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08 - modintro - The creation of a three dimensional...

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Protein Structure Modelling –What is it? The creation of a three dimensional structural image of a protein, using its amino acid sequence and the principles, and our knowledge, of protein structure. An application of theory, not experiment, resulting in a theoretical model. Why do this? Structure allows protein molecules to function. We will see that sequence, structure and function are interrelated in ways that allow us to connect each to the others. Building models of proteins allows us to understand function and plan experiments more effectively. Why Model? Just Solve All the Structures! X-ray methods need proteins that form crystals. NMR methods need proteins that are soluble (at millimolar concentrations). Both take months to years per protein. A model based on a known structure can be made quickly. Models can be used to test mutations or rebuilt and refined if new information becomes available. Some Genomic Thoughts The Yeast Genome has 6,000 (protein coding) genes. The Human Genome has 20-25,000 (40,000?) genes. A large proportion of genes found in new genomes cannot be assigned a function. Exploring sequence-structure compatibility will help assign functions. There are 1000 times as many sequences as structures and the gap is widening. Theoretical means, such as modelling, are the only way we can manage the task of inferring function (and so directing experiments) for new genomes. Database Growth Log scale – exponential growth! There are 48,638 structures but 80,388,382 nucleic acid sequences ( 83,874,179,730 nucleotides ). A vast sequence/structure mismatch. New sequences are found faster than we can solve structures. The apparently small number of folds helps us to predict structures for sequences. Comparison methods are of great importance.
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Should You Model? Some Crystallographers say No! Modelling is - not experimental! - a guess! - wrong! - to some degree - how much? / how little? Many “Gels and Cells” People Think Not! But! How do you: • explain your mutations?
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