Solution structure of the DNA-binding domain of a human papillomavirus E2 protein: evidence for flexible DNA-binding regions

Molecular cloning, biophysical and in silico studies of Human papillomavirus 33 E2 DNA binding domain

Human papillomavirus 33, a high-risk HPV strain, is mainly responsible for HPV infection and cervical cancer in Asian countries. The E2 protein of HPV 33 is a DNA-binding protein that plays a crucial role in viral replication and transcription. We have cloned, overexpressed, and purified the DNA binding domain of the E2 protein. Size exclusion chromatography results suggested that the protein exists in a homodimeric state in the native form. Circular dichroism data showed that the protein has a higher content of β-sheet. The melting temperature obtained from differential scanning calorimetry is 52.59 °C, and the protein is stable at pH 8 and is in a dimeric form at basic pH. The protein is monomeric or unfolded at a very low pH. Chemical denaturation studies suggested that the protein denatured and dissociated simultaneously. The DNA binding activity of the protein was also confirmed and it showed binding affinity in the order of 106 M-1. The protein structure was modeled using homology modeling and other bioinformatic tools. The virtual screening and molecular dynamic simulation studies were performed to find compounds that can act as potent inhibitors against E2 DBD. This study expands the understanding of the conserved structural and binding properties of HPV33 E2 DBD and provides the first report on the characterization of the viral protein.Communicated by Ramaswamy H. Sarma.

KSHV but not MHV-68 LANA induces a strong bend upon binding to terminal repeat viral DNA

Latency-associated nuclear antigen (LANA) is central to episomal tethering, replication and transcriptional regulation of γ2-herpesviruses. LANA binds cooperatively to the terminal repeat (TR) region of the viral episome via adjacent LANA binding sites (LBS), but the molecular mechanism by which LANA assembles on the TR remains elusive. We show that KSHV LANA and MHV-68 LANA proteins bind LBS DNA using strikingly different modes. Solution structure of LANA complexes revealed that while kLANA tetramer is intrinsically bent both in the free and bound state to LBS1-2 DNA, mLANA oligomers instead adopt a rigid linear conformation. In addition, we report a novel non-ring kLANA structure that displays more flexibility at its assembly interface than previously demonstrated. We identified a hydrophobic pivot point located at the dimer-dimer assembly interface, which gives rotational freedom for kLANA to adopt variable conformations to accommodate both LBS1-2 and LBS2-1-3 DNA. Alterations in the arrangement of LBS within TR or at the tetramer assembly interface have a drastic effect on the ability of kLANA binding. We also show kLANA and mLANA DNA binding functions can be reciprocated. Although KSHV and MHV-68 are closely related, the findings provide new insights into how the structure, oligomerization, and DNA binding of LANA have evolved differently to assemble on the TR DNA.

Design and characterization of an enhanced repressor of human papillomavirus E2 protein

Papillomaviruses are causative agents of cervical and anogenital cancers. The viral E2 protein mediates viral DNA replication and transactivation of viral oncogenes and thus represents a specific target for therapeutic intervention. Short forms of E2, E2R, contain only the C-terminal dimerization domain, and repress the normal function of E2 due to formation of an inactive heterodimer. Using structure-guided design, we replaced conserved residues at the dimer interface to design a heterodimer with increased stability. One E2R mutant in which histidine was replaced by a glutamate residue showed preferential heterodimer formation in vitro, as well as an increase in plasticity at the interface, as a result of histidine-glutamate pair formation, as observed spectroscopically and in the crystal structure, determined to 2.2-Å resolution. In addition, the enhanced E2R showed greater repression of transcription from E2-responsive reporter plasmids in mammalian cell culture. Recent advances in protein delivery into the cell raise the possibility of using exogenously added proteins as therapeutic agents. More generally, this approach may be used to target the subunit interfaces of any multisubunit protein having a similar mechanism of action.

Small molecule inhibitors of the human papillomavirus E1-E2 interaction

Human papillomaviruses are responsible for multiple human diseases, including cervical cancer caused by multiple high-risk types and genital warts caused by the low-risk types 6 and 11. Based on the research indicating that low-risk HPV could be successfully targeted by inhibitors of viral DNA replication, we carried out several high-throughput screens for inhibitors of DNA replication activities. Two series were identified in screens for inhibitors of the interaction between the viral proteins E1 and E2. The two series were demonstrated to bind to overlapping sites on the transactivation domain of E2, at the E1-binding interface, by a series of biochemical and biophysical experiments. A member of the first series was also cocrystallized with the E2 transactivation domain. For both series, structure-activity investigations are described, which resulted in several hundred fold improvements in activity. The best compounds in each series had low nanomolar activity against the HPV11 E1-E2 interaction, and EC(50) values in cellular DNA replication assays of approximately 1 μM. Binding modes for the two series are compared, and some general conclusions about the discovery of protein-protein interaction inhibitors are drawn from the work described.

Protein flexibility directs DNA recognition by the papillomavirus E2 proteins

Although DNA flexibility is known to play an important role in DNA–protein interactions, the importance of protein flexibility is less well understood. Here, we show that protein dynamics are important in DNA recognition using the well-characterized human papillomavirus (HPV) type 6 E2 protein as a model system. We have compared the DNA binding properties of the HPV 6 E2 DNA binding domain (DBD) and a mutant lacking two C-terminal leucine residues that form part of the hydrophobic core of the protein. Deletion of these residues results in increased specific and non-specific DNA binding and an overall decrease in DNA binding specificity. Using ¹⁵N NMR relaxation and hydrogen/deuterium exchange, we demonstrate that the mutation results in increased flexibility within the hydrophobic core and loop regions that orient the DNA binding helices. Stopped-flow kinetic studies indicate that increased flexibility alters DNA binding by increasing initial interactions with DNA but has little or no effect on the structural rearrangements that follow this step. Taken together these data demonstrate that subtle changes in protein dynamics have a major influence on protein–DNA interactions.

Interaction of the papillomavirus E8--E2C protein with the cellular CHD6 protein contributes to transcriptional repression

Expression of the E6 and E7 oncogenes of high-risk human papillomaviruses (HPV) is controlled by cellular transcription factors and by viral E2 and E8--E2C proteins, which are both derived from the HPV E2 gene. Both proteins bind to and repress the HPV E6/E7 promoter. Promoter inhibition has been suggested to be due to binding site competition with cellular transcription factors and to interactions of different cellular transcription modulators with the different amino termini of E2 and E8--E2C. We have now identified the cellular chromodomain helicase DNA binding domain 6 protein (CHD6) as a novel interactor with HPV31 E8--E2C by using yeast two-hybrid screening. Pull-down and coimmunoprecipitation assays indicate that CHD6 interacts with the HPV31 E8--E2C protein via the E2C domain. This interaction is conserved, as it occurs also with the E8--E2C proteins expressed by HPV16 and -18 and with the HPV31 E2 protein. Both RNA knockdown experiments and mutational analyses of the E2C domain suggest that binding of CHD6 to E8--E2C contributes to the transcriptional repression of the HPV E6/E7 oncogene promoter. We provide evidence that CHD6 is also involved in transcriptional repression but not activation by E2. Taken together our results indicate that the E2C domain not only mediates specific DNA binding but also has an additional role in transcriptional repression by recruitment of the CHD6 protein. This suggests that repression of the E6/E7 promoter by E2 and E8--E2C involves multiple interactions with host cell proteins through different protein domains.

Mutational analysis of the latency-associated nuclear antigen DNA-binding domain of Kaposi's sarcoma-associated herpesvirus reveals structural conservation among gammaherpesvirus origin-binding proteins

The latency-associated nuclear antigen (LANA) of Kaposi's sarcoma-associated herpesvirus functions as an origin-binding protein (OBP) and transcriptional regulator. LANA binds the terminal repeats via the C-terminal DNA-binding domain (DBD) to support latent DNA replication. To date, the structure of LANA has not been solved. Sequence alignments among OBPs of gammaherpesviruses have revealed that the C terminus of LANA is structurally related to EBNA1, the OBP of Epstein-Barr virus. Based on secondary structure predictions for LANA(DBD) and published structures of EBNA1(DBD), this study used bioinformatics tools to model a putative structure for LANA(DBD) bound to DNA. To validate the predicted model, 38 mutants targeting the most conserved motifs, namely three alpha-helices and a conserved proline loop, were constructed and functionally tested. In agreement with data for EBNA1, residues in helices 1 and 2 mainly contributed to sequence-specific DNA binding and replication activity, whilst mutations in helix 3 affected replication activity and multimer formation. Additionally, several mutants were isolated with discordant phenotypes, which may aid further studies into LANA function. In summary, these data suggest that the secondary and tertiary structures of LANA and EBNA1 DBDs are conserved and are critical for (i) sequence-specific DNA binding, (ii) multimer formation, (iii) LANA-dependent transcriptional repression, and (iv) DNA replication.

Drugging challenging targets using fragment-based approaches

Fragment-based approaches have now become firmly established in the drug discovery armoury. After notable early successes against protein kinases, the versatility and power of fragment-based approaches are increasingly being demonstrated on more diverse and difficult protein targets. This review highlights seven examples including targeting protein-protein interactions, a RNA polymerase and a DNA-binding protein. It shows how fragment-based approaches using small libraries have been successful when large HTS screens have failed. It also highlights the range of biophysical approaches being used and the interplay between experimental and in silico screens. The examples all show the iterative way in which potency is built up by synthetic elaboration of the initial fragment hits.

A strained DNA binding helix is conserved for site recognition, folding nucleation, and conformational modulation

Nucleic acid recognition is often mediated by alpha-helices or disordered regions that fold into alpha-helix on binding. A peptide bearing the DNA recognition helix of HPV16 E2 displays type II polyproline (PII) structure as judged by pH, temperature, and solvent effects on the CD spectra. NMR experiments indicate that the canonical alpha-helix is stabilized at the N-terminus, while the PII forms at the C-terminus half of the peptide. Re-examination of the dihedral angles of the DNA binding helix in the crystal structure and analysis of the NMR chemical shift indexes confirm that the N-terminus half is a canonical alpha-helix, while the C-terminal half adopts a 3(10) helix structure. These regions precisely match two locally driven folding nucleii, which partake in the native hydrophobic core and modulate a conformational switch in the DNA binding helix. The peptide shows only weak and unspecific residual DNA binding, 10(4)-fold lower affinity, and 500-fold lower discrimination capacity compared with the domain. Thus, the precise side chain conformation required for modulated and tight physiological binding by HPV E2 is largely determined by the noncanonical strained alpha-helix conformation, "presented" by this unique architecture. (c) 2009 Wiley Periodicals, Inc. Biopolymers 91: 432-443, 2009.

Evolutionary and biophysical relationships among the papillomavirus E2 proteins

Infection by human papillomavirus (HPV) may result in clinical conditions ranging from benign warts to invasive cancer. The HPV E2 protein represses oncoprotein transcription and is required for viral replication. HPV E2 binds to palindromic DNA sequences of highly conserved four base pair sequences flanking an identical length variable 'spacer'. E2 proteins directly contact the conserved but not the spacer DNA. Variation in naturally occurring spacer sequences results in differential protein affinity that is dependent on their sensitivity to the spacer DNA's unique conformational and/or dynamic properties. This article explores the biophysical character of this core viral protein with the goal of identifying characteristics that associated with risk of virally caused malignancy. The amino acid sequence, 3d structure and electrostatic features of the E2 protein DNA binding domain are highly conserved; specific interactions with DNA binding sites have also been conserved. In contrast, the E2 protein's transactivation domain does not have extensive surfaces of highly conserved residues. Rather, regions of high conservation are localized to small surface patches. Implications to cancer biology are discussed.

Comprehensive comparison of the interaction of the E2 master regulator with its cognate target DNA sites in 73 human papillomavirus types by sequence statistics

Mucosal human papillomaviruses (HPVs) are etiological agents of oral, anal and genital cancer. Properties of high- and low-risk HPV types cannot be reduced to discrete molecular traits. The E2 protein regulates viral replication and transcription through a finely tuned interaction with four sites at the upstream regulatory region of the genome. A computational study of the E2–DNA interaction in all 73 types within the alpha papillomavirus genus, including all known mucosal types, indicates that E2 proteins have similar DNA discrimination properties. Differences in E2–DNA interaction among HPV types lie mostly in the target DNA sequence, as opposed to the amino acid sequence of the conserved DNA-binding alpha helix of E2. Sequence logos of natural and in vitro selected sites show an asymmetric pattern of conservation arising from indirect readout, and reveal evolutionary pressure for a putative methylation site. Based on DNA sequences only, we could predict differences in binding energies with a standard deviation of 0.64 kcal/mol. These energies cluster into six discrete affinity hierarchies and uncovered a fifth E2-binding site in the genome of six HPV types. Finally, certain distances between sites, affinity hierarchies and their eventual changes upon methylation, are statistically associated with high-risk types.

A quasi-spontaneous amyloid route in a DNA binding gene regulatory domain: The papillomavirus HPV16 E2 protein

The DNA binding domain of papillomavirus E2 proteins is at the center of the regulation of gene transcription and replication of the virus. Its unique fold consists of a beta-barrel domain that combines an eight-stranded dimeric beta-barrel core interface with two symmetrical DNA binding alpha-helices and other two helices, packed against the central barrel. Treatment with low amounts of trifluoroethanol readily leads to a mostly beta-sheet oligomeric species, with a loss of near-UV circular dichroism signal and increase in its ANS binding capacity, indicating that buried hydrophobic surfaces become accessible to the solvent. This species subsequently undergoes a slow transition into amyloid aggregates as determined by light scattering and Congo red and thioflavin T binding. Electron microscopy shows short amyloid fibers with a curly aspect as the end product. The amyloid route is completely prevented by addition of stoichiometrical amounts of specific DNA, strongly suggesting that unfolding of the DNA binding alpha-helix is required for the formation of the intermediate. The slow nature of this expanded beta-oligomeric species and the availability of several different conformational probes make it an excellent model for investigating amyloid mechanisms. The mild perturbation required for entering an amyloid route is indicative of a preexisting equilibrium. Oligomerization processes are required for the assembly of transcription initiation and DNA replication machineries, where proteins from different viruses must come together with host cell proteins. The E2 protein is a virus-encoded multifunctional master regulator that may exert one of its multiple functions through its ability to oligomerize.

Molecular dynamics of the DNA-binding domain of the papillomavirus E2 transcriptional regulator uncover differential properties for DNA target accommodation

Papillomaviruses are small DNA tumor viruses that infect mammalian hosts, with consequences from benign to cancerous lesions. The Early protein 2 is the master regulator for the virus life cycle, participating in gene transcription, DNA replication, and viral episome migration. All of these functions rely on primary target recognition by its dimeric DNA-binding domain. In this work, we performed molecular dynamics simulations in order to gain insights into the structural dynamics of the DNA-binding domains of two prototypic strains, human papillomavirus strain 16 and the bovine papillomavirus strain 1. The simulations underline different dynamic features in the two proteins. The human papillomavirus strain 16 domain displays a higher flexibility of the beta2-beta3 connecting loop in comparison with the bovine papillomavirus strain 1 domain, with a consequent effect on the DNA-binding helices, and thus on the modulation of DNA recognition. A compact beta-barrel is found in human papillomavirus strain 16, whereas the bovine papillomavirus strain 1 protein is characterized by a loose beta-barrel with a large number of cavities filled by water, which provides great flexibility. The rigidity of the human papillomavirus strain 16 beta-barrel prevents protein deformation, and, as a consequence, deformable spacers are the preferred targets in complex formation. In contrast, in bovine papillomavirus strain 1, a more deformable beta-barrel confers greater adaptability to the protein, allowing the binding of less flexible DNA regions. The flexibility data are confirmed by the experimental NMR S2 values, which are reproduced well by calculation. This feature may provide the protein with an ability to discriminate between spacer sequences. Clearly, the deformability required for the formation of the Early protein 2 C-terminal DNA-binding domain-DNA complexes of various types is based not only on the rigidity of the base sequences in the DNA spacers, but also on the intrinsic deformability properties of each domain.

Papillomavirus proteins and their potential as drug design targets

The papillomaviruses are a family of small, double-stranded DNA viruses that infect the basal cells of cutaneous and mucosal epithelium. While a large percentage of the population is benignly infected with various strains of human papillomavirus (HPV), long-term infection by a subset of HPV strains is associated with malignant transformation. The prospects for prophylaxis against HPV infection have recently received an enormous boost with the approval by the US FDA of a vaccine targeted against the most common cancer-associated HPV strains. However, the large number of people already infected, the high cost of the vaccination regimen (particularly in poorer countries) and the HPV infections that these vaccines do not protect against underscore the need for therapeutic strategies. The elucidation of molecular details underlying fundamental processes in the viral life cycle, such as virus replication, transcription and HPV-induced carcinogenesis, is required to meet this aim. This article provides an overview of high-resolution structures of papillomavirus proteins and their functional complexes, with particular reference to mechanistic and structural features that could be exploited in the rational design of antiviral agents.

The recognition of local DNA conformation by the human papillomavirus type 6 E2 protein

The E2 proteins are transcription/replication factors from papillomaviruses. Human papillomaviruses (HPVs) can be broadly divided in two groups; low-risk HPV subtypes cause benign warts while high-risk HPVs give rise to cervical cancer. Although a range of crystal structures of E2 DNA-binding domains (DBD) from both high- and low-risk HPV subtypes have been reported previously, structures of E2 DBD:DNA complexes have only been available for high-risk HPV18 and bovine papillomavirus (BPV1). In the present study we report the unliganded and DNA complex structures of the E2 DBD from the low-risk HPV6. As in the previous E2-DNA structures, complex formation results in considerable bending of the DNA, which is facilitated by sequences with A:T-rich spacers that adopt a pre-bent conformation. The low-risk HPV6 E2-DNA complex differs from the earlier structures in that minimal deformation of the protein accompanies complex formation. Stopped-flow kinetic studies confirm that both high- and low-risk E2 proteins adapt their structures on binding to DNA, although this is achieved more readily for HPV6 E2. It therefore appears that the higher selectivity of the HPV6 E2 protein may arise from its limited molecular adaptability, a property that might distinguish the behaviour of E2 proteins from high- and low-risk HPV subtypes.

Specificity in DNA recognition by a peptide from papillomavirus E2 protein

The E2 proteins of papillomavirus specifically bind to double-stranded DNA containing the consensus sequence ACCG-N4-CGGT, where N is any nucleotide. Here, we show the binding and recognition of dissimilar DNA sequences by an 18 amino-acid peptide (alpha1E2), which corresponds to the DNA-recognition helix, alpha-helix-1. Isothermal DNA binding assays performed with the DNA consensus sequence show saturable curves with alpha1E2 peptide, and the alpha1E2 peptide is converted to an ordered conformation upon complexation. Measurements performed with non-specific DNA sequence fail to saturate, a behavior characteristic of non-specific binding. Binding of the alpha1E2 peptide to these DNA sequences display a different counter-ion dependence, indicating a dissimilar, sequence-dependent mechanism of interaction. Quantitative stoichiometric measurements revealed the specificity in alpha1E2 peptide recognition of the ACCG half-site, demonstrating capacity for discrimination of nucleic acid bases sequences without the need of a whole protein architecture.

Indirect readout of DNA sequence by papillomavirus E2 proteins depends upon net cation uptake

The papillomavirus E2 proteins bind with high affinity to palindromic DNA sequences consisting of two highly conserved four base-pair sequences flanking a variable "spacer" of identical length (ACCG NNNN CGGT). While intimate contacts are observed between the bound proteins and conserved DNA in the available co-crystal structures, no contact is seen between the proteins and the spacer DNA. The ability of human papillomavirus strain 16 (HPV-16) E2 and bovine papillomavirus strain 1 (BPV-1) E2 to discriminate among binding sites with different spacer sequences is dependent on their sensitivity to the unique conformational and/or dynamic properties of the spacer DNA in a process termed "indirect readout". Differential sequence-specific K(+) uptake in low ionic strength solutions lacking Mg(2+) is observed upon E2 protein binding to sites containing the AATT, TTAA or ACGT spacer sequences. In contrast, the cation displacement typical of protein-DNA complex formation is observed at high K(+) concentrations or in the presence of Mg(2+). These results are interpreted to reflect the sequence-specific stabilization of bent DNA conformations by cations localized within the narrowed minor grooves of the protein-bound DNA and the intrinsic structure and flexibility of the DNA target. Mg(2+) differentially affects the binding of the HPV-16 E2 DNA binding domain (HPV16-E2/D) and the BPV-1 E2 DNA binding domain (BPV1-E2/D) to sites bearing different spacer sequences. This study suggests that monovalent and divalent cations contribute to the discrimination of DNA structure and flexibility that could in turn contribute to the specificity with which HPV16-E2/D and BPV1-E2/D mediate DNA replication and gene transcription.

Free energy contributions to direct readout of a DNA sequence

The energetic contributions of individual DNA-contacting side chains to specific DNA recognition in the human papillomavirus 16 E2C-DNA complex is small (less than 1.0 kcal mol(-1)), independent of the physical and chemical nature of the interaction, and is strictly additive. The sum of the individual contributions differs 1.0 kcal mol(-1) from the binding energy of the wild-type protein. This difference corresponds to the contribution from the deformability of the DNA, known as "indirect readout." Thus, we can dissect the energetic contribution to DNA binding into 90% direct and 10% indirect readout components. The lack of high energy interactions indicates the absence of "hot spots," such as those found in protein-protein interfaces. These results are compatible with a highly dynamic and "wet" protein-DNA interface, yet highly specific and tight, where individual interactions are constantly being formed and broken.

Emerging therapies for human papillomavirus infection

Human papillomavirus (HPV) is the most common sexually transmitted infection, with > 50% of sexually active women being affected. The virus causes a wide variety of benign and pre-malignant epithelial tumours and although most infections are transient, it is estimated that 1% of the sexually active population in the US have clinically apparent genital warts. A subset of genital HPVs, termed high-risk HPVs, is highly associated with the development of genital cancers including cervical carcinoma. Therapies for these HPV related cancers are however outside of the scope of this review. The absence of a simple monolayer cell culture system for analysis and propagation of the virus has substantially retarded progress in the development of diagnostic and therapeutic strategies for HPV infection. In spite of these difficulties, great progress has been made in the elucidation of the molecular controls of virus gene expression, replication and pathogenesis, and there has been some progress in the development of prophylactic and therapeutic vaccines and of other therapies.

Positive contribution of hydration on DNA binding by E2c protein from papillomavirus

Protein-nucleic acid interactions are responsible for the regulation of key biological events such as genomic transcription and recombination and viral replication. However, the recognition mechanisms involved in these processes are not completely understood. Here, we investigate the dominant forces involved in protein-protein and protein-DNA interactions for the 80-amino-acid C-terminal domain of the E2 protein (E2c) from human papillomavirus (HPV-16). The E2c protein is a homodimer that specifically binds to double-stranded DNA containing the consensus sequence ACCG-N(4)-CGGT, where N is any nucleotide. DNA binding affinity is reduced by lowering water chemical potential, accompanied by an increase in cooperativity. Wyman linkage relations between affinity and water chemical potential indicate that 11 additional water molecules are bound in the formation of the complex between E2c and DNA. Salt dissociation isotherms showed that 10 counterions are released upon association, even at low water activity, indicating that this latter variable does not change the electrostatic component of the interaction. Further analysis demonstrates a strong dependence of cooperativity of binding on the protein concentration. Altogether, these results reveal a novel binding pathway in which the consolidated complex may achieve its final form via a monomer-DNA intermediate, which favors the binding of a second monomer. This molecular mechanism reveals the contributions of multiple conformers in a tight virus genome modulation that seems to be important in the cell infection scenario.

Functionally significant mobile regions of Escherichia coli SecA ATPase identified by NMR

SecA, a 204-kDa homodimeric protein, is a major component of the cellular machinery that mediates the translocation of proteins across the Escherichia coli plasma membrane. SecA promotes translocation by nucleotide-modulated insertion and deinsertion into the cytoplasmic membrane once bound to both the signal sequence and portions of the mature domain of the preprotein. SecA is proposed to undergo major conformational changes during translocation. These conformational changes are accompanied by major rearrangements of SecA structural domains. To understand the interdomain rearrangements, we have examined SecA by NMR and identified regions that display narrow resonances indicating high mobility. The mobile regions of SecA have been assigned to a sequence from the second of two domains with nucleotide-binding folds (NBF-II; residues 564-579) and to the extreme C-terminal segment of SecA (residues 864-901), both of which are essential for preprotein translocation activity. Interactions with ligands suggest that the mobile regions are involved in functionally critical regulatory steps in SecA.

The papillomavirus E2 proteins: structure, function, and biology

Nearly twenty years after the first high-resolution crystal structures of specific protein-DNA complexes were determined, the stereo-chemical basis for protein-DNA recognition remains an active area of investigation. One outstanding question is, how are proteins able to detect noncontacted sequences in their binding sites? The papillomavirus E2 proteins represent a particularly suitable group of proteins in which to examine the mechanisms of "indirect readout." Coordinated structural and thermodynamic studies of the E2-DNA interaction conducted over the past five years are summarized in this review. The data support a model in which the electrostatic properties of the individual E2 proteins correlate with their affinities for intrinsically flexible or rigidly prebent DNA targets.

DNA tightens the dimeric DNA-binding domain of human papillomavirus E2 protein without changes in volume

The recognition of palindromic specific DNA sequences by the human papillomavirus (HPV) E2 proteins is responsible for regulation of virus transcription. The dimeric E2 DNA-binding domain of HPV-16 (E2c) dissociates into a partially folded state under high hydrostatic pressure. We show here that pressure-induced monomers of E2c are highly structured, as evidenced by NMR hydrogen-deuterium exchange measurements. On binding to both specific and nonspecific DNA, E2c becomes stable against pressure. Competitive binding studies using fluorescence polarization of fluorescein-labeled DNA demonstrate the reversibility of the specific binding. To assess the thermodynamic parameters for the linkage between protein dissociation and DNA binding, urea denaturation curves were obtained at different pressures in the presence of specific and nonspecific DNA sequences. The change in free energy on denaturation fell linearly with increase in pressure for both protein-DNA complexes, and the measured volume change was similar to that obtained for E2c alone. The data show that the free energy of dissociation increases when E2c binds to a nonspecific DNA sequence but increases even more when the protein binds to the specific DNA sequence. Thus, specific complexes are tighter but do not entail variation in the volume change. The thermodynamic data indicate that DNA-bound E2c dissociates into monomers bound to DNA. The existence of monomeric units of E2c bound to DNA may have implications for the formation of DNA loops, as an additional target for viral and host factors binding to the loosely associated dimer of the N-terminal module of the E2 protein.

The structural basis of DNA target discrimination by papillomavirus E2 proteins

The papillomavirus E2 proteins regulate the transcription of all papillomavirus genes and are necessary for viral DNA replication. Disruption of the E2 gene is commonly associated with malignancy in cervical carcinoma, indicating that E2 has a role in regulating tumor progression. Although the E2 proteins from all characterized papillomaviruses bind specifically to the same 12-base pair DNA sequence, the cancer-associated human papillomavirus E2 proteins display a unique ability to detect DNA flexibility and intrinsic curvature. To understand the structural basis for this phenomenon, we have determined the crystal structures of the human papillomavirus-18 E2 DNA-binding domain and its complexes with high and low affinity binding sites. The E2 protein is a dimeric beta-barrel and the E2-DNA interaction is accompanied by a large deformation of the DNA as it conforms to the E2 surface. DNA conformation and E2-DNA contacts are similar in both high and low affinity complexes. The differences in affinity correlate with the flexibility of the DNA sequence. Preferences of E2 proteins from different papillomavirus strains for flexible or prevent DNA targets correlate with the distribution of positive charge on their DNA interaction surfaces, suggesting a role for electrostatic forces in the recognition of DNA deformability.

Recent advances in diagnosis and therapy of human papillomaviruses

Infection with human papillomavirus is extremely common throughout the world. Almost 50% of sexually active young women are infected with human papillomavirus and although most infections are transient, a subset has the potential to progress to invasive cancer. During the last 20 years, our understanding of the human papillomavirus life cycle and the role of human papillomavirus in human cancer has dramatically increased. Recent technological advances in human papillomavirus detection have provided the means to detect the presence of human papillomavirus with great sensitivity. In the context of patient care, there is still substantial debate regarding the optimal diagnostic and prognostic use of information derived from hybrid capture or polymerase chain reaction-based detection. The inventory of available treatment options is growing somewhat slowly. The most promising advances are being made in the clinical evaluation of candidates for prophylactic vaccination. This review is focused on the current status and future directions of prevention, diagnosis and therapy.

Two domains of the epstein-barr virus origin DNA-binding protein, EBNA1, orchestrate sequence-specific DNA binding

The EBNA1 (for Epstein-Barr nuclear antigen 1) protein of Epstein-Barr virus governs the replication and partitioning of the viral genomes during latent infection by binding to specific recognition sites in the viral origin of DNA replication. The crystal structure of the DNA binding portion of the EBNA1 protein revealed that this region comprises two structural motifs; a core domain, which mediates protein dimerization and is structurally homologous to the DNA binding domain of the papillomavirus E2 protein, and a flanking domain, which mediated all the observed sequence-specific contacts. To test the possibility that the EBNA1 core domain plays a role in sequence-specific DNA binding not revealed in the crystal structure, we examined the effects of point mutations in potential hydrogen bond donors located in an alpha-helix of the EBNA1 core domain whose structural homologue in E2 mediates sequence-specific DNA binding. We show that these mutations severely reduce the affinity of EBNA1 for its recognition site, and that the core domain, when expressed in the absence of the flanking domain, has sequence-specific DNA binding activity. Flanking domain residues were also found to contribute to the DNA binding activity of EBNA1. Thus, both the core and flanking domains of EBNA1 play direct roles in DNA recognition.

Searching for Antiviral Drugs for Human Papillomaviruses

The human papillomaviruses (HPVs) are ubiquitous human pathogens that cause a wide variety of benign and pre-malignant epithelial tumours. Of the almost 100 different types of HPV that have been characterized to date, approximately two dozen specifically infect genital and oral mucosa. Mucosal HPVs are most frequently sexually transmitted and, with an incidence roughly twice that of herpes simplex virus infection, are considered one of the most common sexually transmitted diseases throughout the world. A subset of genital HPVs, termed ‘high-risk’ HPVs, is highly associated with the development of genital cancers including cervical carcinoma. The absence of a simple monolayer cell culture system for analysis and propagation of the virus has substantially retarded progress in the development of diagnostic and therapeutic strategies for HPV infection. In spite of these difficulties, great progress has been made in the elucidation of the molecular controls of virus gene expression, replication and pathogenesis. With this knowledge and some important new tools, there is great potential for the development of improved diagnostic and prognostic tests, prophylactic and therapeutic vaccines, and traditional antiviral medicines.

Folding of a dimeric beta-barrel: residual structure in the urea denatured state of the human papillomavirus E2 DNA binding domain

The dimeric beta-barrel is a characteristic topology initially found in the transcriptional regulatory domain of the E2 DNA binding domain from papillomaviruses. We have previously described the kinetic folding mechanism of the human HPV-16 domain, and, as part of these studies, we present a structural characterization of the urea-denatured state of the protein. We have obtained a set of chemical shift assignments for the C-terminal domain in urea using heteronuclear NMR methods and found regions with persistent residual structure. Based on chemical shift deviations from random coil values, 3'J(NHN alpha) coupling constants, heteronuclear single quantum coherence peak intensities, and nuclear Overhauser effect data, we have determined clusters of residual structure in regions corresponding to the DNA binding helix and the second beta-strand in the folded conformation. Most of the structures found are of nonnative nature, including turn-like conformations. Urea denaturation at equilibrium displayed a loss in protein concentration dependence, in absolute parallel to a similar deviation observed in the folding rate constant from kinetic experiments. These results strongly suggest an alternative folding pathway in which a dimeric intermediate is formed and the rate-limiting step becomes first order at high protein concentrations. The structural elements found in the denatured state would collide to yield productive interactions, establishing an intermolecular folding nucleus at high protein concentrations. We discuss our results in terms of the folding mechanism of this particular topology in an attempt to contribute to a better understanding of the folding of dimers in general and intertwined dimeric proteins such as transcription factors in particular.

A structural model for the rolA protein and its interaction with DNA

The study of the plant oncogene rolA has been hampered by a lack of structural information. Here we show that, despite a lack of significant sequence similarity to proteins of known structure, the rolA sequence adopts a known fold; that of the papillomavirus E2 DNA-binding domain. This fold is reliably identified by modern threading programs, which consider predicted secondary structure, but not by others. Although the rolA sequence is only around 16% identical to those of the available template structures, a structural model could be built that performed well against protein structure verification programs. The adopted strategy involved alignment corrections, justified by multiple model building and evaluation, with particular attention paid to the hydrophobic core residues. We find that rolA protein is predicted to resemble the template proteins in two key aspects; existence as a dimer and ability to bind DNA. rolA protein has recently been shown experimentally to possess DNA binding ability. This model predicts Lys 24 and Arg 27 to be involved in sequence-specific interactions and eight other residues to hydrogen-bond phosphate groups of the DNA.

Backbone dynamics of a short PU.1 ETS domain

The resonance assignments, secondary structure and backbone dynamics of the ETS domain of the transcription factor PU.1 have been determined for the free protein in solution by NMR spectroscopy. The secondary structure for the free ETS domain is similar to that observed in the crystal structure of the PU.1 protein complexed with DNA, except that helix alpha2 and recognition helix alpha3 are shorter for the free protein in solution. Backbone dynamics of the protein have been examined using amide hydrogen-deuterium exchange and (15)N laboratory-frame spin relaxation measurements. A significant probability of local unfolding of helix alpha2, which precedes the loop-helix-loop DNA recognition domain, is inferred from the very fast hydrogen-deuterium exchange for amide protons in this helix. The (15)N relaxation measurements indicate that the protein is partially oligomerized at a concentration of 2.5 mM, but monomeric at a concentration of 0.3 mM. The (15)N relaxation data for the low concentration sample were interpreted, using the model-free formalism, to provide insight into protein dynamics on picosecond-nanosecond and microsecond-millisecond time scales. High flexibility of the protein backbone is observed for the residues in the loop between alpha2 and alpha3. This loop is variable in length and in structure within the class of winged helix proteins and is partially responsible for binding to DNA. The dynamic properties observed for alpha2, alpha3 and the intervening loop may indicate a correlation between protein plasticity in particular structural elements and recognition of specific DNA sequences.

Solution structure of the DNA-binding domain of NtrC with three alanine substitutions

The structure of the 20 kDa C-terminal DNA-binding domain of NtrC from Salmonella typhimurium (residues Asp380-Glu469) with alanine replacing Arg456, Asn457, and Arg461, was determined by NMR spectroscopy. NtrC is a homodimeric enhancer-binding protein that activates the transcription of genes whose products are required for nitrogen metabolism. The 91-residue C-terminal domain contains the determinants necessary for dimerization and DNA-binding of the full length protein. The mutant protein does not bind to DNA but retains many characteristics of the wild-type protein, and the mutant domain expresses at high yield (20 mg/l) in minimal medium. Three-dimensional (1)H/(13)C/(15)N triple-resonance, (1)H-(13)C-(13)C-(1)H correlation and (15)N-separated nuclear Overhauser effect (NOE) spectroscopy experiments were used to make backbone and side-chain (1)H,(15)N, and (13)C assignments. The structures were calculated using a total of 1580 intra and inter-monomer distance and hydrogen bond restraints (88 hydrogen bonds; 44 hydrogen bond restraints), and 88 phi dihedral restraints for residues Asp400 through Glu469 in both monomers. A total of 54 ambiguous restraints (intra or inter-monomer) involving residues close to the 2-fold symmetry axis were also included. Each monomer consists of four helical segments. Helices A (Trp402-Leu414) and B (Leu421-His440) join with those of another monomer to form an antiparallel four-helix bundle. Helices C (Gln446-Leu451) and D (Ala456-Met468) of each monomer adopt a classic helix-turn-helix DNA-binding fold at either end of the protein. The backbone rms deviation for the 28 best of 40 starting structures is 0.6 (+/-0.2) A. Structural differences between the C-terminal domain of NtrC and the homologous Factor for Inversion Stimulation are discussed.

Crystal structure of the human papillomavirus type 18 E2 activation domain

The papillomavirus E2 protein regulates viral transcription and DNA replication through interactions with cellular and viral proteins. The amino-terminal activation domain, which represents a protein class whose structural themes are poorly understood, contains key residues that mediate these functional contacts. The crystal structure of a protease-resistant core of the human papillomavirus type 18 E2 activation domain reveals a novel fold creating a cashew-shaped form with a glutamine-rich alpha helix packed against a beta-sheet framework. The protein surface shows extensive overlap of determinants for replication and transcription. The structure broadens the concept of activators to include proteins with potentially malleable, but certainly ordered, structures.

Crystal structure of the E2 DNA-binding domain from human papillomavirus type 16: implications for its DNA binding-site selection mechanism

The crystal structure of the E2 DNA-binding domain from the high-risk cervical cancer-associated strain human papillomavirus type 16 (HPV-16) is described here. The papillomavirus E2 proteins regulate transcription from all viral promoters and are required for the initiation of replication in vivo. They belong to a family of viral proteins that form dimeric beta-barrels and use surface alpha-helices for DNA interaction. Although all E2 proteins recognize the same consensus, palindromic DNA sequence, proteins from different viral strains differ in their abilities to discriminate among their specific DNA-binding sites. The structure reported here reveals that while the overall fold of the HPV-16 E2 DNA-binding domain resembles that of its counterpart from the related viral strain bovine papillomavirus type 1, the precise placement of the recognition helices is significantly different. Additionally, the charge distribution on the DNA-binding surfaces of the two proteins varies; HPV-16 E2 has a much less electropositive surface. HPV-16 E2 is thus less able to utilize charge neutralization of the phosphate groups on DNA to induce bending. These results correlate well with previous solution studies that showed decreased affinity between HPV-16 E2 and flexible DNA target sequences, and enhanced affinity towards A-tract-containing, pre-bent sequences. In summary, the crystal structure of the HPV-16 E2 DNA-binding domain shows that the protein presents a stereo-chemically and electrostatically unique surface to DNA, characteristics that can contribute to its mechanism of DNA target discrimination.

Therapeutic evaluation of compounds in the SCID-RA papillomavirus model

A previous study by Kreider (Kreider et al., 1979) indicated that rabbit skin, which had been transplanted to immunodeficient nude mice, could be successfully infected with cottontail rabbit papillomavirus (CRPV). We have extended this observation in developing a rodent model for evaluation of compounds for activity against the papillomaviruses. In this model (called the SCID-Ra model), rabbit ear skin is transplanted to the dorsum of SCID mice and allowed to heal for 3 weeks. Infection with CRPV by scarification leads to the growth of warty lesions within 2 3 weeks in >95% of the animals. Topical and/or systemic therapy can be initiated at various times post infection (PI). Weekly lesion scores are recorded and compounds are evaluated for their ability to suppress wart growth when compared to untreated control mice. Ribavirin, which has had a suppressive effect both in the clinic for the treatment of respiratory papillomatosis and on the growth of warts in the rabbit back model, was evaluated and showed significant anti-proliferative activity with oral dosing. Both antiviral and antiproliferative compounds including podophyllin and 5-fluorouracil, which have been used clinically for the treatment of human papillomavirus (HPV) infections, were evaluated in this model. The anti-mitotic compound, Navelbine (vinorelbine tartrate), which is used for the treatment of non-small cell lung carcinoma was evaluated in this system and showed significant inhibition of wart growth with somewhat less topical cytotoxicity when compared to podophyllotoxin.

Molecular targets for human papillomaviruses: prospects for antiviral therapy

A substantial medical need exists for the development of antiviral medicines for the treatment of diseases associated with infection by human papillomaviruses (HPVs). HPVs are associated with various benign and malignant lesions including benign genital condyloma, common skin warts, laryngeal papillomas and anogenital cancer. Since treatment options are limited and typically not very satisfactory, the development of safe and effective antiviral drugs for HPV could have substantial clinical impact. In the last few years, exciting advances have been made in our understanding of papillomavirus replication and the effects that the virus has on growth of the host cell. Although still somewhat rudimentary, techniques have been developed for limited virion production in vitro offering the promise of more rapid advances in the dissection and understanding of the virus life cycle. Of the 8-10 HPV gene products that are made during infection, only one encodes enzymatic activities, the E1 helicase. Successful antiviral therapies have traditionally targeted viral enzymes such as polymerases, kinases and proteases. In contrast, macromolecular interactions which mediate the functions of E6, E7 and E2 are thought to be more difficult targets for small molecule therapy.

Towards a mutant analysis of the tertiary structures of functional DNA-binding motifs

Transcription factors have specific regions, often alpha helices, with which they recognise DNA. These regions are more or less disordered off DNA. Some examples are listed here. However, a detailed mutant analysis of this phenomenon is missing. It could show to what extent DNA binding in vitro and in vivo is harmed when such a region is artificially made rigid by suitable substitutions and could reveal how much transcription factors have improved by having been selected to carry unstable recognition domains.

Characterization of a partially folded monomer of the DNA-binding domain of human papillomavirus E2 protein obtained at high pressure

The pressure-induced dissociation of the dimeric DNA binding domain of the E2 protein of human papillomavirus (E2-DBD) is a reversible process with a Kd of 5.6 x 10(-8) M at pH 5.5. The complete exposure of the intersubunit tryptophans to water, together with the concentration dependence of the pressure effect, is indicative of dissociation. Dissociation is accompanied by a decrease in volume of 76 ml/mol, which corresponds to an estimated increase in solvent-exposed area of 2775 A2. There is a decrease in fluorescence polarization of tryptophan overlapping the red shift of fluorescence emission, supporting the idea that dissociation of E2-DBD occurs in parallel with major changes in the tertiary structure. The dimer binds bis(8-anilinonaphthalene-1-sulfonate), and pressure reduces the binding by about 30%, in contrast with the almost complete loss of dye binding in the urea-unfolded state. These results strongly suggest the persistence of substantial residual structure in the high pressure state. Further unfolding of the high pressure state was produced by low concentrations of urea, as evidenced by the complete loss of bis(8-anilinonaphthalene-1-sulfonate) binding with less than 1 M urea. Following pressure dissociation, a partially folded state is also apparent from the distribution of excited state lifetimes of tryptophan. The combined data show that the tryptophans of the protein in the pressure-dissociated state are exposed long enough to undergo solvent relaxation, but the persistence of structure is evident from the observed internal quenching, which is absent in the completely unfolded state. The average rotational relaxation time (derived from polarization and lifetime data) of the pressure-induced monomer is shorter than the urea-denatured state, suggesting that the species obtained under pressure are more compact than that unfolded by urea.

Mutagenesis of histidine 26 demonstrates the importance of loop-loop and loop-protein interactions for the function of iso-1-cytochrome c

In yeast iso-1-cytochrome c, the side chain of histidine 26 (His26) attaches omega loop A to the main body of the protein by forming a hydrogen bond to the backbone atom carbonyl of glutamic acid 44. The His26 side chain also forms a stabilizing intra-loop interaction through a hydrogen bond to the backbone amide of asparagine 31. To investigate the importance of loop-protein attachment and intra-loop interactions to the structure and function of this protein, a series of site-directed and random-directed mutations were produced at His26. Yeast strains expressing these variant proteins were analyzed for their ability to grow on non-fermentable carbon sources and for their intracellular production of cytochrome c. While the data show that mutations at His26 lead to slightly decreased intracellular amounts of cytochrome c, the level of cytochrome c function is decreased more. The data suggest that cytochrome c reductase binding is affected more than cytochrome c oxidase or lactate dehydrogenase binding. We propose that mutations at this residue increase loop mobility, which, in turn, decreases the protein's ability to bind redox partners.

Subunit rearrangement accompanies sequence-specific DNA binding by the bovine papillomavirus-1 E2 protein

The 2.5 A crystal structures of the DNA-binding domain of the E2 protein from bovine papillomavirus strain 1 and its complex with DNA are presented. E2 is a transcriptional regulatory protein that is also involved in viral DNA replication. It is the structural prototype for a novel class of DNA-binding proteins: dimeric beta-barrels with surface alpha-helices that serve as recognition helices. These helices contain the amino-acid residues involved in sequence-specifying interactions. The E2 proteins from different papillomavirus strains recognize and bind to the same consensus 12 base-pair DNA sequence. However, recent evidence from solution studies points to differences in the mechanisms by which E2 from the related viral strains bovine papillomavirus-1 and human papillomavirus-16 discriminate between DNA targets based on non-contacted nucleotide sequences. This report provides evidence that sequence-specific DNA-binding is accompanied by a rearrangement of protein subunits and deformation of the DNA. These results suggest that, along with DNA sequence-dependent conformational properties, protein subunit orientation plays a significant role in the mechanisms of target selection utilized by E2.

Origin DNA-binding proteins

The first step in DNA replication involves the recognition of origin DNA sequences by origin-binding proteins. The three-dimensional structures of three different origin DNA-binding proteins have recently been solved. These proteins form a structural class distinct from other DNA-binding proteins. One of the origin-binding proteins, Epstein-Barr virus nuclear antigen 1, most likely has two modes of DNA binding; the sequential use of these modes may be important for the initiation of DNA replication.

Conformational changes and stabilization induced by ligand binding in the DNA-binding domain of the E2 protein from human papillomavirus

We are investigating the folding of the 81-residue recombinant dimeric DNA binding domain of the E2 protein from human papillomavirus and how it is coupled to the binding of its DNA ligand. Modifications in buffer composition, such as ionic strength and phosphate, cause an approximately 5.0 kcal mol-1 stabilization of the domain to urea unfolding, based on very similar conformational changes as measured by far UV circular dichroism. Binding of DNA produces an even greater stabilization, magnitude similar to that caused by the nonspecific polymer ligand heparin, which shifts the urea midpoint 2.5-fold. The DNA-bound complex displays substantial changes similar to those caused by ionic strength and phosphate in terms of overall secondary structure. Bis-8-anilino-1-naphthalenesulfonate provides a very sensitive conformational probe, which shows alterations in the domain caused by the above mentioned compounds. In general terms, binding of DNA involves an overall conformational readjustment in the protein but maintains the beta-barrel scaffold intact. This conformational plasticity seems to be of importance in the regulatory functions of this type of DNA-binding protein. The extremely long half-life of the E2-DNA complex, together with its very high stability, suggests that, in the absence of other factors that may affect its stability in vivo, the possibility of dissociation once formed is restricted.

The dimeric DNA binding domain of the human papillomavirus E2 protein folds through a monomeric intermediate which cannot be native-like

The dimeric DNA binding domain of the human papillomavirus E2 protein displays a two-state concerted unfolding and dissociation, with no detectable monomeric intermediate species accumulated at equilibrium. We investigated the kinetic folding mechanism of the dimeric domain using stopped-flow spectroscopic techniques and observed a fast forming monomeric intermediate, followed by a slower bimolecular reaction. Both phases involve secondary structure rearrangements of similar magnitude. Our results support a folding pathway in which the formation of an early monomeric intermediate, with characteristics of hydrophobic collapse, is followed by a bimolecular step encompassing association and folding. The interwoven folding topology of this particular type of dimeric beta-barrel found in the E2 DNA binding domain strongly suggests that any monomeric species formed could not be native-like.