understanding biology through structures course work 2006 protein-nucleic acid interactions: general...

Understanding biology through structures Course work 2006

Protein-Nucleic Acid Interactions:

General Principles


Role: RegulatoryExample: Transcription factors

Function: Gene Regulation

Role: StructuralExample: Histones & chromosomal proteins

Function: DNA packaged into chromosomes

Role: EnzymaticExample: Polymerases, Restriction Endonucleases

Function: Replication & Transcription

Roles of Protein Nucleic acid complexes


Nucleic Acid Structure

Stabilizing forces

hydrogen bonding

van der Waals attractions

Hydrophobic interactions


A.T Watson-Crick A.A N1-amino symmetric

G.C Watson-Crick A.C Reverse WobbleA.U Watson-Crick A.A N7-amino symmetricG.U Wobble G.G N1-carbonyl symmetricA.U Reverse Hoogsteen G.G N3-amino symmetricA.C Reverse Hoogsteen G.G N1-carbonyl,N7-aminoSheared G.A G.A N7-N1 amino-carbonylG.A imino A.G N3-amino,amino-N1A.A.N7-amino C.C N3-amino symmetric

G.G.N7-imino U.U 4-carbonyl-imino symmetricU.U imino-carbonyl U.U 2-carbonyl-imino symmetricU.C 4-carbonyl-amino U.C 2-carbonyl-amino

A.U Reverse Watson-CrickG.C Reverse Watson-CrickG.U Reverse WobbleG.C N3-amino,amino-N3 A.U Hoogsteen

Base Pair Types


DNA is not a straight tube

The morphology of DNA is dependent on the DNA sequence. Some sequences introduce bends in DNA for example

These structural features are recognised by proteins, much like in the ‘lock and key model’ for enzymes

Local DNA structure


DNA binding proteins ‘see’ the edges of the basepairs in the major or minor groove

Major groove

Minor groove


Structure of Glucocorticoid receptor


What is it that these proteins interact with:

Hydrogen bond donorsHydrogen bond acceptorsHydrophobic residues

The protein ‘sees’ a particular array of these, which is different for each of the four base pairs

Note that the edge pattern for G:C is different than the one for C:G


These are the edge patterns a DNA binding protein would ‘see’

Notice that in the major groove, every base pair has a unique pattern, wherease the minor groove only has two distinct patterns.

The major groove is therefore more informative than the minor groove


Protein structure

DNA binding Motif in protein molecules

• Helix-turn-helix• Zn fingers (steroid receptor type)• Bzip (leucine zipper)• Parallel alpha helices • Anti-parallel beta strands

Unbound conformation bound conformation

Conformational Changes


Zinc-finger motif

• Present in proteins that bind nucleic acids

• Zn2+ ion is held between a pair of strands and helix


Zn-Finger motif


Leucine Zipper Motif

1YSA - Gcn4 Complex With Ap-1 Dna from Saccharomyces cerevisiae.

Front SideTop


Front Side

Top

Helix Turn Helix Motif

3CRO – 434 Cro Protein Complex With DNA Containing Operator OR1 from Bacteriophage 434


What parts of the protein are involved in DNA recognition

Based on structure comparisons it turned out that many bacterial DNA binding proteins contain a conserved domain of two alpha helices: helix-turn-helix motif

Mutations in helix 2 prevent DNA binding, which can be suppressed by mutations in the DNA sequence of the operator

This shows that helix 2 is involved in DNA recognition

Swapping helix 2 between two different repressors also swapped the operator to which the proteins bind


Helix 2 inserts into the major groove of DNA, whereas helix 1 lies across the groove

Helix 2 interacts with the base pair edges

Helix 1 contacts the sugar phosphate backbone


Specific amino acids, on the side of the helix facing DNA, interact with the base pair edges through hydrogen bonding

Helix turn helix motif of Cro repressor protein (phage Lambda)

Explains why the same protein can bind to different, yet related sequences with different affinities. We saw this for the LysR type proteins!

The number of interactions between helix 2 and the DNA sequence determines the strenghth of DNA binding.

Interaction between Cro and DNA


Many DNA binding proteins are dimers, e.g, the LysR type proteins and CAP

This means that there are two helix-turn-helix motifs per dimeric protein

These will interact with two adjacent major grooves, ie 10 bp apart

The DNA recognition site is therefore frequently an inverted repeat

GCCACTTCAGATTTCCTGAATGCCTAC

helix helix

(CbbR binding site, lecture 5)


The 434 cro molecule contains 71 amino acid residues that show 48% sequence identity to the 69 residues that form the N-terminal DNA-binding of 434 repressor. It is not surprising, therefore, that their three-dimensional structures are very similar. Like its lambda counterpart, the subunit structure of the DNA-binding domain of 434 repressor, as well as that of 434 cro, consist of a cluster of four helices, with helices 2 and 3 forming the helix-turn-helix motif.

The two HTH motifs are at either end of the dimer and contribute the main protein-DNA interactions, while protein-protein interactions at the C-terminal part of the chains hold the two subunits together in the complexes. Both 434 cro and repressor fragment are monomers in solution even at high protein concentrations, whereas they form dimers when they are bound to DNA.


The protein-DNA interactions have been analyzed in detail. Residues of the recognition helix project their side chains into the major groove and interact with the edges of the DNA base pairs on the floor of the groove. Gln(Q)28 forms two hydrogen bonds to N6 and N7 of Ade1 in the base pair 1(T14’-A1), and Gln29 forms hydrogen bonds both to O6 and N7 of G13’ in base pair 2 (G13’-C2). At base pair 3 (T12’-A3) no hydrogen bonding to the protein occurs and direct contacts are all hydrophobic; The methyl groups of the side chains of Thr27 and Gln29 form a hydrophobic pocket to receive the methyl group of T12’.


The first three base pairs in all six operator regions recognized by phage 434 repressor are identical. This means that interactions between these three base pairs and the two glutamine residues (28 and 29) cannot contribute to the discrimination between the six binding sites in the DNA; rather, these interactions provide a general recognition site for operator regions. This simple paattern of hydrogen bonds and hydrophobic interactions therefore accounts for the specificity of phage 434 cro and repressor protein for 434 operator regions.

Note that when glutamines 28 and 29 are replaced by any other amino acid, the mutant phages are no longer viable.


It is apparent from crystal structures of these protein-DNA complexes that the differential affinities of 434 repressor and cro for the different operator regions are not determined by sequence-specific interactions between amino acid side chains of the recognition helix and base pairs in the major groove of DNA. Instead, they seem to be determined mainly by the ability of the DNA to undergo specific structural changes so that complementary surfaces are formed between the proteins and the DNA. Nonspecific interactions between the DNA sugar-phosphate backbone and the proteins are one important factor in establishing such structural changes.

In all complexes studies the protein subunit is anchored across the major groove with extensive contacts along two segment of the sugar-phosphate backbone, one to either side of the groove. Hydrogen bonds between the DNA phosphate groups and peptide backbone NH groups are remarkably prevalent in these contacts.


One of these interaction regions involves the loop after the recognition helix, where three main-chain NH groups form hydrogen bonds with phosphatess 9’ and 10’. All residues in this loop, which are outside the HTH motif, contribute to the surface complementarity between the protein and the sugar-phosspahte surfaces of nucleotides 9’ and 10’.

These and other nonspecific interactions, which stabilize the appropriate DNA conformation, involve a large number of residues that are distributed along most of the polypeptide chain. Thus the « unit » that is responsable for differential binding to different operator DNA regions is really an entire binding domain, and nearly all the protein-DNA contacts contribute to this specificity.


Tata-box bindingproteinPDBcode: 1cdwR = 1.9 Å R factor = 0.189

The ternary complexes DNA/TBP/TFIIA and DNA/TBP/TFIIB are now available. The superposition gives the following multicomplex structure.


Histone octamer


Histone tails between DNA gyres


Two halves of DNA wrapped around an octamer


RNA polymerase II (Δ4/7)Crystal structure at 2.8Å resolution

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RNA polymerase II (Δ4/7)Crystal structure at 2.8Å resolution


Four crystal structures of RNA polymerase II transcribing complexes

1. NTP enters into the E site

2. NTP rotates into the A site

4. Post-translocation 3. Pre-translocation

understanding biology through structures course work 2006 protein-nucleic acid interactions: general...

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