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

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.

Lymphocyte subsets predictive value and possible involvement of human papilloma virus infection on breast cancer molecular subtypes

AIM

To detect human papilloma virus (HPV) presence and to characterize cellular immune response in breast cancer patients.

METHODS

A total of 74 women were included, of which 48 samples were from patients diagnosed with breast cancer and 26 patients with benign pathology of the breast. Molecular subtype classification was performed based on the immunohistochemical reports of the tumor piece. HPV genome detection and genotyping from fresh breast biopsies was performed using the INNO-LIPA HPV Genotyping Extra test (Innogenetics, Ghent, Belgium). CD3+, CD4+, CD8+ and natural killer (NK)+ cells levels from peripheral blood samples from patients with breast cancer and benign pathology were measured by flow cytometry.

RESULTS

Luminal A was the most frequent breast cancer molecular subtype (33.33%). HPV was detected in 25% of the breast cancer patients, and genotype 18 was the most frequent in the studied population. The mean of CD3+, CD4+ and CD8+ subpopulations were decreased in patients with breast cancer, in relation to those with benign pathology, with a statistically significant difference in CD8+ values (P = 0.048). The mean of NK+ cells was increased in the benign pathology group. The average level of CD3+, CD4+, CD8+ and NK+ cells decreased as the disease progressed. HER2+ and Luminal B HER2+ tumors had the lowest counts of cell subsets. HPV breast cancer patients had elevated counts of cellular subsets.

CONCLUSION

Determining level changes in cellular subsets in breast cancer patients is a useful tool to evaluate treatment response.

Importance of β2-β3 Loop Motion for the Increased Binding and Decreased Selectivity of the ΔLL Mutant of the Human Papillomavirus Type 6 E2 Protein

The binding affinity of the human papillomavirus type 6 E2 protein is strongly mediated by the sequence of the DNA linker region, with high affinity for the AATT linker and low affinity for the CCGG linker. When two terminal leucine residues are removed from the protein, the level of binding to both strands increases, but unequally, resulting in a significant decrease in selectivity for the AATT linker strand. To rationalize this behavior, we performed molecular dynamics simulations of the wild-type and mutant protein in the apo state and bound to DNA with high-affinity AATT and low-affinity CCGG linker strands. While no stable contacts were made between the β2-β3 loop and DNA in the wild type, this loop was repositioned in the mutant complexes and formed electrostatic contacts with the DNA backbone. More contacts were formed when the mutant was bound to the CCGG linker strand than to the AATT linker strand, resulting in a more favorable change in interaction energy for the CCGG strand. In addition, significant differences in correlated motions were found, which further explained the differences in binding. The simulations suggest that β2-β3 loop motions are responsible for the increased affinity and decreased selectivity of the mutant protein.

Presence of human papillomavirus in breast cancer and its association with prognostic factors

Breast cancer accounts for 16% of all female cancers worldwide, and in Venezuela, it is the leading cause of death among women. Recently, the presence of high-risk genotypes of human papillomavirus (HPV) has been demonstrated in breast cancer and has been associated with histopathological features of the tumours. In Venezuela, there is no study which determines the association between the presence of HPV in breast cancer and the histopathological features. The aim of this investigation is to evaluate the presence of HPV in the different types of breast cancer, according to their molecular classification, based on the expression of ER, PR, HER2 and Ki67. With this purpose in mind, we assessed the presence of the HPV genome in 24 breast cancer samples diagnosed with infiltrating ductal carcinoma, ductal carcinoma in situ (DCIS) and lobular carcinoma, by the INNO-LIPA genotyping extra kit and the evaluation of the markers ER, PR, HER2, and Ki67 by immunohistochemistry. The viral genome was found in 41.67% of the total number of samples, 51 being the most frequent genotype with 30.77%, followed by types 18 and 33, with 23.08%, respectively. Most tumours were found in the group of luminal A, with a low range of Ki67 expression. The presence of HPV in breast tumours could affect their growth pattern and metastatic power.

The papillomavirus E2 proteins

The papillomavirus E2 proteins are pivotal to the viral life cycle and have well characterized functions in transcriptional regulation, initiation of DNA replication and partitioning the viral genome. The E2 proteins also function in vegetative DNA replication, post-transcriptional processes and possibly packaging. This review describes structural and functional aspects of the E2 proteins and their binding sites on the viral genome. It is intended to be a reference guide to this viral protein.

HPV associated with recurrent respiratory papillomatosis

Papillomaviruses are members of the Papillomaviridae family. Over 150 HPV types have been identified. Recurrent respiratory papillomatosis (RRP) is a chronic condition caused by HPV characterized by recurrent papillomas of the respiratory tract, mainly the larynx. During the early stages, the condition presents with hoarseness, while more advanced disease presents with stridor and respiratory distress. There is no specific cure and treatment consists of repeated surgical procedures to remove the papillomas. Most patients eventually go into remission, but some suffer for many years with this condition, which may be fatal. HPV-6 and HPV-11 are the HPV types most commonly associated with RRP. Although most studies have found RRP due to HPV-11 to be more aggressive than disease due to HPV-6, the variability in disease aggressiveness is probably multifactorial. Information regarding the current epidemiology, molecular diversity and host immune responses is important for strategizing ways to reduce disease. Data on HPV genotypes associated with RRP would provide valuable information for vaccination programs to reduce the incidence of these genotypes in mothers and, in the long term, reduce the incidence of RRP in children. This review focuses on HPV-6 and HPV-11 as the HPV types that cause RRP, and discusses the viral genome and replication, clinical presentation of RRP, current techniques of diagnosis and genotyping, and the molecular diversity of HPV-6 and HPV-11.

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.

Thermodynamics of cooperative DNA recognition at a replication origin and transcription regulatory site

Binding cooperativity guides the formation of protein−nucleic acid complexes, in particular those that are highly regulated such as replication origins and transcription sites. Using the DNA binding domain of the origin binding and transcriptional regulator protein E2 from human papillomavirus type 16 as model, and through isothermal titration calorimetry analysis, we determined a positive, entropy-driven cooperativity upon binding of the protein to its cognate tandem double E2 site. This cooperativity is associated with a change in DNA structure, where the overall B conformation is maintained. Two homologous E2 domains, those of HPV18 and HPV11, showed that the enthalpic−entropic components of the reaction and DNA deformation can diverge. Because the DNA binding helix is almost identical in the three domains, the differences must lie dispersed throughout this unique dimeric β-barrel fold. This is in surprising agreement with previous results for this domain, which revealed a strong coupling between global dynamics and DNA recognition.

Experimental snapshots of a protein-DNA binding landscape

Protein recognition of DNA sites is a primary event for gene function. Its ultimate mechanistic understanding requires an integrated structural, dynamic, kinetic, and thermodynamic dissection that is currently limited considering the hundreds of structures of protein-DNA complexes available. We describe a protein-DNA-binding pathway in which an initial, diffuse, transition state ensemble with some nonnative contacts is followed by formation of extensive nonnative interactions that drive the system into a kinetic trap. Finally, nonnative contacts are slowly rearranged into native-like interactions with the DNA backbone. Dissimilar protein-DNA interfaces that populate along the DNA-binding route are explained by a temporary degeneracy of protein-DNA interactions, centered on "dual-role" residues. The nonnative species slow down the reaction allowing for extended functionality.

Human papillomavirus (HPV) type 18 induces extended growth in primary human cervical, tonsillar, or foreskin keratinocytes more effectively than other high-risk mucosal HPVs

Mucosal high-risk (HR) human papillomaviruses (HPVs) that cause cervical and other anogenital cancers also are found in approximately 25% of head and neck carcinomas (HNCs), especially those arising in the oropharynx and the tonsils. While many HR HPV types are common in anogenital cancer, over 90% of HPV-positive HNCs harbor HPV type 16 (HPV-16). Using a quantitative colony-forming assay, we compared the ability of full-length mucosal HPV genomes, i.e., the low-risk HPV-11 and HR HPV-16, -18, and -31, to persist in and alter the growth of primary human keratinocytes from the foreskin, cervix, and tonsils. The HR HPV types led to the formation of growing keratinocyte colonies in culture independent of the site of epithelial origin. However, HPV-18 induced colony growth in all keratinocytes >4-fold more effectively than HPV-16 or HPV-31 and >20-fold more efficiently than HPV-11 or controls. HPV-11-transfected or control colonies failed to expand beyond 32 to 36 population doublings postexplantation. In contrast, individual HR HPV-transfected clones exhibited no apparent slowdown of growth or "crisis," and many maintained HPV plasmid persistence beyond 60 population doublings. Keratinocyte clones harboring extrachromosomal HR HPV genomes had shorter population doubling times and formed dysplastic stratified epithelia in organotypic raft cultures, mirroring the pathological features of higher-grade intraepithelial lesions, yet did not exhibit chromosomal instability. We conclude that, in culture, the HR HPV type, rather than the site of epithelial origin of the cells, determines the efficacy of inducing continued growth of individual keratinocytes, with HPV-18 being the most aggressive mucosal HR HPV type tested.

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.

Transition state for protein-DNA recognition

We describe the formation of protein-DNA contacts in the two-state route for DNA sequence recognition by a transcriptional regulator. Surprisingly, direct sequence readout establishes in the transition state and constitutes the bottleneck of complex formation. Although a few nonspecific ionic interactions are formed at this early stage, they mainly play a stabilizing role in the final consolidated complex. The interface is fairly plastic in the transition state, likely because of a high level of hydration. The overall picture of this two-state route largely agrees with a smooth energy landscape for binding that speeds up DNA recognition. This "direct" two-state route differs from the parallel multistep pathway described for this system, which involves nonspecific contacts and at least two intermediate species that must involve substantial conformational rearrangement in either or both macromolecules.

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.