1
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Khaykelson D, Asor R, Zhao Z, Schlicksup CJ, Zlotnick A, Raviv U. Guanidine Hydrochloride-Induced Hepatitis B Virus Capsid Disassembly Hysteresis. Biochemistry 2024; 63:1543-1552. [PMID: 38787909 PMCID: PMC11191408 DOI: 10.1021/acs.biochem.4c00077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/20/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024]
Abstract
Hepatitis B virus (HBV) displays remarkable self-assembly capabilities that interest the scientific community and biotechnological industries as HBV is leading to an annual mortality of up to 1 million people worldwide (especially in Africa and Southeast Asia). When the ionic strength is increased, hepatitis B virus-like particles (VLPs) can assemble from dimers of the first 149 residues of the HBV capsid protein core assembly domain (Cp149). Using solution small-angle X-ray scattering, we investigated the disassembly of the VLPs by titrating guanidine hydrochloride (GuHCl). Measurements were performed with and without 1 M NaCl, added either before or after titrating GuHCl. Fitting the scattering curves to a linear combination of atomic models of Cp149 dimer (the subunit) and T = 3 and T = 4 icosahedral capsids revealed the mass fraction of the dimer in each structure in all the titration points. Based on the mass fractions, the variation in the dimer-dimer association standard free energy was calculated as a function of added GuHCl, showing a linear relation between the interaction strength and GuHCl concentration. Using the data, we estimated the energy barriers for assembly and disassembly and the critical nucleus size for all of the assembly reactions. Extrapolating the standard free energy to [GuHCl] = 0 showed an evident hysteresis in the assembly process, manifested by differences in the dimer-dimer association standard free energy obtained for the disassembly reactions compared with the equivalent assembly reactions. Similar hysteresis was observed in the energy barriers for assembly and disassembly and the critical nucleus size. The results suggest that above 1.5 M, GuHCl disassembled the capsids by attaching to the protein and adding steric repulsion, thereby weakening the hydrophobic attraction.
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Affiliation(s)
- Daniel Khaykelson
- Institute
of Chemistry and the Center for Nanoscience and Nanotechnology, the Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Roi Asor
- Institute
of Chemistry and the Center for Nanoscience and Nanotechnology, the Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Zhongchao Zhao
- Department
of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Christopher John Schlicksup
- Department
of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Adam Zlotnick
- Department
of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Uri Raviv
- Institute
of Chemistry and the Center for Nanoscience and Nanotechnology, the Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
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2
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Timmermans SBPE, Ramezani A, Montalvo T, Nguyen M, van der Schoot P, van Hest JCM, Zandi R. The Dynamics of Viruslike Capsid Assembly and Disassembly. J Am Chem Soc 2022; 144:12608-12612. [PMID: 35792573 PMCID: PMC9305980 DOI: 10.1021/jacs.2c04074] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Cowpea chlorotic
mottle virus (CCMV) is a widely used model for
virus replication studies. A major challenge lies in distinguishing
between the roles of the interaction between coat proteins and that
between the coat proteins and the viral RNA in assembly and disassembly
processes. Here, we report on the spontaneous and reversible size
conversion of the empty capsids of a CCMV capsid protein functionalized
with a hydrophobic elastin-like polypeptide which occurs following
a pH jump. We monitor the concentrations of T = 3
and T = 1 capsids as a function of time and show
that the time evolution of the conversion from one T number to another is not symmetric: The conversion from T = 1 to T = 3 is a factor of 10 slower
than that of T = 3 to T = 1. We
explain our experimental findings using a simple model based on classical
nucleation theory applied to virus capsids, in which we account for
the change in the free protein concentration, as the different types
of shells assemble and disassemble by shedding or absorbing single
protein subunits. As far as we are aware, this is the first study
confirming that both the assembly and disassembly of viruslike shells
can be explained through classical nucleation theory, reproducing
quantitatively results from time-resolved experiments
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Affiliation(s)
- Suzanne B. P. E. Timmermans
- Bio-Organic Chemistry Research Group, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Alireza Ramezani
- Department of Physics and Astronomy, University of California, Riverside, California 92521, United States
| | - Toni Montalvo
- Department of Physics and Astronomy, University of California, Riverside, California 92521, United States
| | - Mark Nguyen
- Department of Physics and Astronomy, University of California, Riverside, California 92521, United States
| | - Paul van der Schoot
- Soft Matter and Biological Physics Group, Department of Applied Physics, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Jan C. M. van Hest
- Bio-Organic Chemistry Research Group, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Roya Zandi
- Department of Physics and Astronomy, University of California, Riverside, California 92521, United States
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3
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Indelicato G, Cermelli P, Twarock R. Local rules for the self-assembly of a non-quasi-equivalent viral capsid. Phys Rev E 2022; 105:064403. [PMID: 35854534 DOI: 10.1103/physreve.105.064403] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
The structures of many large bacteriophages, such as the P23-77 capsids, do not adhere strictly to the quasi-equivalence principle of viral architecture. Although the general architecture of the P23-77 capsids is classed as T=28d, it self-assembles from multiple copies of two types of coat protein subunits, and the resulting hexameric capsomers do not conform to the Caspar-Klug paradigm. There are two types of hexamers with distinct internal organization, that are located at specific positions in the capsid. It is an open problem which assembly mechanism can lead to such a complex capsid organization. Here we propose a simple set of local rules that can explain how such non-quasi-equivalent capsid structures can arise as a result of self-assembly.
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Affiliation(s)
| | - Paolo Cermelli
- Dipartimento di Matematica, Università di Torino, 10123 Torino TO, Italy
| | - Reidun Twarock
- Department of Mathematics and Department of Biology, University of York, York, YO10 5DD, United Kingdom
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4
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Evolving and assembling to pierce through: Evolutionary and structural aspects of antimicrobial peptides. Comput Struct Biotechnol J 2022; 20:2247-2258. [PMID: 35615024 PMCID: PMC9117813 DOI: 10.1016/j.csbj.2022.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/27/2022] [Accepted: 05/01/2022] [Indexed: 11/24/2022] Open
Abstract
The burgeoning menace of antimicrobial resistance across the globe has necessitated investigations into other chemotherapeutic strategies to combat infections. Antimicrobial peptides, or host defense peptides, are a set of promising therapeutic candidates in this regard. Most of them cause membrane permeabilization and are a key component of the innate immune response to pathogenic invasion. It has also been reported that peptide self-assembly is a driving factor governing the microbicidal activity of these peptide candidates. While efforts have been made to develop novel synthetic peptides against various microbes, many clinical trials of such peptides have failed due to toxicity and hemolytic activity to the host. A function-guided rational peptide engineering, based on evolutionary principles, physicochemical properties and activity determinants of AMP activity, is expected to help in targeting specific microbes. Furthermore, it is important to develop a unified understanding of the evolution of AMPs in order to fully appreciate their importance in host defense. This review seeks to explore the evolution of AMPs and the physicochemical determinants of AMP activity. The specific interactions driving AMP self-assembly have also been reviewed, emphasizing implications of this self-assembly on microbicidal and immunomodulatory activity.
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5
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Deciphering the Assembly of Enveloped Viruses Using Model Lipid Membranes. MEMBRANES 2022; 12:membranes12050441. [PMID: 35629766 PMCID: PMC9142974 DOI: 10.3390/membranes12050441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/01/2022] [Accepted: 04/09/2022] [Indexed: 01/09/2023]
Abstract
The cell plasma membrane is mainly composed of phospholipids, cholesterol and embedded proteins, presenting a complex interface with the environment. It maintains a barrier to control matter fluxes between the cell cytosol and its outer environment. Enveloped viruses are also surrounded by a lipidic membrane derived from the host-cell membrane and acquired while exiting the host cell during the assembly and budding steps of their viral cycle. Thus, model membranes composed of selected lipid mixtures mimicking plasma membrane properties are the tools of choice and were used to decipher the first step in the assembly of enveloped viruses. Amongst these viruses, we choose to report the three most frequently studied viruses responsible for lethal human diseases, i.e., Human Immunodeficiency Type 1 (HIV-1), Influenza A Virus (IAV) and Ebola Virus (EBOV), which assemble at the host-cell plasma membrane. Here, we review how model membranes such as Langmuir monolayers, bicelles, large and small unilamellar vesicles (LUVs and SUVs), supported lipid bilayers (SLBs), tethered-bilayer lipid membranes (tBLM) and giant unilamellar vesicles (GUVs) contribute to the understanding of viral assembly mechanisms and dynamics using biophysical approaches.
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6
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Complete and cooperative in vitro assembly of computationally designed self-assembling protein nanomaterials. Nat Commun 2021; 12:883. [PMID: 33563988 PMCID: PMC7873210 DOI: 10.1038/s41467-021-21251-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/15/2021] [Indexed: 01/03/2023] Open
Abstract
Recent advances in computational methods have enabled the predictive design of self-assembling protein nanomaterials with atomic-level accuracy. These design strategies focus exclusively on a single target structure, without consideration of the mechanism or dynamics of assembly. However, understanding the assembly process, and in particular its robustness to perturbation, will be critical for translating this class of materials into useful technologies. Here we investigate the assembly of two computationally designed, 120-subunit icosahedral complexes in detail using several complementary biochemical methods. We found that assembly of each material from its two constituent protein building blocks was highly cooperative and yielded exclusively complete, 120-subunit complexes except in one non-stoichiometric regime for one of the materials. Our results suggest that in vitro assembly provides a robust and controllable route for the manufacture of designed protein nanomaterials and confirm that cooperative assembly can be an intrinsic, rather than evolved, feature of hierarchically structured protein complexes. Recent advances in computational methods have enabled the predictive design of self-assembling protein nanomaterials with atomic-level accuracy. Here authors investigate the assembly of two computationally designed, 120-subunit icosahedral complexes and find that assembly of each material from its two constituent protein building blocks was highly cooperative.
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7
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Bruinsma RF, Wuite GJL, Roos WH. Physics of viral dynamics. NATURE REVIEWS. PHYSICS 2021; 3:76-91. [PMID: 33728406 PMCID: PMC7802615 DOI: 10.1038/s42254-020-00267-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/20/2020] [Indexed: 05/12/2023]
Abstract
Viral capsids are often regarded as inert structural units, but in actuality they display fascinating dynamics during different stages of their life cycle. With the advent of single-particle approaches and high-resolution techniques, it is now possible to scrutinize viral dynamics during and after their assembly and during the subsequent development pathway into infectious viruses. In this Review, the focus is on the dynamical properties of viruses, the different physical virology techniques that are being used to study them, and the physical concepts that have been developed to describe viral dynamics.
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Affiliation(s)
- Robijn F. Bruinsma
- Department of Physics and Astronomy, University of California, Los Angeles, California, USA
| | - Gijs J. L. Wuite
- Fysica van levende systemen, Vrije Universiteit, Amsterdam, the Netherlands
| | - Wouter H. Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, the Netherlands
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8
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Schlicksup CJ, Laughlin P, Dunkelbarger S, Wang JCY, Zlotnick A. Local Stabilization of Subunit-Subunit Contacts Causes Global Destabilization of Hepatitis B Virus Capsids. ACS Chem Biol 2020; 15:1708-1717. [PMID: 32369333 DOI: 10.1021/acschembio.0c00320] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Development of antiviral molecules that bind virion is a strategy that remains in its infancy, and the details of their mechanisms are poorly understood. Here we investigate the behavior of DBT1, a dibenzothiazepine that specifically interacts with the capsid protein of hepatitis B virus (HBV). We found that DBT1 stabilizes protein-protein interaction, accelerates capsid assembly, and can induce formation of aberrant particles. Paradoxically, DBT1 can cause preformed capsids to dissociate. These activities may lead to (i) assembly of empty and defective capsids, inhibiting formation of new virus, and (ii) disruption of mature viruses, which are metastable, to inhibit new infection. Using cryo-electron microscopy, we observed that DBT1 led to asymmetric capsids where well-defined DBT1 density was bound at all intersubunit contacts. These results suggest that DBT1 can support assembly by increasing buried surface area but induce disassembly of metastable capsids by favoring asymmetry to induce structural defects.
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Affiliation(s)
- Christopher John Schlicksup
- Molecular and Cellular Biology Department, Indiana University—Bloomington, Bloomington, Indiana 47401, United States
| | - Patrick Laughlin
- Molecular and Cellular Biology Department, Indiana University—Bloomington, Bloomington, Indiana 47401, United States
| | - Steven Dunkelbarger
- Molecular and Cellular Biology Department, Indiana University—Bloomington, Bloomington, Indiana 47401, United States
| | - Joseph Che-Yen Wang
- Molecular and Cellular Biology Department, Indiana University—Bloomington, Bloomington, Indiana 47401, United States
- Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Adam Zlotnick
- Molecular and Cellular Biology Department, Indiana University—Bloomington, Bloomington, Indiana 47401, United States
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9
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Gartner FM, Graf IR, Wilke P, Geiger PM, Frey E. Stochastic yield catastrophes and robustness in self-assembly. eLife 2020; 9:51020. [PMID: 32022683 PMCID: PMC7089767 DOI: 10.7554/elife.51020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 02/04/2020] [Indexed: 12/02/2022] Open
Abstract
A guiding principle in self-assembly is that, for high production yield, nucleation of structures must be significantly slower than their growth. However, details of the mechanism that impedes nucleation are broadly considered irrelevant. Here, we analyze self-assembly into finite-sized target structures employing mathematical modeling. We investigate two key scenarios to delay nucleation: (i) by introducing a slow activation step for the assembling constituents and, (ii) by decreasing the dimerization rate. These scenarios have widely different characteristics. While the dimerization scenario exhibits robust behavior, the activation scenario is highly sensitive to demographic fluctuations. These demographic fluctuations ultimately disfavor growth compared to nucleation and can suppress yield completely. The occurrence of this stochastic yield catastrophe does not depend on model details but is generic as soon as number fluctuations between constituents are taken into account. On a broader perspective, our results reveal that stochasticity is an important limiting factor for self-assembly and that the specific implementation of the nucleation process plays a significant role in determining the yield. The self-assembly of a large biological molecule from small building blocks is like finishing a puzzle of magnetic pieces by shaking the box. Even though each piece of the puzzle is attracted to its correct neighbours, the limited control makes it very hard to finish the puzzle in a short amount of time. The problem becomes even more difficult if several copies of the same puzzle are assembled in one box. If several puzzles start at the same time, the different parts might steal pieces from each other, making it impossible to successfully complete any of the puzzles. This is called a depletion trap. If the box is only shaken and there is no real control over individual pieces, these traps occur at random. Overcoming these random depletion traps is an important challenge when assembling nanostructures and other artificial molecules designed by humans without wasting many, potentially expensive, components. Previous studies have shown that when multiple copies of the same structure are assembled simultaneously, slowing the rate of initiation increases the yield of correctly-made structures. This prevents new structures from stealing pieces from existing structures before they are fully completed. Now, Gartner, Graf, Wilke et al. have used a mathematical model to show that changing the way initiation is delayed leads to different yields. This was especially true for small systems where fluctuations in the availability of the different pieces strongly enhanced the initiation of new structures. In these cases, the self-assembly process terminated undesirably with many incomplete structures. Nanostructures have various applications ranging from drug delivery to robotics. These findings suggest that in order to efficiently assemble biological molecules, the concentrations of the different building blocks need to be tightly controlled. A question for further research is to investigate strategies that reduce fluctuations in the availability of the building blocks to develop more efficient assembly protocols.
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Affiliation(s)
- Florian M Gartner
- Arnold Sommerfeld Center for Theoretical Physics (ASC) and Center for NanoScience (CeNS), Department of Physics, Ludwig-Maximilians-Universität München, München, Germany
| | - Isabella R Graf
- Arnold Sommerfeld Center for Theoretical Physics (ASC) and Center for NanoScience (CeNS), Department of Physics, Ludwig-Maximilians-Universität München, München, Germany
| | - Patrick Wilke
- Arnold Sommerfeld Center for Theoretical Physics (ASC) and Center for NanoScience (CeNS), Department of Physics, Ludwig-Maximilians-Universität München, München, Germany
| | - Philipp M Geiger
- Arnold Sommerfeld Center for Theoretical Physics (ASC) and Center for NanoScience (CeNS), Department of Physics, Ludwig-Maximilians-Universität München, München, Germany
| | - Erwin Frey
- Arnold Sommerfeld Center for Theoretical Physics (ASC) and Center for NanoScience (CeNS), Department of Physics, Ludwig-Maximilians-Universität München, München, Germany
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10
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Buzón P, Maity S, Roos WH. Physical virology: From virus self-assembly to particle mechanics. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2020; 12:e1613. [PMID: 31960585 PMCID: PMC7317356 DOI: 10.1002/wnan.1613] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 10/01/2019] [Accepted: 12/11/2019] [Indexed: 12/19/2022]
Abstract
Viruses are highly ordered supramolecular complexes that have evolved to propagate by hijacking the host cell's machinery. Although viruses are very diverse, spreading through cells of all kingdoms of life, they share common functions and properties. Next to the general interest in virology, fundamental viral mechanisms are of growing importance in other disciplines such as biomedicine and (bio)nanotechnology. However, in order to optimally make use of viruses and virus-like particles, for instance as vehicle for targeted drug delivery or as building blocks in electronics, it is essential to understand their basic chemical and physical properties and characteristics. In this context, the number of studies addressing the mechanisms governing viral properties and processes has recently grown drastically. This review summarizes a specific part of these scientific achievements, particularly addressing physical virology approaches aimed to understand the self-assembly of viruses and the mechanical properties of viral particles. Using a physicochemical perspective, we have focused on fundamental studies providing an overview of the molecular basis governing these key aspects of viral systems. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.
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Affiliation(s)
- Pedro Buzón
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, The Netherlands
| | - Sourav Maity
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, The Netherlands
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, The Netherlands
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11
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Mesoscale model of the assembly and cross-linking of HPV virus-like particles. Virology 2019; 537:53-64. [PMID: 31450047 DOI: 10.1016/j.virol.2019.08.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/16/2019] [Accepted: 08/19/2019] [Indexed: 11/22/2022]
Abstract
We present a novel kinetic Monte Carlo model to simulate the real process time-scale of the assembly of Human Papillomavirus (HPV) virus-like particles (VLPs) incorporating the formation of intercapsomeric disulfide bonds. The objective was to develop insights into the underlying mechanisms of HPV VLP assembly and cross-linking during in vitro production of the HPV vaccine. The model integrates actual experimental data and detailed information of VLP geometrical structure in microscopic mechanistic steps. The principal novelty of this model is in the concurrent simulation of VLP assembly and cross-linking including a variable for spatial angular arrangement of capsomeres during their assembly that affects the overall rates of VLP assembly and cross-linking. The cross-linking modeled by using the mechanistic probability rules between involved cysteine residues. The model was utilized to better understand the actual process data and check on the hypothesis related to factors affecting the rates of HPV growth and maturation.
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12
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Asor R, Selzer L, Schlicksup CJ, Zhao Z, Zlotnick A, Raviv U. Assembly Reactions of Hepatitis B Capsid Protein into Capsid Nanoparticles Follow a Narrow Path through a Complex Reaction Landscape. ACS NANO 2019; 13:7610-7626. [PMID: 31173689 PMCID: PMC7243059 DOI: 10.1021/acsnano.9b00648] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
For many viruses, capsids (biological nanoparticles) assemble to protect genetic material and dissociate to release their cargo. To understand these contradictory properties, we analyzed capsid assembly for hepatitis B virus; an endemic pathogen with an icosahedral, 120-homodimer capsid. We used solution X-ray scattering to examine trapped and equilibrated assembly reactions. To fit experimental results, we generated a library of distinct intermediates, selected by umbrella sampling of Monte Carlo simulations. The number of possible capsid intermediates is immense, ∼1030, yet assembly reactions are rapid and completed with high fidelity. If the huge number of possible intermediates were actually present, maximum entropy analysis shows that assembly reactions would be blocked by an entropic barrier, resulting in incomplete nanoparticles. When an energetic term was applied to select the stable species that dominated the reaction mixture, we found only a few hundred intermediates, mapping out a narrow path through the immense reaction landscape. This is a solution to a viral application of the Levinthal paradox. With the correct energetic term, the match between predicted intermediates and scattering data was striking. The grand canonical free energy landscape for assembly, calibrated by our experimental results, supports a detailed analysis of this complex reaction. There is a narrow range of energies that supports on-path assembly. If association energy is too weak or too strong, progressively more intermediates will be entropically blocked, spilling into paths leading to dissociation or trapped incomplete nanoparticles, respectively. These results are relevant to many viruses and provide a basis for simplifying assembly models and identifying new targets for antiviral intervention. They provide a basis for understanding and designing biological and abiological self-assembly reactions.
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Affiliation(s)
- Roi Asor
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology , The Hebrew University of Jerusalem , Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401 , Israel
| | - Lisa Selzer
- Department of Molecular and Cellular Biochemistry , Indiana University , Bloomington , Indiana 47405 , United States
- Department of Genetics , Stanford University School of Medicine , Stanford , California 94305 , United States
| | - Christopher John Schlicksup
- Department of Molecular and Cellular Biochemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Zhongchao Zhao
- Department of Molecular and Cellular Biochemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Adam Zlotnick
- Department of Molecular and Cellular Biochemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Uri Raviv
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology , The Hebrew University of Jerusalem , Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401 , Israel
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13
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Roth-Konforti ME, Comune M, Halperin-Sternfeld M, Grigoriants I, Shabat D, Adler-Abramovich L. UV Light-Responsive Peptide-Based Supramolecular Hydrogel for Controlled Drug Delivery. Macromol Rapid Commun 2018; 39:e1800588. [DOI: 10.1002/marc.201800588] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 09/08/2018] [Indexed: 12/17/2022]
Affiliation(s)
| | - Michela Comune
- Department of Oral Biology; The Goldschleger School of Dental Medicine; Sackler Faculty of Medicine; Tel Aviv University; Tel Aviv 69978 Israel
| | - Michal Halperin-Sternfeld
- Department of Oral Biology; The Goldschleger School of Dental Medicine; Sackler Faculty of Medicine; Tel Aviv University; Tel Aviv 69978 Israel
| | - Irena Grigoriants
- Department of Oral Biology; The Goldschleger School of Dental Medicine; Sackler Faculty of Medicine; Tel Aviv University; Tel Aviv 69978 Israel
| | - Doron Shabat
- School of Chemistry, Faculty of Exact Sciences; Tel Aviv University; Tel Aviv 69978 Israel
| | - Lihi Adler-Abramovich
- Department of Oral Biology; The Goldschleger School of Dental Medicine; Sackler Faculty of Medicine; Tel Aviv University; Tel Aviv 69978 Israel
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14
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Zhou J, Kondylis P, Haywood DG, Harms ZD, Lee LS, Zlotnick A, Jacobson SC. Characterization of Virus Capsids and Their Assembly Intermediates by Multicycle Resistive-Pulse Sensing with Four Pores in Series. Anal Chem 2018; 90:7267-7274. [PMID: 29708733 PMCID: PMC6039186 DOI: 10.1021/acs.analchem.8b00452] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Virus self-assembly is a critical step in the virus lifecycle. Understanding how viruses assemble and disassemble provides needed insight into developing antiviral pharmaceuticals. Few tools offer sufficient resolution to study assembly intermediates that differ in size by a few dimers. Our goal is to improve resistive-pulse sensing on nanofluidic devices to offer better particle-size and temporal resolution to study intermediates and capsids generated along the assembly pathway. To increase the particle-size resolution of the resistive-pulse technique, we measured the same, single virus particles up to a thousand times, cycling them back and forth across a series of nanopores by switching the polarity of the applied potential, i.e., virus ping-pong. Multiple pores in series provide a unique multipulse signature during each cycle that improves particle tracking and, therefore, identification of a single particle and reduces the number of cycles needed to make the requisite number of measurements. With T = 3 and T = 4 hepatitis B virus (HBV) capsids, we showed the standard deviation of the particle-size distribution decreased with the square root of the number of measurements and approached discriminating particles differing in size by single dimers. We then studied in vitro assembly of HBV capsids and observed that the ensemble of intermediates shift to larger sizes over 2 days of annealing. On the contrary, assembly reactions diluted to lower dimer concentrations an hour after initiation had fewer intermediates that persisted after the 2 day incubation and had a higher ratio of T = 4 to T = 3 capsids. These reactions indicate that labile T = 4 intermediates are formed rapidly, and dependent on conditions, intermediates may be trapped as metastable species or progress to yield complete capsids.
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Affiliation(s)
- Jinsheng Zhou
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | | | | | - Zachary D. Harms
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | - Lye Siang Lee
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405
| | - Adam Zlotnick
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405
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van der Holst B, Kegel WK, Zandi R, van der Schoot P. The different faces of mass action in virus assembly. J Biol Phys 2018; 44:163-179. [PMID: 29616429 PMCID: PMC5928020 DOI: 10.1007/s10867-018-9487-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/16/2018] [Indexed: 02/06/2023] Open
Abstract
The spontaneous encapsulation of genomic and non-genomic polyanions by coat proteins of simple icosahedral viruses is driven, in the first instance, by electrostatic interactions with polycationic RNA binding domains on these proteins. The efficiency with which the polyanions can be encapsulated in vitro, and presumably also in vivo, must in addition be governed by the loss of translational and mixing entropy associated with co-assembly, at least if this co-assembly constitutes a reversible process. These forms of entropy counteract the impact of attractive interactions between the constituents and hence they counteract complexation. By invoking mass action-type arguments and a simple model describing electrostatic interactions, we show how these forms of entropy might settle the competition between negatively charged polymers of different molecular weights for co-assembly with the coat proteins. In direct competition, mass action turns out to strongly work against the encapsulation of RNAs that are significantly shorter, which is typically the case for non-viral (host) RNAs. We also find that coat proteins favor forming virus particles over nonspecific binding to other proteins in the cytosol even if these are present in vast excess. Our results rationalize a number of recent in vitro co-assembly experiments showing that short polyanions are less effective at attracting virus coat proteins to form virus-like particles than long ones do, even if both are present at equal weight concentrations in the assembly mixture.
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Affiliation(s)
- Bart van der Holst
- Department of Applied Physics, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Willem K Kegel
- Department of Chemistry, Utrecht University, Utrecht, The Netherlands
| | - Roya Zandi
- Department of Physics and Astronomy, University of California Riverside, Riverside, USA
| | - Paul van der Schoot
- Department of Applied Physics, Eindhoven University of Technology, Eindhoven, The Netherlands. .,Institute for Theoretical Physics, Utrecht University, Utrecht, The Netherlands.
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