1
|
Sleutel M, Pradhan B, Volkov AN, Remaut H. Structural analysis and architectural principles of the bacterial amyloid curli. Nat Commun 2023; 14:2822. [PMID: 37198180 DOI: 10.1038/s41467-023-38204-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 04/20/2023] [Indexed: 05/19/2023] Open
Abstract
Two decades have passed since the initial proposition that amyloids are not only (toxic) byproducts of an unintended aggregation cascade, but that they can also be produced by an organism to serve a defined biological function. That revolutionary idea was borne out of the realization that a large fraction of the extracellular matrix that holds Gram-negative cells into a persistent biofilm is composed of protein fibers (curli; tafi) with cross-β architecture, nucleation-dependent polymerization kinetics and classic amyloid tinctorial properties. The list of proteins shown to form so-called functional amyloid fibers in vivo has greatly expanded over the years, but detailed structural insights have not followed at a similar pace in part due to the associated experimental barriers. Here we combine extensive AlphaFold2 modelling and cryo-electron transmission microscopy to propose an atomic model of curli protofibrils, and their higher modes of organization. We uncover an unexpected structural diversity of curli building blocks and fibril architectures. Our results allow for a rationalization of the extreme physico-chemical robustness of curli, as well as earlier observations of inter-species curli promiscuity, and should facilitate further engineering efforts to expand the repertoire of curli-based functional materials.
Collapse
Affiliation(s)
- Mike Sleutel
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.
- Structural and Molecular Microbiology, VIB-VUB Center for Structural Biology, Brussels, Belgium.
| | - Brajabandhu Pradhan
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Structural and Molecular Microbiology, VIB-VUB Center for Structural Biology, Brussels, Belgium
| | - Alexander N Volkov
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Jean Jeener NMR Center, Brussel, Belgium
| | - Han Remaut
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.
- Structural and Molecular Microbiology, VIB-VUB Center for Structural Biology, Brussels, Belgium.
| |
Collapse
|
2
|
Morales CG, Jimenez NR, Herbst-Kralovetz MM, Lee NR. Novel Vaccine Strategies and Factors to Consider in Addressing Health Disparities of HPV Infection and Cervical Cancer Development among Native American Women. Med Sci (Basel) 2022; 10:52. [PMID: 36135837 PMCID: PMC9503187 DOI: 10.3390/medsci10030052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/31/2022] [Accepted: 09/05/2022] [Indexed: 12/24/2022] Open
Abstract
Cervical cancer is the 4th most common type of cancer in women world-wide. Many factors play a role in cervical cancer development/progression that include genetics, social behaviors, social determinants of health, and even the microbiome. The prevalence of HPV infections and cervical cancer is high and often understudied among Native American communities. While effective HPV vaccines exist, less than 60% of 13- to 17-year-olds in the general population are up to date on their HPV vaccination as of 2020. Vaccination rates are higher among Native American adolescents, approximately 85% for females and 60% for males in the same age group. Unfortunately, the burden of cervical cancer remains high in many Native American populations. In this paper, we will discuss HPV infection, vaccination and the cervicovaginal microbiome with a Native American perspective. We will also provide insight into new strategies for developing novel methods and therapeutics to prevent HPV infections and limit HPV persistence and progression to cervical cancer in all populations.
Collapse
Affiliation(s)
- Crystal G. Morales
- Department of Biology, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Nicole R. Jimenez
- Department of Obstetrics and Gynecology, College of Medicine, University of Arizona, Phoenix, AZ 85004, USA
| | - Melissa M. Herbst-Kralovetz
- Department of Obstetrics and Gynecology, College of Medicine, University of Arizona, Phoenix, AZ 85004, USA
- Department of Basic Medical Sciences, College of Medicine, University of Arizona, Phoenix, AZ 85004, USA
| | - Naomi R. Lee
- Department of Chemistry and Biochemistry, Northern Arizona University, Flagstaff, AZ 86011, USA
| |
Collapse
|
3
|
Miller JG, Hughes SA, Modlin C, Conticello VP. Structures of synthetic helical filaments and tubes based on peptide and peptido-mimetic polymers. Q Rev Biophys 2022; 55:1-103. [PMID: 35307042 DOI: 10.1017/s0033583522000014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
AbstractSynthetic peptide and peptido-mimetic filaments and tubes represent a diverse class of nanomaterials with a broad range of potential applications, such as drug delivery, vaccine development, synthetic catalyst design, encapsulation, and energy transduction. The structures of these filaments comprise supramolecular polymers based on helical arrangements of subunits that can be derived from self-assembly of monomers based on diverse structural motifs. In recent years, structural analyses of these materials at near-atomic resolution (NAR) have yielded critical insights into the relationship between sequence, local conformation, and higher-order structure and morphology. This structural information offers the opportunity for development of new tools to facilitate the predictable and reproduciblede novodesign of synthetic helical filaments. However, these studies have also revealed several significant impediments to the latter process – most notably, the common occurrence of structural polymorphism due to the lability of helical symmetry in structural space. This article summarizes the current state of knowledge on the structures of designed peptide and peptido-mimetic filamentous assemblies, with a focus on structures that have been solved to NAR for which reliable atomic models are available.
Collapse
Affiliation(s)
- Jessalyn G Miller
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA30322
| | - Spencer A Hughes
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA30322
| | - Charles Modlin
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA30322
| | | |
Collapse
|
4
|
Ostermeier L, de Oliveira GAP, Dzwolak W, Silva JL, Winter R. Exploring the polymorphism, conformational dynamics and function of amyloidogenic peptides and proteins by temperature and pressure modulation. Biophys Chem 2020; 268:106506. [PMID: 33221697 DOI: 10.1016/j.bpc.2020.106506] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/06/2020] [Accepted: 11/06/2020] [Indexed: 11/15/2022]
Abstract
Our understanding of amyloid structures and the mechanisms by which disease-associated peptides and proteins self-assemble into these fibrillar aggregates, has advanced considerably in recent years. It is also established that amyloid fibrils are generally polymorphic. The molecular structures of the aggregation intermediates and the causes of molecular and structural polymorphism are less understood, however. Such information is mandatory to explain the pathological diversity of amyloid diseases. What is also clear is that not only protein mutations, but also the physiological milieu, i.e. pH, cosolutes, crowding and surface interactions, have an impact on fibril formation. In this minireview, we focus on the effect of the less explored physical parameters temperature and pressure on the fibrillization propensity of proteins and how these variables can be used to reveal additional mechanistic information about intermediate states of fibril formation and molecular and structural polymorphism. Generally, amyloids are very stable and can resist harsh environmental conditions, such as extreme pH, high temperature and high pressure, and can hence serve as valuable functional amyloid. As an example, we discuss the effect of temperature and pressure on the catalytic activity of peptide amyloid fibrils that exhibit enzymatic activity.
Collapse
Affiliation(s)
- Lena Ostermeier
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Street 4a, 44227 Dortmund, Germany
| | - Guilherme A P de Oliveira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-901, Brazil
| | - Wojciech Dzwolak
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Pasteur 1 Str., 02-093 Warsaw, Poland.
| | - Jerson L Silva
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-901, Brazil.
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Street 4a, 44227 Dortmund, Germany.
| |
Collapse
|
5
|
Jang J, Kim K, Yoon J, Park CB. Piezoelectric materials for ultrasound-driven dissociation of Alzheimer's β-amyloid aggregate structure. Biomaterials 2020; 255:120165. [PMID: 32540759 DOI: 10.1016/j.biomaterials.2020.120165] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 05/22/2020] [Accepted: 05/30/2020] [Indexed: 01/22/2023]
Abstract
Piezoelectric materials can evoke electrochemical reactions by transferring charge carriers to reactants upon receiving mechanical stimuli. We report a newly discovered function of piezoelectric bismuth oxychloride (BiOCl) nanosheets for dissociating Alzheimer's β-amyloid (Aβ) aggregates through ultrasound-induced redox reactions. The accumulation of Aβ aggregates (e.g., Aβ fibrils, plaques) in the central nervous system is a major pathological hallmark of Alzheimer's disease (AD). Thus, clearing Aβ aggregates is considered a key for treating AD, but the dissociation of Aβ aggregates is challenging due to their extremely robust structure consisting of β-sheets. BiOCl nanosheets are a biocompatible piezoelectric material with piezocatalytic activity in response to ultrasound. Our analyses using multiple spectroscopic and microscopic tools have revealed that BiOCl nanosheets effectively disassemble Aβ fibrils under ultrasound stimulation. Sono-activated BiOCl nanosheets produce piezo-induced oxidative stress, which effectively destabilizes the β-sheets in Aβ fibrils. In vitro evolution has also shown that sono-activated BiOCl nanosheets can effectively alleviate the neuro-toxicity of Aβ fibrils. Furthermore, ex vivo evolution demonstrated that amount of Aβ plaques in AD mouse's brain slices was drastically reduced by treatment with sono-activated BiOCl nanosheets.
Collapse
Affiliation(s)
- Jinhyeong Jang
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), 335 Science Road, Daejeon, 34141, Republic of Korea
| | - Kayoung Kim
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), 335 Science Road, Daejeon, 34141, Republic of Korea
| | - Jaeho Yoon
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), 335 Science Road, Daejeon, 34141, Republic of Korea
| | - Chan Beum Park
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), 335 Science Road, Daejeon, 34141, Republic of Korea.
| |
Collapse
|
6
|
Heo Y, Kim K, Kim J, Jang J, Park CB. Near-Infrared-Active Copper Bismuth Oxide Electrodes for Targeted Dissociation of Alzheimer's β-Amyloid Aggregates. ACS APPLIED MATERIALS & INTERFACES 2020; 12:23667-23676. [PMID: 32364368 DOI: 10.1021/acsami.0c02349] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The abnormal accumulation of β-amyloid (Aβ) aggregates in the brain is a major pathological hallmark of Alzheimer's disease. We report a near-infrared (NIR)-active CuBi2O4-based photocathodic platform that can target intact Aβ aggregates and dissociate them into nontoxic species. Because of its relatively narrow band gap, CuBi2O4 exhibits strong absorption of NIR light, which allows for deeper tissue penetration and causes less photodamage to tissues compared to visible light. Furthermore, its high stability in aqueous media, biocompatibility, and robustness against photocorrosion make CuBi2O4 an ideal material for medical applications. For the targeted clearance of Aβ aggregates, we have conjugated the KLVFF peptide which specifically recognizes and captures Aβ aggregates on the surface of silver-doped CuBi2O4 (Ag:CuBi2O4). Upon illumination of NIR light under a cathodic bias, the KLVFF-immobilized Ag:CuBi2O4 (KLVFF-Ag:CuBi2O4) effectively dissociated β-sheet-rich, long, and entangled Aβ fibrillary aggregates into small fragmented, soluble species through photo-oxygenation. We also verified that the KLVFF-Ag:CuBi2O4 photocathode is biocompatible and effective in reducing Aβ aggregate-induced neurotoxicity. Our work demonstrates the potential of the KLVFF-Ag:CuBi2O4 platform for the targeted disassembly of cytotoxic, robust Aβ aggregates with the aid of NIR energy and cathodic bias.
Collapse
Affiliation(s)
- Yerin Heo
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), 335 Science Road, Daejeon 305-701, Republic of Korea
| | - Kayoung Kim
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), 335 Science Road, Daejeon 305-701, Republic of Korea
| | - Jinhyun Kim
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), 335 Science Road, Daejeon 305-701, Republic of Korea
| | - Jinhyeong Jang
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), 335 Science Road, Daejeon 305-701, Republic of Korea
| | - Chan Beum Park
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), 335 Science Road, Daejeon 305-701, Republic of Korea
| |
Collapse
|
7
|
Peng Z, Peralta MDR, Cox DL, Toney MD. Bottom-up synthesis of protein-based nanomaterials from engineered β-solenoid proteins. PLoS One 2020; 15:e0229319. [PMID: 32084222 PMCID: PMC7034853 DOI: 10.1371/journal.pone.0229319] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 01/02/2020] [Indexed: 02/04/2023] Open
Abstract
Biomolecular self-assembly is an emerging bottom-up approach for the synthesis of novel nanomaterials. DNA and viruses have both been used to create scaffolds but the former lacks chemical diversity and the latter lack spatial control. To date, the use of protein scaffolds to template materials on the nanoscale has focused on amyloidogenic proteins that are known to form fibrils or two-protein systems where a second protein acts as a cross-linker. We previously developed a unique approach for self-assembly of nanomaterials based on engineering β-solenoid proteins (BSPs) to polymerize into micrometer-length fibrils. BSPs have highly regular geometries, tunable lengths, and flat surfaces that are amenable to engineering and functionalization. Here, we present a newly engineered BSP based on the antifreeze protein of the beetle Rhagium inquisitor (RiAFP-m9), which polymerizes into stable fibrils under benign conditions. Gold nanoparticles were used to functionalize the RiAFP-m9 fibrils as well as those assembled from the previously described SBAFP-m1 protein. Cysteines incorporated into the sequences provide site-specific gold attachment. Additionally, silver was deposited on the gold-labelled fibrils by electroless plating to create nanowires. These results bolster prospects for programable self-assembly of BSPs to create scaffolds for functional nanomaterials.
Collapse
Affiliation(s)
- Zeyu Peng
- Department of Chemistry, University of California Davis, Davis, California, United States of America
- * E-mail:
| | - Maria D. R. Peralta
- Department of Chemistry, University of California Davis, Davis, California, United States of America
| | - Daniel L. Cox
- Department of Physics, University of California Davis, Davis, California, United States of America
| | - Michael D. Toney
- Department of Chemistry, University of California Davis, Davis, California, United States of America
| |
Collapse
|
8
|
Iadanza MG, Jackson MP, Hewitt EW, Ranson NA, Radford SE. A new era for understanding amyloid structures and disease. Nat Rev Mol Cell Biol 2019; 19:755-773. [PMID: 30237470 DOI: 10.1038/s41580-018-0060-8] [Citation(s) in RCA: 568] [Impact Index Per Article: 113.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The aggregation of proteins into amyloid fibrils and their deposition into plaques and intracellular inclusions is the hallmark of amyloid disease. The accumulation and deposition of amyloid fibrils, collectively known as amyloidosis, is associated with many pathological conditions that can be associated with ageing, such as Alzheimer disease, Parkinson disease, type II diabetes and dialysis-related amyloidosis. However, elucidation of the atomic structure of amyloid fibrils formed from their intact protein precursors and how fibril formation relates to disease has remained elusive. Recent advances in structural biology techniques, including cryo-electron microscopy and solid-state NMR spectroscopy, have finally broken this impasse. The first near-atomic-resolution structures of amyloid fibrils formed in vitro, seeded from plaque material and analysed directly ex vivo are now available. The results reveal cross-β structures that are far more intricate than anticipated. Here, we describe these structures, highlighting their similarities and differences, and the basis for their toxicity. We discuss how amyloid structure may affect the ability of fibrils to spread to different sites in the cell and between organisms in a prion-like manner, along with their roles in disease. These molecular insights will aid in understanding the development and spread of amyloid diseases and are inspiring new strategies for therapeutic intervention.
Collapse
Affiliation(s)
- Matthew G Iadanza
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Matthew P Jackson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Eric W Hewitt
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
| |
Collapse
|
9
|
Holtrup S, Heimerl T, Linne U, Altegoer F, Noll F, Waidner B. Biochemical characterization of the Helicobacter pylori bactofilin-homolog HP1542. PLoS One 2019; 14:e0218474. [PMID: 31233532 PMCID: PMC6590870 DOI: 10.1371/journal.pone.0218474] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 06/03/2019] [Indexed: 01/11/2023] Open
Abstract
The human pathogen Helicobacter pylori is known for its colonization of the upper digestive system, where it escapes the harsh acidic environment by hiding in the mucus layer. One factor promoting this colonization is the helical cell shape of H. pylori. Among shape determining proteins are cytoskeletal elements like the recently discovered bactofilins. Bactofilins constitute a widespread family of polymer-forming bacterial proteins whose biology is still poorly investigated. Here we describe the first biochemical analysis of the bactofilin HP1542 of H. pylori reference strain 26695. Purified HP1542 forms sheet-like 2D crystalline assemblies, which clearly depend on a natively structured C-terminus. Polymerization properties and protein stability were investigated. Additionally, we also could demarcate HP1542 from amyloid proteins that share similarities with the bactofilin DUF domain. By using zonal centrifugation of total H. pylori cell lysates and immunfluorescence analysis we revealed peripheral membrane association of HP1542 mostly pronounced near mid-cell. Interestingly our results indicate that H. pylori bactofilin does not contribute to cell wall stability. This study might act as a starting point for biophysical studies of the H. pylori bactofilin biology as well as for the investigation of bactofilin cell physiology in this organism. Importantly, this study is the first biochemical analysis of a bactofilin in a human pathogen.
Collapse
Affiliation(s)
- Sven Holtrup
- LOEWE Center for Synthetic Microbiology, Philipps-Universität, Marburg, Germany
- Faculty of Chemistry, Philipps-Universität, Marburg, Germany
| | - Thomas Heimerl
- LOEWE Center for Synthetic Microbiology, Philipps-Universität, Marburg, Germany
- Faculty of Biology, Philipps-Universität, Marburg, Germany
| | - Uwe Linne
- Faculty of Chemistry, Philipps-Universität, Marburg, Germany
| | - Florian Altegoer
- LOEWE Center for Synthetic Microbiology, Philipps-Universität, Marburg, Germany
- Faculty of Chemistry, Philipps-Universität, Marburg, Germany
| | - Frank Noll
- Faculty of Chemistry, Philipps-Universität, Marburg, Germany
| | - Barbara Waidner
- LOEWE Center for Synthetic Microbiology, Philipps-Universität, Marburg, Germany
- Faculty of Chemistry, Philipps-Universität, Marburg, Germany
| |
Collapse
|
10
|
Vance TDR, Bayer-Giraldi M, Davies PL, Mangiagalli M. Ice-binding proteins and the 'domain of unknown function' 3494 family. FEBS J 2019; 286:855-873. [PMID: 30680879 DOI: 10.1111/febs.14764] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/03/2019] [Accepted: 01/22/2019] [Indexed: 02/03/2023]
Abstract
Ice-binding proteins (IBPs) control the growth and shape of ice crystals to cope with subzero temperatures in psychrophilic and freeze-tolerant organisms. Recently, numerous proteins containing the domain of unknown function (DUF) 3494 were found to bind ice crystals and, hence, are classified as IBPs. DUF3494 IBPs constitute today the most widespread of the known IBP families. They can be found in different organisms including bacteria, yeasts and microalgae, supporting the hypothesis of horizontal transfer of its gene. Although the 3D structure is always a discontinuous β-solenoid with a triangular cross-section and an adjacent alpha-helix, DUF3494 IBPs present very diverse activities in terms of the magnitude of their thermal hysteresis and inhibition of ice recrystallization. The proteins are secreted into the environments around the host cells or are anchored on their cell membranes. This review covers several aspects of this new class of IBPs, which promise to leave their mark on several research fields including structural biology, protein biochemistry and cryobiology.
Collapse
Affiliation(s)
- Tyler D R Vance
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
| | - Maddalena Bayer-Giraldi
- Department of Glaciology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
| | - Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| |
Collapse
|
11
|
Baarda RA, Marianchuk TL, Toney MD, Cox DL. In silico stress-strain measurements on self-assembled protein lattices. SOFT MATTER 2018; 14:8095-8104. [PMID: 30159554 DOI: 10.1039/c8sm00412a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Due to their large mechanical strength and potential for functionalization, beta-solenoid proteins show promise as building blocks in biomaterials applications such as two- and three-dimensional scaffolds. We have designed simulation models of two-dimensional square and honeycomb protein lattices by covalently linking a beta-solenoid protein, the spruce budworm antifreeze protein (SBAFP), to symmetric protein multimers. Periodic boundary conditions applied to the simulation cell allow for the simulation of an infinite lattice. We use molecular dynamics to strain the lattice by deforming the simulation cell and measuring the resulting stress tensor. We evaluate the linear portion of stress-strain curves to extract the corresponding bulk and shear elastic moduli. When strained at a rate of 0.3 nm ps-1, the lattices yield a bulk modulus of approximately 3 GPa. This large elastic modulus demonstrates that 2-dimensional structures designed from beta-solenoid proteins can be expected to retain the exceptional material strength of their building blocks.
Collapse
Affiliation(s)
- Rachel A Baarda
- Department of Physics, University of California, Davis, California, USA.
| | | | - Michael D Toney
- Department of Chemistry, University of California, Davis, California, USA
| | - Daniel L Cox
- Department of Physics, University of California, Davis, California, USA.
| |
Collapse
|
12
|
Impact of membrane curvature on amyloid aggregation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1741-1764. [PMID: 29709613 DOI: 10.1016/j.bbamem.2018.04.012] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/23/2018] [Accepted: 04/25/2018] [Indexed: 12/11/2022]
Abstract
The misfolding, amyloid aggregation, and fibril formation of intrinsically disordered proteins/peptides (or amyloid proteins) have been shown to cause a number of disorders. The underlying mechanisms of amyloid fibrillation and structural properties of amyloidogenic precursors, intermediates, and amyloid fibrils have been elucidated in detail; however, in-depth examinations on physiologically relevant contributing factors that induce amyloidogenesis and lead to cell death remain challenging. A large number of studies have attempted to characterize the roles of biomembranes on protein aggregation and membrane-mediated cell death by designing various membrane components, such as gangliosides, cholesterol, and other lipid compositions, and by using various membrane mimetics, including liposomes, bicelles, and different types of lipid-nanodiscs. We herein review the dynamic effects of membrane curvature on amyloid generation and the inhibition of amyloidogenic proteins and peptides, and also discuss how amyloid formation affects membrane curvature and integrity, which are key for understanding relationships with cell death. Small unilamellar vesicles with high curvature and large unilamellar vesicles with low curvature have been demonstrated to exhibit different capabilities to induce the nucleation, amyloid formation, and inhibition of amyloid-β peptides and α-synuclein. Polymorphic amyloidogenesis in small unilamellar vesicles was revealed and may be viewed as one of the generic properties of interprotein interaction-dominated amyloid formation. Several mechanical models and phase diagrams are comprehensively shown to better explain experimental findings. The negative membrane curvature-mediated mechanisms responsible for the toxicity of pancreatic β cells by the amyloid aggregation of human islet amyloid polypeptide (IAPP) and binding of the precursors of the semen-derived enhancer of viral infection (SEVI) are also described. The curvature-dependent binding modes of several types of islet amyloid polypeptides with high-resolution NMR structures are also discussed.
Collapse
|