DNA binding domain with Helix turn Helix structuresNaveed asif (MS)BiochemistryCOMSATS-IslamabadPakistan2013-14

It’s a DOMAIN that binds to DNA

•The proteins that Bind to DNA consist of fallowing parts

1-Ligend binding Domain3-Activation or repression Domain (C-terminal)2-DNA binding Domain (N-terminal)

•Presentation constitutes

1-Structure of Helix turns Helix Domain2-Its interaction with DNA3-Its Functionsa-In Activatorsb-In Repressors

•1-Sturcture of Helix turn Helix Domain

Secondary structure (Helix) + Secondarystructure(Helix)

Supersecondary structure (motif) Mofit + Motif

Domain

• Structure of helix turn helix motif

Two alpha helixes joined by a turnDIFFERENCE between turn & loop

• Structure of a loop

Difference1-Loop is larger than turn. 2-loop has 7 to 16 amino acids. turn has 4 to 6 amino acidsSimilaritiesBoth has charged amino acids

•General Mechanism of formation of a Domain

Secondary structure (Helix or Beta) + Secondary structure (HelixorBeta) Supersecondary structure (motif) Mofit + Motif

Domain

•Formation of Complex Domains

•BACK to helix turn helix motife.g. HOMEO-DOMAIN

They are formed by homeoboxes. Homeoboxes are conserved sequences of 180 base pairs; the proteins formed by these boxes give rise to domains that are called homeodomains

• Mechanism of interaction with DNA

PARTS of HELIX turn HELIX motif

1-HORIZONTAL one is recognition helix

ANGEL 90◦2-VETICAL helix is going to interact with back bone3-Recognition helix goes into the major groove C-terminal (Recognition helix) and-N terminal (helix that interact with backbone)

• Mechanism Cont.Interaction is between charged amino acids, phosphate back bone and nitrogenous basesArginine (positively charged), Asparagines-Asn (neutral) and serine-Ser (neutral)

THIS BINDING COULD BE OF ACTIVATOR HTH motif

•Mechanism cont.HTH-Motif(Charge on Amino Acids)CHARGE on the AMINO ACID plays the key roleNeutral, (--) and (+)1-This untimely effect the polypeptide polarity2-this also gives a sequence specific binding between DNA & ProteinAnd can be modified1-Phosphorilation2-Aceylation3-methylation These modifications are very important in activator and repressor proteins

•FunctionsTranscription Repression & Activation

1-Repression function of helix turn helix motif2-Activation function of helix turn helix motife.g.:- Lac repressor &CAP(catabolite activator

protein)

• Normal• DNA

• ↓ bending

• ↓ Bending

• ↓ ●• ↓

•Lac repressor (helix turn helix motif)SEQUENCE

Glutamic acid (negative charge)Asparagines(neutral) Leucine(neutral)Under the normal circumstances repressor keeps on binding the operator.It BENDS the DNAWhat type of bending?No Transcription.

Lactose→ AllolactoseAllolactose binds to the allostaric site→ Conformational changeWhat kind of change? The distance between the two helix’s changesNow repressor is unable to bind leading to transcription

• Normal DNA• ↓• Open bend• ↓• ●

SEQUENCE Arginine (Positively charged) Asparagines (neutral) Serine (neutral)

cAMP INTERACTIONMechanism

CAP+cAMPConfirmation change in the CAP Protein What change?Distance between the two helix’s changesNow DNA bendsActivates the Transcription

•2-CAP (Catabolite Activator Protein) helix turn helix Motif

Thanks for your PATEINCE ReferencesMolecular genetics lectures, Dr. SaeedCOMSATS-Islamabad, PakistanBiosciences resource; Massey University, New ZealandIshaque P.K , Pondicherry University