DNA-binding Proteins and Their Attachment

Sites

• X-ray crystallography

• nuclear magnetic resonance (NMR) spectroscopy

THE STRUCTURES OF MANY PROTEINS HAVE BEEN DETERMINED BY :

Motifs are structural characteristics domains are functional regions

Helix-turn-helix (HTH)• turn made up of four amino acids, the second of which is usually glycine• second a-helix is therefore the recognition helix • lactose repressor• The Homeodomain is an extended HTH motif (antennapodia , pax, SRY)•POU domain which is usually found in proteins that also have a homeodomain• winged helix–turn–helix ( GABP )

Zinc fingers• very common in eukaryotes•There are at least six different versions of the zinc finger

Cys2His2 finger-comprises a series of 12 or so amino acids, including two cysteines and two histidines- α helix is recognition-the zinc atom holds the b-sheet and a-helix in the appropriate positions relative to one another-TFIIIA , SW15- multicysteine zinc fingers (steroid receptor)

OTHER NUCLEIC ACID–BINDING MOTIFS basic domain : DNA recognition structure is an a-helix that contains a high number of basic amino acids (ser ,arg,thr) ribbon–helix–helix : use of two strands of a b-sheet as the recognition structure (Met J)

TBP domain: the recognition structure is a b-sheet (the main contacts are with the minor, not major, groove of the DNA)leucine zipper : is an a-helix that coils more tightly than normal and presents a series of leucines on one of its faces (c-Jun , c-Fos )

helix–loop–helix :

- E1 , E2 , Myo D , Myc

RNA-BINDING PROTEINS : Ribonucleoprotein (RNP) domain : comprises four β-strands and two α-helices in the order β-α-β-β-α-β

double-stranded RNA binding domain (dsRBD) : the structure α-β-β-β-α

κ-homology domain : the structure β-α-α-β-β-α

GEL RETARDATION IDENTIFIES DNA FRAGMENTS THAT BIND TO PROTEINS

MODIFICATION PROTECTION

MODIFICATION INTERFERENCE

Mutations in the GLI3 gene cause Greig cephalopolysyndactyly syndromeThe GLI3 gene provides instructions for making a protein that controls gene expression

GREIG CEPHALOPOLYSYNDACTYLY SYNDROME

WILMS TUMOR AND DENYS-DRASH SYNDROME•The WT1 gene provides instructions for making a protein that is necessary for the development of the kidneys and gonads .

•The mutations that cause Denys-Drash syndrome lead to the production of an abnormal WT1 protein that cannot bind to DNA

HOLOPROSENCEPHALY• Mutations in 11 genes have been found to cause nonsyndromic holoprosencephaly.•The ZIC2 protein regulates genes involved in both early and late stages of forebrain development

Mahdevar