NMR studies of Arc repressor mutants: proton assignments, secondary structure, and long-range contacts for the thermostable proline-8----leucine variant of Arc

Targeting the Major Groove of the Palindromic d(GGCGCC)2 Sequence by Oligopeptide Derivatives of Anthraquinone Intercalators

GC-rich sequences are recurring motifs in oncogenes and retroviruses and could be targeted by noncovalent major-groove therapeutic ligands. We considered the palindromic sequence d(G₁G₂C₃G₄C₅C₆)₂, and designed several oligopeptide derivatives of the anticancer intercalator mitoxantrone. The stability of their complexes with an 18-mer oligonucleotide encompassing this sequence in its center was validated using polarizable molecular dynamics. We report the most salient structural features of two novel compounds, having a dialkylammonium group as a side chain on both arms. The anthraquinone ring is intercalated in the central d(CpG)₂ sequence with its long axis perpendicular to that of the two base pairs. On each strand, this enables each ammonium group to bind in-register to O₆/N₇ of the two facing G bases upstream. We subsequently designed tris-intercalating derivatives, each dialkylammonium substituted with a connector to an N₉-aminoacridine intercalator extending our target range from a six- to a ten-base-pair palindromic sequence, d(C₁G₂G₃G₄C₅G₆C₇C₈C₉G₁₀)₂. The structural features of the complex of the most promising derivative are reported. The present design strategy paves the way for designing intercalator-oligopeptide derivatives with even higher selectivity, targeting an increased number of DNA bases, going beyond ten.

Wiggle-predicting functionally flexible regions from primary sequence

The Wiggle series are support vector machine-based predictors that identify regions of functional flexibility using only protein sequence information. Functionally flexible regions are defined as regions that can adopt different conformational states and are assumed to be necessary for bioactivity. Many advances have been made in understanding the relationship between protein sequence and structure. This work contributes to those efforts by making strides to understand the relationship between protein sequence and flexibility. A coarse-grained protein dynamic modeling approach was used to generate the dataset required for support vector machine training. We define our regions of interest based on the participation of residues in correlated large-scale fluctuations. Even with this structure-based approach to computationally define regions of functional flexibility, predictors successfully extract sequence-flexibility relationships that have been experimentally confirmed to be functionally important. Thus, a sequence-based tool to identify flexible regions important for protein function has been created. The ability to identify functional flexibility using a sequence based approach complements structure-based definitions and will be especially useful for the large majority of proteins with unknown structures. The methodology offers promise to identify structural genomics targets amenable to crystallization and the possibility to engineer more flexible or rigid regions within proteins to modify their bioactivity.

1H and 13C NMR assignments and molecular modelling of a minor groove DNA-binding peptide from the HMG-I protein

The HMG-I subfamily of high mobility group (HMG) chromatin proteins consists of DNA-binding proteins that preferentially bind to stretches of A.T-rich sequence both in vitro and in vivo. Recently, members of the HMG-I family have been suggested to bind in vitro to the narrow minor groove of A.T-DNA by means of an 11 amino acid peptide binding domain (BD) which, because of its predicted structure, is called the 'A.T-hook motif' [Reeves, R. & Nissen, M. (1990) J. Biol. Chem. 265, 8573-8582], and would appear to be crescent-shaped. A BD peptide with 13 amino-acid residues was synthesized and examined by proton and carbon-13 nuclear magnetic resonance (NMR) spectroscopy. The peptide contains four proline residues, and on the basis of NOEs and 13C chemical shifts was found to exist in an all-trans conformation. Molecular modelling based on this result provides evidence for a dynamic equilibrium between turn-like conformations in solution, the most populated of which is likely to be an S-shaped conformer, on the basis of amide exchange data.

Energy coupling between DNA binding and subunit association is responsible for the specificity of DNA-Arc interaction

The effects of several DNA molecules on the free energy of subunit association of Arc repressor were measured. The association studies under equilibrium conditions were performed by the dissociating perturbation of hydrostatic pressure. The magnitude of stabilization of the subunit interaction was determined by the specificity of the protein-DNA interaction. Operator DNA stabilized the free energy of association by about 2.2 kcal/mol of monomeric unit, whereas poly(dG-dC) stabilized the subunit interaction by only 0.26 kcal. Measurements of the stabilizing free energy at different DNA concentrations revealed a stoichiometry of two dimers per 21 bp for the operator DNA sequence and for the nonspecific DNA poly(dA-dT). However, the maximum stabilization was much larger for operator sequence (delta p = 1,750 bar) as compared for poly(dA-dT) (delta p = 750 bar). The importance of the free-energy linkage for the recognition process was corroborated by its absence in a mutant Arc protein (PL8) that binds to operator and nonspecific DNA sequences with equal, low affinity. We conclude that the coupling accounts for the high specificity of the Arc-operator DNA interaction. We hypothesize a mutual coupling between the protein subunits and the two DNA strands, in which the much higher persistency of the associated form when Arc is bound to operator would stabilize the interactions between the two DNA strands.

Characterization of the Escherichia coli F factor traY gene product and its binding sites

The traY gene product (TraYp) from the Escherichia coli F factor has previously been purified and shown to bind a DNA fragment containing the F plasmid oriT region (E. E. Lahue and S. W. Matson, J. Bacteriol. 172:1385-1391, 1990). To determine the precise nucleotide sequence bound by TraYp, DNase I footprinting was performed. The TraYp-binding site is near, but not coincident with, the site that is nicked to initiate conjugative DNA transfer. In addition, a second TraYp binding site, which is coincident with the mRNA start site at the traYI promoter, is described. The Kd for each binding site was determined by a gel mobility shift assay. TraYp exhibits a fivefold higher affinity for the oriT binding site compared with the traYI promoter binding site. Hydrodynamic studies were performed to show that TraYp is a monomer in solution under the conditions used in DNA binding assays. Early genetic experiments implicated the traY gene product in the site- and strand-specific endonuclease activity that nicks at oriT (R. Everett and N. Willetts, J. Mol. Biol. 136:129-150, 1980; S. McIntire and N. Willetts, Mol. Gen. Genet. 178:165-172, 1980). As this activity has recently been ascribed to helicase I, it was of interest to see whether TraYp had any effect on this reaction. Addition of TraYp to nicking reactions catalyzed by helicase I showed no effect on the rate or efficiency of oriT nicking. Roles for TraYp in conjugative DNA transfer and a possible mode of binding to DNA are discussed.

Molten-globule conformation of Arc repressor monomers determined by high-pressure 1H NMR spectroscopy

The conformation of the pressure-dissociated monomer of Arc repressor was characterized by 1H NMR spectroscopy. The NMR spectra of the monomer under pressure (up to 5.0 kbar; 1 bar = 100 kPa) are typical of a molten globule and they are considerably different from those of the native dimer and thermally denatured monomer. The two-dimensional nuclear Overhauser effect spectra suggest that the pressure-induced molten globule retains some secondary structure. The presence of nuclear Overhauser effects in the beta-sheet region in the dissociated state suggests that the intermonomer beta-sheet (residues 8-14) in the native dimer is replaced by an intramonomer beta-sheet. Changes in one-dimensional and two-dimensional NMR spectra prior to pressure dissociation were found and suggest the existence of a "predissociated" state.

Dissociation of a native dimer to a molten globule monomer. Effects of pressure and dilution on the association equilibrium of arc repressor

The monomer-dimer association reaction of Arc repressor was studied by pressure-induced dissociation and by dilution. The dissociation was measured by the decrease (red shift) in the average energy of emission of the tryptophan fluorescence. Pressure dissociation also promoted a decrease in the excited-state lifetime of the single tryptophanyl residue, Trp14. These observations suggest that Trp14 becomes exposed to an aqueous environment following dissociation. The pressure-dissociation curves were concentration dependent, with p1/2 (half-dissociation pressure) shifting to higher pressures as the concentration increased. The dissociation constant (KdO) obtained by extrapolating the pressure-dissociation curves to atmospheric pressure was similar to that determined from the dilution curve (KdO = 30 nM). An anomalous steepness of dissociation in response to dilution was observed, suggesting that conformational changes occur as a result of dissociation of Arc repressor. Binding of bis(8-anilinonaphthalene-1-sulfonate) to Arc repressor was not significantly affected by pressure dissociation, whereas thermal or urea denaturation was accompanied by a dramatic decrease in binding. These results suggest that the conformational changes that follow dissociation induced by pressure are more limited than those following denaturation. The tryptophan anisotropy decreased by about one-half, suggesting the dissociation of a globular dimer to a compact monomer. On the other hand, denaturation by urea promoted an increase in anisotropy, as expected for a random-coil conformation. Dissociated Arc has the hydrodynamic properties of a folded monomer. On the other hand, dissociated Arc has a high degree of exposure of hydrophobic side-chains, and the distribution of conformations is much broader than that in the folded dimer. These features suggest that the dissociated subunit is a molten globule. The subunit interaction was substantially increased by a single amino acid substitution (Pro8----Leu), and the free energy of stabilization amounted to -2.9 kcal/mol. This increased stability suggests that residue 8 is located in the dimer interface and that part of the tertiary and most of the quaternary structure constraints result from the interaction between the intersubunit beta-strands.

Structural aspects of protein-DNA recognition

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Theoretical design of a bistetrapeptide derivative of mitoxantrone targeted towards the double-stranded hexanucleotide sequence d(GGCGCC)2

The hexanucleotide d(GGCGCC)2 is encountered in recurrent fashion within transcriptional activating sequences in retroviruses and protooncogenes. Our first theoretical design of novel oligopeptide derivatives of mitoxantrone, MTX (1), had enabled us to predict derivatives depsiGly-Lys(L) and depsiGly-Gly-Orn(D) to preferentially target the tetrameric core d(CCGG)2. Owing to the crucial importance of hexamer d(GGCGCC)2, we have attempted to extend the realm of our approach by now targeting this specific hexanucleotide. For that purpose, we undertook the design of further oligopeptide derivatives of MTX, in which each arm was identically amidated (rather than esterified as in (1)) by tri- or tetrapeptides of varying sequences and individual residue configurations. The binding affinities of these derivatives to the palindromic sequences d(GGCGCC)2, d(CGCGCG)2, d(GCCGGC)2 and d(CCCGGG)2, were compared by energy-minimization. We report here the results obtained with the most promising derivative, having the sequence Arg(L)-Gly-Val(L)-Glu(L), and displaying a considerable energy preference for d(GGCGCC)2 over the other candidate hexameric sites (referred to as I). In the corresponding complexes, the two arms are in two mutually antiparallel directions in the major groove, and adopt a beta-sheet like arrangement stabilized by two H-bonds involving the carbonyl and amide groups of the Gly residues. Each Arg side chain on a given arm chelates O6 and N7 atoms of G1, G2/G1', G2' with its imino and cis amino hydrogen, and is simultaneously bound through two amino hydrogens in a bidentate interaction with the Glu residue.

Structure of Arc repressor in solution: evidence for a family of beta-sheet DNA-binding proteins

The Arc repressor, which is involved in the switch between lysis and lysogeny of Salmonella bacteriophage P22, does not belong to any of the known classes of DNA-binding proteins. Mutagenesis studies show that the DNA-binding region is located in the 15 N-terminal amino-acid residues. We have now determined the three-dimensional structure of the Arc dimer from an extensive set of interproton-distance data obtained from 1H NMR spectroscopy. A priori, intra- and inter-monomer nuclear Overhauser effects (NOEs) cannot be distinguished for a symmetric dimer. But by using the homology with the Escherichia coli Met repressor we could interpret the NOEs unambiguously in an iterative structure refinement procedure. The final structure satisfies a large set of NOE constraints (1,352 for the dimer). It shows a strongly intertwined dimer, in which residues 8-14 of different monomers form an antiparallel beta-sheet. A model for the Arc repressor-operator complex can account for all available biochemical and genetic data. In this model two Arc dimers bind with their beta-sheet regions in successive major grooves on one side of the DNA helix, similar to the Met repressor interaction. Thus, Arc and Met repressors are members of the same family of proteins, which contain an antiparallel beta-sheet as the DNA-binding motif.

Deciphering the message in protein sequences: tolerance to amino acid substitutions

An amino acid sequence encodes a message that determines the shape and function of a protein. This message is highly degenerate in that many different sequences can code for proteins with essentially the same structure and activity. Comparison of different sequences with similar messages can reveal key features of the code and improve understanding of how a protein folds and how it performs its function.