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DNA-PROTEIN INTERACTIONS

DNA-PROTEIN INTERACTIONS. AN IN-CLASS PROJECT. DNA-PROTEIN INTERACTIONS. NONSPECIFIC LOOSE BETWEEN PROTEIN FUNCTIONAL GROUPS AND DNA BACKBONE IONIC H-BONDS VANDERWAALS SPECIFIC (SEQUENCE-SPECIFIC) TIGHT BINDING DIRECT H-BONDING INDIRECT H-BONDING “INDIRECT READOUT”.

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DNA-PROTEIN INTERACTIONS

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  1. DNA-PROTEIN INTERACTIONS AN IN-CLASS PROJECT

  2. DNA-PROTEIN INTERACTIONS • NONSPECIFIC • LOOSE • BETWEEN PROTEIN FUNCTIONAL GROUPS AND DNA BACKBONE • IONIC • H-BONDS • VANDERWAALS • SPECIFIC (SEQUENCE-SPECIFIC) • TIGHT BINDING • DIRECT H-BONDING • INDIRECT H-BONDING • “INDIRECT READOUT”

  3. PROKARYOTIC CONTROL MOTIFS • STUDY THE FOLLOWING MOTIFS • 434 PHAGE REPRESSOR WITH TARGET DNA (PDBid 2OR1) • E.coli Trp REPRESSOR-OPERATOR COMPLEX (PDBid 1TRO) • E.COLI Met REPRESSOR-SAM OPERATOR COMPLEX (PDBid 1CMA) • ANSWER ALL QUESTIONS • FILL OUT THE SUMMARY SHEET

  4. EUKARYOTIC TRANSCRIPTION CONTROL FACTORS • LOOK AT THE FOLLOWING CONTROL FACTORS • Cys2 – His2 ZINC FINGER BINDING MOTIFS (PDBidS 1ZNF AND 1AIF) • Cys4 ESTROGEN RECEPTOR (PDBid 1HCQ) • Cys6 YEAST TRANSCRIPTION FACTOR GAL4 (PDBid 1D66) • GCN4 LEUCINE ZIPPER MOTIF (PDBid 1YSA) • ANSWER ALL QUESTIONS • FILL OUT THE SUMMARY SHEET

  5. IN-CLASS PROJECT ON TRANSCRIPTION FACTORS • WORK TOGETHER IN SMALL GROUPS OF 2 OR 3 STUDENTS WHEN LOOKING AT THE STRUCTURES AND ANSWERING THE QUESTIONS • EACH STUDENT IN EACH GROUP WILL FILL OUT EACH OF THE TWO “SUMMARY SHEETS” AND HAND THEM IN FOR GRADING NO LATER THAN MONDAY, APRIL 20, 2009 AT 2:00 PM IN CLASS. • BEFORE HANDING IN THE SHEETS, PUT THE NAME OF EACH GROUP MEMBER ON THEM. THERE SHOULD BE NO COLLABORATION AMONG GROUPS WHEN FILLING THESE OUT. • THIS WILL COUNT FOR 25 POINTS OF YOUR LAST EXAM.

  6. CONCLUSIONS • NATURE USES A NUMBER OF DEVICES WHICH CAN BE VARIED TO MAXIMIZE DIVERSITY BUT MINIMIZE COMPLEXITY OF DNA-PROTEIN INTERACTIONS: • MOTIF TYPE • DIMERIZATION • PALINDROMIC DNA SEQUENCES • BONDING TYPES • CONTACT SITE ON DNA • NEED FOR ADDITIONAL SUBSTRATE

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