Protein Solubility Prediction-Presentation

Protein Solubility Prediction-Presentation - Protein...

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Unformatted text preview: Protein Solubility Prediction Reese Lennarson Rex Richard Project Relevance s Recombinant DNA Technology: Insert gene of protein of interest into Escherichia coli accessory DNA s E. coli uses these new instructions from new DNA and becomes a reactor for the production of the protein of interest s Proteins not native to E. coli may be soluble or insoluble when expressed s Insoluble proteins form pellets that are difficult to recover and are not desired in production s Accurate predictions can save time performing experiments Project Objectives s Develop models that can predict whether a protein will be soluble or insoluble when expressed in Escherichia coli based on trends in parameters for collected proteins s Evaluate different methods for prediction and see which is best s Identify most important parameters for accurate prediction of solubility Protein Background: Amino Acids s Proteins composed of building blocks called amino acids s R groups responsible for protein folding and ultimately function s 20 amino acids each with different R group Protein Background: Amino Acids (cont’d) s R groups characterized by H-bond character, charge, size, shape, hydrophobicity Serine (hydrophilic) Valine (hydrophobic) s Sequence of amino acid’s R groups (primary structure) determines how protein folds Protein Background: Secondary Structure s Secondary structure (local 3-D structure) has three common motifs: α-helix, β-sheet, and turns s Alpha helix forms stabilizing H-bonds along adjacent coil strands s Secondary structure can be predicted fairly well with knowledge of amino acid sequence Β sheet Alpha helix Creating a Protein Database s 226 proteins found in research for which solubility status on expression in E. coli is known at set conditions (37 C, no chaperones or fusion partners) s Amino acid sequences catalogued for each found protein s 17 parameters based on amino acid sequence and hypothesized to affect solubility calculated for each protein Protein Parameters Parameters based on fraction of specific amino acids: cysteine fraction proline fraction asparagine fraction threonine fraction tyrosine fraction combined fraction of asn, thr, and tyr Parameters based on protein-solvent interaction: hydrophilicity index hydrophobic residue fraction average number of contiguous hydrophobic residues aliphatic index approximate charge average Protein Parameters (cont’d) Parameters based on secondary structure: alpha helix propensity beta sheet propensity alpha helix propensity/beta sheet propensity turn-forming residue fraction Parameters based on protein size: molecular weight, total number of residues Developing a Model that Can Predict Solubility s Three methods used for prediction: discriminant analysis, logistic regression, and neural network s Models look for parameter trends from protein to protein in the database s Each model develops an equation to predict solubility for new proteins Statistical Analyses s Discriminant Analysis (DA) b Used in all previous solubility studies...
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This note was uploaded on 08/31/2011 for the course CHE 4273 taught by Professor Staff during the Spring '10 term at Oklahoma State.

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Protein Solubility Prediction-Presentation - Protein...

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