Protein_Structure.ppt

Lecture 9.1 February, 2003 Boris Steipe ? 2003 CBW/CGDN The Structure Lectures Boris Steipe boris.steipe@utoronto.ca http://biochemistry.utoronto.ca/steipe Departments of Biochemistry and Molecular and Medical Genetics Program in Proteomics and Bioinformatics University of Toronto Lecture 9.0:Use of Protein Structure Boris Steipe boris.steipe@utoronto.ca http://biochemistry.utoronto.ca/steipe Departments of Biochemistry and Molecular and Medical Genetics Program in Proteomics and Bioinformatics University of Toronto ( Some slides have been adapted from material by Chris Hogue, Toronto, prepared for CBW in 2002) Concepts Sequence and structure are abstractions of biopolymers. Structure can be determined experimentally. Structure abstractions can be stored, retrieved and visualized. Knowledge of structure allows mechanistic explanations. Structure is not arbitrary, but comes in units - motifs, helices, strands, domains and complexes. Domains are folding units, functional units and units of inheritance. Concept 1: Sequence and structure are abstractions of biopolymers. Physical Amino Acids andAmino Acid Abstractions The Concept of Abstract Amino Acids Allows Highly Compressed Information The Concept of Abstract Amino Acid Similarity is Lossy Structure Contextualizes Sequence Structural Abstraction To store structures we need: - coordinate - topology, and - chemical type information. Concept 2: Structure can be determined experimentally. Experimental sources of structure X-ray NMR Experimental sources of structure Experimental sources of structure X-ray NMR Experimental sources of structure Assessing structure quality Metrics: Resolution, R-factor and R-free Bond length and angle deviations Coordinate error can be estimated from diffraction data Concept 3: Structure abstractions can be stored, retrieved and visualized. ThePDB What’s in a Structure File? Population experiments X-ray, 1 structure NMR - sometimes many