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1.
Bioorg Chem ; 147: 107415, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38701597

ABSTRACT

The tobacco mosaic virus coat protein (TMV-CP) is indispensable for the virus's replication, movement and transmission, as well as for the host plant's immune system to recognize it. It constitutes the outermost layer of the virus particle, and serves as an essential component of the virus structure. TMV-CP is essential for initiating and extending viral assembly, playing a crucial role in the self-assembly process of Tobacco Mosaic Virus (TMV). This research employed TMV-CP as a primary target for virtual screening, from which a library of 43,417 compounds was sourced and SH-05 was chosen as the lead compound. Consequently, a series of α-amide phosphate derivatives were designed and synthesized, exhibiting remarkable anti-TMV efficacy. The synthesized compounds were found to be beneficial in treating TMV, with compound 3g displaying a slightly better curative effect than Ningnanmycin (NNM) (EC50 = 304.54 µg/mL) at an EC50 of 291.9 µg/mL. Additionally, 3g exhibited comparable inactivation activity (EC50 = 63.2 µg/mL) to NNM (EC50 = 67.5 µg/mL) and similar protective activity (EC50 = 228.9 µg/mL) to NNM (EC50 = 219.7 µg/mL). Microscale thermal analysis revealed that the binding of 3g (Kd = 4.5 ± 1.9 µM) to TMV-CP showed the same level with NNM (Kd = 5.5 ± 2.6 µM). Results from transmission electron microscopy indicated that 3g could disrupt the structure of TMV virus particles. The toxicity prediction indicated that 3g was low toxicity. Molecular docking showed that 3g interacted with TMV-CP through hydrogen bond, attractive charge interaction and π-Cation interaction. This research provided a novel α-amide phosphate structure target TMV-CP, which may help the discovery of new anti-TMV agents in the future.


Subject(s)
Antiviral Agents , Capsid Proteins , Phosphates , Tobacco Mosaic Virus , Tobacco Mosaic Virus/drug effects , Antiviral Agents/pharmacology , Antiviral Agents/chemistry , Antiviral Agents/chemical synthesis , Phosphates/chemistry , Phosphates/pharmacology , Structure-Activity Relationship , Molecular Structure , Capsid Proteins/antagonists & inhibitors , Capsid Proteins/chemistry , Capsid Proteins/metabolism , Drug Design , Microbial Sensitivity Tests , Amides/chemistry , Amides/pharmacology , Amides/chemical synthesis , Dose-Response Relationship, Drug , Drug Discovery , Molecular Docking Simulation
2.
Sci Rep ; 14(1): 10253, 2024 05 04.
Article in English | MEDLINE | ID: mdl-38704431

ABSTRACT

The tegument protein pp150 of Human Cytomegalovirus (HCMV) is known to be essential for the final stages of virus maturation and mediates its functions by interacting with capsid proteins. Our laboratory has previously identified the critical regions in pp150 important for pp150-capsid interactions and designed peptides similar in sequence to these regions, with a goal to competitively inhibit capsid maturation. Treatment with a specific peptide (PepCR2 or P10) targeted to pp150 conserved region 2 led to a significant reduction in murine CMV (MCMV) growth in cell culture, paving the way for in vivo testing in a mouse model of CMV infection. However, the general pharmacokinetic parameters of peptides, including rapid degradation and limited tissue and cell membrane permeability, pose a challenge to their successful use in vivo. Therefore, we designed a biopolymer-stabilized elastin-like polypeptide (ELP) fusion construct (ELP-P10) to enhance the bioavailability of P10. Antiviral efficacy and cytotoxic effects of ELP-P10 were studied in cell culture, and pharmacokinetics, biodistribution, and antiviral efficacy were studied in a mouse model of CMV infection. ELP-P10 maintained significant antiviral activity in cell culture, and this conjugation significantly enhanced P10 bioavailability in mouse tissues. The fluorescently labeled ELP-P10 accumulated to higher levels in mouse liver and kidneys as compared to the unconjugated P10. Moreover, viral titers from vital organs of MCMV-infected mice indicated a significant reduction of virus load upon ELP-P10 treatment. Therefore, ELP-P10 has the potential to be developed into an effective antiviral against CMV infection.


Subject(s)
Antiviral Agents , Cytomegalovirus Infections , Elastin , Muromegalovirus , Peptides , Phosphoproteins , Viral Matrix Proteins , Animals , Elastin/chemistry , Elastin/metabolism , Cytomegalovirus Infections/drug therapy , Cytomegalovirus Infections/virology , Mice , Antiviral Agents/pharmacology , Antiviral Agents/pharmacokinetics , Antiviral Agents/chemistry , Peptides/pharmacology , Peptides/chemistry , Muromegalovirus/drug effects , Humans , Capsid Proteins/metabolism , Capsid Proteins/chemistry , Cytomegalovirus/drug effects , Capsid/metabolism , Capsid/drug effects , Recombinant Fusion Proteins/pharmacology , Recombinant Fusion Proteins/pharmacokinetics , Disease Models, Animal , Elastin-Like Polypeptides
3.
Proc Natl Acad Sci U S A ; 121(20): e2321260121, 2024 May 14.
Article in English | MEDLINE | ID: mdl-38722807

ABSTRACT

Protein capsids are a widespread form of compartmentalization in nature. Icosahedral symmetry is ubiquitous in capsids derived from spherical viruses, as this geometry maximizes the internal volume that can be enclosed within. Despite the strong preference for icosahedral symmetry, we show that simple point mutations in a virus-like capsid can drive the assembly of unique symmetry-reduced structures. Starting with the encapsulin from Myxococcus xanthus, a 180-mer bacterial capsid that adopts the well-studied viral HK97 fold, we use mass photometry and native charge detection mass spectrometry to identify a triple histidine point mutant that forms smaller dimorphic assemblies. Using cryoelectron microscopy, we determine the structures of a precedented 60-mer icosahedral assembly and an unexpected 36-mer tetrahedron that features significant geometric rearrangements around a new interaction surface between capsid protomers. We subsequently find that the tetrahedral assembly can be generated by triple-point mutation to various amino acids and that even a single histidine point mutation is sufficient to form tetrahedra. These findings represent a unique example of tetrahedral geometry when surveying all characterized encapsulins, HK97-like capsids, or indeed any virus-derived capsids reported in the Protein Data Bank, revealing the surprising plasticity of capsid self-assembly that can be accessed through minimal changes in the protein sequence.


Subject(s)
Capsid Proteins , Capsid , Cryoelectron Microscopy , Point Mutation , Capsid/metabolism , Capsid/chemistry , Capsid/ultrastructure , Capsid Proteins/genetics , Capsid Proteins/chemistry , Capsid Proteins/metabolism , Myxococcus xanthus/genetics , Myxococcus xanthus/metabolism , Models, Molecular
4.
Cell ; 187(9): 2236-2249.e17, 2024 Apr 25.
Article in English | MEDLINE | ID: mdl-38614100

ABSTRACT

Unlike those of double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), and ssRNA viruses, the mechanism of genome packaging of dsRNA viruses is poorly understood. Here, we combined the techniques of high-resolution cryoelectron microscopy (cryo-EM), cellular cryoelectron tomography (cryo-ET), and structure-guided mutagenesis to investigate genome packaging and capsid assembly of bluetongue virus (BTV), a member of the Reoviridae family of dsRNA viruses. A total of eleven assembly states of BTV capsid were captured, with resolutions up to 2.8 Å, with most visualized in the host cytoplasm. ATPase VP6 was found underneath the vertices of capsid shell protein VP3 as an RNA-harboring pentamer, facilitating RNA packaging. RNA packaging expands the VP3 shell, which then engages middle- and outer-layer proteins to generate infectious virions. These revealed "duality" characteristics of the BTV assembly mechanism reconcile previous contradictory co-assembly and core-filling models and provide insights into the mysterious RNA packaging and capsid assembly of Reoviridae members and beyond.


Subject(s)
Bluetongue virus , Capsid Proteins , Capsid , Cryoelectron Microscopy , RNA, Viral , Viral Genome Packaging , Bluetongue virus/genetics , Bluetongue virus/physiology , Bluetongue virus/metabolism , Capsid/metabolism , Capsid/ultrastructure , Capsid Proteins/metabolism , Capsid Proteins/genetics , Capsid Proteins/chemistry , Animals , RNA, Viral/metabolism , RNA, Viral/genetics , Genome, Viral/genetics , Virus Assembly , Electron Microscope Tomography , Virion/metabolism , Virion/genetics , Virion/ultrastructure , Models, Molecular , Cell Line , Cricetinae
5.
Nat Commun ; 15(1): 3576, 2024 Apr 27.
Article in English | MEDLINE | ID: mdl-38678040

ABSTRACT

Controlled assembly of a protein shell around a viral genome is a key step in the life cycle of many viruses. Here we report a strategy for regulating the co-assembly of nonviral proteins and nucleic acids into highly ordered nucleocapsids in vitro. By fusing maltose binding protein to the subunits of NC-4, an engineered protein cage that encapsulates its own encoding mRNA, we successfully blocked spontaneous capsid assembly, allowing isolation of the individual monomers in soluble form. To initiate RNA-templated nucleocapsid formation, the steric block can be simply removed by selective proteolysis. Analyses by transmission and cryo-electron microscopy confirmed that the resulting assemblies are structurally identical to their RNA-containing counterparts produced in vivo. Enzymatically triggered cage formation broadens the range of RNA molecules that can be encapsulated by NC-4, provides unique opportunities to study the co-assembly of capsid and cargo, and could be useful for studying other nonviral and viral assemblies.


Subject(s)
Cryoelectron Microscopy , Maltose-Binding Proteins , Nucleocapsid , Nucleocapsid/metabolism , Nucleocapsid/ultrastructure , Maltose-Binding Proteins/metabolism , Maltose-Binding Proteins/genetics , Virus Assembly , Capsid/metabolism , RNA, Viral/metabolism , RNA, Viral/genetics , Capsid Proteins/metabolism , Capsid Proteins/genetics , Capsid Proteins/chemistry , RNA, Messenger/metabolism , RNA, Messenger/genetics
6.
Phys Chem Chem Phys ; 26(17): 13094-13105, 2024 May 01.
Article in English | MEDLINE | ID: mdl-38628116

ABSTRACT

Collision induced unfolding (CIU) is a method used with ion mobility mass spectrometry to examine protein structures and their stability. Such experiments yield information about higher order protein structures, yet are unable to provide details about the underlying processes. That information can however be provided using molecular dynamics simulations. Here, we investigate the gas-phase unfolding of norovirus capsid dimers from the Norwalk and Kawasaki strains by employing molecular dynamics simulations over a range of temperatures, representing different levels of activation, together with CIU experiments. The dimers have highly similar structures, but their CIU reveals different stability that can be explained by the different dynamics that arises in response to the activation seen in the simulations, including a part of the sequence with previously observed strain-specific dynamics in solution. Our findings show how similar protein variants can be examined using mass spectrometric techniques in conjunction with atomistic molecular dynamics simulations to reveal differences in stability as well as differences in how and where unfolding takes place upon activation.


Subject(s)
Capsid Proteins , Molecular Dynamics Simulation , Norovirus , Protein Unfolding , Norovirus/chemistry , Capsid Proteins/chemistry , Capsid Proteins/metabolism , Protein Stability , Capsid/chemistry , Protein Multimerization
7.
Biosci Rep ; 44(5)2024 May 29.
Article in English | MEDLINE | ID: mdl-38592735

ABSTRACT

The rotavirus capsid protein VP6 forms the middle of three protein layers and is responsible for many critical steps in the viral life cycle. VP6 as a structural protein can be used in various applications including as a subunit vaccine component. The head domain of VP6 (VP6H) contains key sequences that allow the protein to trimerize and that represent epitopes that are recognized by human antibodies in the viral particle. The domain is rich in ß-sheet secondary structures. Here, VP6H was solubilised from bacterial inclusion bodies and purified using a single affinity chromatography step. Spectral (far-UV circular dichroism and intrinsic tryptophan fluorescence) analysis revealed that the purified domain had native-like secondary and tertiary structures. The domain could maintain structure up to 44°C during thermal denaturation following which structural changes result in an intermediate forming and finally irreversible aggregation and denaturation. The chemical denaturation with urea and guanidinium hydrochloride produces intermediates that represent a loss in the cooperativity. The VP6H domain is stable and can fold to produce its native structure in the absence of the VP6 base domain but cannot be defined as an independent folding unit.


Subject(s)
Antigens, Viral , Capsid Proteins , Rotavirus , Capsid Proteins/chemistry , Capsid Proteins/genetics , Antigens, Viral/chemistry , Antigens, Viral/genetics , Rotavirus/chemistry , Protein Denaturation , Protein Domains , Circular Dichroism , Protein Folding , Escherichia coli/genetics , Escherichia coli/metabolism , Humans , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism
8.
J Virol ; 98(5): e0006824, 2024 May 14.
Article in English | MEDLINE | ID: mdl-38661364

ABSTRACT

The portal protein of tailed bacteriophage plays essential roles in various aspects of capsid assembly, motor assembly, genome packaging, connector formation, and infection processes. After DNA packaging is complete, additional proteins are assembled onto the portal to form the connector complex, which is crucial as it bridges the mature head and tail. In this study, we report high-resolution cryo-electron microscopy (cryo-EM) structures of the portal vertex from bacteriophage lambda in both its prohead and mature virion states. Comparison of these structures shows that during head maturation, in addition to capsid expansion, the portal protein undergoes conformational changes to establish interactions with the connector proteins. Additionally, the independently assembled tail undergoes morphological alterations at its proximal end, facilitating its connection to the head-tail joining protein and resulting in the formation of a stable portal-connector-tail complex. The B-DNA molecule spirally glides through the tube, interacting with the nozzle blade region of the middle-ring connector protein. These insights elucidate a mechanism for portal maturation and DNA translocation within the phage lambda system. IMPORTANCE: The tailed bacteriophages possess a distinct portal vertex that consists of a ring of 12 portal proteins associated with a 5-fold capsid shell. This portal protein is crucial in multiple stages of virus assembly and infection. Our research focused on examining the structures of the portal vertex in both its preliminary prohead state and the fully mature virion state of bacteriophage lambda. By analyzing these structures, we were able to understand how the portal protein undergoes conformational changes during maturation, the mechanism by which it prevents DNA from escaping, and the process of DNA spirally gliding.


Subject(s)
Bacteriophage lambda , Capsid Proteins , Capsid , Cryoelectron Microscopy , Virion , Virus Assembly , Bacteriophage lambda/physiology , Bacteriophage lambda/genetics , Capsid Proteins/metabolism , Capsid Proteins/chemistry , Virion/metabolism , Virion/ultrastructure , Capsid/metabolism , Capsid/ultrastructure , DNA, Viral/genetics , DNA, Viral/metabolism , DNA Packaging , Models, Molecular , Protein Conformation
9.
J Virol ; 98(5): e0019724, 2024 May 14.
Article in English | MEDLINE | ID: mdl-38593321

ABSTRACT

Noroviruses are major causative agents of acute nonbacterial gastroenteritis in humans. There are neither antiviral therapeutic agents nor vaccines for noroviruses at this time. To evaluate the potential usefulness of two previously isolated human monoclonal antibody fragments, CV-1A1 and CV-2F5, we first conducted a single-particle analysis to determine the cryo-electron microscopy structure of virus-like particles (VLPs) from the genogroup I genotype 4 (GI.4) Chiba strain uniformly coated with CV-1A1 fragments. The results revealed that the GI.4-specific CV-1A1 antibody bound to the P2 subdomain, in which amino acids are less conserved and variable. Interestingly, a part of the CV-1A1 intrudes into the histo-blood group antigen-binding site, suggesting that this antibody might exert neutralizing activity. Next, we determined the crystal structure of the protruding (P) domain of the capsid protein in the complex form with the CV-2F5 antibody fragment. Consistent with the cross-reactivity, the CV-2F5 bound to the P1 subdomain, which is rich in amino acids conserved among the GI strains, and moreover induced a disruption of Chiba VLPs. These results suggest that the broadly reactive CV-2F5 antibody can be used as both a universal detection reagent and an antiviral drug for GI noroviruses. IMPORTANCE: We conducted the structural analyses of the VP1 protein from the GI.4 Chiba norovirus to identify the binding sites of the previously isolated human monoclonal antibodies CV-1A1 and CV-2F5. The cryo-electron microscopy of the Chiba virus-like particles (VLPs) complexed with the Fv-clasp forms of GI.4-specific CV-1A1 revealed that this antibody binds to the highly variable P2 subdomain, suggesting that this antibody may have neutralizing ability against the GI.4 strains. X-ray crystallography revealed that the CV-2F5 antibody bound to the P1 subdomain, which is rich in conserved amino acids. This result is consistent with the ability of the CV-2F5 antibody to react with a wide variety of GI norovirus strains. It is also found that the CV-2F5 antibody caused a disruption of VLPs. Our findings, together with previous reports on the structures of VP1 proteins and VLPs, are expected to open a path for the structure-based development of antivirals and vaccines against norovirus disease.


Subject(s)
Antibodies, Monoclonal , Antibodies, Viral , Capsid Proteins , Cryoelectron Microscopy , Norovirus , Norovirus/immunology , Cryoelectron Microscopy/methods , Humans , Antibodies, Monoclonal/immunology , Crystallography, X-Ray , Capsid Proteins/immunology , Capsid Proteins/chemistry , Capsid Proteins/metabolism , Binding Sites , Antibodies, Viral/immunology , Antibodies, Neutralizing/immunology , Models, Molecular
10.
Viruses ; 16(4)2024 03 23.
Article in English | MEDLINE | ID: mdl-38675835

ABSTRACT

Many protein expression systems are primarily utilised to produce a single, specific recombinant protein. In contrast, most biological processes such as virus assembly rely upon a complex of several interacting proteins rather than the activity of a sole protein. The high complexity of the baculovirus genome, coupled with a multiphase replication cycle incorporating distinct transcriptional steps, made it the ideal system to manipulate for high-level expression of a single, or co-expression of multiple, foreign proteins within a single cell. We have developed and utilised a series of recombinant baculovirus systems to unravel the sequential assembly process of a complex non-enveloped model virus, bluetongue virus (BTV). The high protein yields expressed by the baculovirus system not only facilitated structure-function analysis of each viral protein but were also advantageous to crystallography studies and supported the first atomic-level resolution of a recombinant viral protein, the major BTV capsid protein. Further, the formation of recombinant double-shelled virus-like particles (VLPs) provided insights into the structure-function relationships among the four major structural proteins of the BTV whilst also representing a potential candidate for a viral vaccine. The baculovirus multi-gene expression system facilitated the study of structurally complex viruses (both non-enveloped and enveloped viruses) and heralded a new generation of viral vaccines.


Subject(s)
Baculoviridae , Recombinant Proteins , Baculoviridae/genetics , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Animals , Gene Expression , Bluetongue virus/genetics , Genetic Vectors/genetics , Virus Assembly , Viral Proteins/genetics , Viral Proteins/metabolism , Capsid Proteins/genetics , Capsid Proteins/metabolism , Capsid Proteins/chemistry
11.
Viruses ; 16(4)2024 03 27.
Article in English | MEDLINE | ID: mdl-38675855

ABSTRACT

The foot-and-mouth disease virus is a highly contagious and economically devastating virus of cloven-hooved animals, including cattle, buffalo, sheep, and goats, causing reduced animal productivity and posing international trade restrictions. For decades, chemically inactivated vaccines have been serving as the most effective strategy for the management of foot-and-mouth disease. Inactivated vaccines are commercially produced in cell culture systems, which require successful propagation and adaptation of field isolates, demanding a high cost and laborious time. Cell culture adaptation is chiefly indebted to amino acid substitutions in surface-exposed capsid proteins, altering the necessity of RGD-dependent receptors to heparan sulfate macromolecules for virus binding. Several amino acid substations in VP1, VP2, and VP3 capsid proteins of FMDV, both at structural and functional levels, have been characterized previously. This literature review combines frequently reported amino acid substitutions in virus capsid proteins, their critical roles in virus adaptation, and functional characterization of the substitutions. Furthermore, this data can facilitate molecular virologists to develop new vaccine strains against the foot-and-mouth disease virus, revolutionizing vaccinology via reverse genetic engineering and synthetic biology.


Subject(s)
Amino Acid Substitution , Capsid Proteins , Foot-and-Mouth Disease Virus , Foot-and-Mouth Disease , Viral Tropism , Foot-and-Mouth Disease Virus/genetics , Foot-and-Mouth Disease Virus/metabolism , Animals , Capsid Proteins/genetics , Capsid Proteins/metabolism , Capsid Proteins/chemistry , Foot-and-Mouth Disease/virology , Receptors, Virus/metabolism , Receptors, Virus/genetics , Viral Structural Proteins/genetics , Viral Structural Proteins/metabolism , Cell Culture Techniques
12.
Viruses ; 16(4)2024 04 10.
Article in English | MEDLINE | ID: mdl-38675928

ABSTRACT

The higher-order structure (HOS) is a critical quality attribute of recombinant adeno-associated viruses (rAAVs). Evaluating the HOS of the entire rAAV capsid is challenging because of the flexibility and/or less folded nature of the VP1 unique (VP1u) and VP1/VP2 common regions, which are structural features essential for these regions to exert their functions following viral infection. In this study, hydrogen/deuterium exchange mass spectrometry (HDX-MS) was used for the structural analysis of full and empty rAAV8 capsids. We obtained 486 peptides representing 85% sequence coverage. Surprisingly, the VP1u region showed rapid deuterium uptake even though this region contains the phospholipase A2 domain composed primarily of α-helices. The comparison of deuterium uptake between full and empty capsids showed significant protection from hydrogen/deuterium exchange in the full capsid at the channel structure of the 5-fold symmetry axis. This corresponds to cryo-electron microscopy studies in which the extended densities were observed only in the full capsid. In addition, deuterium uptake was reduced in the VP1u region of the full capsid, suggesting the folding and/or interaction of this region with the encapsidated genome. This study demonstrated HDX-MS as a powerful method for probing the structure of the entire rAAV capsid.


Subject(s)
Capsid Proteins , Capsid , Dependovirus , Dependovirus/chemistry , Dependovirus/genetics , Capsid Proteins/chemistry , Capsid Proteins/metabolism , Capsid Proteins/genetics , Capsid/chemistry , Capsid/metabolism , Serogroup , Deuterium Exchange Measurement , Hydrogen Deuterium Exchange-Mass Spectrometry/methods , Humans , Deuterium/chemistry , Mass Spectrometry , Cryoelectron Microscopy , Models, Molecular
13.
Sci Rep ; 14(1): 9828, 2024 04 29.
Article in English | MEDLINE | ID: mdl-38684729

ABSTRACT

The pharmacological effects of limonene, especially their derivatives, are currently at the forefront of research for drug development and discovery as well and structure-based drug design using huge chemical libraries are already widespread in the early stages of therapeutic and drug development. Here, various limonene derivatives are studied computationally for their potential utilization against the capsid protein of Herpes Simplex Virus-1. Firstly, limonene derivatives were designed by structural modification followed by conducting a molecular docking experiment against the capsid protein of Herpes Simplex Virus-1. In this research, the obtained molecular docking score exhibited better efficiency against the capsid protein of Herpes Simplex Virus-1 and hence we conducted further in silico investigation including molecular dynamic simulation, quantum calculation, and ADMET analysis. Molecular docking experiment has documented that Ligands 02 and 03 had much better binding affinities (- 7.4 kcal/mol and - 7.1 kcal/mol) to capsid protein of Herpes Simplex Virus-1 than Standard Acyclovir (- 6.5 kcal/mol). Upon further investigation, the binding affinities of primary limonene were observed to be slightly poor. But including the various functional groups also increases the affinities and capacity to prevent viral infection of the capsid protein of Herpes Simplex Virus-1. Then, the molecular dynamic simulation confirmed that the mentioned ligands might be stable during the formation of drug-protein complexes. Finally, the analysis of ADMET was essential in establishing them as safe and human-useable prospective chemicals. According to the present findings, limonene derivatives might be a promising candidate against the capsid protein of Herpes Simplex Virus-1 which ultimately inhibits Herpes Simplex Virus-induced encephalitis that causes interventions in brain inflammation. Our findings suggested further experimental screening to determine their practical value and utility.


Subject(s)
Antiviral Agents , Capsid Proteins , Drug Design , Herpesvirus 1, Human , Limonene , Molecular Docking Simulation , Molecular Dynamics Simulation , Limonene/chemistry , Limonene/pharmacology , Herpesvirus 1, Human/drug effects , Capsid Proteins/metabolism , Capsid Proteins/chemistry , Ligands , Antiviral Agents/pharmacology , Antiviral Agents/chemistry , Humans , Computer Simulation , Protein Binding
14.
Biomacromolecules ; 25(5): 2890-2901, 2024 May 13.
Article in English | MEDLINE | ID: mdl-38683736

ABSTRACT

While adeno-associated virus is a leading vector for gene therapy, significant gaps remain in understanding AAV degradation and stability. In this work, we study the degradation of an engineered AAV serotype at physiological pH and ionic strength. Viral particles of varying fractions of encapsulated DNA were incubated between 30 and 60 °C, with changes in molecular weight measured by changes in total light scattering intensity at 90° over time. Mostly full vectors demonstrated a rapid decrease in molecular weight corresponding to the release of capsid DNA, followed by slow aggregation. In contrast, empty vectors demonstrated immediate, rapid colloid-type aggregation. Mixtures of full and empty capsids showed a pronounced decrease in initial aggregation that cannot be explained by a linear superposition of empty and full degradation scattering signatures, indicating interactions between capsids and ejected DNA that influenced aggregation mechanisms. This demonstrates key interactions between AAV capsids and their cargo that influence capsid degradation, aggregation, and DNA release mechanisms in a physiological solution.


Subject(s)
Capsid , DNA, Viral , Dependovirus , Dependovirus/genetics , Dependovirus/chemistry , Capsid/chemistry , Capsid/metabolism , Kinetics , DNA, Viral/chemistry , Humans , Genetic Vectors/chemistry , Genetic Vectors/metabolism , Capsid Proteins/chemistry , Capsid Proteins/metabolism , Hydrogen-Ion Concentration
15.
Int J Mol Sci ; 25(5)2024 Feb 20.
Article in English | MEDLINE | ID: mdl-38473709

ABSTRACT

Porcine circovirus 4 (PCV4) is a newly identified virus belonging to PCV of the Circoviridae family, the Circovirus genus. We previously found that PCV4 is pathogenic in vitro, while the virus's replication in cells is still unknown. In this study, we evaluated the N-terminal of the PCV4 capsid (Cap) and identified an NLS at amino acid residues 4-37 of the N-terminus of the PCV4 Cap, 4RSRYSRRRRNRRNQRRRGLWPRASRRRYRWRRKN37. The NLS was further divided into two fragments (NLS-A and NLS-B) based on the predicted structure, including two α-helixes, which were located at 4RSRYSRRRRNRRNQRR19 and 24PRASRRRYRWRRK36, respectively. Further studies showed that the NLS, especially the first α-helixes formed by the NLS-A fragment, determined the nuclear localization of the Cap protein, and the amino acid 4RSRY7 in the NLS of the PCV4 Cap was the critical motif affecting the VLP packaging. These results will provide a theoretical basis for elucidating the infection mechanism of PCV4 and developing subunit vaccines based on VLPs.


Subject(s)
Circovirus , Nuclear Localization Signals , Animals , Swine , Nuclear Localization Signals/metabolism , Capsid/metabolism , Capsid Proteins/chemistry , Amino Acids/metabolism
16.
Phys Rev E ; 109(2-1): 024402, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38491620

ABSTRACT

A minimal coarse-grained model for T=1 viral capsids assembled from 20 protein rigid trimers has been designed by extending a previously proposed form of the interaction energy written as a sum of anisotropic pairwise interactions between the trimeric capsomers. The extension of the model has been performed to properly account for the coupling between two internal coordinates: the one that measures the intercapsomer distance and the other that gives the intercapsomer dihedral angle. The model has been able to fit with less than a 10% error the atomic force microscopy (AFM) indentation experimental data for the empty capsid of the minute virus of mice (MVM), providing in this way an admissible picture of the main mechanisms behind the capsid deformations. In this scenario, the bending of the intercapsomer dihedral angle is the angular internal coordinate that can support larger deformations away from its equilibrium values, determining important features of the AFM indentation experiments as the elastic constants along the three symmetry axes of the capsid and the critical indentations. From the value of one of the parameters of our model, we conclude that trimers in the MVM must be quite oblate tops, in excellent agreement with their known structure. The transition from the linear to the nonlinear regimes sampled in the indentation process appears to be an interesting topic for future research in physical virology.


Subject(s)
Minute Virus of Mice , Viruses , Animals , Mice , Capsid/chemistry , Capsid Proteins/chemistry , Microscopy, Atomic Force
17.
Nature ; 627(8005): 905-914, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38448589

ABSTRACT

A string of nucleotides confined within a protein capsid contains all the instructions necessary to make a functional virus particle, a virion. Although the structure of the protein capsid is known for many virus species1,2, the three-dimensional organization of viral genomes has mostly eluded experimental probes3,4. Here we report all-atom structural models of an HK97 virion5, including its entire 39,732 base pair genome, obtained through multiresolution simulations. Mimicking the action of a packaging motor6, the genome was gradually loaded into the capsid. The structure of the packaged capsid was then refined through simulations of increasing resolution, which produced a 26 million atom model of the complete virion, including water and ions confined within the capsid. DNA packaging occurs through a loop extrusion mechanism7 that produces globally different configurations of the packaged genome and gives each viral particle individual traits. Multiple microsecond-long all-atom simulations characterized the effect of the packaged genome on capsid structure, internal pressure, electrostatics and diffusion of water, ions and DNA, and revealed the structural imprints of the capsid onto the genome. Our approach can be generalized to obtain complete all-atom structural models of other virus species, thereby potentially revealing new drug targets at the genome-capsid interface.


Subject(s)
Bacteriophages , Capsid , DNA, Viral , Genome, Viral , Virion , Virus Assembly , Bacteriophages/chemistry , Bacteriophages/genetics , Bacteriophages/growth & development , Bacteriophages/metabolism , Capsid/chemistry , Capsid/metabolism , Capsid Proteins/chemistry , Capsid Proteins/metabolism , Diffusion , DNA, Viral/chemistry , DNA, Viral/genetics , DNA, Viral/metabolism , Ions/analysis , Ions/chemistry , Ions/metabolism , Static Electricity , Virion/chemistry , Virion/genetics , Virion/metabolism , Virus Assembly/genetics , Water/analysis , Water/chemistry , Water/metabolism
18.
Environ Sci Technol ; 58(12): 5279-5289, 2024 Mar 26.
Article in English | MEDLINE | ID: mdl-38488515

ABSTRACT

The sensitivity of enteroviruses to disinfectants varies among genetically similar variants and coincides with amino acid changes in capsid proteins, although the effect of individual substitutions remains unknown. Here, we employed reverse genetics to investigate how amino acid substitutions in coxsackievirus B5 (CVB5) capsid proteins affect the virus' sensitivity to free chlorine and heat treatment. Of ten amino acid changes observed in CVB5 variants with free chlorine resistance, none significantly reduced the chlorine sensitivity, indicating a minor role of the capsid composition in chlorine sensitivity of CVB5. Conversely, a subset of these amino acid changes located at the C-terminal region of viral protein 1 led to reduced heat sensitivity. Cryo-electron microscopy revealed that these changes affect the assembly of intermediate viral states (altered and empty particles), suggesting that the mechanism for reduced heat sensitivity could be related to improved molecular packing of CVB5, resulting in greater stability or altered dynamics of virus uncoating during infection.


Subject(s)
Capsid Proteins , Chlorine , Capsid Proteins/genetics , Capsid Proteins/chemistry , Chlorine/pharmacology , Cryoelectron Microscopy , Amino Acid Substitution , Enterovirus B, Human/genetics , Amino Acids
19.
Nat Commun ; 15(1): 2654, 2024 Mar 26.
Article in English | MEDLINE | ID: mdl-38531972

ABSTRACT

The Myoviridae cyanophage A-1(L) specifically infects the model cyanobacteria Anabaena sp. PCC 7120. Following our recent report on the capsid structure of A-1(L), here we present the high-resolution cryo-EM structure of its intact tail machine including the neck, tail and attached fibers. Besides the dodecameric portal, the neck contains a canonical hexamer connected to a unique pentadecamer that anchors five extended bead-chain-like neck fibers. The 1045-Å-long contractile tail is composed of a helical bundle of tape measure proteins surrounded by a layer of tube proteins and a layer of sheath proteins, ended with a five-component baseplate. The six long and six short tail fibers are folded back pairwise, each with one end anchoring to the baseplate and the distal end pointing to the capsid. Structural analysis combined with biochemical assays further enable us to identify the dual hydrolytic activities of the baseplate hub, in addition to two host receptor binding domains in the tail fibers. Moreover, the structure of the intact A-1(L) also helps us to reannotate its genome. These findings will facilitate the application of A-1(L) as a chassis cyanophage in synthetic biology.


Subject(s)
Anabaena , Myoviridae , Capsid Proteins/chemistry , Capsid
20.
Sci Adv ; 10(8): eadj1640, 2024 Feb 23.
Article in English | MEDLINE | ID: mdl-38394211

ABSTRACT

The compartmentalization of eukaryotic cells presents considerable challenges to the herpesvirus life cycle. The herpesvirus tegument, a bulky proteinaceous aggregate sandwiched between herpesviruses' capsid and envelope, is uniquely evolved to address these challenges, yet tegument structure and organization remain poorly characterized. We use deep-learning-enhanced cryogenic electron microscopy to investigate the tegument of human cytomegalovirus virions and noninfectious enveloped particles (NIEPs; a genome packaging-aborted state), revealing a portal-biased tegumentation scheme. We resolve atomic structures of portal vertex-associated tegument (PVAT) and identify multiple configurations of PVAT arising from layered reorganization of pUL77, pUL48 (large tegument protein), and pUL47 (inner tegument protein) assemblies. Analyses show that pUL77 seals the last-packaged viral genome end through electrostatic interactions, pUL77 and pUL48 harbor a head-linker-capsid-binding motif conducive to PVAT reconfiguration, and pUL47/48 dimers form 45-nm-long filaments extending from the portal vertex. These results provide a structural framework for understanding how herpesvirus tegument facilitates and evolves during processes spanning viral genome packaging to delivery.


Subject(s)
Capsid Proteins , Cytomegalovirus , Humans , Cytomegalovirus/chemistry , Cytomegalovirus/genetics , Cytomegalovirus/metabolism , Cryoelectron Microscopy , Capsid Proteins/chemistry , Capsid/chemistry , Virion/chemistry , Artificial Intelligence
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