8 - LECTURE 8 ANNOUNCEMENTS 1. THIS WEEK: LG PROBLEMS 10 -...

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LECTURE 8 ANNOUNCEMENTS 1. THIS WEEK: LG PROBLEMS 10 - 17; PyMOL ASSIGNMENT #3, PROTEIN FOLDS. 5. ANY STUDENT WHO HAS JUST ADDED THIS CLASS: MEET PROF RIGHT AFTER LECTURE TO DISCUSS HOW TO CATCH UP. FRIDAY’S LECTURE: β -SHEETS, TURNS, COLLAGEN STRUCTURE FOLDS, SUPERFAMILIES, FAMILIES: ONLY ABOUT 1000 DIFFERENT KINDS OF "FOLDS" TODAY'S LECTURE: SUPERFAMILY OF EUKARYOTIC PROTEIN KINASES MULTI-FOLD PROTEINS QUATERNARY STRUCTURE (IV) PROTEIN STABILITY 2. RE-GRADING POLICY: PUT QUIZ, WITH WRITTEN EXPLANATION/REQUEST FIRMLY ATTACHED , IN THE PURPLE RE-GRADE FOLDER ON THE TABLE AT THE FRONT OF THE LECTURE ROOM. NO ORAL ARGUMENTS-- ONLY WRITTEN REQUESTS ATTACHED TO QUIZ . 4. OFFICE HRS TODAY 2 - 4PM IN BIOTECH RM. 402 . REVIEW SESSION 5:30 - 7PM IN ROCKEFELLER 104. 3. DID NOT PICK UP YOUR QUIZ ON FRIDAY? FIND IT AT THE BIO CENTER RESERVE DESK (2nd FLOOR STIMSON HALL).
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e.g. 1CD8 PROTEIN CLASSIFICATION DEFINITIONS FOLD : ALSO KNOWN AS STRUCTURAL DOMAIN, FOLDING UNIT, MOTIF. A CHARACTERISTIC ARRANGEMENT OF THE MAJOR SECONDARY STRUCTURES, INCLUDING THE SAME TOPOLOGICAL CONNECTIONS. PDB IDENTIFIER : PROTEIN DATA BANK CODE SUPERFAMILY : THESE PROTEINS VARY IN SEQUENCE IDENTITY FROM HIGH TO NEARLY ZERO. PROTEINS IN THE SAME SUPERFAMILY HAVE STRUCTURAL (AND SOMETIMES FUNCTIONAL) SIMILARITIES THAT SUGGEST A COMMON EVOLUTIONARY ORIGIN. A SUPERFAMILY CAN CONTAIN ONLY ONE, OR MANY DIFFERENT FAMILIES. FAMILY : THESE PROTEINS HAVE A COMMON EVOLUTIONARY ORIGIN BASED ON EITHER OF TWO CRITERIA: (1) RESIDUE IDENTITIES OF > 30%; OR (2) LOWER SEQUENCE IDENTITY BUT HAVING SIMILAR STRUCTURES AND FUNCTIONS, FOR EXAMPLE: GLOBINS WITH SEQUENCE IDENTITIES OF ~ 15%. SIMILAR FUNCTION, CLEAR EVOL. RELATION PROTEIN : THE NAME OF THIS SPECIFIC PROTEIN. THE SAME PROTEIN FROM DIFFERENT SPECIES SHOWS A RANGE OF AMINO ACID SEQUENCE DIFFERENCES. SPECIES : THE ORGANISM IN WHICH THIS PROTEIN IS FOUND. FROM SCOP = S TRUCTURAL C LASSIFICATION O F P ROTEINS http://scop.mrc-lmb.cam.ac.uk/scop/
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SOME FAMILIES WITHIN THE SUPERFAMILY: THE HUMAN "KINOME" THE KINASE SUPERFAMILY ALL CATALYZE PO 4 CHEM. MOD. OF TYR, THR, OR SER = TK TYROSINE IS TARGET TKL TYROSINE KINASE-LIKE AGC INCLUDES PROTEIN KINASE A, PROTEIN KINASE G, AND PROTEIN KINASE C CONTAINS 8 FAMILIES; THE PROTEINS WITHIN EACH FAMILY ARE CLOSELY RELATED TO EACH OTHER BY AA SEQUENCE AND ENZYME BEHAVIOR THE KINASE SUPERFAMILY PROTEINS IN THIS SUPERFAMILY HAVE SAME FOLD: "PROTEIN KINASE-LIKE" ; ALL 518 PROTEINS HAVE STRUCTURAL MOST KINASE PROTEINS EVOLVED TO HAVE FUNCTIONS ADDITIONAL TO BEING A KINASE.
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8 - LECTURE 8 ANNOUNCEMENTS 1. THIS WEEK: LG PROBLEMS 10 -...

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