1
|
Wańczura P, Aebisher D, Iwański MA, Myśliwiec A, Dynarowicz K, Bartusik-Aebisher D. The Essence of Lipoproteins in Cardiovascular Health and Diseases Treated by Photodynamic Therapy. Biomedicines 2024; 12:961. [PMID: 38790923 PMCID: PMC11117957 DOI: 10.3390/biomedicines12050961] [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: 03/10/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Lipids, together with lipoprotein particles, are the cause of atherosclerosis, which is a pathology of the cardiovascular system. In addition, it affects inflammatory processes and affects the vessels and heart. In pharmaceutical answer to this, statins are considered a first-stage treatment method to block cholesterol synthesis. Many times, additional drugs are also used with this method to lower lipid concentrations in order to achieve certain values of low-density lipoprotein (LDL) cholesterol. Recent advances in photodynamic therapy (PDT) as a new cancer treatment have gained the therapy much attention as a minimally invasive and highly selective method. Photodynamic therapy has been proven more effective than chemotherapy, radiotherapy, and immunotherapy alone in numerous studies. Consequently, photodynamic therapy research has expanded in many fields of medicine due to its increased therapeutic effects and reduced side effects. Currently, PDT is the most commonly used therapy for treating age-related macular degeneration, as well as inflammatory diseases, and skin infections. The effectiveness of photodynamic therapy against a number of pathogens has also been demonstrated in various studies. Also, PDT has been used in the treatment of cardiovascular diseases, such as atherosclerosis and hyperplasia of the arterial intima. This review evaluates the effectiveness and usefulness of photodynamic therapy in cardiovascular diseases. According to the analysis, photodynamic therapy is a promising approach for treating cardiovascular diseases and may lead to new clinical trials and management standards. Our review addresses the used therapeutic strategies and also describes new therapeutic strategies to reduce the cardiovascular burden that is induced by lipids.
Collapse
Affiliation(s)
- Piotr Wańczura
- Department of Cardiology, Medical College of the University of Rzeszów, 35-310 Rzeszów, Poland
| | - David Aebisher
- Department of Photomedicine and Physical Chemistry, Medical College of the University of Rzeszów, 35-310 Rzeszów, Poland
| | - Mateusz A Iwański
- English Division Science Club, Medical College of the University of Rzeszów, 35-310 Rzeszów, Poland
| | - Angelika Myśliwiec
- Center for Innovative Research in Medical and Natural Sciences, Medical College of the University of Rzeszów, 35-310 Rzeszów, Poland
| | - Klaudia Dynarowicz
- Center for Innovative Research in Medical and Natural Sciences, Medical College of the University of Rzeszów, 35-310 Rzeszów, Poland
| | - Dorota Bartusik-Aebisher
- Department of Biochemistry and General Chemistry, Medical College of the University of Rzeszów, 35-310 Rzeszów, Poland
| |
Collapse
|
2
|
Tan FH, Ng JF, Mohamed Alitheen NB, Muhamad A, Yong CY, Lee KW. A simple and high efficiency purification of His-tagged turnip yellow mosaic virus-like particle (TYMV-VLP) by nickel ion affinity precipitation. J Virol Methods 2023; 319:114771. [PMID: 37437780 DOI: 10.1016/j.jviromet.2023.114771] [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: 04/11/2023] [Revised: 07/05/2023] [Accepted: 07/08/2023] [Indexed: 07/14/2023]
Abstract
Virus-like particles (VLPs) is one of the most favourable subjects of study, especially in the field of nanobiotechnology and vaccine development because they possess good immunogenicity and self-adjuvant properties. Conventionally, VLPs can be tagged and purified using affinity chromatography or density gradient ultracentrifugation which is costly and time-consuming. Turnip yellow mosaic virus (TYMV) is a plant virus, where expression of the viral coat protein (TYMVc) in Escherichia coli (E. coli) has been shown to form VLP. In this study, we report a non-chromatographic method for VLP purification using C-terminally His-tagged TYMVc (TYMVcHis6) as a protein model. Firstly, the TYMVcHis6 was cloned and expressed in E. coli. Upon clarification of cell lysate, nickel (II) chloride [NiCl2; 15µM or equivalent to 0.0000194% (w/v)] was added to precipitate TYMVcHis6. Following centrifugation, the pellet was resuspended in buffer containing 1mM EDTA to chelate Ni2+, which is then removed via dialysis. A total of 50% of TYMVcHis6 was successfully recovered with purity above 0.90. Later, the purified TYMVcHis6 was analysed with sucrose density ultracentrifugation, dynamic light scattering (DLS), and transmission electron microscopy (TEM) to confirm VLP formation, which is comparable to TYMVcHis6 purified using the standard immobilized metal affinity chromatography (IMAC) column. As the current method omitted the need for IMAC column and beads while significantly reducing the time needed for column washing, nickel affinity precipitation represents a novel method for the purification of VLPs displaying poly-histidine tags (His-tags).
Collapse
Affiliation(s)
- Foo Hou Tan
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia
| | - Jeck Fei Ng
- School of Pharmacy, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia
| | | | - Azira Muhamad
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Kajang, Selangor, Malaysia
| | - Chean Yeah Yong
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, Selangor, Malaysia
| | - Khai Wooi Lee
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia.
| |
Collapse
|
3
|
Xue H, Zhang M, Liu J, Wang J, Ren G. Structure-based mechanism and inhibition of cholesteryl ester transfer protein. Curr Atheroscler Rep 2023; 25:155-166. [PMID: 36881278 PMCID: PMC10027838 DOI: 10.1007/s11883-023-01087-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2023] [Indexed: 03/08/2023]
Abstract
PURPOSE OF REVIEW Cholesteryl ester transfer proteins (CETP) regulate plasma cholesterol levels by transferring cholesteryl esters (CEs) among lipoproteins. Lipoprotein cholesterol levels correlate with the risk factors for atherosclerotic cardiovascular disease (ASCVD). This article reviews recent research on CETP structure, lipid transfer mechanism, and its inhibition. RECENT FINDINGS Genetic deficiency in CETP is associated with a low plasma level of low-density lipoprotein cholesterol (LDL-C) and a profoundly elevated plasma level of high-density lipoprotein cholesterol (HDL-C), which correlates with a lower risk of atherosclerotic cardiovascular disease (ASCVD). However, a very high concentration of HDL-C also correlates with increased ASCVD mortality. Considering that the elevated CETP activity is a major determinant of the atherogenic dyslipidemia, i.e., pro-atherogenic reductions in HDL and LDL particle size, inhibition of CETP emerged as a promising pharmacological target during the past two decades. CETP inhibitors, including torcetrapib, dalcetrapib, evacetrapib, anacetrapib and obicetrapib, were designed and evaluated in phase III clinical trials for the treatment of ASCVD or dyslipidemia. Although these inhibitors increase in plasma HDL-C levels and/or reduce LDL-C levels, the poor efficacy against ASCVD ended interest in CETP as an anti-ASCVD target. Nevertheless, interest in CETP and the molecular mechanism by which it inhibits CE transfer among lipoproteins persisted. Insights into the structural-based CETP-lipoprotein interactions can unravel CETP inhibition machinery, which can hopefully guide the design of more effective CETP inhibitors that combat ASCVD. Individual-molecule 3D structures of CETP bound to lipoproteins provide a model for understanding the mechanism by which CETP mediates lipid transfer and which in turn, guide the rational design of new anti-ASCVD therapeutics.
Collapse
Affiliation(s)
- Han Xue
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Meng Zhang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jianjun Wang
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| |
Collapse
|
4
|
Solé R, Sardanyés J, Elena SF. Phase transitions in virology. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2021; 84:115901. [PMID: 34584031 DOI: 10.1088/1361-6633/ac2ab0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
Viruses have established relationships with almost every other living organism on Earth and at all levels of biological organization: from other viruses up to entire ecosystems. In most cases, they peacefully coexist with their hosts, but in most relevant cases, they parasitize them and induce diseases and pandemics, such as the AIDS and the most recent avian influenza and COVID-19 pandemic events, causing a huge impact on health, society, and economy. Viruses play an essential role in shaping the eco-evolutionary dynamics of their hosts, and have been also involved in some of the major evolutionary innovations either by working as vectors of genetic information or by being themselves coopted by the host into their genomes. Viruses can be studied at different levels of biological organization, from the molecular mechanisms of genome replication, gene expression and encapsidation, to global pandemics. All these levels are different and yet connected through the presence of threshold conditions allowing for the formation of a capsid, the loss of genetic information or epidemic spreading. These thresholds, as occurs with temperature separating phases in a liquid, define sharp qualitative types of behaviour. Thesephase transitionsare very well known in physics. They have been studied by means of simple, but powerful models able to capture their essential properties, allowing us to better understand them. Can the physics of phase transitions be an inspiration for our understanding of viral dynamics at different scales? Here we review well-known mathematical models of transition phenomena in virology. We suggest that the advantages of abstract, simplified pictures used in physics are also the key to properly understanding the origins and evolution of complexity in viruses. By means of several examples, we explore this multilevel landscape and how minimal models provide deep insights into a diverse array of problems. The relevance of these transitions in connecting dynamical patterns across scales and their evolutionary and clinical implications are outlined.
Collapse
Affiliation(s)
- Ricard Solé
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra-PRBB, Dr Aiguader 80, 08003 Barcelona, Spain
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Passeig Maritim de la Barceloneta 37, 08003 Barcelona, Spain
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe NM 87501, United States of America
| | - Josep Sardanyés
- Centre de Recerca Matemàtica (CRM), Edifici C, Campus de Bellaterra, Cerdanyola del Vallès, 08193 Barcelona, Spain
- Dynamical Systems and Computational Virology, CSIC Associated Unit, Institute for Integrative Systems Biology (I2SysBio)-CRM, Spain
| | - Santiago F Elena
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe NM 87501, United States of America
- Evolutionary Systems Virology Lab (I2SysBio), CSIC-Universitat de València, Catedrático Agustín Escardino 9, Paterna, 46980 València, Spain
| |
Collapse
|
5
|
Icosadeltahedral Geometry of Geodesic Domes, Fullerenes and Viruses: A Tutorial on the T-Number. Symmetry (Basel) 2020. [DOI: 10.3390/sym12040556] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The Caspar–Klug (CK) classification of viruses is discussed by parallel examination of geometry of icosahedral geodesic domes, fullerenes, and viruses. The underlying symmetry of all structures is explained and thoroughly visually represented. Euler’s theorem on polyhedra is used to calculate the number of vertices, edges, and faces in domes, number of atoms, bonds, and pentagonal and hexagonal rings in fullerenes, and number of proteins and protein–protein contacts in viruses. The T-number, the characteristic for the CK classification, is defined and discussed. The superposition of fullerene and dome designs is used to obtain a representation of a CK virus with all the proteins indicated. Some modifications of the CK classifications are sketched, including elongation of the CK blueprint, fusion of two CK blueprints, dodecahedral view of the CK shapes, and generalized CK designs without a clearly visible geometry of the icosahedron. These are compared to cases of existing viruses.
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Cieplak M, Roos WH. Special Issue on the Physics of Viral Capsids. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:290201. [PMID: 29882747 DOI: 10.1088/1361-648x/aacb6c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- Marek Cieplak
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland. Zernike Instituut, Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | | |
Collapse
|
8
|
Abstract
The spread of bacterial resistance to antibiotics poses the need for antimicrobial discovery. With traditional search paradigms being exhausted, approaches that are altogether different from antibiotics may offer promising and creative solutions. Here, we introduce a de novo peptide topology that—by emulating the virus architecture—assembles into discrete antimicrobial capsids. Using the combination of high-resolution and real-time imaging, we demonstrate that these artificial capsids assemble as 20-nm hollow shells that attack bacterial membranes and upon landing on phospholipid bilayers instantaneously (seconds) convert into rapidly expanding pores causing membrane lysis (minutes). The designed capsids show broad antimicrobial activities, thus executing one primary function—they destroy bacteria on contact. With the growing threat of antibiotic resistance, unconventional approaches to antimicrobial discovery are needed. Here, the authors present a peptide topology that mimics virus architecture and assembles into antimicrobial capsids that disrupt bacterial membranes upon contact.
Collapse
|
9
|
Kononova O, Snijder J, Kholodov Y, Marx KA, Wuite GJL, Roos WH, Barsegov V. Fluctuating Nonlinear Spring Model of Mechanical Deformation of Biological Particles. PLoS Comput Biol 2016; 12:e1004729. [PMID: 26821264 PMCID: PMC4731076 DOI: 10.1371/journal.pcbi.1004729] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 01/05/2016] [Indexed: 12/17/2022] Open
Abstract
The mechanical properties of virus capsids correlate with local conformational dynamics in the capsid structure. They also reflect the required stability needed to withstand high internal pressures generated upon genome loading and contribute to the success of important events in viral infectivity, such as capsid maturation, genome uncoating and receptor binding. The mechanical properties of biological nanoparticles are often determined from monitoring their dynamic deformations in Atomic Force Microscopy nanoindentation experiments; but a comprehensive theory describing the full range of observed deformation behaviors has not previously been described. We present a new theory for modeling dynamic deformations of biological nanoparticles, which considers the non-linear Hertzian deformation, resulting from an indenter-particle physical contact, and the bending of curved elements (beams) modeling the particle structure. The beams’ deformation beyond the critical point triggers a dynamic transition of the particle to the collapsed state. This extreme event is accompanied by a catastrophic force drop as observed in the experimental or simulated force (F)-deformation (X) spectra. The theory interprets fine features of the spectra, including the nonlinear components of the FX-curves, in terms of the Young’s moduli for Hertzian and bending deformations, and the structural damage dependent beams’ survival probability, in terms of the maximum strength and the cooperativity parameter. The theory is exemplified by successfully describing the deformation dynamics of natural nanoparticles through comparing theoretical curves with experimental force-deformation spectra for several virus particles. This approach provides a comprehensive description of the dynamic structural transitions in biological and artificial nanoparticles, which is essential for their optimal use in nanotechnology and nanomedicine applications. Dynamic force experiments, which have become available to explore the physical properties of biological assemblies, oftentimes reveal results that are difficult to understand without theoretical framework. We employed a multiscale modeling approach—a combination of Molecular Dynamics simulations of atomic structures with Langevin simulations of coarse-grained models of virus shells—to characterize the degrees of freedom defining the deformation and structural collapse of biological particles tested mechanically. This enabled us to develop an analytical model that provides meaningful interpretation of force-deformation spectra available from single-particle nanoindentation experiments. The Fluctuating Nonlinear Spring (FNS) model of uniaxial particle’s deformation captures essential features of the force-deformation spectra as observed in nanomanipulations in vitro and in silico: initial non-linearity, then a subsequent force decrease transition due to structural collapse. Our theory uniquely combines the elements of continuum mechanics with the statistics of extremes, enabling one to gather mechanical and statistical characteristics of nanoparticles, which determine the Hertzian deformation of the particle’s protein layer, and bending deformation and structural damage to the particle structure. We have demonstrated how the FNS theory can accurately model the deformation of several viral shells, showing promising model applications for describing a variety of natural and synthetic nanoparticles.
Collapse
Affiliation(s)
- Olga Kononova
- Department of Chemistry, University of Massachusetts, Lowell, Massachusetts, United States of America
- Moscow Institute of Physics and Technology, Moscow Region, Russia
| | - Joost Snijder
- Natuur- en Sterrenkunde and LaserLab, Vrije Universiteit, Amsterdam, The Netherlands
| | - Yaroslav Kholodov
- Moscow Institute of Physics and Technology, Moscow Region, Russia
- Institute of Computer Aided Design Russian Academy of Science, Moscow, Russia
| | - Kenneth A. Marx
- Department of Chemistry, University of Massachusetts, Lowell, Massachusetts, United States of America
| | - Gijs J. L. Wuite
- Natuur- en Sterrenkunde and LaserLab, Vrije Universiteit, Amsterdam, The Netherlands
| | - Wouter H. Roos
- Moleculaire Biofysica, Zernike instituut, Rijksuniversiteit Groningen, Groningen, The Netherlands
- * E-mail: (WHR); (VB)
| | - Valeri Barsegov
- Department of Chemistry, University of Massachusetts, Lowell, Massachusetts, United States of America
- Moscow Institute of Physics and Technology, Moscow Region, Russia
- * E-mail: (WHR); (VB)
| |
Collapse
|
10
|
Kim J, Wu J. A molecular thermodynamic model for the stability of hepatitis B capsids. J Chem Phys 2015; 140:235101. [PMID: 24952568 DOI: 10.1063/1.4882068] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Self-assembly of capsid proteins and genome encapsidation are two critical steps in the life cycle of most plant and animal viruses. A theoretical description of such processes from a physiochemical perspective may help better understand viral replication and morphogenesis thus provide fresh insights into the experimental studies of antiviral strategies. In this work, we propose a molecular thermodynamic model for predicting the stability of Hepatitis B virus (HBV) capsids either with or without loading nucleic materials. With the key components represented by coarse-grained thermodynamic models, the theoretical predictions are in excellent agreement with experimental data for the formation free energies of empty T4 capsids over a broad range of temperature and ion concentrations. The theoretical model predicts T3/T4 dimorphism also in good agreement with the capsid formation at in vivo and in vitro conditions. In addition, we have studied the stability of the viral particles in response to physiological cellular conditions with the explicit consideration of the hydrophobic association of capsid subunits, electrostatic interactions, molecular excluded volume effects, entropy of mixing, and conformational changes of the biomolecular species. The course-grained model captures the essential features of the HBV nucleocapsid stability revealed by recent experiments.
Collapse
Affiliation(s)
- Jehoon Kim
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, USA
| | - Jianzhong Wu
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, USA
| |
Collapse
|
11
|
Segrest JP, Jones MK, Catte A. MD simulations suggest important surface differences between reconstituted and circulating spherical HDL. J Lipid Res 2013; 54:2718-32. [PMID: 23856070 DOI: 10.1194/jlr.m039206] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Since spheroidal HDL particles (sHDL) are highly dynamic, molecular dynamics (MD) simulations are useful for obtaining structural models. Here we use MD to simulate sHDL with stoichiometries of reconstituted and circulating particles. The hydrophobic effect during simulations rapidly remodels discoidal HDL containing mixed lipids to sHDL containing a cholesteryl ester/triglyceride (CE/TG) core. We compare the results of simulations of previously characterized reconstituted sHDL particles containing two or three apoA-I created in the absence of phospholipid transfer protein (PLTP) with simulations of circulating human HDL containing two or three apoA-I without apoA-II. We find that circulating sHDL compared with reconstituted sHDL with the same number of apoA-I per particle contain approximately equal volumes of core lipid but significantly less surface lipid monolayers. We conclude that in vitro reconstituted sHDL particles contain kinetically trapped excess phospholipid and are less than ideal models for circulating sHDL particles. In the circulation, phospholipid transfer via PLTP decreases the ratio of phospholipid to apolipoprotein for all sHDL particles. Further, sHDL containing two or three apoA-I adapt to changes in surface area by condensation of common conformational motifs. These results represent an important step toward resolving the complicated issue of the protein and lipid stoichiometry of circulating HDL.
Collapse
Affiliation(s)
- Jere P Segrest
- Department of Medicine and Center for Computational and Structural Dynamics, University of Alabama at Birmingham, Birmingham, AL 35294
| | | | | |
Collapse
|
12
|
Segrest JP, Jones MK, Catte A, Thirumuruganandham SP. Validation of previous computer models and MD simulations of discoidal HDL by a recent crystal structure of apoA-I. J Lipid Res 2012; 53:1851-63. [PMID: 22773698 DOI: 10.1194/jlr.m026229] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HDL is a population of apoA-I-containing particles inversely correlated with heart disease. Because HDL is a soft form of matter deformable by thermal fluctuations, structure determination has been difficult. Here, we compare the recently published crystal structure of lipid-free (Δ185-243)apoA-I with apoA-I structure from models and molecular dynamics (MD) simulations of discoidal HDL. These analyses validate four of our previous structural findings for apoA-I: i) a baseline double belt diameter of 105 Å ii) central α helixes with an 11/3 pitch; iii) a "presentation tunnel" gap between pairwise helix 5 repeats hypothesized to move acyl chains and unesterified cholesterol from the lipid bilayer to the active sites of LCAT; and iv) interchain salt bridges hypothesized to stabilize the LL5/5 chain registry. These analyses are also consistent with our finding that multiple salt bridge-forming residues in the N-terminus of apoA-I render that conserved domain "sticky." Additionally, our crystal MD comparisons led to two new hypotheses: i) the interchain leucine-zippers previously reported between the pair-wise helix 5 repeats drive lipid-free apoA-I registration; ii) lipidation induces rotations of helix 5 to allow formation of interchain salt bridges, creating the LCAT presentation tunnel and "zip-locking" apoA-I into its full LL5/5 registration.
Collapse
Affiliation(s)
- Jere P Segrest
- Department of Medicine, Atherosclerosis Research Unit, and Center for Computational and Structural Dynamics, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | | | | | | |
Collapse
|
13
|
Siber A, Božič AL, Podgornik R. Energies and pressures in viruses: contribution of nonspecific electrostatic interactions. Phys Chem Chem Phys 2011; 14:3746-65. [PMID: 22143065 DOI: 10.1039/c1cp22756d] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We summarize some aspects of electrostatic interactions in the context of viruses. A simplified but, within well defined limitations, reliable approach is used to derive expressions for electrostatic energies and the corresponding osmotic pressures in single-stranded RNA viruses and double-stranded DNA bacteriophages. The two types of viruses differ crucially in the spatial distribution of their genome charge which leads to essential differences in their free energies, depending on the capsid size and total charge in a quite different fashion. Differences in the free energies are trailed by the corresponding characteristics and variations in the osmotic pressure between the inside of the virus and the external bathing solution.
Collapse
|
14
|
Jones MK, Gu F, Catte A, Li L, Segrest JP. "Sticky" and "promiscuous", the yin and yang of apolipoprotein A-I termini in discoidal high-density lipoproteins: a combined computational-experimental approach. Biochemistry 2011; 50:2249-63. [PMID: 21329368 DOI: 10.1021/bi101301g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Apolipoprotein (apo) A-I-containing lipoproteins in the form of high-density lipoproteins (HDL) are inversely correlated with atherosclerosis. Because HDL is a soft form of condensed matter easily deformable by thermal fluctuations, the molecular mechanisms for HDL remodeling are not well understood. A promising approach to understanding HDL structure and dynamics is molecular dynamics (MD). In the present study, two computational strategies, MD simulated annealing (MDSA) and MD temperature jump, were combined with experimental particle reconstitution to explore molecular mechanisms for phospholipid- (PL-) rich HDL particle remodeling. The N-terminal domains of full-length apoA-I were shown to be "sticky", acting as a molecular latch largely driven by salt bridges, until, at a critical threshold of particle size, the associated domains released to expose extensive hydrocarbon regions of the PL to solvent. The "sticky" N-termini also associate with other apoA-I domains, perhaps being involved in N-terminal loops suggested by other laboratories. Alternatively, the overlapping helix 10 C-terminal domains of apoA-I were observed to be extremely mobile or "promiscuous", transiently exposing limited hydrocarbon regions of PL. Based upon these models and reconstitution studies, we propose that separation of the N-terminal domains, as particles exceed a critical size, triggers fusion between particles or between particles and membranes, while the C-terminal domains of apoA-I drive the exchange of polar lipids down concentration gradients between particles. This hypothesis has significant biological relevance since lipid exchange and particle remodeling are critically important processes during metabolism of HDL particles at every step in the antiatherogenic process of reverse cholesterol transport.
Collapse
Affiliation(s)
- Martin K Jones
- Department of Medicine and Atherosclerosis Research Unit, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | | | | | | | | |
Collapse
|
15
|
Pease LF, Tsai DH, Brorson KA, Guha S, Zachariah MR, Tarlov MJ. Physical Characterization of Icosahedral Virus Ultra Structure, Stability, and Integrity Using Electrospray Differential Mobility Analysis. Anal Chem 2011; 83:1753-9. [DOI: 10.1021/ac1030094] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Leonard F. Pease
- National Institute of Standards and Technology (NIST), 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
- Departments of Chemical Engineering, Pharmaceutics and Pharmaceutical Chemistry, and Internal Medicine, The University of Utah, Salt Lake City, Utah 84112, United States
| | - De-Hao Tsai
- National Institute of Standards and Technology (NIST), 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
- Departments of Chemistry and Mechanical Engineering, The University of Maryland, College Park, Maryland 20742, United States
| | - Kurt A. Brorson
- Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20903, United States
| | - Suvajyoti Guha
- National Institute of Standards and Technology (NIST), 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
- Departments of Chemistry and Mechanical Engineering, The University of Maryland, College Park, Maryland 20742, United States
| | - Michael R. Zachariah
- National Institute of Standards and Technology (NIST), 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
- Departments of Chemistry and Mechanical Engineering, The University of Maryland, College Park, Maryland 20742, United States
| | - Michael J. Tarlov
- National Institute of Standards and Technology (NIST), 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| |
Collapse
|
16
|
Bashtovyy D, Jones MK, Anantharamaiah GM, Segrest JP. Sequence conservation of apolipoprotein A-I affords novel insights into HDL structure-function. J Lipid Res 2010; 52:435-50. [PMID: 21159667 DOI: 10.1194/jlr.r012658] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We performed alignment of apolipoprotein A-I (apoA-I) sequences from 31 species of animals. We found there is specific conservation of salt bridge-forming residues in the first 30 residues of apoA-I and general conservation of a variety of residue types in the central domain, helix 2/3 to helix 7/8. In the lipid-associating domain, helix 7 and helix 10 are the most and least conserved helixes, respectively. Furthermore, eight residues are completely conserved: P66, R83, P121, E191, and P220, and three of seven Tyr residues in human apoA-I, Y18, Y115, and Y192, are conserved. Residue Y18 appears to be important for assembly of HDL. E191-Y192 represents the only completely conserved pair of adjacent residues in apoA-I; Y192 is a preferred target for site-specific oxidative modification within atheroma, and molecular dynamic simulations suggest that the conserved pair E191-Y192 is in a solvent-exposed loop-helix-loop. Molecular dynamics testing of human apoA-I showed that M112 and M148 interact with Y115, a microenvironment unique to human apoA-I. Finally, conservation of Arg residues in the α11/3 helical wheel position 7 supports several possibilities: interactions with adjacent phospholipid molecules and/or oxidized lipids and/or binding of antioxidant enzymes through cation-π orbital interactions. We conclude that sequence alignment of apoA-I provides unique insights into apoA-I structure-function relationship.
Collapse
Affiliation(s)
- Denys Bashtovyy
- Department of Medicine, Atherosclerosis Research Unit, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | | | | | | |
Collapse
|
17
|
Rochal SB, Lorman VL. Theory of a reconstructive structural transformation in capsids of icosahedral viruses. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 80:051905. [PMID: 20365004 DOI: 10.1103/physreve.80.051905] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Revised: 07/07/2009] [Indexed: 05/29/2023]
Abstract
A theory of a reconstructive structural transformation in icosahedral capsid shells is developed for a whole family of virulent human viruses. It is shown that the reversible rearrangement of proteins during the virus maturation transformation is driven by the variation in the wave number l associated with the protein density distribution function. The collective displacement field of protein centers from their positions in the initial (procapsid) and the final (capsid) two-dimensional icosahderal structures is derived. The amplitude of the displacement field is shown to be small and it minimizes the calculated free energy of the transformation. The theory allows us to propose a continuous thermodynamical mechanism of the reconstructive procapsid-to-capsid transformation. In the frame of the density-wave approach, we also propose to take an equivalent plane-wave vector as a common structural feature for different icosahedral capsid shells formed by the same proteins. Using these characteristics, we explain the relation between the radii of the procapsid and capsid shells and generalize it to the case of the viral capsid polymorphism.
Collapse
Affiliation(s)
- S B Rochal
- Physical Faculty, South Federal University, 5 Zorge Str., 344090 Rostov-on-Don, Russia
| | | |
Collapse
|
18
|
Lauck F, Helms V, Geyer T. Graph Measures Reveal Fine Structure of Complexes Forming in Multiparticle Simulations. J Chem Theory Comput 2009; 5:641-8. [DOI: 10.1021/ct800396v] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Florian Lauck
- Zentrum für Bioinformatik, Universität des Saarlandes, D-66041 Saarbrücken, Germany
| | - Volkhard Helms
- Zentrum für Bioinformatik, Universität des Saarlandes, D-66041 Saarbrücken, Germany
| | - Tihamér Geyer
- Zentrum für Bioinformatik, Universität des Saarlandes, D-66041 Saarbrücken, Germany
| |
Collapse
|
19
|
Abstract
Virus capsid assembly is a critical step in the viral life cycle. The underlying basis of capsid stability is key to understanding this process. Capsid subunits interact with weak individual contact energies to form a globally stable icosahedral lattice; this structure is ideal for encapsidating the viral genome and host partners and protecting its contents upon secretion, yet the unique properties of its assembly and inter-subunit contacts allow the capsid to dissociate upon entering a new host cell. The stability of the capsid can be analyzed by treating capsid assembly as an equilibrium polymerization reaction, modified from the traditional polymer model to account for the fact that a separate nucleus is formed for each individual capsid. From the concentrations of reactants and products in an equilibrated assembly reaction, it is possible to extract the thermodynamic parameters of assembly for a wide array of icosahedral viruses using well-characterized biochemical and biophysical methods. In this chapter we describe this basic analysis and provide examples of thermodynamic assembly data for several different icosahedral viruses. These data provide new insights into the assembly mechanisms of spherical virus capsids, as well as into the biology of the viral life cycle.
Collapse
Affiliation(s)
- Sarah Katen
- Department of Biology, Indiana University, Bloomington, IN 47405
| | - Adam Zlotnick
- Department of Biology, Indiana University, Bloomington, IN 47405
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| |
Collapse
|
20
|
Levy HC, Bowman VD, Govindasamy L, McKenna R, Nash K, Warrington K, Chen W, Muzyczka N, Yan X, Baker TS, Agbandje-McKenna M. Heparin binding induces conformational changes in Adeno-associated virus serotype 2. J Struct Biol 2008; 165:146-56. [PMID: 19121398 DOI: 10.1016/j.jsb.2008.12.002] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Revised: 11/29/2008] [Accepted: 12/03/2008] [Indexed: 01/08/2023]
Abstract
Adeno-associated virus serotype 2 (AAV2) uses heparan sulfate proteoglycan as a cell surface-attachment receptor. In this study the structures of AAV2 alone and complexed with heparin were determined to approximately 18A resolution using cryo-electron microscopy and three-dimensional image reconstruction. A difference map showed positive density, modeled as heparin, close to the icosahedral twofold axes and between the protrusions that surround the threefold axes of the capsid. Regions of the model near the threefold place the receptor in close proximity to basic residues previously identified as part of the heparin binding site. The region of the model near the twofold axes identifies a second contact site, not previously characterized but which is also possibly configured by heparin binding. The difference map also revealed two significant conformational changes: (I) at the tops of the threefold protrusions, which have become flattened in the complex, and (II) at the fivefold axes where the top of the channel is widened possibly in response to movement of the HI loops in the capsid proteins. Ordered density in the interior of the capsid in the AAV2-heparin complex was interpreted as nucleic acid, consistent with the presence of non-viral DNA in the expressed capsids.
Collapse
Affiliation(s)
- Hazel C Levy
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, 1600 SW Archer Road, P.O. Box 100245, University of Florida, Gainesville, FL 32610, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Morton VL, Stockley PG, Stonehouse NJ, Ashcroft AE. Insights into virus capsid assembly from non-covalent mass spectrometry. MASS SPECTROMETRY REVIEWS 2008; 27:575-95. [PMID: 18498137 PMCID: PMC7168407 DOI: 10.1002/mas.20176] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Revised: 03/07/2008] [Accepted: 03/07/2008] [Indexed: 05/25/2023]
Abstract
The assembly of viral proteins into a range of macromolecular complexes of strictly defined architecture is one of Nature's wonders. Unraveling the details of these complex structures and the associated self-assembly pathways that lead to their efficient and precise construction will play an important role in the development of anti-viral therapeutics. It will also be important in bio-nanotechnology where there is a plethora of applications for such well-defined macromolecular complexes, including cell-specific drug delivery and as substrates for the formation of novel materials with unique electrical and magnetic properties. Mass spectrometry has the ability not only to measure masses accurately but also to provide vital details regarding the composition and stoichiometry of intact, non-covalently bound macromolecular complexes under near-physiological conditions. It is thus ideal for exploring the assembly and function of viruses. Over the past decade or so, significant advances have been made in this field, and these advances are summarized in this review, which covers the literature up to the end of 2007.
Collapse
Affiliation(s)
- Victoria L. Morton
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Peter G. Stockley
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Nicola J. Stonehouse
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Alison E. Ashcroft
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| |
Collapse
|
22
|
Angelova A, Angelov B, Lesieur S, Mutafchieva R, M.Ollivon, Bourgaux C, Willumeit R, Couvreur P. Dynamic control of nanofluidic channels in protein drug delivery vehicles. J Drug Deliv Sci Technol 2008. [DOI: 10.1016/s1773-2247(08)50005-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
23
|
Lorman VL, Rochal SB. Density-wave theory of the capsid structure of small icosahedral viruses. PHYSICAL REVIEW LETTERS 2007; 98:185502. [PMID: 17501583 DOI: 10.1103/physrevlett.98.185502] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2006] [Indexed: 05/15/2023]
Abstract
We apply Landau theory of crystallization to explain and to classify the capsid structures of small viruses with spherical topology and icosahedral symmetry. We develop an explicit method which predicts the positions of centers of mass for the proteins constituting the viral capsid shell. Corresponding density distribution function which generates the positions has a universal form without any fitting parameter. The theory describes in a uniform way both the structures satisfying the well-known Caspar and Klug geometrical model for capsid construction and those violating it.
Collapse
Affiliation(s)
- V L Lorman
- Laboratoire de Physique Theorique et Astroparticules, CNRS-Universite Montpellier 2, Place Eugene Bataillon, 34095 Montpellier, France
| | | |
Collapse
|
24
|
Gonçalves RB, Mendes YS, Soares MR, Katpally U, Smith TJ, Silva JL, Oliveira AC. VP4 protein from human rhinovirus 14 is released by pressure and locked in the capsid by the antiviral compound WIN. J Mol Biol 2006; 366:295-306. [PMID: 17161425 PMCID: PMC1995025 DOI: 10.1016/j.jmb.2006.11.033] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2006] [Revised: 11/05/2006] [Accepted: 11/08/2006] [Indexed: 11/29/2022]
Abstract
Rhinoviruses are the major causative agents of the common cold in humans. Here, we studied the stability of human rhinovirus type 14 (HRV14) under conditions of high hydrostatic pressure, low temperature, and urea in the absence and presence of an antiviral drug. Capsid dissociation and changes in the protein conformation were monitored by fluorescence spectroscopy, light scattering, circular dichroism, gel filtration chromatography, mass spectrometry and infectivity assays. The data show that high pressure induces the dissociation of HRV14 and that this process is inhibited by WIN 52084. MALDI-TOF mass spectrometry experiments demonstrate that VP4, the most internal viral protein, is released from the capsid by pressure treatment. This release of VP4 is concomitant with loss of infectivity. Our studies also show that at least one antiviral effect of the WIN drugs involves the locking of VP4 inside the capsid by blocking the dynamics associated with cell attachment.
Collapse
Affiliation(s)
- Rafael B. Gonçalves
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica, CCS, Universidade Federal do Rio de Janeiro, RJ, Brazil, 21941-590
| | - Ygara S. Mendes
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica, CCS, Universidade Federal do Rio de Janeiro, RJ, Brazil, 21941-590
| | - Marcia R. Soares
- Unidade Multidisciplinar de Genômica, IBCCF, UFRJ, RJ, Brazil, 21941-590
| | - Umesh Katpally
- Donald Danforth Plant Science Center, 63132, Saint Louis, MO, USA
| | - Thomas J. Smith
- Donald Danforth Plant Science Center, 63132, Saint Louis, MO, USA
| | - Jerson L. Silva
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica, CCS, Universidade Federal do Rio de Janeiro, RJ, Brazil, 21941-590
- § To whom correspondence should be addressed: Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Av. Bauhinia, 400 - CCS/Sl. E1-008, Cidade Universitária, 21941-590, Rio de Janeiro, RJ, Brazil. Tel./Fax: + 55 21 2562-6756; e-mail: ;
| | - Andréa C. Oliveira
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica, CCS, Universidade Federal do Rio de Janeiro, RJ, Brazil, 21941-590
- § To whom correspondence should be addressed: Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Av. Bauhinia, 400 - CCS/Sl. E1-008, Cidade Universitária, 21941-590, Rio de Janeiro, RJ, Brazil. Tel./Fax: + 55 21 2562-6756; e-mail: ;
| |
Collapse
|
25
|
Lima SMB, Vaz ACQ, Souza TLF, Peabody DS, Silva JL, Oliveira AC. Dissecting the role of protein-protein and protein-nucleic acid interactions in MS2 bacteriophage stability. FEBS J 2006; 273:1463-75. [PMID: 16689932 DOI: 10.1111/j.1742-4658.2006.05167.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To investigate the role of protein-protein and protein-nucleic acid interactions in virus assembly, we compared the stabilities of native bacteriophage MS2, virus-like particles (VLPs) containing nonviral RNAs, and an assembly-defective coat protein mutant (dlFG) and its single-chain variant (sc-dlFG). Physical (high pressure) and chemical (urea and guanidine hydrochloride) agents were used to promote virus disassembly and protein denaturation, and the changes in virus and protein structure were monitored by measuring tryptophan intrinsic fluorescence, bis-ANS probe fluorescence, and light scattering. We found that VLPs dissociate into capsid proteins that remain folded and more stable than the proteins dissociated from authentic particles. The proposed model is that the capsid disassembles but the protein remains bound to the heterologous RNA encased by VLPs. The dlFG dimerizes correctly, but fails to assemble into capsids, because it lacks the 15-amino acid FG loop involved in inter-dimer interactions at the viral fivefold and quasi-sixfold axes. This protein was very unstable and, when compared with the dissociation/denaturation of the VLPs and the wild-type virus, it was much more susceptible to chemical and physical perturbation. Genetic fusion of the two subunits of the dimer in the single-chain dimer sc-dlFG stabilized the protein, as did the presence of 34-bp poly(GC) DNA. These studies reveal mechanisms by which interactions in the capsid lattice can be sufficiently stable and specific to ensure assembly, and they shed light on the processes that lead to the formation of infectious viral particles.
Collapse
Affiliation(s)
- Sheila M B Lima
- Programa de Biologia Estrutural and Centro Nacional de Ressonância Magnética Nuclear de Macromoléculas, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Brazil
| | | | | | | | | | | |
Collapse
|
26
|
Van Workum K, Douglas JF. Symmetry, equivalence, and molecular self-assembly. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2006; 73:031502. [PMID: 16605527 DOI: 10.1103/physreve.73.031502] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2005] [Indexed: 05/08/2023]
Abstract
Molecular self-assembly at equilibrium is fundamental to the fields of biological self-organization, the development of novel environmentally responsive polymeric materials, and nanofabrication. Our approach to understanding the principles governing this process is inspired by existing models and measurements for the self-assembly of actin, tubulin, and the ubiquitous icosahedral shell structures of viral capsids. We introduce a family of simple potentials that give rise to the self-assembly of linear polymeric, random surface ("membrane"), tubular ("nanotube"), and hollow icosahedral structures that are similar in many respects to their biological counterparts. The potentials involve equivalent particles and an interplay between directional (dipolar, multipolar) and short-range (van der Waals) interactions. Specifically, we find that the dipolar potential, having a continuous rotational symmetry about the dipolar axis, gives rise to chain formation, while particles with multipolar potentials, having discrete rotational symmetries (square quadrupole or triangular ring of dipoles or "hexapole"), lead to the self-assembly of open sheet, nanotube, and hollow icosahedral geometries. These changes in the geometry of self-assembly are accompanied by significant changes in the kinetics of the organization.
Collapse
Affiliation(s)
- Kevin Van Workum
- National Institute of Standards and Technology, Polymers Division, Gaithersburg, Maryland 20899, USA.
| | | |
Collapse
|
27
|
Hemberg M, Yaliraki SN, Barahona M. Stochastic kinetics of viral capsid assembly based on detailed protein structures. Biophys J 2006; 90:3029-42. [PMID: 16473916 PMCID: PMC1432130 DOI: 10.1529/biophysj.105.076737] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present a generic computational framework for the simulation of viral capsid assembly which is quantitative and specific. Starting from PDB files containing atomic coordinates, the algorithm builds a coarse-grained description of protein oligomers based on graph rigidity. These reduced protein descriptions are used in an extended Gillespie algorithm to investigate the stochastic kinetics of the assembly process. The association rates are obtained from a diffusive Smoluchowski equation for rapid coagulation, modified to account for water shielding and protein structure. The dissociation rates are derived by interpreting the splitting of oligomers as a process of graph partitioning akin to the escape from a multidimensional well. This modular framework is quantitative yet computationally tractable, with a small number of physically motivated parameters. The methodology is illustrated using two different viruses which are shown to follow quantitatively different assembly pathways. We also show how in this model the quasi-stationary kinetics of assembly can be described as a Markovian cascading process, in which only a few intermediates and a small proportion of pathways are present. The observed pathways and intermediates can be related a posteriori to structural and energetic properties of the capsid oligomers.
Collapse
Affiliation(s)
- Martin Hemberg
- Department of Bioengineering and Department of Chemistry, Imperial College London, London, United Kingdom
| | | | | |
Collapse
|
28
|
Abstract
Thermodynamic and dynamic properties of biomolecules can be calculated using a coarse-grained approach based upon sampling stationary points of the underlying potential energy surface. The superposition approximation provides an overall partition function as a sum of contributions from the local minima, and hence functions such as internal energy, entropy, free energy and the heat capacity. To obtain rates we must also sample transition states that link the local minima, and the discrete path sampling method provides a systematic means to achieve this goal. A coarse-grained picture is also helpful in locating the global minimum using the basin-hopping approach. Here we can exploit a fictitious dynamics between the basins of attraction of local minima, since the objective is to find the lowest minimum, rather than to reproduce the thermodynamics or dynamics.
Collapse
Affiliation(s)
- David J Wales
- Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK.
| |
Collapse
|
29
|
Saugar I, Luque D, Oña A, Rodríguez JF, Carrascosa JL, Trus BL, Castón JR. Structural Polymorphism of the Major Capsid Protein of a Double-Stranded RNA Virus: An Amphipathic α Helix as a Molecular Switch. Structure 2005; 13:1007-17. [PMID: 16004873 DOI: 10.1016/j.str.2005.04.012] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2004] [Revised: 04/05/2005] [Accepted: 04/05/2005] [Indexed: 11/26/2022]
Abstract
The infectious bursal disease virus T=13 viral particle is composed of two major proteins, VP2 and VP3. Here, we show that the molecular basis of the conformational flexibility of the major capsid protein precursor, pVP2, is an amphipatic alpha helix formed by the sequence GFKDIIRAIR. VP2 containing this alpha helix is able to assemble into the T=13 capsid only when expressed as a chimeric protein with an N-terminal His tag. An amphiphilic alpha helix, which acts as a conformational switch, is thus responsible for the inherent structural polymorphism of VP2. The His tag mimics the VP3 C-terminal region closely and acts as a molecular triggering factor. Using cryo-electron microscopy difference imaging, both polypeptide elements were detected on the capsid inner surface. We propose that electrostatic interactions between these two morphogenic elements are transmitted to VP2 to acquire the competent conformations for capsid assembly.
Collapse
Affiliation(s)
- Irene Saugar
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología/CSIC, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | | | | | | | | | | | | |
Collapse
|