The human papillomavirus (HPV) E2 protein is essential for regulating the initiation of viral DNA replication as well as the regulation of transcription of certain HPV-encoded genes. Its ability to ...recognize and bind to its four recognition sequences in the viral origin is a key step in the initiation of HPV DNA replication. Thus, understanding the mechanism of DNA binding by E2 protein and the unique roles played by individual DNA sequence elements of the replication origin is essential. We have purified the recombinant full-length HPV type 11 E2 protein. Quantitative DNA binding analysis indicated E2 protein bound all four DNA binding sites with reasonably high affinities but with distinct preferences. It bound its cognate binding sites 1, 2, and 4 with higher affinities, but bound binding site 3 with lower affinity. Analysis of binding to these sites unraveled multiple sequence elements that appeared to influence E2 binding affinity and target discrimination, including the sequence of spacer region, flanking sequences, and proximity of E2 binding sites. Thermodynamic analysis indicated hydrophobic interaction in the protein-DNA complex formation. Our studies indicate a large multi-protein complex formation on the HPV-origin DNA, likely due to reasonably high binding affinities as well as intrinsic oligomerization propensity of E2 dimers.
The retina-specific ATP-binding cassette transporter protein ABCA4 is responsible for properly continuing the visual cycle by removing toxic retinoid byproducts of phototransduction. Functional ...impairment caused by ABCA4 sequence variations is the leading cause of autosomal recessive inherited retinal disorders, including Stargardt disease, retinitis pigmentosa, and cone-rod dystrophy. To date, more than 3000
genetic variants have been identified, approximately 40 percent of which have not been able to be classified for pathogenicity assessments. This study examined 30 missense
variants using AlphaFold2 protein modeling and computational structure analysis for pathogenicity prediction. All variants classified as pathogenic (n = 10) were found to have deleterious structural consequences. Eight of the ten benign variants were structurally neutral, while the remaining two resulted in mild structural changes. This study's results provided multiple lines of computational pathogenicity evidence for eight
variants of uncertain clinical significance. Overall, in silico analyses of ABCA4 can provide a valuable tool for understanding the molecular mechanisms of retinal degeneration and their pathogenic impact.
Human papillomavirus (HPV) is a group of alpha papillomaviruses that cause various illnesses, including cancer. There are more than 160 types of HPV, with many being "high-risk" types that have been ...clinically linked to cervical and other types of cancer. "Low-risk" types of HPV cause less severe conditions, such as genital warts. Over the past few decades, numerous studies have shed light on how HPV induces carcinogenesis. The HPV genome is a circular double-stranded DNA molecule that is approximately 8 kilobases in size. Replication of this genome is strictly regulated and requires two virus-encoded proteins, E1 and E2. E1 is a DNA helicase that is necessary for replisome assembly and replication of the HPV genome. On the other hand, E2 is responsible for initiating DNA replication and regulating the transcription of HPV-encoded genes, most importantly the E6 and E7 oncogenes. This article explores the genetic characteristics of high-risk HPV types, the roles of HPV-encoded proteins in HPV DNA replication, the regulation of transcription of E6 and E7 oncogenes, and the development of oncogenesis.
The human retina-specific ATP binding cassette transporter, ABCA4, plays a significant role in the visual cycle. Mutations in the ABCA4 gene result in a broad spectrum of severe, blinding, retinal ...degenerative diseases, including Stargardt macular dystrophy, fundus flavimaculatus, autosomal recessive (ar)-retinitis pigmentosa, and ar-cone-rod dystrophy. Genetic testing frequently yields novel variants of unknown significance, making accurate prognosis and therapeutic approaches difficult.
Recently, we have reported a novel variant of ABCA4 corresponding to a four-nucleotide deletion which led to a premature stop codon and loss of the last 161 amino acids, including the highly-conserved VFVNFA motif. Despite the presence of this motif among other ABCA proteins, knowledge of the functional significance of this sequence remains limited. In this study, we have conducted structural and functional analyses of recombinant ABCA4 polypeptides with altered VFVNFA motifs to evaluate the importance of this sequence. Further investigation of ABCA4 subdomain interactions, using Fluorescence Resonance Energy Transfer, demonstrated a loss of interaction between nucleotide binding domains in the absence of the VFVNFA motif.
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•ABCA4 transporter harbors a well-conserved VFVNFA motif in the C-terminal domain.•Presence of the VFVNFA motif is crucial for ATP binding and ATPase activity.•VFVNFA motif is necessary for ATP-driven nucleotide binding domain interaction.•Overall transporter function relies on the integrity of the VFVNFA motif.•Disruption of the C-terminal domain of ABCA4 leads to inherited visual disease.
ABCA4 is a retina‐specific member of the ATP‐binding cassette transporter protein family. It is responsible for the transport and clearance of retinal derivatives produced in the visual cycle in the ...photoreceptor cells. More than a thousand mutations in the ABCA4 gene are associated with a series of autosomal recessive inherited retinal diseases, including Stargardt disease, retinitis pigmentosa, and cone‐rod dystrophy, and also linked with susceptibility for age‐related macular degeneration. Determining disease‐causing variants is a crucial part of clinical management, yet, a limited number of the ABCA4 variants have been studied in vitro and relatively few of them have been functionally characterized. Bioinformatics approaches can be highly effective to interpret the consequences of the mutations more rapidly. In this study, we aim to analyze the pathogenicity of ABCA4 clinical and prospective variants utilizing two methods to infer mutation effects: prediction software and computational protein models. We hypothesize that these two approaches in combination will allow us to identify the consequences of the ABCA4 variants and gain insight into the overall structure and function of the protein. We found that the pathogenicity prediction software results align well with the structural analysis results in most instances. The clinical in silico prediction tools were found to predict pathogenicity more frequently than structural analyses, albeit with high sensitivity and low specificity. On the other hand, structure prediction tools are high specificity and thus, predict more accurately. Our results also indicate a correlation between disease severity and structural changes in protein models induced by genetic variations. Our findings suggest that computational analyses are promising tools to predict pathogenicity and can aid in the understanding of disease‐associated ABCA4 genetic variants. These computational approaches have additional applications in protein analysis and provide a strong framework for future in vitro studies.
Human papillomaviruses (HPVs) encompass a large family of viruses that range from benign to highly carcinogenic. The crucial differences between benign and carcinogenic types of HPV remain unknown, ...except that the two HPV types differ in the frequency of DNA replication. We have systematically analyzed the mechanism of HPV DNA replication initiation in low-risk and high-risk HPVs. Our results demonstrate that HPV-encoded E2 initiator protein and its four binding sites in the replication origin play pivotal roles in determining the destiny of the HPV-infected cell. We have identified strain-specific single nucleotide variations in E2 binding sites found only in the high-risk HPVs. We have demonstrated that these variations result in attenuated formation of the E2-DNA complex. E2 binding to these sites is linked to the activation of the DNA replication origin as well as initiation of DNA replication. Both electrophoretic mobility shift assay and atomic force microscopy studies demonstrated that binding of E2 from either low- or high-risk HPVs with variant binding sequences lacked multimeric E2-DNA complex formation in vitro. These results provided a molecular basis of differential DNA replication in the two types of HPVs and pointed to a correlation with the development of cancer.
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•High-risk (HPV-16) E2 protein bound to three of its four binding sites efficiently. The binding affinities are likely as follows: BS4>BS2≈BS1>>BS3.•A common feature amongst the high-risk genotypes was found to be a single nucleotide variation (SNV) in a E2 binding site (BS2 or BS3) which led to attenuation in E2 multimer formation on the origin DNA.•The SNVs in E2 binding sites in the origin correlated well with the HPV-associated carcinogenicity.•Based on the evidence presented here, a model for the interplay of E2 and its binding sites in HPV DNA replication and modulation of carcinogenicity was proposed.
DnaA protein is the initiator of genomic DNA replication in prokaryotes. It binds to specific DNA sequences in the origin of DNA replication and unwinds small AT-rich sequences downstream for the ...assembly of the replisome. The mechanism of activation of DnaA that enables it to bind and organize the origin DNA and leads to replication initiation remains unclear. In this study, we have developed double-labeled fluorescent DnaA probes to analyze conformational states of DnaA protein upon binding DNA, nucleotide, and Soj sporulation protein using Fluorescence Resonance Energy Transfer (FRET). Our studies demonstrate that DnaA protein undergoes large conformational changes upon binding to substrates and there are multiple distinct conformational states that enable it to initiate DNA replication. DnaA protein adopted a relaxed conformation by expanding ~15Å upon binding ATP and DNA to form the ATP·DnaA·DNA complex. Hydrolysis of bound ATP to ADP led to a contraction of DnaA within the complex. The relaxed conformation of DnaA is likely required for the formation of the multi-protein ATP·DnaA·DNA complex. In the initiation of sporulation, Soj binding to DnaA prevented relaxation of its conformation. Soj·ADP appeared to block the activation of DnaA, suggesting a mechanism for Soj·ADP in switching initiation of DNA replication to sporulation. Our studies demonstrate that multiple conformational states of DnaA protein regulate its binding to DNA in the initiation of DNA replication.
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•DnaA protein undergoes large conformational changes upon binding to substrates, nucleotides and DnaA box.•DnaA protein adopted a relaxed conformation by expanding ~15Å upon binding ATP and DNA to form the ATP·DnaA·DNA complex.•Hydrolysis of bound ATP to ADP led to a contraction of DnaA within the complex.•The relaxed conformation of DnaA is likely required for the formation of the multi-protein ATP·DnaA·DNA complex.•Binding of sporulation protein, Soj to DnaA prevented relaxation of its conformation.•Soj·ADP appeared to block the activation of DnaA, suggesting its mechanism in switching DNA replication to sporulation.
Human papillomavirus (HPV) infection and cervical cancer are leading health problems and causes of death in many parts of the world. There are ~ 200 HPV types that can infect humans. This study aims ...to understand the spectrum of HPV infections in Nigerian women with normal or abnormal cytology.
We screened cervical samples from 90 women with possible HPV infections collected in two regional hospitals in Nigeria. The first screening was done using next-generation DNA sequencing (NGS), identifying multiple HPV types in many samples. Thereafter, type-specific PCR analysis was used to verify the NGS-identified HPV types in each sample.
NGS analysis of the 90 samples from the Nigerian cohort identified 44 HPV types. The type-specific PCR confirmed 25 HPV types out of the 44 HPV types detected by NGS, and ~ 10 of these types were the most prevalent. The top five prevalent types found in the Nigerian cohort were HPV71 (17%), HPV82 (15%), HPV16 (16%), HPV6 (10%), and HPV20 (7%). Among the PCR-confirmed HPV types, we found 40.98% high-risk HPV types, 27.22% low-risk HPV types, and 31.15% undetermined HPV types. Among these 25 HPV types in Nigeria, only six were included in the current nine-valent HPV vaccine. We also observed strikingly high multiple HPV infections in most patients, with as many as nine HPV types in a few single samples.
Our NGS-PCR approach of HPV typing in the Nigerian cohort samples unveiled all possible HPV types currently circulating in Nigerian people. We confirmed 25 HPV types using NGS and PCR, with many samples infected with multiple HPV types. However, only six of these types are part of the nine-valent HPV vaccines indicating the need to develop region-specific selective vaccines.
The retina-specific ATP binding cassette transporter, ABCA4 protein, is associated with a broad range of inherited macular degenerations, including Stargardt disease, autosomal recessive cone rod ...dystrophy, and fundus flavimaculatus. In order to understand its role in retinal transport in rod out segment discs, we have investigated the interactions of the soluble domains of ABCA4 with both 11-cis- and all-trans-retinal. Using fluorescence anisotropy-based binding analysis and recombinant polypeptides derived from the amino acid sequences of the four soluble domains of ABCA4, we demonstrated that the nucleotide binding domain 1 (NBD1) specifically bound 11-cis-retinal. Its affinity for all-trans-retinal was markedly reduced. Stargardt disease-associated mutations in this domain resulted in attenuation of 11-cis-retinal binding. Significant differences in 11-cis-retinal binding affinities were observed between NBD1 and other cytoplasmic and lumenal domains of ABCA4. The results suggest a possible role of ABCA4 and, in particular, the NBD1 domain in 11-cis-retinal binding. These results also correlate well with a recent report on the in vivo role of ABCA4 in 11-cis-retinal transport.
The ABCA4 protein is proposed to transport all-trans-retinal from the outer segment discs of retinal rod and cone photoreceptors.
11-cis-Retinal bound specifically and with high affinity to the NBD1 domain of hABCA4.
The NBD1 domain plays further roles in addition to nucleotide hydrolysis.
ABCA4 may play a novel role in the visual transduction cycle involving 11-cis-retinal.
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•Insertion of a Cys4 sequence and single Cys motif allowedsite-specific labeling with FlAsH and Alexa568 of a protein.•FRET is a well-known technique useful for analysis of structural ...changes of proteins labeled with donor and accepter fluorophores.•Inter-fluorophore distances and proximity ratios of the peakintensities are used to understand structural changes.
Fluorescence Resonance Energy Transfer (FRET) is a well-known methodology for detection and quantitation of structural changes of proteins in solution. FRET requires site-specific protein labeling with two fluorophores, one of which functions as an energy donor and the other one as an energy acceptor. However, the site-specific labeling of protein is often complex and difficult, particularly when inserting two fluorophores in specific sites. We have examined several protein labeling approaches with a varying degree of success. Described here is a dual labeling strategy that worked reproducibly in a number of protein targets and we believe will be applicable to a variety of proteins, which have few or no native cysteine (Cys) residues. We have successfully double-labeled DnaA protein of Bacillus anthracis, which lacks intrinsic Cys residues. A cysteine residue was inserted at the N-terminus by in vitro mutagenesis and a Cys-Cys-Phe-Gly-Cys-Cys (CCPGCC) sequence at the C-terminus by PCR. This protein was labeled site-specifically with a fluorescein derivative, FlAsH, at the CCPGCC sequence followed by Alexa568 maleimide at the N-terminus Cys residue. Structural changes of the protein with nucleotide, DNA and an inhibitor protein binding were determined by FRET analysis of the double-labeled protein. This comprehensive novel methodology for site-specific protein labeling with different fluorophores is applicable for understanding different in vitro proteomic structural studies. Here, we describe a verified technique used for FRET spectral analysis and quantitative evaluation of structural changes using fluorophore labeled DnaA protein constructs as an example.
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