1
|
van Ewijk C, Xu F, Maity S, Sheng J, Stuart MCA, Feringa BL, Roos WH. Light-Triggered Disassembly of Molecular Motor-based Supramolecular Polymers Revealed by High-Speed AFM. Angew Chem Int Ed Engl 2024; 63:e202319387. [PMID: 38372499 DOI: 10.1002/anie.202319387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/02/2024] [Accepted: 02/14/2024] [Indexed: 02/20/2024]
Abstract
Photoresponsive supramolecular polymers have a major potential for applications in responsive materials that are externally triggered by light with spatio-temporal control of their polymerisation state. While changes in macroscopic properties revealed the adaptive nature of these materials, it remains challenging to capture the dynamic depolymerisation process at the molecular level, which requires fast observation techniques combined with in situ irradiation. By implementing in situ UV illumination into a High-Speed Atomic Force Microscope (HS-AFM) setup, we have been able to capture the disassembly of a light-driven molecular motor-based supramolecular polymer. The real-time visualisation of the light-triggered disassembly process not only reveals cooperative depolymerisation, it also shows that this process continues after illumination is halted. Combining the data with cryo-electron microscopy and spectroscopy approaches, we obtain a molecular-level description of the motor-based polymer dynamics reminiscent of actin chain-end depolymerisation. Our detailed understanding of supramolecular depolymerisation will drive the development of future responsive polymer systems.
Collapse
Affiliation(s)
- Chris van Ewijk
- Molecular Biophysics, Zernike Institute for Advanced Materials Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG, Groningen, The, Netherlands
| | - Fan Xu
- Synthetic Organic Chemistry, Stratingh Institute for Chemistry Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG, Groningen, The, Netherlands
| | - Sourav Maity
- Molecular Biophysics, Zernike Institute for Advanced Materials Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG, Groningen, The, Netherlands
| | - Jinyu Sheng
- Synthetic Organic Chemistry, Stratingh Institute for Chemistry Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG, Groningen, The, Netherlands
| | - Marc C A Stuart
- Synthetic Organic Chemistry, Stratingh Institute for Chemistry Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG, Groningen, The, Netherlands
| | - Ben L Feringa
- Synthetic Organic Chemistry, Stratingh Institute for Chemistry Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG, Groningen, The, Netherlands
| | - Wouter H Roos
- Molecular Biophysics, Zernike Institute for Advanced Materials Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG, Groningen, The, Netherlands
| |
Collapse
|
2
|
Valbuena A, Strobl K, Gil-Redondo JC, Valiente L, de Pablo PJ, Mateu MG. Single-Molecule Analysis of Genome Uncoating from Individual Human Rhinovirus Particles, and Modulation by Antiviral Drugs. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2304722. [PMID: 37806749 DOI: 10.1002/smll.202304722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/26/2023] [Indexed: 10/10/2023]
Abstract
Infection of humans by many viruses is typically initiated by the internalization of a single virion in each of a few susceptible cells. Thus, the outcome of the infection process may depend on stochastic single-molecule events. A crucial process for viral infection, and thus a target for developing antiviral drugs, is the uncoating of the viral genome. Here a force spectroscopy procedure using an atomic force microscope is implemented to study uncoating for individual human rhinovirus particles. Application of an increasing mechanical force on a virion led to a high force-induced structural transition that facilitated extrusion of the viral RNA molecule without loss of capsid integrity. Application of force to virions that h ad previously extruded the RNA, or to RNA-free capsids, led to a lower force-induced event associated with capsid disruption. The kinetic parameters are determined for each reaction. The high-force event is a stochastic process governed by a moderate free energy barrier (≈20 kcal mol-1 ), which results in a heterogeneous population of structurally weakened virions in which different fractions of the RNA molecule are externalized. The effects of antiviral compounds or capsid mutation on the kinetics of this reaction reveal a correlation between the reaction rate and virus infectivity.
Collapse
Affiliation(s)
- Alejandro Valbuena
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Klara Strobl
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Juan Carlos Gil-Redondo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Luis Valiente
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Pedro J de Pablo
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Instituto de Física de la Materia Condensada (IFIMAC), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| |
Collapse
|
3
|
Sha H, Zhu F. Hexagonal Lattices of HIV Capsid Proteins Explored by Simulations Based on a Thermodynamically Consistent Model. J Phys Chem B 2024; 128:960-972. [PMID: 38251836 DOI: 10.1021/acs.jpcb.3c06881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
HIV capsid proteins (CAs) may self-assemble into a variety of shapes under in vivo and in vitro conditions. Here, we employed simulations based on a residue-level coarse-grained (CG) model with full conformational flexibility to investigate hexagonal lattices, which are the underlying structural pattern for CA aggregations. Facilitated by enhanced sampling simulations to rigorously calculate CA dimerization and polymerization affinities, we calibrated our model to reproduce the experimentally measured affinities. Using the calibrated model, we performed unbiased simulations on several large systems consisting of 1512 CA subunits, allowing reversible binding and unbinding of the CAs in a thermodynamically consistent manner. In one simulation, a preassembled hexagonal CA sheet developed spontaneous curvatures reminiscent of those observed in experiments, and the edges of the sheet exhibited local curvatures larger than those of the interior. In other simulations starting with randomly distributed CAs at different concentrations, existing CA assemblies grew by binding free capsomeres to the edges and by merging with other assemblies. At high CA concentrations, rapid establishment of predominant aggregates was followed by much slower adjustments toward more regular hexagonal lattices, with increasing numbers of intact CA hexamers and pentamers being formed. Our approach of adapting a general CG model to specific systems by using experimental binding data represents a practical and effective strategy for simulating and elucidating intricate protein aggregations.
Collapse
Affiliation(s)
- Hao Sha
- Department of Physics, Indiana University─Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Fangqiang Zhu
- Department of Physics, Indiana University─Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
- Biochemical and Biophysical Systems Group, Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| |
Collapse
|
4
|
Liu K, Blokhuis A, van Ewijk C, Kiani A, Wu J, Roos WH, Otto S. Light-driven eco-evolutionary dynamics in a synthetic replicator system. Nat Chem 2024; 16:79-88. [PMID: 37653230 DOI: 10.1038/s41557-023-01301-2] [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: 06/07/2022] [Accepted: 07/21/2023] [Indexed: 09/02/2023]
Abstract
Darwinian evolution involves the inheritance and selection of variations in reproducing entities. Selection can be based on, among others, interactions with the environment. Conversely, the replicating entities can also affect their environment generating a reciprocal feedback on evolutionary dynamics. The onset of such eco-evolutionary dynamics marks a stepping stone in the transition from chemistry to biology. Yet the bottom-up creation of a molecular system that exhibits eco-evolutionary dynamics has remained elusive. Here we describe the onset of such dynamics in a minimal system containing two synthetic self-replicators. The replicators are capable of binding and activating a co-factor, enabling them to change the oxidation state of their environment through photoredox catalysis. The replicator distribution adapts to this change and, depending on light intensity, one or the other replicator becomes dominant. This study shows how behaviour analogous to eco-evolutionary dynamics-which until now has been restricted to biology-can be created using an artificial minimal replicator system.
Collapse
Affiliation(s)
- Kai Liu
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Groningen, the Netherlands
| | - Alex Blokhuis
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Groningen, the Netherlands
| | - Chris van Ewijk
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Armin Kiani
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Groningen, the Netherlands
| | - Juntian Wu
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Groningen, the Netherlands
| | - Wouter H Roos
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Groningen, the Netherlands.
| |
Collapse
|
5
|
van Ewijk C, Maity S, Roos WH. Visualizing Molecular Dynamics by High-Speed Atomic Force Microscopy. Methods Mol Biol 2024; 2694:355-372. [PMID: 37824013 DOI: 10.1007/978-1-0716-3377-9_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Dynamic processes and structural changes of biological molecules are essential to life. While conventional atomic force microscopy (AFM) is able to visualize molecules and supramolecular assemblies at sub-nanometer resolution, it cannot capture dynamics because of its low imaging rate. The introduction of high-speed atomic force microscopy (HS-AFM) solved this problem by providing a large increase in imaging velocity. Using HS-AFM, one is able to visualize dynamic molecular events with high spatiotemporal resolution under near-to physiological conditions. This approach opened new windows as finally dynamics of biomolecules at sub-nanometer resolution could be studied. Here we describe the working principles and an operation protocol for HS-AFM imaging and characterization of biological samples in liquid.
Collapse
Affiliation(s)
- Chris van Ewijk
- Molecular Biophysics, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, The Netherlands
| | - Sourav Maity
- Molecular Biophysics, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, The Netherlands
| | - Wouter H Roos
- Molecular Biophysics, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, The Netherlands.
| |
Collapse
|
6
|
Feng Y, Roos WH. Atomic Force Microscopy: An Introduction. Methods Mol Biol 2024; 2694:295-316. [PMID: 37824010 DOI: 10.1007/978-1-0716-3377-9_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Imaging of nano-sized particles and sample features is crucial in a variety of research fields, for instance, in biological sciences, where it is paramount to investigate structures at the single particle level. Often, two-dimensional images are not sufficient, and further information such as topography and mechanical properties are required. Furthermore, to increase the biological relevance, it is desired to perform the imaging in close to physiological environments. Atomic force microscopy (AFM) meets these demands in an all-in-one instrument. It provides high-resolution images including surface height information leading to three-dimensional information on sample morphology. AFM can be operated both in air and in buffer solutions. Moreover, it has the capacity to determine protein and membrane material properties via the force spectroscopy mode. Here we discuss the principles of AFM operation and provide examples of how biomolecules can be studied. New developments in AFM are discussed, and by including approaches such as bimodal AFM and high-speed AFM (HS-AFM), we show how AFM can be used to study a variety of static and dynamic single biomolecules and biomolecular assemblies.
Collapse
Affiliation(s)
- Yuzhen Feng
- Moleculaire Biofysica, Zernike instituut, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike instituut, Rijksuniversiteit Groningen, Groningen, the Netherlands.
| |
Collapse
|
7
|
Gisbert VG, Garcia R. Insights and guidelines to interpret forces and deformations at the nanoscale by using a tapping mode AFM simulator: dForce 2.0. SOFT MATTER 2023; 19:5857-5868. [PMID: 37305960 DOI: 10.1039/d3sm00334e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Amplitude modulation (tapping mode) AFM is the most versatile AFM mode for imaging surfaces at the nanoscale in air and liquid environments. However, it remains challenging to estimate the forces and deformations exerted by the tip. We introduce a new simulator environment to predict the values of the observables in tapping mode AFM experiments. The relevant feature of dForce 2.0 is the incorporation of contact mechanics models aimed to describe the properties of ultrathin samples. These models were essential to determine the forces applied on samples such as proteins, self-assembled monolayers, lipid bilayers, and few-layered materials. The simulator incorporates two types of long-range magnetic forces. The simulator is written in an open-source code (Python) and it can be run from a personal computer.
Collapse
Affiliation(s)
- Victor G Gisbert
- Instituto de Ciencia de Materiales de Madrid, CSIC c/Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain.
| | - Ricardo Garcia
- Instituto de Ciencia de Materiales de Madrid, CSIC c/Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain.
| |
Collapse
|
8
|
Zhou AXZ, Hammond JA, Sheng K, Millar DP, Williamson JR. Early HIV-1 Gag Assembly on Lipid Membrane with vRNA. RESEARCH SQUARE 2023:rs.3.rs-3060076. [PMID: 37461524 PMCID: PMC10350206 DOI: 10.21203/rs.3.rs-3060076/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
HIV-1 capsid assembly is an essential process in the virus infection cycle. Initiation of capsid assembly involves viral proteins, genomic RNA, and the inner leaflet of the plasma membrane, facilitated by a number of cellular factors1. The viral structural protein Gag plays a number of central roles in this process, including association with the membrane, selective binding of genomic RNA, and oligomerization and packaging to ultimately produce an immature budded pro-viral particle2. While there have been intensive studies regarding the early stages of Gag assembly, there is a lack of consensus on the mechanism for nucleation and growth of Gag complexes3-7. Here we show that myristoylated Gag forms a trimer nucleus in a model membrane that can selectively bind a dimeric RNA containing the packaging signal. Subsequent growth of myristoyl-Gag oligomers requires vRNA, and occurs by addition of 1 or 2 Gag monomers at a time from solution. These data support a model where the immature capsid lattice formation occurs by a gradual lattice edge expansion, following a trimeric nucleation event. The dynamic single molecule data that support this model were recorded using mass photometry, involving full length myristoylated protein, RNA, and lipid together. These data are the first to support a lattice edge expansion model of Gag during early stages of assembly in a biological-relevant setting, providing insights to the fundamental models of virus structural protein assembly process.
Collapse
Affiliation(s)
- Anne X.-Z. Zhou
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - John A. Hammond
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - Kai Sheng
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - David P. Millar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - James R. Williamson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
| |
Collapse
|
9
|
Lynch DL, Pavlova A, Fan Z, Gumbart JC. Understanding Virus Structure and Dynamics through Molecular Simulations. J Chem Theory Comput 2023. [PMID: 37192279 DOI: 10.1021/acs.jctc.3c00116] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Viral outbreaks remain a serious threat to human and animal populations and motivate the continued development of antiviral drugs and vaccines, which in turn benefits from a detailed understanding of both viral structure and dynamics. While great strides have been made in characterizing these systems experimentally, molecular simulations have proven to be an essential, complementary approach. In this work, we review the contributions of molecular simulations to the understanding of viral structure, functional dynamics, and processes related to the viral life cycle. Approaches ranging from coarse-grained to all-atom representations are discussed, including current efforts at modeling complete viral systems. Overall, this review demonstrates that computational virology plays an essential role in understanding these systems.
Collapse
Affiliation(s)
- Diane L Lynch
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Zixing Fan
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| |
Collapse
|
10
|
Sergeeva IA, Klinov DV, Schäffer TE, Dubrovin EV. Characterization of the effect of chromium salts on tropocollagen molecules and molecular aggregates. Int J Biol Macromol 2023; 242:124835. [PMID: 37201883 DOI: 10.1016/j.ijbiomac.2023.124835] [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: 03/23/2023] [Revised: 05/06/2023] [Accepted: 05/08/2023] [Indexed: 05/20/2023]
Abstract
Though the capability of chromium treatment to improve the stability and mechanical properties of collagen fibrils is well-known, the influence of different chromium salts on collagen molecules (tropocollagen) is not well characterized. In this study, the effect of Cr3+ treatment on the conformation and hydrodynamic properties of collagen was studied using atomic force microscopy (AFM) and dynamic light scattering (DLS). Statistical analysis of contours of adsorbed tropocollagen molecules using the two-dimensional worm-like chain model revealed a reduction of the persistence length (i.e., the increase of flexibility) from ≈72 nm in water to ≈56-57 nm in chromium (III) salt solutions. DLS studies demonstrated an increase of the hydrodynamic radius from ≈140 nm in water to ≈190 nm in chromium (III) salt solutions, which is associated with protein aggregation. The kinetics of collagen aggregation was shown to be ionic strength dependent. Collagen molecules treated with three different chromium (III) salts demonstrated similar properties such as flexibility, aggregation kinetics, and susceptibility to enzymatic cleavage. The observed effects are explained by a model that considers the formation of chromium-associated intra- and intermolecular crosslinks. The obtained results provide novel insights into the effect of chromium salts on the conformation and properties of tropocollagen molecules.
Collapse
Affiliation(s)
- Irina A Sergeeva
- Lomonosov Moscow State University, Faculty of Physics, Leninskie Gory 1 bld 2, 119991 Moscow, Russia.
| | - Dmitry V Klinov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya 1a, 119435 Moscow, Russia
| | - Tilman E Schäffer
- University of Tübingen, Institute of Applied Physics, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Evgeniy V Dubrovin
- Lomonosov Moscow State University, Faculty of Physics, Leninskie Gory 1 bld 2, 119991 Moscow, Russia.
| |
Collapse
|
11
|
Lostao A, Lim K, Pallarés MC, Ptak A, Marcuello C. Recent advances in sensing the inter-biomolecular interactions at the nanoscale - A comprehensive review of AFM-based force spectroscopy. Int J Biol Macromol 2023; 238:124089. [PMID: 36948336 DOI: 10.1016/j.ijbiomac.2023.124089] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 03/24/2023]
Abstract
Biomolecular interactions underpin most processes inside the cell. Hence, a precise and quantitative understanding of molecular association and dissociation events is crucial, not only from a fundamental perspective, but also for the rational design of biomolecular platforms for state-of-the-art biomedical and industrial applications. In this context, atomic force microscopy (AFM) appears as an invaluable experimental technique, allowing the measurement of the mechanical strength of biomolecular complexes to provide a quantitative characterization of their interaction properties from a single molecule perspective. In the present review, the most recent methodological advances in this field are presented with special focus on bioconjugation, immobilization and AFM tip functionalization, dynamic force spectroscopy measurements, molecular recognition imaging and theoretical modeling. We expect this work to significantly aid in grasping the principles of AFM-based force spectroscopy (AFM-FS) technique and provide the necessary tools to acquaint the type of data that can be achieved from this type of experiments. Furthermore, a critical assessment is done with other nanotechnology techniques to better visualize the future prospects of AFM-FS.
Collapse
Affiliation(s)
- Anabel Lostao
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain; Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, Zaragoza 50018, Spain; Fundación ARAID, Aragón, Spain.
| | - KeeSiang Lim
- WPI-Nano Life Science Institute, Kanazawa University, Ishikawa 920-1192, Japan
| | - María Carmen Pallarés
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain; Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, Zaragoza 50018, Spain
| | - Arkadiusz Ptak
- Institute of Physics, Faculty of Materials Engineering and Technical Physics, Poznan University of Technology, Poznan 60-925, Poland
| | - Carlos Marcuello
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain; Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, Zaragoza 50018, Spain.
| |
Collapse
|
12
|
Kikuchi K, Date K, Ueno T. Design of a Hierarchical Assembly at a Solid-Liquid Interface Using an Asymmetric Protein Needle. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:2389-2397. [PMID: 36734675 DOI: 10.1021/acs.langmuir.2c03146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Design and control of processes for a hierarchical assembly of proteins remain challenging because it requires consideration of design principles with atomic-level accuracy. Previous studies have adopted symmetry-based strategies to minimize the complexity of protein-protein interactions and this has placed constraints on the structures of the resulting protein assemblies. In the present work, we used an anisotropic-shaped protein needle, gene product 5 (gp5) from bacteriophage T4 with a C-terminal hexahistidine-tag (His-tag) (gp5_CHis), to construct a hierarchical assembly with two distinct protein-protein interaction sites. High-speed atomic force microscopy (HS-AFM) measurements reveal that it forms unique tetrameric clusters through its N-terminal head on a mica surface. The clusters further self-assemble into a monolayer through the C-terminal His-tag. The HS-AFM images and displacement analyses show that the monolayer is a network-like structure rather than a crystalline lattice. Our results expand the toolbox for constructing hierarchical protein assemblies based on structural anisotropy.
Collapse
Affiliation(s)
- Kosuke Kikuchi
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B-55, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Koki Date
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B-55, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B-55, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
- Living Systems Materialogy (LiSM) Research Group, International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan
| |
Collapse
|
13
|
Zhou AXZ, Hammond JA, Sheng K, Millar DP, Williamson JR. Early HIV-1 Gag Assembly on Lipid Membrane with vRNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.27.525415. [PMID: 36747785 PMCID: PMC9901173 DOI: 10.1101/2023.01.27.525415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Mass photometry (MP) was used to investigate the assembly of myristoylated full-length HIV-1 Gag (myr-Gag) and vRNA 5’ UTR fragment in a supported lipid bilayer (SLB) model system. The MP trajectories demonstrated that Gag trimerization on the membrane is a key step of early Gag assembly in the presence of vRNA. Growth of myr-Gag oligomers requires vRNA, occuring by addition of 1 or 2 monomers at a time from solution. These data support a model where formation of the Gag hexamers characteristic of the immature capsid lattice occurs by a gradual edge expansion, following a trimeric nucleation event. These dynamic single molecule data involving protein, RNA, and lipid components together, provide novel and fundamental insights into the initiation of virus capsid assembly.
Collapse
|
14
|
Teixobactin kills bacteria by a two-pronged attack on the cell envelope. Nature 2022; 608:390-396. [PMID: 35922513 PMCID: PMC9365693 DOI: 10.1038/s41586-022-05019-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/23/2022] [Indexed: 01/08/2023]
Abstract
Antibiotics that use novel mechanisms are needed to combat antimicrobial resistance1–3. Teixobactin4 represents a new class of antibiotics with a unique chemical scaffold and lack of detectable resistance. Teixobactin targets lipid II, a precursor of peptidoglycan5. Here we unravel the mechanism of teixobactin at the atomic level using a combination of solid-state NMR, microscopy, in vivo assays and molecular dynamics simulations. The unique enduracididine C-terminal headgroup of teixobactin specifically binds to the pyrophosphate-sugar moiety of lipid II, whereas the N terminus coordinates the pyrophosphate of another lipid II molecule. This configuration favours the formation of a β-sheet of teixobactins bound to the target, creating a supramolecular fibrillar structure. Specific binding to the conserved pyrophosphate-sugar moiety accounts for the lack of resistance to teixobactin4. The supramolecular structure compromises membrane integrity. Atomic force microscopy and molecular dynamics simulations show that the supramolecular structure displaces phospholipids, thinning the membrane. The long hydrophobic tails of lipid II concentrated within the supramolecular structure apparently contribute to membrane disruption. Teixobactin hijacks lipid II to help destroy the membrane. Known membrane-acting antibiotics also damage human cells, producing undesirable side effects. Teixobactin damages only membranes that contain lipid II, which is absent in eukaryotes, elegantly resolving the toxicity problem. The two-pronged action against cell wall synthesis and cytoplasmic membrane produces a highly effective compound targeting the bacterial cell envelope. Structural knowledge of the mechanism of teixobactin will enable the rational design of improved drug candidates. Using a combination of methods, the mechanism of the antibiotic teixobactin is revealed.
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Majsterkiewicz K, Biela AP, Maity S, Sharma M, Piette BMAG, Kowalczyk A, Gaweł S, Chakraborti S, Roos WH, Heddle JG. Artificial Protein Cage with Unusual Geometry and Regularly Embedded Gold Nanoparticles. NANO LETTERS 2022; 22:3187-3195. [PMID: 35254086 PMCID: PMC9052746 DOI: 10.1021/acs.nanolett.1c04222] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Artificial protein cages have great potential in a number of areas including cargo capture and delivery and as artificial vaccines. Here, we investigate an artificial protein cage whose assembly is triggered by gold nanoparticles. Using biochemical and biophysical methods we were able to determine both the mechanical properties and the gross compositional features of the cage which, combined with mathematical models and biophysical data, allowed the structure of the cage to be predicted. The accuracy of the overall geometrical prediction was confirmed by the cryo-EM structure determined to sub-5 Å resolution. This showed the cage to be nonregular but similar to a dodecahedron, being constructed from 12 11-membered rings. Surprisingly, the structure revealed that the cage also contained a single, small gold nanoparticle at each 3-fold axis meaning that each cage acts as a synthetic framework for regular arrangement of 20 gold nanoparticles in a three-dimensional lattice.
Collapse
Affiliation(s)
- Karolina Majsterkiewicz
- Małopolska
Centre of Biotechnology, Jagiellonian University, Kraków 30-387, Poland
- Postgraduate
School of Molecular Medicine, ul. Żwirki i Wigury 61, Warsaw 02-091, Poland
| | - Artur P. Biela
- Małopolska
Centre of Biotechnology, Jagiellonian University, Kraków 30-387, Poland
- Institute
of Zoology and Biomedical Research, Department of Cell Biology and
Imaging, Jagiellonian University, Kraków 30-387, Poland
| | - Sourav Maity
- Moleculaire
Biofysica, Zernike Instituut, Rijksuniversiteit
Groningen, Groningen 9747 AG, Netherlands
| | - Mohit Sharma
- Małopolska
Centre of Biotechnology, Jagiellonian University, Kraków 30-387, Poland
- Postgraduate
School of Molecular Medicine, ul. Żwirki i Wigury 61, Warsaw 02-091, Poland
| | | | - Agnieszka Kowalczyk
- Małopolska
Centre of Biotechnology, Jagiellonian University, Kraków 30-387, Poland
- Faculty of
Mathematics and Computer Science, Jagiellonian
University, Kraków 30-348, Poland
| | - Szymon Gaweł
- Małopolska
Centre of Biotechnology, Jagiellonian University, Kraków 30-387, Poland
| | | | - Wouter H. Roos
- Moleculaire
Biofysica, Zernike Instituut, Rijksuniversiteit
Groningen, Groningen 9747 AG, Netherlands
| | - Jonathan G. Heddle
- Małopolska
Centre of Biotechnology, Jagiellonian University, Kraków 30-387, Poland
| |
Collapse
|
17
|
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: 7] [Impact Index Per Article: 3.5] [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.
Collapse
|
18
|
Sumner C, Ono A. Relationship between HIV-1 Gag Multimerization and Membrane Binding. Viruses 2022; 14:v14030622. [PMID: 35337029 PMCID: PMC8949992 DOI: 10.3390/v14030622] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/06/2022] [Accepted: 03/09/2022] [Indexed: 12/11/2022] Open
Abstract
HIV-1 viral particle assembly occurs specifically at the plasma membrane and is driven primarily by the viral polyprotein Gag. Selective association of Gag with the plasma membrane is a key step in the viral assembly pathway, which is traditionally attributed to the MA domain. MA regulates specific plasma membrane binding through two primary mechanisms including: (1) specific interaction of the MA highly basic region (HBR) with the plasma membrane phospholipid phosphatidylinositol (4,5) bisphosphate [PI(4,5)P2], and (2) tRNA binding to the MA HBR, which prevents Gag association with non-PI(4,5)P2 containing membranes. Gag multimerization, driven by both CA–CA inter-protein interactions and NC-RNA binding, also plays an essential role in viral particle assembly, mediating the establishment and growth of the immature Gag lattice on the plasma membrane. In addition to these functions, the multimerization of HIV-1 Gag has also been demonstrated to enhance its membrane binding activity through the MA domain. This review provides an overview of the mechanisms regulating Gag membrane binding through the MA domain and multimerization through the CA and NC domains, and examines how these two functions are intertwined, allowing for multimerization mediated enhancement of Gag membrane binding.
Collapse
|
19
|
Domínguez-Zotes S, Valbuena A, Mateu MG. Antiviral compounds modulate elasticity, strength and material fatigue of a virus capsid framework. Biophys J 2022; 121:919-931. [PMID: 35151634 PMCID: PMC8943814 DOI: 10.1016/j.bpj.2022.02.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/18/2022] [Accepted: 02/09/2022] [Indexed: 11/30/2022] Open
Abstract
This study investigates whether the biochemical and antiviral effects of organic compounds that bind different sites in the mature human immunodeficiency virus capsid may be related to the modulation of different mechanical properties of the protein lattice from which the capsid is built. Mechanical force was used as a probe to quantify, in atomic force microscopy experiments at physiological pH and ionic strength, ligand-mediated changes in capsid lattice elasticity, breathing, strength against local dislocation by mechanical stress, and resistance to material fatigue. The results indicate that the effects of the tested compounds on assembly or biochemical stability can be linked, from a physics-based perspective, to their interference with the mechanical behavior of the viral capsid framework. The antivirals CAP-1 and CAI-55 increased the intrinsic elasticity and breathing of the capsid protein lattice and may entropically decrease the probability of the capsid protein to assemble into a functionally competent conformation. Antiviral PF74 increased the resistance of the capsid protein lattice to disruption by mechanical stress and material fatigue and may enthalpically strengthen the basal capsid lattice against breakage and disintegration. This study provides proof of concept that the interrogation of the mechanical properties of the nanostructured protein material that makes a virus capsid may provide fundamental insights into the biophysical action of capsid-binding antiviral agents. The implications for drug design by specifically targeting the biomechanics of viruses are discussed.
Collapse
Affiliation(s)
- Santos Domínguez-Zotes
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - Alejandro Valbuena
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain.
| | - Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain.
| |
Collapse
|
20
|
Hills RA, Howarth M. Virus-like particles against infectious disease and cancer: guidance for the nano-architect. Curr Opin Biotechnol 2022; 73:346-354. [PMID: 34735984 PMCID: PMC8555979 DOI: 10.1016/j.copbio.2021.09.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/24/2021] [Accepted: 09/29/2021] [Indexed: 02/07/2023]
Abstract
Virus-like particles (VLPs) can play important roles in prevention and therapy for infectious diseases and cancer. Here we describe recent advances in rational construction of VLP assemblies, as well as new approaches to enhance long-lasting antibody and CD8+ T cell responses. DNA origami and computational protein design identified optimal spacing of antigens. Chemical biology advances enabled simple and irreversible VLP decoration with protein or polysaccharide antigens. Mosaic VLPs co-displayed antigens to generate cross-reactive antibodies against different influenza strains and coronaviruses. The mode of action of adjuvants inside VLPs was established through knock-outs and repackaging of innate immune stimuli. VLPs themselves showed their power as adjuvants in cancer models. Finally, landmark clinical results were obtained against malaria and the SARS-CoV-2 pandemic.
Collapse
|
21
|
High-speed atomic force microscopy reveals a three-state elevator mechanism in the citrate transporter CitS. Proc Natl Acad Sci U S A 2022; 119:2113927119. [PMID: 35101979 PMCID: PMC8833178 DOI: 10.1073/pnas.2113927119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2021] [Indexed: 12/16/2022] Open
Abstract
As cellular membranes are impermeable to most molecules, transporter proteins are typically present in the membrane to transport small molecules in or out of the cell. Due to the small, nanometer size of these transporters, it is challenging to study their transport mechanism. Here, we use advanced microscopy approaches to study in real time and at the single-molecule level the mode of action of the dimeric CitS tranpsorter. Using high-speed atomic force microscopy, we visualize the dynamic, elevator-like movement of the transporter, and we reveal that the two protomers move independently. We also discovered an intermediate state, reminiscent of another, unrelated transporter, indicating that independent evolutionary pathways have led to similar three-state elevator mechanisms. The secondary active transporter CitS shuttles citrate across the cytoplasmic membrane of gram-negative bacteria by coupling substrate translocation to the transport of two Na+ ions. Static crystal structures suggest an elevator type of transport mechanism with two states: up and down. However, no dynamic measurements have been performed to substantiate this assumption. Here, we use high-speed atomic force microscopy for real-time visualization of the transport cycle at the level of single transporters. Unexpectedly, instead of a bimodal height distribution for the up and down states, the experiments reveal movements between three distinguishable states, with protrusions of ∼0.5 nm, ∼1.0 nm, and ∼1.6 nm above the membrane, respectively. Furthermore, the real-time measurements show that the individual protomers of the CitS dimer move up and down independently. A three-state elevator model of independently operating protomers resembles the mechanism proposed for the aspartate transporter GltPh. Since CitS and GltPh are structurally unrelated, we conclude that the three-state elevators have evolved independently.
Collapse
|
22
|
Sukeník L, Mukhamedova L, Procházková M, Škubník K, Plevka P, Vácha R. Cargo Release from Nonenveloped Viruses and Virus-like Nanoparticles: Capsid Rupture or Pore Formation. ACS NANO 2021; 15:19233-19243. [PMID: 34881874 DOI: 10.1021/acsnano.1c04814] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Virus-like nanoparticles are protein shells similar to wild-type viruses, and both aim to deliver their content into a cell. Unfortunately, the release mechanism of their cargo/genome remains elusive. Pores on the symmetry axes were proposed to enable the slow release of the viral genome. In contrast, cryo-EM images showed that capsids of nonenveloped RNA viruses can crack open and rapidly release the genome. We combined in vitro cryo-EM observations of the genome release of three viruses with coarse-grained simulations of generic virus-like nanoparticles to investigate the cargo/genome release pathways. Simulations provided details on both slow and rapid release pathways, including the success rates of individual releases. Moreover, the simulated structures from the rapid release pathway were in agreement with the experiment. Slow release occurred when interactions between capsid subunits were long-ranged, and the cargo/genome was noncompact. In contrast, rapid release was preferred when the interaction range was short and/or the cargo/genome was compact. These findings indicate a design strategy of virus-like nanoparticles for drug delivery.
Collapse
Affiliation(s)
- Lukáš Sukeník
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
- Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Kotlářská 267/2, 611 37 Brno, Czech Republic
| | - Liya Mukhamedova
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Michaela Procházková
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Karel Škubník
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Pavel Plevka
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Robert Vácha
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
- Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Kotlářská 267/2, 611 37 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| |
Collapse
|
23
|
Buzón P, Maity S, Christodoulis P, Wiertsema MJ, Dunkelbarger S, Kim C, Wuite GJ, Zlotnick A, Roos WH. Virus self-assembly proceeds through contact-rich energy minima. SCIENCE ADVANCES 2021; 7:eabg0811. [PMID: 34730996 PMCID: PMC8565845 DOI: 10.1126/sciadv.abg0811] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Self-assembly of supramolecular complexes such as viral capsids occurs prominently in nature. Nonetheless, the mechanisms underlying these processes remain poorly understood. Here, we uncover the assembly pathway of hepatitis B virus (HBV), applying fluorescence optical tweezers and high-speed atomic force microscopy. This allows tracking the assembly process in real time with single-molecule resolution. Our results identify a specific, contact-rich pentameric arrangement of HBV capsid proteins as a key on-path assembly intermediate and reveal the energy balance of the self-assembly process. Real-time nucleic acid packaging experiments show that a free energy change of ~1.4 kBT per condensed nucleotide is used to drive protein oligomerization. The finding that HBV assembly occurs via contact-rich energy minima has implications for our understanding of the assembly of HBV and other viruses and also for the development of new antiviral strategies and the rational design of self-assembling nanomaterials.
Collapse
Affiliation(s)
- Pedro Buzón
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, Netherlands
| | - Sourav Maity
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, Netherlands
| | | | - Monique J. Wiertsema
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, Netherlands
| | - Steven Dunkelbarger
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN, USA
| | - Christine Kim
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN, USA
| | - Gijs J.L. Wuite
- Physics of Living Systems, Vrije Universiteit, Amsterdam, Netherlands
| | - Adam Zlotnick
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN, USA
| | - Wouter H. Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, Netherlands
- Corresponding author.
| |
Collapse
|
24
|
Zhao X, Meng X, Ragauskas AJ, Lai C, Ling Z, Huang C, Yong Q. Unlocking the secret of lignin-enzyme interactions: Recent advances in developing state-of-the-art analytical techniques. Biotechnol Adv 2021; 54:107830. [PMID: 34480987 DOI: 10.1016/j.biotechadv.2021.107830] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/07/2021] [Accepted: 08/29/2021] [Indexed: 02/08/2023]
Abstract
Bioconversion of renewable lignocellulosics to produce liquid fuels and chemicals is one of the most effective ways to solve the problem of fossil resource shortage, energy security, and environmental challenges. Among the many biorefinery pathways, hydrolysis of lignocellulosics to fermentable monosaccharides by cellulase is arguably the most critical step of lignocellulose bioconversion. In the process of enzymatic hydrolysis, the direct physical contact between enzymes and cellulose is an essential prerequisite for the hydrolysis to occur. However, lignin is considered one of the most recalcitrant factors hindering the accessibility of cellulose by binding to cellulase unproductively, which reduces the saccharification rate and yield of sugars. This results in high costs for the saccharification of carbohydrates. The various interactions between enzymes and lignin have been explored from different perspectives in literature, and a basic lignin inhibition mechanism has been proposed. However, the exact interaction between lignin and enzyme as well as the recently reported promotion of some types of lignin on enzymatic hydrolysis is still unclear at the molecular level. Multiple analytical techniques have been developed, and fully unlocking the secret of lignin-enzyme interactions would require a continuous improvement of the currently available analytical techniques. This review summarizes the current commonly used advanced research analytical techniques for investigating the interaction between lignin and enzyme, including quartz crystal microbalance with dissipation (QCM-D), surface plasmon resonance (SPR), attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy, atomic force microscopy (AFM), nuclear magnetic resonance (NMR) spectroscopy, fluorescence spectroscopy (FLS), and molecular dynamics (MD) simulations. Interdisciplinary integration of these analytical methods is pursued to provide new insight into the interactions between lignin and enzymes. This review will serve as a resource for future research seeking to develop new methodologies for a better understanding of the basic mechanism of lignin-enzyme binding during the critical hydrolysis process.
Collapse
Affiliation(s)
- Xiaoxue Zhao
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China
| | - Xianzhi Meng
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Arthur J Ragauskas
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA; Center for Renewable Carbon, Department of Forestry, Wildlife and Fisheries, University of Tennessee, Knoxville, TN 37996, USA; Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Chenhuan Lai
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China
| | - Zhe Ling
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China
| | - Caoxing Huang
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China.
| | - Qiang Yong
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China.
| |
Collapse
|
25
|
Chaudhari HV, Inamdar MM, Kondabagil K. Scaling relation between genome length and particle size of viruses provides insights into viral life history. iScience 2021; 24:102452. [PMID: 34113814 PMCID: PMC8169800 DOI: 10.1016/j.isci.2021.102452] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/23/2021] [Accepted: 04/15/2021] [Indexed: 12/12/2022] Open
Abstract
In terms of genome and particle sizes, viruses exhibit great diversity. With the discovery of several nucleocytoplasmic large DNA viruses (NCLDVs) and jumbo phages, the relationship between particle and genome sizes has emerged as an important criterion for understanding virus evolution. We use allometric scaling of capsid volume with the genome length of different groups of viruses to shed light on its relationship with virus life history. The allometric exponents for icosahedral dsDNA bacteriophages and NCDLVs were found to be 1 and 2, respectively, indicating that with increasing capsid size DNA packaging density remains the same in bacteriophages but decreases for NCLDVs. We argue that the exponents are largely shaped by their entry mechanism and capsid mechanical stability. We further show that these allometric size parameters are also intricately linked to the relative energy costs of translation and replication in viruses and can have further implications on viral life history. Capsid and genome size allometric exponent gives insights into viral life history The allometric exponent of NCLDVs is almost twice that of bacteriophages The exponent is largely shaped by the viral entry mechanism and capsid stability The relaxed genome size constraint allows large viruses to evolve greater autonomy
Collapse
Affiliation(s)
- Harshali V Chaudhari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Mandar M Inamdar
- Department of Civil Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| |
Collapse
|
26
|
Le DT, Müller KM. In Vitro Assembly of Virus-Like Particles and Their Applications. Life (Basel) 2021; 11:334. [PMID: 33920215 PMCID: PMC8069851 DOI: 10.3390/life11040334] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 02/06/2023] Open
Abstract
Virus-like particles (VLPs) are increasingly used for vaccine development and drug delivery. Assembly of VLPs from purified monomers in a chemically defined reaction is advantageous compared to in vivo assembly, because it avoids encapsidation of host-derived components and enables loading with added cargoes. This review provides an overview of ex cella VLP production methods focusing on capsid protein production, factors that impact the in vitro assembly, and approaches to characterize in vitro VLPs. The uses of in vitro produced VLPs as vaccines and for therapeutic delivery are also reported.
Collapse
Affiliation(s)
| | - Kristian M. Müller
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany;
| |
Collapse
|
27
|
Gisbert V, Benaglia S, Uhlig MR, Proksch R, Garcia R. High-Speed Nanomechanical Mapping of the Early Stages of Collagen Growth by Bimodal Force Microscopy. ACS NANO 2021; 15:1850-1857. [PMID: 33412008 PMCID: PMC8477367 DOI: 10.1021/acsnano.0c10159] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/05/2021] [Indexed: 05/07/2023]
Abstract
High-speed atomic force microscopy (AFM) enabled the imaging of protein interactions with millisecond time resolutions (10 fps). However, the acquisition of nanomechanical maps of proteins is about 100 times slower. Here, we developed a high-speed bimodal AFM that provided high-spatial resolution maps of the elastic modulus, the loss tangent, and the topography at imaging rates of 5 fps. The microscope was applied to identify the initial stages of the self-assembly of the collagen structures. By following the changes in the physical properties, we identified four stages, nucleation and growth of collagen precursors, formation of tropocollagen molecules, assembly of tropocollagens into microfibrils, and alignment of microfibrils to generate microribbons. Some emerging collagen structures never matured, and after an existence of several seconds, they disappeared into the solution. The elastic modulus of a microfibril (∼4 MPa) implied very small stiffness (∼3 × 10-6 N/m). Those values amplified the amplitude of the collagen thermal fluctuations on the mica plane, which facilitated microribbon build-up.
Collapse
Affiliation(s)
- Victor
G. Gisbert
- Instituto
de Ciencia de Materiales de Madrid, CSIC, c/Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain
| | - Simone Benaglia
- Instituto
de Ciencia de Materiales de Madrid, CSIC, c/Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain
| | - Manuel R. Uhlig
- Instituto
de Ciencia de Materiales de Madrid, CSIC, c/Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain
| | - Roger Proksch
- Asylum
Research an Oxford Instruments Company, Santa Barbara, California 93117, United States
| | - Ricardo Garcia
- Instituto
de Ciencia de Materiales de Madrid, CSIC, c/Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain
| |
Collapse
|
28
|
Wenzel M, Celik Gulsoy IN, Gao Y, Teng Z, Willemse J, Middelkamp M, van Rosmalen MGM, Larsen PWB, van der Wel NN, Wuite GJL, Roos WH, Hamoen LW. Control of septum thickness by the curvature of SepF polymers. Proc Natl Acad Sci U S A 2021; 118:e2002635118. [PMID: 33443155 PMCID: PMC7812789 DOI: 10.1073/pnas.2002635118] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Gram-positive bacteria divide by forming a thick cross wall. How the thickness of this septal wall is controlled is unknown. In this type of bacteria, the key cell division protein FtsZ is anchored to the cell membrane by two proteins, FtsA and/or SepF. We have isolated SepF homologs from different bacterial species and found that they all polymerize into large protein rings with diameters varying from 19 to 44 nm. Interestingly, these values correlated well with the thickness of their septa. To test whether ring diameter determines septal thickness, we tried to construct different SepF chimeras with the purpose to manipulate the diameter of the SepF protein ring. This was indeed possible and confirmed that the conserved core domain of SepF regulates ring diameter. Importantly, when SepF chimeras with different diameters were expressed in the bacterial host Bacillus subtilis, the thickness of its septa changed accordingly. These results strongly support a model in which septal thickness is controlled by curved molecular clamps formed by SepF polymers attached to the leading edge of nascent septa. This also implies that the intrinsic shape of a protein polymer can function as a mold to shape the cell wall.
Collapse
Affiliation(s)
- Michaela Wenzel
- Bacterial Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Ilkay N Celik Gulsoy
- Bacterial Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Yongqiang Gao
- Bacterial Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Zihao Teng
- Bacterial Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Joost Willemse
- Molecular Biotechnology, Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands
| | - Martijn Middelkamp
- Molecular Biophysics, Zernike Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Mariska G M van Rosmalen
- Department of Physics and Astronomy and Laser Lab, Free University of Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Per W B Larsen
- Department of Medical Biology, Electron Microscopy Center Amsterdam, Amsterdam UMC, 1105 AZ Amsterdam, The Netherlands
| | - Nicole N van der Wel
- Department of Medical Biology, Electron Microscopy Center Amsterdam, Amsterdam UMC, 1105 AZ Amsterdam, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy and Laser Lab, Free University of Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Wouter H Roos
- Molecular Biophysics, Zernike Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Leendert W Hamoen
- Bacterial Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands;
| |
Collapse
|
29
|
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.
Collapse
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
| |
Collapse
|