DNA - Protein Interactions

 

We have begun considering the issue of control of the readout of the genetic information that is stored in DNA by looking at the flexibility inherent in DNA because of its geometric conformations and by studying the topology of DNA supercoiling. The genetic information must be accessible to proteins that transcribe it onto RNA or that assist in duplicating the DNA. Control of these two processes is modulated by varying the accessibility of the encoded information. This will affect whether or not a specific gene is active in a particular cell type and, if it is, at what rate does it direct synthesis of its protein.

Proteins can interact with DNA either specifically or non-specifically. In the case of non-specific interactions, the sequence of nucleotides does not matter, as far as the binding interactions are concerned. Histone (protein) - DNA interactions, which we have recently looked at, are an example of such interactions, and they occur between functional groups on the protein and the sugar-phosphate backbone of DNA. Specific DNA - protein interactions, however, depend upon the sequence of bases in the DNA and, as we have already discussed, on the orientation of the bases that can vary with twisting and writhing. These DNA - protein interactions are strong, and are mediated by:

        Hydrogen bonding : Can be direct H-bonds, or indirect, mediated by water molecules

        Ionic interactions: Salt bridges; protein side chains - DNA backbone interactions

        Other forces: van der Waals, hydrophobic

In this lecture, we will be concerned with specific DNA- protein interactions, in particular, the interactions that we will see when we consider the processe of DNA transcription. Specifically, we will look at  common supersecondary structures ("motifs") that are found in proteins that control transcription in prokaryotes and eukaryotes and how and why these structures interact with DNA.

Although we will look at transcription of information encoded in the DNA onto RNA in great detail in the next lecture, it is reasonable to mention a few of the highlights here. RNA polymerases are enzymes that carry out transcription. In order to begin transcription, the RNA polymerase must recognize the beginning of a gene (or operons, as are found in prokaryotes). The RNA polymerase recognizes a region of specific base sequences known as the "promoter". "Repressor proteins" can also bind at the promoter, thus blocking initiation of transcription. In addition, "activator proteins" can bind in regions next to the promoters to increase the rate of transcription of a gene. "Enhancer regions" of DNA, which are removed  from the promoter in terms of the number of nucleotides separating them, but may be close in space to the promoter by virtue of the flexibility of DNA, can also bind proteins that can affect the rate of transcription of a particular gene. These interactions, then, act to regulate the rate of transcription. At the extreme, they can also function as "switches", which can turn a gene on and off. In today's lecture, we will use the terms "promoter", "activator" , "repressor", "silencer", "enhancer" and "gene switch" and we will see these terms again in the next lecture.

 

Due to time constraints, I have not yet organized by outline notes into web-page form. Therefore, the following is the outline of this particular lecture as given in class:

 

    SPECIFIC DNA-PROTEIN INTERACTIONS

 

PROKARYOTIC TRANSCRIPTION CONTROL MOTIFS

 

-POLYPEPTIDES, USUALLY < 100 AA RESIDUES

-RECOGNITION VIA DISCRETE DNA-BINDING DOMAINS

    HELIX-TURN-HELIX MOTIF:

        FOUND IN MANY OF THESE DOMAINS

        RECOGNIZES, BINDS SPECIFIC REGUL. REGIONS

-REGULATION THROUGH:

        REPRESSORS: TIGHT BINDING AT PROMOTER

            PREVENTS ACCESS BY RNA POLYMERASE

   à BLOCKS INITIATION OF TRANSCRIPTION

        ACTIVATORS: BIND NEXT TO PROMOTERS

        HELPS RNA POLYMERASE TO BIND ADJACENT TO IT

  à  INCR. RATE OF TRANSCRIPTION OF THE GENE

 

        REPRESSORS AND ACTIVATORS :  

            ACT AT PROTEIN BINDING SITES IN THE       

                    "OPERATOR" REGION OF GENE

            -NOTABLE REGULATOR PROTEINS:

                 PHAGE LAMBDA repressor PROTEIN

    PHAGE LAMBDA Cro PROTEIN

    E.COLI trp REPRESSOR

    CAP : CATABOLITE GENE ACTIVATING    PROTEIN

       E. COLI met REPRESSOR

 

- "SWITCH" MECHANISMS:

repressor AND Cro : SWITCH BETWEEN TWO STABLE STATES OF A BACTERIAL CELL

trp REPRESSOR : ON-OFF SWITCH FOR L-Trp PRODN’

met REPRESSOR : CONTROLS BIOSYNTHESIS OF Met

CAP : A POSITIVE CONTROL PROTEIN THAT ASSISTS RNA POLYMERASE BINDING

(HTH MOTIF FIRST RECOGNIZED IN CAP)

 

STRUCTURE OF HELIX-TURN-HELIX MOTIF:

TWO a -HELICES JOINED BY A LOOP REGION

OFTEN ~ 20 RESIDUES

a -HELICES CROSS AT AN ANGLE OF ~ 120 DEGREES

STRUCTURAL STABILITY ONLY AS A COMPONENT OF OF LARGER PROTEIN

USUALLY DIMERIZATION IS REQUIRED FOR PROPER FUNCTIONIN

THE "RECOGNITION HELIX" :ONE HELIX IN EACH COMPONENT OF DIMER

AA SIDE CHAINS "BIND" TO BASES AND BACK-BONE OF DNA

"PALINDROMIC" NATURE OF SPECIFIC OPERATOR REGIONS: 2 IDENTICAL RECOGNITION SITES

ONE FOR EACH SUBUNIT OF THE DIMER

 

EXAMPLES:

434 (A LYSOGENIC BACTERIOPHAGE) REPRESSOR

SEE BACTERIOPHAGE 434 REPRESSOR BINDING FRAG-

MENT - 20 BP RECOGNITION SEQ. X-RAY STRUCTURE (HARRISON, PDB 2OR1)

TWO-FOLD SYMMETRY:

    EACH DIMER SUBUNIT HAS:

A 4-HELIX CLUSTER

HELICES 2 &3 FORM THE HTH MOTIF

HTH AT FAR END OF EACH SUBUNIT (N-TERM)

"RECOGNITION HELICES" = a 3 HELICES

        BIND IN 2 SUCCESSIVE TURNS OF DNA’S

MAJOR GROOVES

        34 A SEPARATION OF THE TWO a 3s (10 BP)

 

 

 

BINDING TO PALINDROMIC BASE PAIR SEQ.

                ¯                             ¯

5’: TA-TACAA-GAAAGT-TTGTA-CT

                             ·

                           3’: AT-ATGTT- CTTTCA-AACAT-GA

                                        ­                             ­

                        NOTE: CENTERS SEPARATED BY 10 BPs

                                    PSEUDO DYAD AXIS (· )

INTERMOLECULAR FORCES INVOLVED:

H-BONDING

VAN DER WAALS CONTACTS

SALT BRIDGES

 

            C-TERMINAL PROTEIN-PROTEIN INTERACTIONS

      à DIMERIZATION

A 5th HELIX ON EACH ; SEPARATE DOMAIN

NORMAL 20O INCLINATION BETWEEN THEM

        THE DNA-PROTEIN INTERACTIONS:

THE B-FORM OF DNA IS DISTORTED

DNA BENDS AROUND PROTEIN IN AN ARC

(RADIUS = ~ 65 A)

MINOR GROOVE COMPRESSED BY 2.5 A

NEAR CENTER OF PR. DIMER

à OVERWINDING   (TWIST)

MAJOR GROOVE WIDENED BY 2.5 A AT ENDS OF DIMER (TWIST)   à COMPENSATORY UNDERWINDING

LOCAL CONFORMATIONAL CHANGES IN EACH HALF-SITE OF OPERATOR :

    DIFFERENT FOR DIFFERENT AAs THAT INTERACT WITH DNA  BACKBONE

    BINDING à DIFFERENT LOCAL DNA STRS.

    Cro AND repressor IMPOSE DIFF. LOCAL DNA

                        STRUCTURES IN BINDING SITES

 

E. COLI trp REPRESSOR ( SIGLER 1TRO)

18 BP PALINDROME SEQUENCE:

ON ONE STRAND: TGTACTAGTTAACTAGTAC

(1)ALL BUT ONE OF H-BONDS BETWEEN PROTEIN SIDE

CHAINS AND BASES MEDIATED BY WATER BRIDGES

(2)SEVERAL BASE PAIRS IN OPERATOR ARE NOT IN

CONTACT WITH REPRESSOR:

                    MUTATIONS à ¯ REPRESSOR BINDING AFFIN

                        => OPERATOR ASSUMES A SEQUENCE-SPECIFIC

CONFORMATION THAT MAKES FAVORABLE CONTACTS WITH THE REPRESSOR

(1) AND (2), THEN, IMPLY THAT PROTEIN RECOG-

NITION OF DNA BASE SEQUENCE IS NOT MED-

IATED BY PARTICULAR AA-BASE PAIRINGS

 

MEDIATED BY DNA BACKBONE FLEXIBILITY

AND/OR CONFORMATION

"INDIRECT READOUT" PHENOMENON

 

met REPRESSOR

A HOMODIMERIC PROTEIN

A PAIR OF SYMMETRICALLY-RELATED b -STRANDS

S-ADENOSYLMETHIONINE MUST BE BOUND TO

THE REPRESSOR (SEE OVERHEAD)

 

 

 

 

A PROKARYOTIC MOLECULAR ON-OFF GENE SWITCH

GENE PRODUCTION CONTROL SWITCH IN:

LYSOGENIC BACTERIOPHAGES

434

LAMBDA

P22

SWITCH BETWEEN 2 STABLE STATES:

LYSOGEN: DORMANT PHAGE GENOME

LYTIC: ACTIVE PHAGE GENOME

LYSOGEN ==== LYTIC

­

UV LIGHT

THE SWITCH IS IN THE PHAGE GENOME:

2 STRUCTURAL GENES: CODE FOR Cro AND repressor

THE OPERATOR REGION:

OR1,OR2,OR3

PROMOTOR REGIONS

 

 

 

 

                                                    RNA POLYMERASE BINDS

                                                          ¯                          ¯

                                                    | promoter |      promoter  |

_________________________________________________

 

                               repressor GENE     OR3 OR2 OR1     Cro GENE

 

                           __________________________________________________

 

                            ¬ repressor protein                                         Cro protein ®

                                    (THE ARROW = THE DIRECTION OF TRANSCRIPTION)

 THE STATE DEPENDS ON WHICH PROMOTER BINDS RNA POLYMERASE

        THIS DEPENDS ON BINDING OF Cro AND repressor TO:

            OR1                     BOTH BIND AS

            OR2                     DIMERS TO ALL

            OR3                     THREE SITES

Cro BINDS WITH HIGHEST AFFINITY TO OR3 ® ¯ repr pr

repr BINDS TO OR1 WITH HIGHEST AFFINITY ® ¯ Cro

ALSO BINDS TO OR2 ® HELPS POLYMERASE TO

BIND TO ITS OWN PROMOTER

UV light ® CUT repr into 2 pieces ¹ DIMER FORMN’ ® FREE Cro

PROMOTER SITE ® POLYMERASE BINDS ® Cro PROTEIN

® ¯ repr PROTEIN PRODN’ + TRANSCRIPTION OF VIRAL

REPLICATION GENES ® VIRUS PARTICLES +CELL LYSIS

 

 

 

2OR1: COMPLEX BETWEEN 434 PHAGE REPRESSOR

AND TARGET DNA

(ONLY A PORTION OF THE REPRESSOR IS SHOWN)

(1) SELECT ALL AND DISPLAY AS WIREFRAME

(2) SELECT DNA AND DISPLAY AS EITHER:

BACKBONE

RIBBON

IDENTIFY THE MAJOR,MINOR GROOVES OF DNA

(3) SELECT ALL, DISPLAY, CARTOON

IDENTIFY THE PROTEIN DIMER

NOTE THE SYMMETRY BETWEEN SUBUNITS

(WHAT IS THE ROTATIONAL SYMMETRY AXIS?)

HOW MANY HELICES PER SUBUNIT?

ASSIGN A NUMBER TO EACH HELIX IN ONE OF THE SUBUNITS. START WITH THE HELIX AT THE 5:00 POSITION AS #1

WHICH HELIX IS IN THE MAJOR GROOVE?

    (THIS IS THE "RECOGNITION HELIX")

NOTE THAT 2 SUCCESSIVE MAJOR GROOVES OF DNA ARE OCCUPIED, EACH BY ONE HELIX OF EACH SUBUNIT PROTEIN

 

            FIND THE HELIX-TURN-HELIX MOTIF AND NOTE WHICH HELICES ARE         INVOLVED

NOTE THE PROXIMITY OF THE C-TERMINAL

HELICES (AT THE CENTER OF THE DIMER)

THERE APPEARS TO BE SOME INTERACTION

HERE, BUT IT’S NOT THE MAIN PROTEIN-PROTEIN INTERACTION. THE MAIN INTER-

ACTION IS BETWEEN 2 C-TERMINAL DOMAINS

THAT ARE NOT SHOWN HERE.

(4) SELECT , ALL, DISPLAY , WIREFRAME

(5) SELECT PROTEIN

(6) DISPLAY AS VDW SPACEFILL

NOTE HOW THE PROTEIN CONFORMS TO THE

DNA BACKBONE AND MAJOR GROOVES

(7) SELECT ALL , DISPLAY, CARTOON

(8) SELECT PROTEIN SIDE CHAINS

IDENTIFY (BY RESIDUE NUMBER) A FEW OF THE SIDECHAINS ON THE RECOGNITION HELIX THAT

APPEAR TO INTERRACT WITH BASES IN THE MAJOR GROOVE OF THE DNA

IDENTIFY SOME RESIDUES ON HELICES #2 AND #4 THAT APPEAR TO INTERRACT WITH THE DNA BACKBONE

 

 

    (9) SELECT HELICES AND IDENTIFY THE LOOP   PART  

OF THE H-T-H MOTIF

        WHAT RESIDUES COMPRISE THE LOOP?

(10) SELECT WATERS

DO THEY SEEM TO PLAY ANY ROLE IN THE PROTEIN-DNA INTERACTIONS?

                        (11) USING VANDERWAALS DISPLAY OPTION FOR

                 DNA AND ANY OTHER DISPLAY CHOICE FOR THE     PROTEIN, TRY TO IDENTIFY A FEW VANDERWAALS CONTACTS.

FIND SOME NONPOLAR RESIDUES AND DISPLAY

THEM AS BALL AND STICK TO SEE WHICH ARE

IN TOUCHING DISTANCE

 

AS A RESULT OF THE DNA-PROTEIN INTERRACTION,

THE DNA IS BENT IN AN ARC OF RADIUS ~ 65 A.

THIS HAS TWO GEOMETRIC CONSEQUENCES:

(1) MINOR GROOVE IS COMPRESSED ~ 2.5 A AT CENTER

(2) MAJOR GROOVE WIDENS ~ 2.5 A AT ENDS

 

EUKARYOTIC TRANSCRIPTION FACTORS

PROMOTE TRANSCRIPTION OF GENES:

"SELECTIVE ACTIVATION" OF GENES

PROTEINS

BIND AT OR NEAR GENE DNA SEQUENCES (PROMOTER)

DNA BINDING "MOTIFS"

ZINC FINGERS (1985, TFIIIA, Xenopus laevis)

LEUCINE ZIPPERS

HELIX-LOOP-HELIX

ZINC FINGERS : STRUCTURALLY DIVERSE

CYS2-HIS2

CYS4

CYS6

(1) THE CYS2-HIS2 ZINC FINGER DOMAIN

MOST ABUNDANT DNA BINDING MOTIF IN EUKARYOTIC TRANSCRIPTION FACTORS

2 INVARIANT CYS RESIDUES

2 INVARIANT HIS RESIDUES

Zn 2+ TETRAHEDRALLY LIGANDED

(TYR,PHE)-X-CYS-X2-4 –CYS-X3-PHE-X5-LEU-X2-HIS-X3-5-HIS

GENERAL PRINCIPLE: PROTEIN STRUCTURAL DOMAINS

OF < 50 AA RESIDUES DO NOT FOLD AUTONOMOUSLY

ZINC STABILIZES THE FOLD IN Zn FINGER DOMAINS

- ELIMINATES NEED FOR LARGER HYDROPHOBIC CORES

SECONDARY STRUCTURE (Berg, 1989)

A 2-STRANDED ANTIPARALLEL b -SHEET

ONE a -HELIX

HYDROPHOBIC CORE (3 HYDROPHOBIC AAs)

 

MULTIPLE "FINGERS" COMBINED IN TANDEM (2 – 37)

"INDEPENDENT READING HEADS"

Zn FINGER INTERACTS WITH 3-BP SEGMENTS OF DNA

a -HELIX INSERTS INTO MAJOR GROOVE OF B DNA

H-BONDS BETWEEN a -HELIX AND DNA STRAND

H-BONDS TO 2 BASES IN MAJOR GROOVE

H-BONDS TO PHOSPHATE GROUPS (ARG,HIS)

BY BOTH a -HELIX AND b -SHEET

à STABILIZATION OF ATTACHMENT

 

LOOK AT CYS2-HIS2 MOTIF IN A Zn FINGER–DNA COMPLEX : ( Zif268 in mice 1A1F )

3 FINGERS

CURL AROUND ALMOST ONE DNA HELIX

IN MAJOR GROOVE

A FINGER CONTACTS 3 SUCCESSIVE 3-BP SITES

AA IN FIRST TURN OF HELIX:1st BP

AA IN 3rd TURN:3rd BP

a -HELIX POINTS INTO MAJOR GROOVE

1st, 3rd FINGERS WITH IDENTICAL BINDING

(2) CYS4 (ESTROGEN RECEPTOR 1HCQ )

NUCLEAR HORMONE RECEPTORS

NEED BINDING BY SPECIFIC HORMONE, STER-

OID, VITAMIN TO ACTIVATE A GENE

DOMAIN OF 80 AMINO ACIDS

EACH UNIT WITH 2 "FINGERS"

FIRST UNIT BINDS (RECOGNIZES) DNA

SECOND UNIT ALLOWS FOR DIMERIZATION

OF 2 IDENTICAL RECEPTOR MOLECULES

"FINGER" CONSISTS OF:

IRREGULAR LOOP + HELIX

DIMERIZATION:

RECEPTORS BIND AS PAIRS TO DNA

RECOGNIZES ½ OF PALINDROME

DNA DOCKING SITES INCLUDE:

2 "HALF-SITES" (PALINDROMIC)

SPACER

FOR SUCCESSFUL (SPECIFIC) BINDING:

MUST DISTINGUISH:

BP SEQUENCE OF HALF-SITES

SPACING LENGTH

1st UNIT RECOGNIZES HALF-SITE

2nd UNIT "MEASURES" THE SPACING

à RECEPTOR DIMERIZATION

SIMILAR IN FUNCTION TO DNA-RECOGNITION

MOTIFS OF H-T-H AND LEU-ZIPPER

i.e., DISTINCT FROM TFIIIA MOTIF

(3) CYS6 MOTIF (YEAST TF GAL 4 1D66)

BINUCLEAR ZINC FINGER

2 Zn2+ IONS BOUND BY 6 CYS RESIDUES

TETRAHEDRAL COORD. OF EACH Zn2+

2 RESIDUES LIGATE BOTH METAL IONS

 

 

6 INVARIANT CYS RESIDUES ("X" = ANY AA)

CYS-X2-CYS-X6-CYS-X6 CYS-X2-CYS-X6-CYS

 

Xn LENGTHS STRICTLY CONSERVED

AA SEQUENCES VARY

BINUCLEAR ZINC CLUSTER

TETRAHEDRAL COORDINATION

BINDS DNA AS A SYMMETRIC DIMER

EACH SUBUNIT HAS:

Zn FINGER (N-TERM. IN MAJOR GROOVE)

RECOGNIZES CCG SEQUENCE

LINKER

WRAPS INTO MINOR GROOVE

a -HELIX (ASSISTS DIMERIZATION)

POSITIONED OVER MINOR GROOVE

TWO BOUND SUBUNITS ~ 1.5 DNA TURNS

 

 

WHY IS STRUCTURAL DIVERSITY REQUIRED ?

RECOGNIZE SPECIFIC GENE SEQUENCES

(ON-SWITCHES)

GENE SPECIFICITY OF TRANSCRIPTION FACTORS

1% OF HUMAN GENOME SPECIFIES Zn FINGERS

 

 

HIERARCHY OF SWITCH MECHANISMS:

PERMUTE PROTEINS WITH ONE MOTIF TYPE

(CHOICE, ORDER, NUMBER)

WITHIN A MOTIF TYPE: PERMUTE SUB-MOTIFS

(CHOICE, ORDER, NUMBER)

COMBINATORIALS OF SUB-MOTIFS ("MODULES")

RECOGNIZE SPECIFIC BASE PAIR SEQUENCES

 

VERY ECONOMIC

 

WHY IS ZINC IMPORTANT ?

CAN PROVIDE PURELY STRUCTURAL ROLE:

Zn++ HAS A FILLED d-SHELL

à NO LFSE WHEN COORDINATED BY

LIGANDS, REGARDLESS OF GEOMETRY

MOST METALS WITH INCOMPLETE d-ORB

LOSE LFSE WHEN OCTAHEDRAL COORD.

IN WATER à TETRAHEDRAL IN PROTEIN

A "BORDERLINE" ACID ("HARD-SOFT" ACID )

à ALLOWS INTERACTION WITH A

VARIETY OF LIGAND TYPES:

S (CYS) (SOFT BASE)

N (HIS) (HARD BASE)

O (GLU, ASP, H2O) (HARD BASE)

NOT REDOX-ACTIVE UNDER PHYSIOL. COND.

REDOX ACT. CAN à RADICAL REACTIONS

à DNA DAMAGE

KIN. LABILE :RAPID LIGAND EXCHANGE

à EASE OF UPTAKE AND RELEASE OF Zn++

 

 

 

EXAMPLES OF STRUCTURAL ROLE:

ZINC FINGER DOMAINS (SEE ABOVE)

E.COLI ASPARTATE TRANSCARBAMOYLASE

(SEE PYRIMIDINE SYNTHESIS)

4 REGULATORY UNITS CONTAIN BOUND Zn++

REMOVE Zn++ à LOSS OF ALLOSTERIC REGLN’

(BUT NO LOSS OF CATALYTIC ACTIVITY)

ZINC IS DIRECTLY INVOLVED IN CATALYSIS

CATALYTIC ACTIVITY OF CARBONIC ANHYDRASE

CLINICAL DISEASE CORRELATION:

(1) WILM’S TUMOR : FAULTY BINDING BETWEEN

DNA AND PROTEIN (MUTATION IN WT1)

(2) DIETARY ZINC DEFICIENCY : ESTROGEN AND

ANDROGEN RECEPTORS FOLD IMPROPERLY

à DELAYED SEXUAL DEVELOPMENT

(3) BRCA1 BREAST AND OVARIAN CA SUSCPTI-

BILITY GENE

 

 

LEUCINE ZIPPERS (1987)

MEDIATE DIMERIZATION OF SOME DNA-BINDING PRS.

NOT DNA-BINDING MOTIFS THEMSELVES

 

 

FIRST RECOGNIZED IN AA SEQUENCES OF:

(1)C/EBP (A MAMMALIAN TR. FACTOR)

"C" ("CAT") MOTIF, CCATT, IN MANY PRO-

MOTERS

"EBP" (ENHANCER-BINDING PROTEIN)

McNIGHT: CLONED C/EBP GENE

(2) GCN 4 (A YEAST TRANSCRIPTION FACTOR)

(3) 3 NUCLEAR TRANSFORMING ONCOGENE PRODS:

fos

jun

myc

STRUCTURE: ORIGINALLY PROPOSED BY McNIGHT:

REGION IN EACH OF ~ 30 RESIDUES

EVERY 7th RESIDUE IS LEU (HEPTAD REPEATS)

NO PROs OR GLYs (HELIX-BREAKERS)

SUGGESTED HELICAL STRUCTURE

LEUs (HYDROPHOBIC) FORMED A RIDGE IN HELIX

EVERY 2nd TURN OF AN 8-TURN –LONG a -HELIX

ANTIPARALLEL INTERFACING OF 2 HELICES

RIDGES FORM A DIMERIZATION SURFACE

INTERDIGITATION OF LEUs (LIKE A ZIPPER)

SUBSEQUENTLY SHOWN THAT HELICES ARE

PARALLEL; NO INTERDIGITATION

à NOT REALLY ZIPPERS

 

X-RAY STRUCTURE OF GCN 4 (KIM, ALBER, 1YSA)

 

33 RES LEU ZIPPER

FIRST 30 RES CONTAIN ~ 3.6 HEPTAD REPEATS

COIL OF ~ 8 TURN a -HELIX

DIMERS (COILED-COIL) ¼ TURN

LEFT-HANDED

PARALLEL (NOT ANTIPARALLEL)

4 LEU RES OF EACH HELIX IN DIMER REGION

 

DNA-BINDING REGION OF PROTEIN

RICH IN BASIC RES. (ARG, LYS IN C/EBP)

IMMEDIATELY N-TERM. TO ZIPPER

 

ZIPPERING à PROPER BINDING ORIENTATION

"Y"-SHAPED DIMERS

ZIPPER, BINDING REGION SEPARATED BY

6 AAs

EACH HELICAL ARM COMBINES WITH:

½ OF A DYAD-SYMM. RECOGNITION SITE

HELIX IS BROKEN, ALLOWING IT TO BEND

INVARIANT ASN AS A HELIX-BREAKER

 

 

 

 

HETERODIMERIC ZIPPERS

CAN RECOGNIZE 2 DIFFERENT NUCLEOTIDE SEQ.

(­ REPERTOIRE OF USABLE DNA REG. MOTIFS)

BUT HOMODIMERS CAN ALSO BIND ASYM. MOTIFS

­ # OF DISTINGUISHABLE COMBINATIONS OF

PROTEINS IN REGULATORY "PUZZLE"

EACH HALF WITH OWN "ACTIVATION" SITE