Protein_Structure课件.ppt

The Structure Lectures;Lecture 9.0:Use of Protein Structure;Concepts;Concept 1:;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;;;Concept 2:;X-ray NMR;Experimental sources of structure;X-ray NMR;X-ray NMR;Metrics: Resolution, R-factor and R-free Bond length and angle deviations Coordinate error can be estimated from diffraction data;Concept 3:;ThePDB;What’s in a Structure File?;Flat file, column oriented Human readable Human editable Huge legacy problems ;Header;Seqres;Atom;Hetero Atoms;The crystallographic asymmetric units does not necessarily contain a functional molecule;... Biological Unit;NCBI structure group;NDB;PDBsum - and secondary structure databases;PDBsum - Information;Macromolecular Structure Database at EBI (Relibase, PQS ...) http://www.ebi.ac.uk/msd/ Macromolecular structure related resources at the PDB /pdb/links.html Structure links at the Southwestern Biotechnology and Informatics Center /links/.php Molecular Models from Chemistry http://people.ouc.bc.ca/woodcock/molecule/molecule.html Molecular Library /pages/mathmol/library/ many, many more. ;Concept 4:;Structure as an integrated map - Example questions;Geometric relationships;;Dihedral angles;Backbone dihedral angles: Ramachandran plots;Sidechain rotamers;H-bond patterns;Molecular surface;Molecular surface;Molecular surface;Molecular surface;Calculating solvent accessible surfaces;Parameters and assumptions;Mapping properties on surfaces;Concept 5:;Basic building blocks of structure: ;Unbiased structure motifs: alignment with added value;A schematikon motif example: complex loop;A schematikon motif example:strand N-cap;Concept 6:;Domains are ubiquitous in proteins;Domains in proteins:;Domains in proteins:;Domains in proteins:;There is no universal definition of domains;Further complications:;Further complications:;Further complications:;Domains can be elusi