presence of a BFAH in the tRNA binding site of alanyl-tRNA synthetase. www.scanmoment.org.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, University of Puerto Rico - Rio Piedras, PO Box 23360, San Juan, Puerto Rico 00931. stevenemassey@gmail.com

ABSTRACT

Unlabelled: ScanMoment is a webserver designed to identify the presence of the basic faced alpha-helix (BFAH) motif in the nucleic acid binding sites of proteins. The program calculates the 'Basic Moment', a parameter that quantitizes the distribution of basic residues on the surface of an alpha-helix. A sliding window is used to generate a plot displaying regions of the protein sequence that possesses a high Basic Moment and hus likely to possess a BFAH motif. The user may vary the periodicity from that of an alpha-helix (100 degrees ), to those of other secondary structures such as beta sheets and 3(10) helices. The program can also plot the periodicity of basic residues in a protein sequence using a Fourier transformation. The procedure has been used to characterize the presence of BFAHs in the N-terminal extensions of the eukaryotic aminoacyl-tRNA synthetases and to indicate the presence of a BFAH in the tRNA binding site of alanyl-tRNA synthetase.

Availability: www.scanmoment.org.

No MeSH data available.


Related in: MedlinePlus

(a) A helical wheel representaion of an ideal BFAH. Basic residues, indicated by a + sign, are aligned on one side of the α‐helix. Acidic, hydrophilic and hydrophobic residue properties are ignored; (b) Basic Moment plot of yeast cytoplasmic apartyl‐tRNAsynthetase, using a window of 18 residues. The BFAH motif is indicated by arrows (residues 30 to 47); (c) Basic Moment periodicityprofile of yeast cytoplasmic aspartyl‐tRNA synthetase, residues 30 to 47.
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Figure 1: (a) A helical wheel representaion of an ideal BFAH. Basic residues, indicated by a + sign, are aligned on one side of the α‐helix. Acidic, hydrophilic and hydrophobic residue properties are ignored; (b) Basic Moment plot of yeast cytoplasmic apartyl‐tRNAsynthetase, using a window of 18 residues. The BFAH motif is indicated by arrows (residues 30 to 47); (c) Basic Moment periodicityprofile of yeast cytoplasmic aspartyl‐tRNA synthetase, residues 30 to 47.

Mentions: The Basic Moment is a finite Fourier expansion of the distribution of basic residues in an amino acid sequence. ScanMoment has a user defined choice of a 12 or 18 residuesliding window for the calculation of the Basic Moment and plots the resulting value in the centre of the window. An ideal BFAH, with all of the basic residues arrayed on one side of the α‐helix, has a Basic Moment of 33.2 for a window of 18 residues (Figure 1a). A Basic Moment plot of yeast cytoplasmic aspartyl‐tRNA synthetase is displayed in Figure 1b.


ScanMoment: a web server for combinatorial analysis of basic residues in nucleic acid binding sites.

Massey SE - Bioinformation (2009)

(a) A helical wheel representaion of an ideal BFAH. Basic residues, indicated by a + sign, are aligned on one side of the α‐helix. Acidic, hydrophilic and hydrophobic residue properties are ignored; (b) Basic Moment plot of yeast cytoplasmic apartyl‐tRNAsynthetase, using a window of 18 residues. The BFAH motif is indicated by arrows (residues 30 to 47); (c) Basic Moment periodicityprofile of yeast cytoplasmic aspartyl‐tRNA synthetase, residues 30 to 47.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2655046&req=5

Figure 1: (a) A helical wheel representaion of an ideal BFAH. Basic residues, indicated by a + sign, are aligned on one side of the α‐helix. Acidic, hydrophilic and hydrophobic residue properties are ignored; (b) Basic Moment plot of yeast cytoplasmic apartyl‐tRNAsynthetase, using a window of 18 residues. The BFAH motif is indicated by arrows (residues 30 to 47); (c) Basic Moment periodicityprofile of yeast cytoplasmic aspartyl‐tRNA synthetase, residues 30 to 47.
Mentions: The Basic Moment is a finite Fourier expansion of the distribution of basic residues in an amino acid sequence. ScanMoment has a user defined choice of a 12 or 18 residuesliding window for the calculation of the Basic Moment and plots the resulting value in the centre of the window. An ideal BFAH, with all of the basic residues arrayed on one side of the α‐helix, has a Basic Moment of 33.2 for a window of 18 residues (Figure 1a). A Basic Moment plot of yeast cytoplasmic aspartyl‐tRNA synthetase is displayed in Figure 1b.

Bottom Line: A sliding window is used to generate a plot displaying regions of the protein sequence that possesses a high Basic Moment and hus likely to possess a BFAH motif.The user may vary the periodicity from that of an alpha-helix (100 degrees ), to those of other secondary structures such as beta sheets and 3(10) helices.The procedure has been used to characterize the presence of BFAHs in the N-terminal extensions of the eukaryotic aminoacyl-tRNA synthetases and to indicate the presence of a BFAH in the tRNA binding site of alanyl-tRNA synthetase. www.scanmoment.org.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, University of Puerto Rico - Rio Piedras, PO Box 23360, San Juan, Puerto Rico 00931. stevenemassey@gmail.com

ABSTRACT

Unlabelled: ScanMoment is a webserver designed to identify the presence of the basic faced alpha-helix (BFAH) motif in the nucleic acid binding sites of proteins. The program calculates the 'Basic Moment', a parameter that quantitizes the distribution of basic residues on the surface of an alpha-helix. A sliding window is used to generate a plot displaying regions of the protein sequence that possesses a high Basic Moment and hus likely to possess a BFAH motif. The user may vary the periodicity from that of an alpha-helix (100 degrees ), to those of other secondary structures such as beta sheets and 3(10) helices. The program can also plot the periodicity of basic residues in a protein sequence using a Fourier transformation. The procedure has been used to characterize the presence of BFAHs in the N-terminal extensions of the eukaryotic aminoacyl-tRNA synthetases and to indicate the presence of a BFAH in the tRNA binding site of alanyl-tRNA synthetase.

Availability: www.scanmoment.org.

No MeSH data available.


Related in: MedlinePlus