L8: Transcription Factors Flashcards
Transcription factors
Gene regulatory proteins
E.g lac repressor. Early discovered TF, binds DNA and bends it
Domains in TFs
DNA binding domain: binds specific nucleotide sequences close to genes a TF regulates. Binding site usually <20 bp long
Activation/repression domain: interacts with other proteins to regulate transcription
Classes of TFs in eukaryotic genomes
Identified based on:
Type of DNA-binding domain they contain
Sequence similarities of domains
Major groove
Most TFs bind major groove of DNA
More info in major groove than minor groove
Edges of bp exposed at double helix surface
Distinct patterns of features for each of 4 bp configuration. HB acceptors and donors, hydrophobic patches
Surface of TF is complementary to specific surface features of DNA (not bp complementary)
Contacts include: HB, ionic, hydrophobic interactions (individual interaction weak but ~20 interactions add up. Specific & strong), usually alpha helices or beta sheets
Minor groove
Patterns not distinct
G-C & C-G are identical
A-T & T-A are identical
Helix-turn-helix motif
Common in bacterial repressor proteins & eukaryotic TFs
2 alpha helices: connected bu short extended AA chain= the ‘turn’. Held at fixed angle (interactions between helices). Recognition helix=more C-terminal helix: fits into DNA major groove, differ in sequence from TF to TF, interacts with edges of bases. N-terminal helix=structural: positions recognition helix
Helix-turn-helix motif-containing proteins
Outside helix-turn-helix motif, variation in structure of TFs -> variation in presentation of recognition helix to DNA -> increases versatility of motility
In most TFs with hthm, other parts of protein also contact DNA -> fine tuning protein-DNA interactions
Binds DNA as symmetric dimers
DNA target sequences arranged asymmetrical . 2 similar half sites
Increased binding affinity- double the no of contacts (squares the binding affinity constant). The 2 copies of recognition helix in dimer separated by one turn of DNA helix
Zinc finger motif
1 or more Zn2+ ions are part of motif
Regions of protein fold around Zn2+ ions -> resemble finger (because of projection)
Distinct groups:
Cys-Cys-His-His (C2H2) zinc finger motif
Cys-Cys-Cys-Cys (C4) zinc finger motif. Named according to coordinating Zn2+ ion
Cys-Cys-His-His (C2H2) Zinc Finger Motif
Most common DNA-binding motif in genome multicellular animals and common in plants but not dominant
Consists of 23-26 AA
Sequence similarity shared among motifs, including 2 Cys and 2 His residues
Zn2+ ion holds alpha helix and beta sheet of motif together
Alpha helix contacts major groove of DNA
Multiple C2H2 zinc fingers found in many TFS: usually 3 or more, alpha helix of each finger motif interacts with successive groups of bp within major groove. Strong & specific interactions
Cys-Cys-Cys-Cys (C4) Zinc Finger Motif
55 or 56 AA domain, including 4 conserved Cys residues for each Zn2+ ion
2 alpha helices & 2 beta sheets
Zn2+ ions stabilise the DNA recognition alpha helix and loop involved in dimer formation
Bind target DNA as homo- or heterodimers. Heterodimers have 2 fold rotational symmetry. Bind DNA sequences that are inverted repeats
C4 Zinc Finger Motif-Containing Proteins
C4 zinc finger motif found in intracellular receptor proteins
Example glucocorticoid receptor. Binds glucocorticoid steroid hormones like cortisol (produced during starvation and high physical activity). Stimulates liver cells to increase glucose production (genes need to be expressed for metabolism. All have different complex control regions and all require binding of hormone-glucocorticoid receptor complex in control region for maximal expression)
Leucine Zipper Motif
TF
Leucine residues at every 7th position. Amphipathic helix formed (hydrophobic AA along one side of alpha helix)
Coiled-coil structure (hydrophobic interactions of AA side chains)
2 aloha helices held together by hydrophobic pattern
Bind DNA as dimers.
Each monomer composed of alpha helix: contacts between basic AA in N-terminus and -vely charged phosphates in DNA backbone. Each alpha helix binds one half of a symmetric DNA structure.
Dimer contacts 2 adjacent major grooves, separated by half a turn of DNA helix
Helix-Loop-Helix (HLH) motif
Non helical loop connects 2 alpha helical regions in each monomer
Dimerisation: homodimers or heterodimers. C terminal regions of both monomers -> coiled-coil structure
2 alpha helices extending from dimerisation region contact DNA: N terminal regions of alpha helices contain AA with basic side chains that interact with DNA at specific sequences
Two-Stranded Beta-sheet motif
AA side chains extend from beta sheet toward DNA major groove
Example: bacterial methionine (Met) repressor protein. Regulated genes coding for enzymes involved in Met synthesis. When Met is abundant, binds repressor -> conformational change, tight binding to DNA, represses transcription. Works as dimer. One strand from each monomer interacts with DNA sequences in major groove
Loop regions
In gene regulatory proteins
Recognise DNA major and minor grooves
Example: p53. Human tumour suppressor. Arg (R)248 and Lys (K)120 of loops interact with minor and major grooves, respectively. Often mutated in cancer cells. Role: tight regulation of cell growth & proliferation. Gene encoding p53: mutated in ~50% of all human cancers
