1
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Mo XD, Gao LP, Wang QJ, Yin J, Jing YH. Lipid accelerating the fibril of islet amyloid polypeptide aggravated the pancreatic islet injury in vitro and in vivo. Lipids Health Dis 2018. [PMID: 29523142 PMCID: PMC5845206 DOI: 10.1186/s12944-018-0694-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background The fibrillation of islet amyloid polypeptide (IAPP) triggered the amyloid deposition, then enhanced the loss of the pancreatic islet mass. However, it is not clear what factor is the determinant in development of the fibril formation. The aim of this study is to investigate the effects of lipid on IAPP fibril and its injury on pancreatic islet. Methods The fibril form of human IAPP (hIAPP) was tested using thioflavin-T fluorescence assay and transmission electron microscope technology after incubated with palmitate for 5 h at 25 °C. The cytotoxicity of fibril hIAPP was evaluated in INS-1 cells through analyzing the leakage of cell membrane and cell apoptosis. Type 2 diabetes mellitus (T2DM) animal model was induced with low dose streptozotocin combined the high-fat diet feeding for two months in rats. Plasma biochemistry parameters were measured before sacrificed. Pancreatic islet was isolated to evaluate their function. Results The results showed that co-incubation of hIAPP and palmitate induced more fibril form. Fibril hIAPP induced cell lesions including cell membrane leakage and cell apoptosis accompanied insulin mRNA decrease in INS-1 cell lines. In vivo, Plasma glucose, triglyceride, rIAPP and insulin increased in T2DM rats compared with the control group. In addition, IAPP and insulin mRNA increased in pancreatic islet of T2DM rats. Furthermore, T2DM induced the reduction of insulin receptor expression and cleaved caspase-3 overexpression in pancreatic islet. Conclusions Results in vivo and in vitro suggested that lipid and IAPP plays a synergistic effect on pancreatic islet cell damage, which implicated in enhancing the IAPP expression and accelerating the fibril formation of IAPP.
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Affiliation(s)
- Xiao-Dan Mo
- Institute of Anatomy and Histology & Embryology, Neuroscience, School of Basic Medical Sciences, Lanzhou University, No. 199 of Donggang West Road, Lanzhou City, Gansu Province, 730000, People's Republic of China
| | - Li-Ping Gao
- Institute of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Lanzhou University, No. 199 of Donggang West Road, Lanzhou City, Gansu Province, 730000, People's Republic of China
| | - Qing-Jun Wang
- Institute of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Lanzhou University, No. 199 of Donggang West Road, Lanzhou City, Gansu Province, 730000, People's Republic of China
| | - Jie Yin
- Institute of Anatomy and Histology & Embryology, Neuroscience, School of Basic Medical Sciences, Lanzhou University, No. 199 of Donggang West Road, Lanzhou City, Gansu Province, 730000, People's Republic of China
| | - Yu-Hong Jing
- Institute of Anatomy and Histology & Embryology, Neuroscience, School of Basic Medical Sciences, Lanzhou University, No. 199 of Donggang West Road, Lanzhou City, Gansu Province, 730000, People's Republic of China. .,Key Laboratory of Preclinical Study for New Drugs of Gansu province, Lanzhou University, No. 199 of Donggang West Road, Lanzhou City, Gansu Province, 730000, People's Republic of China.
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2
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Li N, Jang H, Yuan M, Li W, Yun X, Lee J, Du Q, Nussinov R, Hou J, Lal R, Zhang F. Graphite-Templated Amyloid Nanostructures Formed by a Potential Pentapeptide Inhibitor for Alzheimer's Disease: A Combined Study of Real-Time Atomic Force Microscopy and Molecular Dynamics Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:6647-6656. [PMID: 28605901 PMCID: PMC7900909 DOI: 10.1021/acs.langmuir.7b00414] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Self-assembly of peptides is closely related to many diseases, including Alzheimer's, Parkinson's, and prion diseases. Understanding the basic mechanism of this assembly is essential for designing ultimate cure and preventive measures. Template-assisted self-assembly (TASA) of peptides on inorganic substrates can provide fundamental understanding of substrate-dependent peptides assemble, including the role of hydrophobic interface on the peptide fibrillization. Here, we have studied the self-assembly process of a potential pentapeptide inhibitor on the surface of highly oriented pyrolytic graphite (HOPG) using real time atomic force microscopy (RT-AFM) as well as molecular dynamics (MD) simulation. Experimental and simulation results show nanofilament formation consisting of β-sheet structures and epitaxial growth on HOPG. Height analysis of the nanofilaments and MD simulation indicate that the peptides adopt a lying down configuration of double-layered antiparallel β-sheets for its epitaxial growth, and the number of nanofilament layers is concentration-dependent. These findings provide new perspective for the mechanism of peptide-based fibrillization in amyloid diseases as well as for designing well-ordered micrometrical and nanometrical structures.
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Affiliation(s)
- Na Li
- Agricultural Nanocenter, School of Life Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
| | - Ming Yuan
- Agricultural Nanocenter, School of Life Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China
| | - Wanrong Li
- Agricultural Nanocenter, School of Life Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China
| | - Xiaolin Yun
- Agricultural Nanocenter, School of Life Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China
| | - Joon Lee
- Materials Science and Engineering Program and Department of Mechanical and Aerospace Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093 United States
| | - Qiqige Du
- Agricultural Nanocenter, School of Life Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jiahua Hou
- Department of Biomedical Engineering, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou 511436, China
| | - Ratnesh Lal
- Materials Science and Engineering Program and Department of Mechanical and Aerospace Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093 United States
| | - Feng Zhang
- Agricultural Nanocenter, School of Life Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093 United States
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3
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Capone R, Jang H, Kotler SA, Connelly L, Teran Arce F, Ramachandran S, Kagan BL, Nussinov R, Lal R. All-d-Enantiomer of β-Amyloid Peptide Forms Ion Channels in Lipid Bilayers. J Chem Theory Comput 2012; 8:1143-1152. [PMID: 22423218 PMCID: PMC3302213 DOI: 10.1021/ct200885r] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Indexed: 12/11/2022]
Abstract
Alzheimer's disease (AD) is the most common type of senile dementia in aging populations. Amyloid β (Aβ)-mediated dysregulation of ionic homeostasis is the prevailing underlying mechanism leading to synaptic degeneration and neuronal death. Aβ-dependent ionic dysregulation most likely occurs either directly via unregulated ionic transport through the membrane or indirectly via Aβ binding to cell membrane receptors and subsequent opening of existing ion channels or transporters. Receptor binding is expected to involve a high degree of stereospecificity. Here, we investigated whether an Aβ peptide enantiomer, whose entire sequence consists of d-amino acids, can form ion-conducting channels; these channels can directly mediate Aβ effects even in the absence of receptor-peptide interactions. Using complementary approaches of planar lipid bilayer (PLB) electrophysiological recordings and molecular dynamics (MD) simulations, we show that the d-Aβ isomer exhibits ion conductance behavior in the bilayer indistinguishable from that described earlier for the l-Aβ isomer. The d isomer forms channel-like pores with heterogeneous ionic conductance similar to the l-Aβ isomer channels, and the d-isomer channel conductance is blocked by Zn(2+), a known blocker of l-Aβ isomer channels. MD simulations further verify formation of β-barrel-like Aβ channels with d- and l-isomers, illustrating that both d- and l-Aβ barrels can conduct cations. The calculated values of the single-channel conductance are approximately in the range of the experimental values. These findings are in agreement with amyloids forming Ca(2+) leaking, unregulated channels in AD, and suggest that Aβ toxicity is mediated through a receptor-independent, nonstereoselective mechanism.
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Affiliation(s)
- Ricardo Capone
- Departments of Bioengineering
and Mechanical and Aerospace Engineering and Material Science Program, University of California—San Diego, La Jolla,
California 92093, United States
| | - Hyunbum Jang
- Center for Cancer Research Nanobiology
Program, SAIC-Frederick, Incorporated,
NCI-Frederick, Frederick, Maryland 21702, United States
| | - Samuel A. Kotler
- Departments of Bioengineering
and Mechanical and Aerospace Engineering and Material Science Program, University of California—San Diego, La Jolla,
California 92093, United States
| | - Laura Connelly
- Departments of Bioengineering
and Mechanical and Aerospace Engineering and Material Science Program, University of California—San Diego, La Jolla,
California 92093, United States
| | - Fernando Teran Arce
- Departments of Bioengineering
and Mechanical and Aerospace Engineering and Material Science Program, University of California—San Diego, La Jolla,
California 92093, United States
| | - Srinivasan Ramachandran
- Departments of Bioengineering
and Mechanical and Aerospace Engineering and Material Science Program, University of California—San Diego, La Jolla,
California 92093, United States
| | - Bruce L. Kagan
- Department of Psychiatry, David
Geffen School of Medicine, Semel Institute for Neuroscience and Human
Behavior, University of California—Los Angeles, Los Angeles, California 90024, United States
| | - Ruth Nussinov
- Center for Cancer Research Nanobiology
Program, SAIC-Frederick, Incorporated,
NCI-Frederick, Frederick, Maryland 21702, United States
- Department of Human Molecular
Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ratnesh Lal
- Departments of Bioengineering
and Mechanical and Aerospace Engineering and Material Science Program, University of California—San Diego, La Jolla,
California 92093, United States
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4
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Toxic effects of expanded ataxin-1 involve mechanical instability of the nuclear membrane. Biochim Biophys Acta Mol Basis Dis 2012; 1822:906-17. [PMID: 22330095 DOI: 10.1016/j.bbadis.2012.01.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 01/26/2012] [Accepted: 01/30/2012] [Indexed: 01/01/2023]
Abstract
Ataxin 1 (ATXN1) is the protein involved in spinocerebellar ataxia type 1, one of nine dominantly inherited neurodegenerative diseases triggered by polyglutamine expansion. One of the isolated polyglutamine tracts properties is to interact with lipid bilayers. Here we used a multidisciplinary approach to test whether one of the mechanisms responsible for neuronal degeneration involves the destabilization of the nuclear membrane. We thus analyzed the interaction between ATXN1 and lipid membranes, both on cellular models and on artificial lipid bilayers, comparing pathological expanded polyglutamine and histidine interrupted non-harmful polyglutamine tracts of the same length. The toxicity of the different constructs was tested in transiently transfected COS1 cells. Cells expressing pathological ATXN1 presented a significantly higher frequency of anomalous nuclei with respect to those expressing non-harmful ATXN1. Immunofluorescence and electron microscopy showed severe damage in the nuclear membrane of cells expressing the pathological protein. Atomic force microscopy on artificial membranes containing interrupted and non-interrupted partial ATXN1 peptides revealed a different arrangement of the peptides within the lipid bilayer. Force-distance measurements indicated that membrane fragility increases with the lengthening of the uninterrupted glutamine. Transmembrane electrical measurements were performed on artificial bilayers and on the inner nuclear membrane of ATXN1 full length transfected cells. Both artificial lipid bilayers and cellular models demonstrated the dynamic appearance of ionic pathways. Uninterrupted polyglutamines showed not only a larger ionic flow, but also an increase in the single event conductance. Collectively, our results suggest that expanded ATXN1 may induce unregulated ionic pathways in the nuclear membrane, causing severe damage to the cell.
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5
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Capone R, Jang H, Kotler S, Kagan BL, Nussinov R, Lal R. Probing structural features of Alzheimer's amyloid-β pores in bilayers using site-specific amino acid substitutions. Biochemistry 2012; 51:776-85. [PMID: 22242635 PMCID: PMC3265145 DOI: 10.1021/bi2017427] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 12/29/2011] [Indexed: 11/28/2022]
Abstract
A current hypothesis for the pathology of Alzheimer's disease (AD) proposes that amyloid-β (Aβ) peptides induce uncontrolled, neurotoxic ion flux across cellular membranes. The mechanism of ion flux is not fully understood because no experiment-based Aβ channel structures at atomic resolution are currently available (only a few polymorphic states have been predicted by computational models). Structural models and experimental evidence lend support to the view that the Aβ channel is an assembly of loosely associated mobile β-sheet subunits. Here, using planar lipid bilayers and molecular dynamics (MD) simulations, we show that amino acid substitutions can be used to infer which residues are essential for channel structure. We created two Aβ(1-42) peptides with point mutations: F19P and F20C. The substitution of Phe19 with Pro inhibited channel conductance. MD simulation suggests a collapsed pore of F19P channels at the lower bilayer leaflet. The kinks at the Pro residues in the pore-lining β-strands induce blockage of the solvated pore by the N-termini of the chains. The cysteine mutant is capable of forming channels, and the conductance behavior of F20C channels is similar to that of the wild type. Overall, the mutational analysis of the channel activity performed in this work tests the proposition that the channels consist of a β-sheet rich organization, with the charged/polar central strand containing the mutation sites lining the pore, and the C-terminal strands facing the hydrophobic lipid tails. A detailed understanding of channel formation and its structure should aid studies of drug design aiming to control unregulated Aβ-dependent ion fluxes.
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Affiliation(s)
- Ricardo Capone
- Department of Bioengineering,
Department of Mechanical and Aerospace Engineering, and Material Science
Program, University of California, San Diego, La Jolla, California 92093, United States
| | - Hyunbum Jang
- Center for Cancer Research Nanobiology
Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick, Maryland 21702, United States
| | - Samuel
A. Kotler
- Department of Bioengineering,
Department of Mechanical and Aerospace Engineering, and Material Science
Program, University of California, San Diego, La Jolla, California 92093, United States
| | - Bruce L. Kagan
- Department of Psychiatry, David
Geffen School of Medicine, Semel Institute for Neuroscience and Human
Behavior, University of California, Los
Angeles, California 90024, United States
| | - Ruth Nussinov
- Center for Cancer Research Nanobiology
Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick, Maryland 21702, United States
- Department of Human Molecular
Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ratnesh Lal
- Department of Bioengineering,
Department of Mechanical and Aerospace Engineering, and Material Science
Program, University of California, San Diego, La Jolla, California 92093, United States
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6
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Zhao LN, Chiu SW, Benoit J, Chew LY, Mu Y. Amyloid β Peptides Aggregation in a Mixed Membrane Bilayer: A Molecular Dynamics Study. J Phys Chem B 2011; 115:12247-56. [DOI: 10.1021/jp2065985] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Li Na Zhao
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
| | - See-Wing Chiu
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jérôme Benoit
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
| | - Lock Yue Chew
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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7
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Chang Z, Luo Y, Zhang Y, Wei G. Interactions of Aβ25−35 β-Barrel-like Oligomers with Anionic Lipid Bilayer and Resulting Membrane Leakage: An All-Atom Molecular Dynamics Study. J Phys Chem B 2010; 115:1165-74. [DOI: 10.1021/jp107558e] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Zhongwen Chang
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, 220 Handan Road, Shanghai, 200433, China
| | - Yin Luo
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, 220 Handan Road, Shanghai, 200433, China
| | - Yun Zhang
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, 220 Handan Road, Shanghai, 200433, China
| | - Guanghong Wei
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, 220 Handan Road, Shanghai, 200433, China
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8
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Jang H, Arce FT, Ramachandran S, Capone R, Lal R, Nussinov R. β-Barrel topology of Alzheimer's β-amyloid ion channels. J Mol Biol 2010; 404:917-34. [PMID: 20970427 PMCID: PMC7291702 DOI: 10.1016/j.jmb.2010.10.025] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 10/06/2010] [Accepted: 10/15/2010] [Indexed: 11/19/2022]
Abstract
Emerging evidence supports the ion channel mechanism for Alzheimer's disease pathophysiology wherein small β-amyloid (Aβ) oligomers insert into the cell membrane, forming toxic ion channels and destabilizing the cellular ionic homeostasis. Solid-state NMR-based data of amyloid oligomers in solution indicate that they consist of a double-layered β-sheets where each monomer folds into β-strand-turn-β-strand and the monomers are stacked atop each other. In the membrane, Aβ peptides are proposed to be β-type structures. Experimental structural data available from atomic force microscopy (AFM) imaging of Aβ oligomers in membranes reveal heterogeneous channel morphologies. Previously, we modeled the channels in a non-tilted organization, parallel with the cross-membrane normal. Here, we modeled a β-barrel-like organization. β-Barrels are common in transmembrane toxin pores, typically consisting of a monomeric chain forming a pore, organized in a single-layered β-sheet with antiparallel β-strands and a right-handed twist. Our explicit solvent molecular dynamics simulations of a range of channel sizes and polymorphic turns and comparisons of these with AFM image dimensions support a β-barrel channel organization. Different from the transmembrane β-barrels where the monomers are folded into a circular β-sheet with antiparallel β-strands stabilized by the connecting loops, these Aβ barrels consist of multimeric chains forming double β-sheets with parallel β-strands, where the strands of each monomer are connected by a turn. Although the Aβ barrels adopt the right-handed β-sheet twist, the barrels still break into heterogeneous, loosely attached subunits, in good agreement with AFM images and previous modeling. The subunits appear mobile, allowing unregulated, hence toxic, ion flux.
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Affiliation(s)
- Hyunbum Jang
- Center for Cancer Research Nanobiology Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick, MD 21702, USA
| | - Fernando Teran Arce
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Srinivasan Ramachandran
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ricardo Capone
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ratnesh Lal
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ruth Nussinov
- Center for Cancer Research Nanobiology Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick, MD 21702, USA
- Department of Human Molecular Genetics, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Department of Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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9
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Jang H, Teran Arce F, Ramachandran S, Capone R, Lal R, Nussinov R. Structural convergence among diverse, toxic beta-sheet ion channels. J Phys Chem B 2010; 114:9445-51. [PMID: 20608696 PMCID: PMC2908347 DOI: 10.1021/jp104073k] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Revised: 06/22/2010] [Indexed: 12/11/2022]
Abstract
Recent studies show that an array of beta-sheet peptides, including N-terminally truncated Abeta peptides (Abeta(11-42/17-42)), K3 (a beta(2)-microglobulin fragment), and protegrin-1 (PG-1) peptides form ion channel-like structures and elicit single channel ion conductance when reconstituted in lipid bilayers and induce cell damage through cell calcium overload. Striking similarities are observed in the dimensions of these toxic channels irrespective of their amino acid sequences. However, the intriguing question of preferred channel sizes is still unresolved. Here, exploiting ssNMR-based, U-shaped, beta-strand-turn-beta-strand coordinates, we modeled truncated Abeta peptide (p3) channels with different sizes (12- to 36-mer). Molecular dynamics (MD) simulations show that optimal channel sizes of the ion channels presenting toxic ionic flux range between 16- and 24-mer. This observation is in good agreement with channel dimensions imaged by AFM for Abeta(9-42), K3 fragment, and PG-1 channels and highlights the bilayer-supported preferred toxic beta-channel sizes and organization, regardless of the peptide sequence.
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Affiliation(s)
| | | | | | | | - Ratnesh Lal
- Corresponding authors. (R.N.) Phone: 301-846-5579. Fax: 301-846-5598. E-mail: . (R.L.) E-mail:
| | - Ruth Nussinov
- Corresponding authors. (R.N.) Phone: 301-846-5579. Fax: 301-846-5598. E-mail: . (R.L.) E-mail:
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10
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Capone R, Mustata M, Jang H, Arce FT, Nussinov R, Lal R. Antimicrobial protegrin-1 forms ion channels: molecular dynamic simulation, atomic force microscopy, and electrical conductance studies. Biophys J 2010; 98:2644-52. [PMID: 20513409 PMCID: PMC2877344 DOI: 10.1016/j.bpj.2010.02.024] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Revised: 01/27/2010] [Accepted: 02/03/2010] [Indexed: 10/19/2022] Open
Abstract
Antimicrobial peptides (AMPs) are an emerging class of antibiotics for controlling health effects of antibiotic-resistant microbial strains. Protegrin-1 (PG-1) is a model antibiotic among beta-sheet AMPs. Antibiotic activity of AMPs involves cell membrane damage, yet their membrane interactions, their 3D membrane-associated structures and the mechanism underlying their ability to disrupt cell membrane are poorly understood. Using complementary approaches, including molecular dynamics simulations, atomic force microscopy (AFM) imaging, and planar lipid bilayer reconstitution, we provide computational and experimental evidence that PG-1, a beta-hairpin peptide, forms ion channels. Simulations indicate that PG-1 forms channel-like structures with loosely attached subunits when reconstituted in anionic lipid bilayers. AFM images show the presence of channel-like structures when PG-1 is reconstituted in dioleoylphosphatidylserine/palmitoyloleoyl phosphatidylethanolamine bilayers or added to preformed bilayers. Planar lipid bilayer electrical recordings show multiple single channel conductances that are consistent with the heterogeneous oligomeric channel structures seen in AFM images. PG-1 channel formation seems to be lipid-dependent: PG-1 does not easily show ion channel electrical activity in phosphatidylcholine membranes, but readily shows channel activity in membranes rich in phosphatidylethanolamine or phosphatidylserine. The combined results support a model wherein the beta-hairpin PG-1 peptide acts as an antibiotic by altering cell ionic homeostasis through ion channel formation in cell membranes.
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Affiliation(s)
- Ricardo Capone
- Center for Nanomedicine and Department of Medicine, University of Chicago, Chicago, Illinois
| | - Mirela Mustata
- Center for Nanomedicine and Department of Medicine, University of Chicago, Chicago, Illinois
| | - Hyunbum Jang
- Center for Cancer Research Nanobiology Program, NCI-Frederick, SAIC-Frederick, Inc., Frederick, Maryland
| | - Fernando Teran Arce
- Center for Nanomedicine and Department of Medicine, University of Chicago, Chicago, Illinois
| | - Ruth Nussinov
- Center for Cancer Research Nanobiology Program, NCI-Frederick, SAIC-Frederick, Inc., Frederick, Maryland
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ratnesh Lal
- Center for Nanomedicine and Department of Medicine, University of Chicago, Chicago, Illinois
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11
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De Simone A, Derreumaux P. Low molecular weight oligomers of amyloid peptides display β-barrel conformations: A replica exchange molecular dynamics study in explicit solvent. J Chem Phys 2010; 132:165103. [DOI: 10.1063/1.3385470] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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12
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Jang H, Arce FT, Ramachandran S, Capone R, Azimova R, Kagan BL, Nussinov R, Lal R. Truncated beta-amyloid peptide channels provide an alternative mechanism for Alzheimer's Disease and Down syndrome. Proc Natl Acad Sci U S A 2010; 107:6538-43. [PMID: 20308552 PMCID: PMC2851998 DOI: 10.1073/pnas.0914251107] [Citation(s) in RCA: 185] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Full-length amyloid beta peptides (Abeta(1-40/42)) form neuritic amyloid plaques in Alzheimer's disease (AD) patients and are implicated in AD pathology. However, recent transgenic animal models cast doubt on their direct role in AD pathology. Nonamyloidogenic truncated amyloid-beta fragments (Abeta(11-42) and Abeta(17-42)) are also found in amyloid plaques of AD and in the preamyloid lesions of Down syndrome, a model system for early-onset AD study. Very little is known about the structure and activity of these smaller peptides, although they could be the primary AD and Down syndrome pathological agents. Using complementary techniques of molecular dynamics simulations, atomic force microscopy, channel conductance measurements, calcium imaging, neuritic degeneration, and cell death assays, we show that nonamyloidogenic Abeta(9-42) and Abeta(17-42) peptides form ion channels with loosely attached subunits and elicit single-channel conductances. The subunits appear mobile, suggesting insertion of small oligomers, followed by dynamic channel assembly and dissociation. These channels allow calcium uptake in amyloid precursor protein-deficient cells. The channel mediated calcium uptake induces neurite degeneration in human cortical neurons. Channel conductance, calcium uptake, and neurite degeneration are selectively inhibited by zinc, a blocker of amyloid ion channel activity. Thus, truncated Abeta fragments could account for undefined roles played by full length Abetas and provide a unique mechanism of AD and Down syndrome pathologies. The toxicity of nonamyloidogenic peptides via an ion channel mechanism necessitates a reevaluation of the current therapeutic approaches targeting the nonamyloidogenic pathway as avenue for AD treatment.
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Affiliation(s)
- Hyunbum Jang
- Center for Cancer Research Nanobiology Program, SAIC-Frederick, Inc., National Cancer Institute, Frederick, MD 21702
| | - Fernando Teran Arce
- Center for Nanomedicine and Department of Medicine, University of Chicago, Chicago, IL 60637
| | - Srinivasan Ramachandran
- Center for Nanomedicine and Department of Medicine, University of Chicago, Chicago, IL 60637
| | - Ricardo Capone
- Center for Nanomedicine and Department of Medicine, University of Chicago, Chicago, IL 60637
| | - Rushana Azimova
- Semel Neuropsychiatric Institute, The David Geffen School of Medicine, University of California at Los Angeles and Greater Los Angeles Veterans Administration Health System, Los Angeles, CA 90024; and
| | - Bruce L. Kagan
- Semel Neuropsychiatric Institute, The David Geffen School of Medicine, University of California at Los Angeles and Greater Los Angeles Veterans Administration Health System, Los Angeles, CA 90024; and
| | - Ruth Nussinov
- Center for Cancer Research Nanobiology Program, SAIC-Frederick, Inc., National Cancer Institute, Frederick, MD 21702
- Department of Human Molecular Genetics and Biochemistry, The Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ratnesh Lal
- Center for Nanomedicine and Department of Medicine, University of Chicago, Chicago, IL 60637
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13
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Jang H, Arce FT, Capone R, Ramachandran S, Lal R, Nussinov R. Misfolded amyloid ion channels present mobile beta-sheet subunits in contrast to conventional ion channels. Biophys J 2010; 97:3029-37. [PMID: 19948133 DOI: 10.1016/j.bpj.2009.09.014] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Revised: 08/31/2009] [Accepted: 09/10/2009] [Indexed: 02/05/2023] Open
Abstract
In Alzheimer's disease, calcium permeability through cellular membranes appears to underlie neuronal cell death. It is increasingly accepted that calcium permeability involves toxic ion channels. We modeled Alzheimer's disease ion channels of different sizes (12-mer to 36-mer) in the lipid bilayer using molecular dynamics simulations. Our Abeta channels consist of the solid-state NMR-based U-shaped beta-strand-turn-beta-strand motif. In the simulations we obtain ion-permeable channels whose subunit morphologies and shapes are consistent with electron microscopy/atomic force microscopy. In agreement with imaged channels, the simulations indicate that beta-sheet channels break into loosely associated mobile beta-sheet subunits. The preferred channel sizes (16- to 24-mer) are compatible with electron microscopy/atomic force microscopy-derived dimensions. Mobile subunits were also observed for beta-sheet channels formed by cytolytic PG-1 beta-hairpins. The emerging picture from our large-scale simulations is that toxic ion channels formed by beta-sheets spontaneously break into loosely interacting dynamic units that associate and dissociate leading to toxic ionic flux. This sharply contrasts intact conventional gated ion channels that consist of tightly interacting alpha-helices that robustly prevent ion leakage, rather than hydrogen-bonded beta-strands. The simulations suggest why conventional gated channels evolved to consist of interacting alpha-helices rather than hydrogen-bonded beta-strands that tend to break in fluidic bilayers. Nature designs folded channels but not misfolded toxic channels.
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Affiliation(s)
- Hyunbum Jang
- Center for Cancer Research Nanobiology Program, NCI-Frederick, SAIC-Frederick, Frederick, Maryland, USA.
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14
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Lindner AB, Demarez A. Protein aggregation as a paradigm of aging. Biochim Biophys Acta Gen Subj 2009; 1790:980-96. [PMID: 19527771 DOI: 10.1016/j.bbagen.2009.06.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Revised: 06/08/2009] [Accepted: 06/09/2009] [Indexed: 12/23/2022]
Abstract
The process of physiological decline leading to death of the individual is driven by the deteriorating capacity to withstand extrinsic and intrinsic hazards, resulting in damage accumulation with age. The dynamic changes with time of the network governing the outcome of misfolded proteins, exemplifying as intrinsic hazards, is considered here as a paradigm of aging. The main features of the network, namely, the non-linear increase of damage and the presence of amplifying feedback loops within the system are presented through a survey of the different components of the network and related cellular processes in aging and disease.
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Affiliation(s)
- Ariel B Lindner
- INSERM U571, Paris Descartes University, Paris, F-75015, France.
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15
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Engel MFM. Membrane permeabilization by Islet Amyloid Polypeptide. Chem Phys Lipids 2009; 160:1-10. [PMID: 19501206 DOI: 10.1016/j.chemphyslip.2009.03.008] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2009] [Revised: 03/26/2009] [Accepted: 03/27/2009] [Indexed: 01/14/2023]
Abstract
Membrane permeabilization by Islet Amyloid Polypeptide (IAPP) is suggested to be the main mechanism for IAPP-induced cytotoxicity and death of insulin-producing beta-cells in type 2 diabetes mellitus (T2DM). The insoluble fibrillar IAPP deposits (amyloid) present in the pancreas of most T2DM patients are not the primary suspects responsible for permeabilization of beta-cell membranes. Instead, soluble IAPP oligomers are thought to be cytotoxic by forming membrane channels or by inducing bilayer disorder. In addition, the elongation of IAPP fibrils at the membrane, but not the fibrils themselves, could cause membrane disruption. Recent reports substantiate the formation of an alpha-helical, membrane-bound IAPP monomer as possible intermediate on the aggregation pathway. Here, the structures and membrane interactions of various IAPP species will be reviewed, and the proposed hypotheses for IAPP-induced membrane permeabilization and cytotoxicity will be discussed.
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Affiliation(s)
- Maarten F M Engel
- Astbury Centre for Structural Molecular Biology and Institute of Molecular and Cellular Biology, University of Leeds, UK.
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16
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Abstract
Hydrophobicity manifests itself differently on large and small length scales. This review focuses on large-length-scale hydrophobicity, particularly on dewetting at single hydrophobic surfaces and drying in regions bounded on two or more sides by hydrophobic surfaces. We review applicable theories, simulations, and experiments pertaining to large-scale hydrophobicity in physical and biomolecular systems and clarify some of the critical issues pertaining to this subject. Given space constraints, we cannot review all the significant and interesting work in this active field.
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Affiliation(s)
- Bruce J Berne
- Department of Chemistry, Columbia University, New York, New York 10027, USA.
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17
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Jang H, Zheng J, Lal R, Nussinov R. New structures help the modeling of toxic amyloidbeta ion channels. Trends Biochem Sci 2008; 33:91-100. [PMID: 18182298 DOI: 10.1016/j.tibs.2007.10.007] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2007] [Revised: 10/18/2007] [Accepted: 10/19/2007] [Indexed: 11/16/2022]
Abstract
The mechanism of amyloid toxicity is poorly understood and there are two schools of thought in this hotly debated field: the first favors membrane destabilization by intermediate-to-large amyloid oligomers, with consequent thinning and non-specific ion leakage; the second favors ion-specific permeable channels lined by small amyloid oligomers. Published results currently support both mechanisms. However, the amyloidbeta (Abeta) peptide has recently been shown to form a U-shaped 'beta-strand-turn-beta-strand' structure. This structure and the available physiological data present a challenge for computational biology--to provide candidate models consistent with the experimental data. Modeling based on small Abeta oligomers containing extramembranous N-termini predicts channels with shapes and dimensions consistent with experimentally derived channel structures. These results support the hypothesis that small Abeta oligomers can form ion channels. Molecular dynamics modeling can provide blueprints of 3D structural conformations for many other amyloids whose membrane association is key to their toxicity.
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Affiliation(s)
- Hyunbum Jang
- Center for Cancer Research Nanobiology Program, SAIC-Frederick Inc. NCI-Frederick, Frederick, MD 21702, USA
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18
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Abstract
Recent NMR experiments have revealed that a single residue mutation W62G on protein hen's-egg white lysozyme can cause a dramatic loss of long-range interactions and protein stability; however, the molecular mechanism for this surprising phenomenon is not completely clear. In this mini-review, we have summarized some of our recent work on the molecular mechanism with large-scale molecular modelling, and also utilized a new wavelet method to analyse the local structural clusters present in both the wild-type and mutant folding trajectories. These extensive MD (Molecular Dynamics) simulations (10+ μs) were performed in 8 M urea, mimicking the experimental condition. Detailed analyses revealed that the Trp62 residue is the key to a co-operative long-range interaction within the wild-type protein: it acts as a bridge between neighbouring basic residues, mainly arginine residues, through π-type hydrogen bonds or π-cation interactions to form an Arg-Trp-Arg ‘sandwich-like’ local structure. The local cluster near Trp62 further extends its interaction to other clusters, such as the one near Trp111, through Arg112, which is involved in such an Arg-Trp-Arg bridging structure, thus achieving the long-range interactions for the wild-type. On the other hand, the mutant does not have this bridging effect and forms much less local clusters or contacts, and therefore results in a much less stable structure. Overall, these findings not only support the general conclusions of the experiment, but also provide a detailed but somewhat different molecular picture of the disruption of the long-range interactions.
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19
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Zhou R, Eleftheriou M, Royyuru AK, Berne BJ. Destruction of long-range interactions by a single mutation in lysozyme. Proc Natl Acad Sci U S A 2007; 104:5824-9. [PMID: 17389393 PMCID: PMC1851576 DOI: 10.1073/pnas.0701249104] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We propose a mechanism, based on a > or =10-micros molecular dynamics simulation, for the surprising misfolding of hen egg-white lysozyme caused by a single mutation (W62G). Our simulations of the wild-type and mutant lysozymes in 8 M urea solution at biological temperature (with both pH 2 and 7) reveal that the mutant structure is much less stable than that of the wild type, with the mutant showing larger fluctuations and less native-like contacts. Analysis of local contacts reveals that the Trp-62 residue is the key to a cooperative long-range interaction within the wild type, where it acts like a bridge between two neighboring basic residues. Thus, a native-like cluster or nucleation site can form near these residues in the wild type but not in the mutant. The time evolution of the secondary structure also exhibits a quicker loss of the beta-sheets in the mutant than in the wild type, whereas some of the alpha-helices persist during the entire simulation in both the wild type and the mutant in 8 M urea (even though the tertiary structures are basically all gone). These findings, while supporting the general conclusions of a recent experimental study by Dobson and coworkers [Klein-Seetharam J, Oikama M, Grimshaw SB, Wirmer J, Duchardt E, Ueda T, Imoto T, Smith LJ, Dobson CM, Schwalbe H (2002) Science 295:1719-1722], provide a detailed but different molecular picture of the misfolding mechanism.
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Affiliation(s)
- Ruhong Zhou
- *Computational Biology Center, Deep Computing Institute, IBM Watson Research Center, Yorktown Heights, NY 10598; and
- Department of Chemistry, Columbia University, New York, NY 10027
- To whom correspondence may be addressed. E-mail: or
| | - Maria Eleftheriou
- *Computational Biology Center, Deep Computing Institute, IBM Watson Research Center, Yorktown Heights, NY 10598; and
| | - Ajay K. Royyuru
- *Computational Biology Center, Deep Computing Institute, IBM Watson Research Center, Yorktown Heights, NY 10598; and
| | - Bruce J. Berne
- *Computational Biology Center, Deep Computing Institute, IBM Watson Research Center, Yorktown Heights, NY 10598; and
- Department of Chemistry, Columbia University, New York, NY 10027
- To whom correspondence may be addressed. E-mail: or
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Eleftheriou M, Germain RS, Royyuru AK, Zhou R. Thermal Denaturing of Mutant Lysozyme with Both the OPLSAA and the CHARMM Force Fields. J Am Chem Soc 2006; 128:13388-95. [PMID: 17031950 DOI: 10.1021/ja060972s] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Biomolecular simulations enabled by massively parallel supercomputers such as BlueGene/L promise to bridge the gap between the currently accessible simulation time scale and the experimental time scale for many important protein folding processes. In this study, molecular dynamics simulations were carried out for both the wild-type and the mutant hen lysozyme (TRP62GLY) to study the single mutation effect on lysozyme stability and misfolding. Our thermal denaturing simulations at 400-500 K with both the OPLSAA and the CHARMM force fields show that the mutant structure is indeed much less stable than the wild-type, which is consistent with the recent urea denaturing experiment (Dobson et al. Science 2002, 295, 1719-1722; Nature 2003, 424, 783-788). Detailed results also reveal that the single mutation TRP62GLY first induces the loss of native contacts in the beta-domain region of the lysozyme protein at high temperatures, and then the unfolding process spreads into the alpha-domain region through Helix C. Even though the OPLSAA force field in general shows a more stable protein structure than does the CHARMM force field at high temperatures, the two force fields examined here display qualitatively similar results for the misfolding process, indicating that the thermal denaturing of the single mutation is robust and reproducible with various modern force fields.
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Affiliation(s)
- Maria Eleftheriou
- Computational Biology Center, Deep Computing Institute, IBM Watson Research Center, Yorktown Heights, NY 10598, USA
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