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Calculating conservation and predicting hENT1 structure using the amino acid sequence

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Title: Calculating conservation and predicting hENT1 structure using the amino acid sequence
Author(s): Ng, Kim
Contributor: University of Helsinki, Faculty of Science, Department of Mathematics and Statistics
Language: English
Acceptance year: 2012
In analysis of structural information for transmembrane (TM) proteins it is ideal to work with a three-dimensional (3D) structure. This is not always possible as determining an accurate 3D structure can be challenging and expensive as pursuing one can take large amounts of time. Sequence analysis is often used as a surrogate to determine a subset of information regarding secondary and tertiary protein structure given the primary structure (an amino acid sequence). Using Equilibrative Nucleoside Transporter member 1 (ENT1) as a model, the objective of predicting secondary and tertiary structure given primary structure is attempted through computational (in silico) methods. The in silico methods include the use of a pipeline of programs spanning both custom made and ready built software. A set of 2034 homologous protein sequences are first obtained from the initial human ENT1 (hENT1) sequence through a BLASTp. This sequence information is then processed to acquire information on variation, conservation, and hydrophobicity through topology prediction, hydropathic moment plots and variation moment plots. Comparing these results with data acquired from Glycerol-3-Phosphate Transporter (GlpT), a protein with a known 3D structure of 3.3 Angstrom resolution is done to assess evidence of evolutionary origin. This in turn allows estimation on the reliability of predictions to be made on aspects of the secondary and tertiary structure for hENT1. The results show that within predicted TM alpha helical regions that there is some level of correlation between the variation of the amino acids within the alpha helical TM region and its orientation towards the membrane. This can be further refined by gathering statistics on other known proteins with a 3D structure for their relationships in TM regions to hydrophobicity and variability. This will aid in secondary and tertiary structure predictions of other TM proteins given further refinement and additional data. In addition, the sequence conservation information obtained should prove to be robust and allow for a large number of sequences to be analyzed to determine conservation of amino acids given a reference protein. Ideally this information will provide aid in determining interesting amino acids for experiments to be done on hENT1.

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