RCSB Protein Data Bank tools for 3D structure-guided cancer research: human papillomavirus (HPV) case study.

Atomic-level three-dimensional (3D) structure data for biological macromolecules often prove critical to dissecting and understanding the precise mechanisms of action of cancer-related proteins and their diverse roles in oncogenic transformation, proliferation, and metastasis. They are also used extensively to identify potentially druggable targets and facilitate discovery and development of both small-molecule and biologic drugs that are today benefiting individuals diagnosed with cancer around the world. 3D structures of biomolecules (including proteins, DNA, RNA, and their complexes with one another, drugs, and other small molecules) are freely distributed by the open-access Protein Data Bank (PDB). This global data repository is used by millions of scientists and educators working in the areas of drug discovery, vaccine design, and biomedical and biotechnology research. The US Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) provides an integrated portal to the PDB archive that streamlines access for millions of worldwide PDB data consumers worldwide. Herein, we review online resources made available free of charge by the RCSB PDB to basic and applied researchers, healthcare providers, educators and their students, patients and their families, and the curious public. We exemplify the value of understanding cancer-related proteins in 3D with a case study focused on human papillomavirus.

The critical residues of helix 5 for in vitro pentamer formation and stability of the papillomavirus capsid protein, L1.

The mono-site mutations of the absolutely conserved residues, (464)LGR(466), in the α-helix 5 (h5) of HPV16 L1 completely disrupted the pentamer formation. The implication of this finding is the potential usage of a h5-like peptide as the reagent to interfere with the pentamer formation and stability as an anti-HPV reagent.

Comparative analysis of recombinant Human Papillomavirus 8 L1 production in plants by a variety of expression systems and purification methods.

Human papillomavirus 8 (HPV-8), one of the high-risk cutaneous papillomaviruses (cHPVs), is associated with epidermodysplasia verruciformis and nonmelanoma skin cancer in immuno-compromised individuals. Currently, no vaccines against cHPVs have been reported; however, recent studies on cross-neutralizing properties of their capsid proteins (CP) have fostered an interest in vaccine production against these viruses. We examined the potential of producing HPV-8 major CP L1 in Nicotiana benthamiana by agroinfiltration of different transient expression vectors: (i) the binary vector pBIN19 with or without silencing suppressor constructs, (ii) the nonreplicating Cowpea mosaic virus-derived expression vector pEAQ-HT and (iii) a replicating Tobacco mosaic virus (TMV)-based vector alone or with signal peptides. Although HPV-8 L1 was successfully expressed using pEAQ-HT and TMV, a 15-fold increase was obtained with pEAQ-HT. In contrast, no L1 protein could be immune detected using pBIN19 irrespective of whether silencing suppressors were coexpressed, although such constructs were required for identifying L1-specific transcripts. A fourfold yield increase in L1 expression was obtained when 22 C-terminal amino acids were deleted (L1ΔC22), possibly eliminating a nuclear localization signal. Electron microscopy showed that plant-made HPV-8 L1 proteins assembled in appropriate virus-like particles (VLPs) of T = 1 or T = 7 symmetry. Ultrathin sections of L1ΔC22-expressing cells revealed their accumulation in the cytoplasm in the form of VLPs or paracrystalline arrays. These results show for the first time the production and localization of HPV-8 L1 protein in planta and its assembly into VLPs representing promising candidate for potential vaccine production.

Molecular and structural characterization of the L1 virus-like particles that are used as vaccine antigens in Cervarix™, the AS04-adjuvanted HPV-16 and -18 cervical cancer vaccine.

Cervarix™ is a prophylactic human papillomavirus (HPV)-16/18 vaccine developed for the prevention of cervical cancer. The vaccine antigens are HPV-16 and HPV-18 L1 virus-like particles (VLPs) made from baculovirus expression vector system (BEVS)-produced HPV-16 and HPV-18 L1 proteins, respectively. In this study, we demonstrate that truncation of the nuclear targeting and DNA binding signals at the C-terminus of the HPV-16 and HPV-18 L1 proteins prevented intranuclear formation of the VLPs in the host cells and led to cytoplasmic localization of the L1 proteins as shown by in situ immunogold detection and electron microscopy. Following purification, these L1 proteins were able to form VLPs. The characteristics of these HPV-16 and HPV-18 L1 VLPs were studied using various physicochemical and immunological techniques. Amino acid analysis, SDS-PAGE and western blotting demonstrated the high purity of the L1 proteins and batch-to-batch consistency. The structure of the VLPs was shown to be similar to that reported for the native virions, as evaluated by microscopic observations, protein tomography and disc centrifugation experiments. The presence of important conformation-dependent neutralizing epitopes, such as U4, V5 and J4, was confirmed by ELISA and surface plasmon resonance. Structural robustness and consistency among batches was also observed by differential scanning calorimetry and electron microscopy. Moreover, adsorption to aluminum was shown not to impair VLP structure. In conclusion, the BEVS-produced HPV-16 and HPV-18 L1 VLPs display key structural and immunological features, which contribute to the efficacy of Cervarix™ vaccination.

One-step chromatographic purification of human papillomavirus type 16 L1 protein from Saccharomyces cerevisiae.

The prophylactic human papillomavirus vaccine is based on recombinant L1 protein produced in yeast or insect cells. L1 is a major capsid protein that self-assembles into virus-like particles (VLP). Conventionally, several chromatography steps are required to purify it; the steps are time consuming, and they result in losses of the target protein. Ultracentrifugation using a sucrose cushions or cesium chloride density gradients, and size-exclusion chromatography, has also been routinely used for small scale purification of L1 protein. However, these methods require a great deal of time and labor, and are not suitable for industrial-scale purification. To resolve these problems, we have developed two simple one-step chromatography methods for purifying recombinant HPV16 L1 protein produced in Saccharomyces cerevisiae. Eighty percent of the contaminating protein was removed by ammonium sulfate precipitation and by precipitating contaminants prior to the chromatography step. One method uses heparin chromatography and the other, cation-exchange chromatography, and recoveries by the two methods were both about 60%, the highest recoveries of L1 protein achieved so far. We confirmed that HPV16 L1 protein purified by either method self-assembles into VLP. We anticipate that these one-step chromatography methods will reduce the time, cost and labor needed for purification of L1 protein, and facilitate the study of prophylactic HPV vaccines.

Translational fusion of chloroplast-expressed human papillomavirus type 16 L1 capsid protein enhances antigen accumulation in transplastomic tobacco.

Human Papillomavirus (HPV) is the causal agent of cervical cancer, one of the most common causes of death for women. The major capsid L1 protein self-assembles in Virus Like Particles (VLPs), which are highly immunogenic and suitable for vaccine production. In this study, a plastid transformation approach was assessed in order to produce a plant-based HPV-16 L1 vaccine. Transplastomic plants were obtained after transformation with vectors carrying a chimeric gene encoding the L1 protein either as the native viral (L1(v) gene) or a synthetic sequence optimized for expression in plant plastids (L1(pt) gene) under control of plastid expression signals. The L1 mRNA was detected in plastids and the L1 antigen accumulated up to 1.5% total leaf proteins only when vectors included the 5'-UTR and a short N-terminal coding segment (Downstream Box) of a plastid gene. The half-life of the engineered L1 protein, determined by pulse-chase experiments, is at least 8 h. Formation of immunogenic VLPs in chloroplasts was confirmed by capture ELISA assay using antibodies recognizing conformational epitopes and by electron microscopy.

Optimum conditions for production and purification of human papillomavirus type 16 L1 protein from Saccharomyces cerevisiae.

Several prophylactic human papillomavirus (HPV) vaccines have been developed based on virus-like particles (VLPs) made from viral L1 proteins. A substantial number of VLPs is necessary for biochemical characterization and diagnostic test development. To establish the optimum conditions for production and purification of HPV L1 in the yeast expression system we varied the amount and nature of the carbon source and evaluated HPV 16 L1 recovery by three purification methods. Maximally threefold more HPV 16 L1 was produced with a 4% carbon source than with a 2% carbon source. In addition, the productivity of HPV 16 L1 varied by 25% depending on the combination of glucose and galactose in the 4% carbon source. We introduced an ammonium sulfate precipitation step in place of the ultracentrifugation using a sucrose cushion routinely used for HPV L1 purification, and optimized the purification by cation-exchange chromatography. Overall L1 protein recovery using the ammonium sulfate precipitation method was 30%, the highest recovery achieved so far. The purified HPV 16 L1 protein successfully self-assembled into VLPs. Purification by ammonium sulfate precipitation was maximally 15 times greater than ultracentrifugation on a sucrose cushion. We anticipate that our procedures for production and purification will reduce the cost, time and labor involved in obtaining sufficient yields of VLPs.

Formation of well-defined soluble aggregates upon fusion to MBP is a generic property of E6 proteins from various human papillomavirus species.

Protein aggregation is a main barrier hindering structural and functional studies of a number of interesting biological targets. The E6 oncoprotein of Human Papillomavirus strain 16 (E6(16)) is difficult to express under a native soluble form in bacteria. Produced as an unfused sequence, it forms inclusion bodies. Fused to the C-terminus of MBP, it is mainly produced in the form of soluble high molecular weight aggregates. Here, we produced as MBP-fusions seven E6 proteins from other HPV strains (5, 11, 18, 33, 45, 52, and 58) belonging to four different species, and we compared their aggregation state to that of MBP-E6(16). Using a fast mutagenesis method, we changed most non-conserved cysteines to the isosteric residue serine to minimize disulfide bridge-mediated aggregation during purification. Static and dynamic light scattering measurements, ultracentrifugation and electron microscopy demonstrated the presence in all MBP-E6 preparations of soluble high-molecular weight aggregates with a well-defined spherical shape. These aggregated particles are relatively monodisperse but their amount and their size vary depending on the conditions of expression and the strain considered. For all strains, minimal aggregate formation occurs when the expression is performed at 15 degrees C. Such observations suggest that the assembly of MBP-E6 aggregates takes place in vivo during protein biosynthesis, rather than occurring during purification. Finally, we show that all MBP-E6 preparations contain two zinc ions per protein monomer, suggesting that E6 domains within the high molecular weight aggregates possess a native-like fold, which enables correct coordination to the metal center.

Papillomavirus capsid protein expression in Escherichia coli: purification and assembly of HPV11 and HPV16 L1.

The L1 major capsid proteins of human papillomavirus (HPV) types 11 and 16 were purified and analyzed for structural integrity and in vitro self-assembly. Proteins were expressed in Escherichia coli as glutathione-S-transferase-L1 (GST-L1) fusions and purified to near homogeneity as pentamers (equivalent to viral capsomeres), after thrombin cleavage from the GST moiety and removal of tightly associated GroEL protein. Sequences at the amino and carboxy termini contributing to formation of L1 pentamers and to in vitro capsid assembly were identified by deletion analysis. For both HPV11 and HPV16 L1, up to at least ten residues could be deleted from the amino terminus (Delta N10) and 30 residues from the carboxy terminus (Delta C30) without affecting pentamer formation. The HPV16 pentamers assembled into relatively regular, 72-pentamer shells ("virus-like particles" or VLPs) at low pH, with the exception of HPV16 L1 Delta N10, which assembled into a 12-pentamer, T=1 capsid (small VLP) under all conditions tested. The production of large quantities of assembly-competent L1, using the expression and purification protocol described here, has been useful for crystallographic analysis, and will be valuable for studies of virus-receptor interactions and potentially for vaccine design.

Structure of small virus-like particles assembled from the L1 protein of human papillomavirus 16.

The papillomavirus major late protein, L1, forms the pentameric assembly unit of the viral shell. Recombinant HPV16 L1 pentamers assemble in vitro into capsid-like structures, and truncation of ten N-terminal residues leads to a homogeneous preparation of 12-pentamer, icosahedral particles. X-ray crystallographic analysis of these particles at 3.5 A resolution shows that L1 closely resembles VP1 from polyomaviruses. Surface loops contain the sites of sequence variation among HPV types and the locations of dominant neutralizing epitopes. The ease with which small virus-like particles may be obtained from L1 expressed in E. coli makes them attractive candidate components of a papillomavirus vaccine. Their crystal structure also provides a starting point for future vaccine design.

In vitro gene transfer using human papillomavirus-like particles.

Recombinant papillomavirus-like particles have recently been shown to be highly effective for the prevention of papillomavirus infections and associated tumors, and a virus-like particle-based vaccine against the most prevalent HPV causing genital infection in humans will be developed in the near future. Another use of these virus-like particles may lie in gene therapy and DNA immunization. We report here that human papillomavirus-like particles composed of the major capsid protein (L1) of HPV-16 are able to package unrelated plasmid DNA in vitro and then to deliver this foreign DNA to eukaryotic cells with the subsequent expression of the encoded gene. The results indicate higher gene transfer than with DNA alone or with liposome. Virus-like particles are a very promising vehicle for delivering genetic material into target cells. Moreover, the preparation of the gene transfer vehicle is relatively easy.

Expression of the major capsid protein of human papillomavirus type 11 in Saccharomyces cerevisae.

The major capsid protein L1 of papillomaviruses expressed recombinantly or in infected cells has the intrinsic ability to form virus-like particles (VLPs) which display conformational epitopes necessary to elicit high-titered, virus-neutralizing antibodies. We have shown previously that the L1 gene of human papillomavirus type 6a (HPV6) can be expressed efficiently in Saccharomyces cerevisae (Sc) as VLPs. However, when we attempted to express the L1 gene cloned from the closely related HPV11 in yeast, few VLPs were observed in crude lysates. The lower expression level of HPV11 L1 protein was found to result from a truncation of the HPV11 L1 mRNA. Since sequence requirements for transcriptional termination in yeast are still unclear, the HPV6 L1 gene was used as the basis for the complete synthetic reconstruction of the entire 1506-bp HPV11 L1 gene. Expression of this HPV6/11 hybrid L1 gene in yeast resulted in predominantly full-length L1 mRNA and a > 7-fold increased level of production of HPV11 VLPs compared to that expressed by the wild-type HPV11 L1 gene. The VLPs were shown to display the conformational epitopes important to elicit virus-neutralizing antibodies.

Dissection of functional domains in the adenovirus 2 early 1B 55K polypeptide by suppressor-linker insertional mutagenesis.

To determine whether the viral replication functions of the adenovirus E1B 55K protein play a role in its ability to transform cloned rat embryo fibroblast cells in culture, we constructed an extensive series of insertion mutations throughout the 55K gene. The mutations were recombined into infectious virus and characterized for their abilities to produce stable 55K protein in HeLa cells, replicate virus in HeLa cells, express late viral proteins efficiently, and transform CREF cells following infection. Mutant 55K transforming activity in primary baby rat kidney cells was also assayed following DNA transfection. The functions required for viral replication are encoded in several patches of the 55K linear sequence, while the CREF transforming functions are sensitive to all of the insertions. An insertion at amino acid 380 created a mutant virus which was reduced in transforming activity, but was not reduced for viral replication. Therefore, a function required for efficient transformation of CREF cells can be separated from functions required for late gene expression and viral replication. Transformation of BRK cells following DNA transfection was reduced by complete disruption of the 55K protein gene, but was not significantly affected by any of the insertions.

Domains required for in vitro association between the cellular p53 and the adenovirus 2 E1B 55K proteins.

The 55K protein encoded by the adenovirus 2 E1B gene is required for complete cellular transformation and binds the cellular protein p53. Using an in vitro immunoprecipitation assay, we mapped the domains in both 55K and p53 required for the interaction of the two proteins. The domain in p53 mapped to the amino terminal 123 residues. There are several domains in the 495 residue 55K polypeptide which contribute to stable association with p53, with the most essential region mapping between residues 224 and 354. Mutations which prevented 55K-p53 binding were not more defective for transformation than other mutations which did not affect binding.

Genetic dissection of the transactivating domain of the E1a 289R protein of adenovirus type 2.

A series of linker-scanning, deletion, and frameshift mutations were made in the pm975 variant of the adenovirus type 2 E1a gene, which expresses only the larger of the two major E1a proteins. Most of these were within the 46-amino-acid segment unique to the larger E1a protein product (the 289R protein), which confers on it the ability to activate in trans the expression of other genes. The mutations were recombined into virus and assayed by in vitro transcription in nuclei isolated from infected cells for their ability to activate the transcription of other viral early genes and of the endogenous hsp70 gene. Mutant E1a proteins from which the 289R-unique segment was removed by deletion or truncation did not completely lose the ability to transactivate by comparison with a virus which makes no E1a at all, indicating that sequences outside this domain are active in the positive regulation of transcription. The E1a mutations tested fell into several classes: those that increased transactivation of virtually all genes, those that severely depressed transactivation of all genes, and those that depressed transactivation only moderately. Each mutation had similar effects on the expression of all transcription units tested, indicating a common process in their transactivation. However, some mutants in the third category decreased transactivation of some induced genes more severely than of others. Such gene-specific defects suggest the existence of subclasses of E1a-responsive transcription units, consistent with the involvement of diverse proteins in the transactivation of different genes. Two specific structural components of the transactivating domain, a putative metal-binding element and a region with high potential for beta-sheet formation at its carboxy-terminus, appear to be important to the transactivation function.