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Wang Z, Zhao C, Li Y, Wang J, Hou D, Wang L, Wang Y, Wang X, Liu X, Wang H, Xu W. Photostable Cascade-Activatable Peptide Self-Assembly on a Cancer Cell Membrane for High-Performance Identification of Human Bladder Cancer. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2210732. [PMID: 37172955 DOI: 10.1002/adma.202210732] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 05/10/2023] [Indexed: 05/15/2023]
Abstract
Missed or residual tumor burden results in high risk for bladder cancer relapse. However, existing fluorescent probes cannot meet the clinical needs because of inevitable photobleaching properties. Performance can be improved by maintaining intensive and sustained fluorescence signals via resistance to intraoperative saline flushing and intrinsic fluorescent decay, providing surgeons with sufficiently clear and high-contrast surgical fields, avoiding residual tumors or missed diagnosis. This study designs and synthesizes a photostable cascade-activatable peptide, a target reaction-induced aggregation peptide (TRAP) system, which can construct polypeptide-based nanofibers in situ on the cell membrane to achieve long-term and stable imaging of bladder cancer. The probe has two parts: a target peptide (TP) targets CD44v6 to recognize bladder cancer cells, and a reaction-induced aggregation peptide (RAP) is introduced, which effectively reacts with the TP via a click reaction to enhance the hydrophobicity of the whole molecule, assembling into nanofibers and further nanonetworks. Accordingly, probe retention on the cell membrane is prolonged, and photostability is significantly improved. Finally, the TRAP system is successfully employed in the high-performance identification of human bladder cancer in ex vivo bladder tumor tissues. This cascade-activatable peptide molecular probe based on the TRAP system enables efficient and stable imaging of bladder cancer.
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Affiliation(s)
- Ziqi Wang
- NHC and CAMS Key Laboratory of Molecular Probes and Targeted Theranostics, Harbin Medical University, Harbin, 150001, China
- Department of Urology, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Changhao Zhao
- NHC and CAMS Key Laboratory of Molecular Probes and Targeted Theranostics, Harbin Medical University, Harbin, 150001, China
- Department of Urology, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Yaowei Li
- NHC and CAMS Key Laboratory of Molecular Probes and Targeted Theranostics, Harbin Medical University, Harbin, 150001, China
- Department of Urology, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Jiaqi Wang
- NHC and CAMS Key Laboratory of Molecular Probes and Targeted Theranostics, Harbin Medical University, Harbin, 150001, China
- Department of Urology, Harbin Medical University Cancer Hospital, Harbin, 150081, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
| | - Dayong Hou
- NHC and CAMS Key Laboratory of Molecular Probes and Targeted Theranostics, Harbin Medical University, Harbin, 150001, China
- Department of Urology, Harbin Medical University Cancer Hospital, Harbin, 150081, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
| | - Lu Wang
- Department of Urology, the Fourth Hospital of Harbin Medical University, Heilongjiang Key Laboratory of Scientific Research in Urology, Harbin, 150001, China
| | - Yueze Wang
- NHC and CAMS Key Laboratory of Molecular Probes and Targeted Theranostics, Harbin Medical University, Harbin, 150001, China
- Department of Urology, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Xunwei Wang
- Department of Urology, the Fourth Hospital of Harbin Medical University, Heilongjiang Key Laboratory of Scientific Research in Urology, Harbin, 150001, China
| | - Xiao Liu
- NHC and CAMS Key Laboratory of Molecular Probes and Targeted Theranostics, Harbin Medical University, Harbin, 150001, China
- Department of Urology, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Hao Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
| | - Wanhai Xu
- NHC and CAMS Key Laboratory of Molecular Probes and Targeted Theranostics, Harbin Medical University, Harbin, 150001, China
- Department of Urology, Harbin Medical University Cancer Hospital, Harbin, 150081, China
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2
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Nguyen PH, Derreumaux P. Multistep molecular mechanisms of Aβ16-22 fibril formation revealed by lattice Monte Carlo simulations. J Chem Phys 2023; 158:235101. [PMID: 37318171 DOI: 10.1063/5.0149419] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/26/2023] [Indexed: 06/16/2023] Open
Abstract
As a model of self-assembly from disordered monomers to fibrils, the amyloid-β fragment Aβ16-22 was subject to past numerous experimental and computational studies. Because dynamics information between milliseconds and seconds cannot be assessed by both studies, we lack a full understanding of its oligomerization. Lattice simulations are particularly well suited to capture pathways to fibrils. In this study, we explored the aggregation of 10 Aβ16-22 peptides using 65 lattice Monte Carlo simulations, each simulation consisting of 3 × 109 steps. Based on a total of 24 and 41 simulations that converge and do not converge to the fibril state, respectively, we are able to reveal the diversity of the pathways leading to fibril structure and the conformational traps slowing down the fibril formation.
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Affiliation(s)
- Phuong H Nguyen
- CNRS, Université Paris Cité, UPR 9080, Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- CNRS, Université Paris Cité, UPR 9080, Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005 Paris, France
- Institut Universitaire de France (IUF), 75005 Paris, France
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3
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Nguyen PH, Sterpone F, Derreumaux P. Metastable alpha-rich and beta-rich conformations of small Aβ42 peptide oligomers. Proteins 2023. [PMID: 37038252 DOI: 10.1002/prot.26495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/15/2023] [Accepted: 03/23/2023] [Indexed: 04/12/2023]
Abstract
Probing the structures of amyloid-β (Aβ) peptides in the early steps of aggregation is extremely difficult experimentally and computationally. Yet, this knowledge is extremely important as small oligomers are the most toxic species. Experiments and simulations on Aβ42 monomer point to random coil conformations with either transient helical or β-strand content. Our current conformational description of small Aβ42 oligomers is funneled toward amorphous aggregates with some β-sheet content and rare high energy states with well-ordered assemblies of β-sheets. In this study, we emphasize another view based on metastable α-helix bundle oligomers spanning the C-terminal residues, which are predicted by the machine-learning AlphaFold2 method and supported indirectly by low-resolution experimental data on many amyloid polypeptides. This finding has consequences in developing novel chemical tools and to design potential therapies to reduce aggregation and toxicity.
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Affiliation(s)
- Phuong H Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Paris Cité, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 rue Pierre et Marie Curie, Paris, 75005, France
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Paris Cité, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 rue Pierre et Marie Curie, Paris, 75005, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Paris Cité, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 rue Pierre et Marie Curie, Paris, 75005, France
- Institut Universitaire de France (IUF), Paris, 75005, France
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4
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Nedaei H, Rezaei-Ghaleh N, Giller K, Becker S, Karami L, Moosavi-Movahedi AA, Griesinger C, Saboury AA. The Calcium-free form of Atorvastatin inhibits amyloid-β(1-42) aggregation in vitro. J Biol Chem 2022; 298:101662. [PMID: 35104501 PMCID: PMC8898965 DOI: 10.1016/j.jbc.2022.101662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/13/2022] [Accepted: 01/16/2022] [Indexed: 11/29/2022] Open
Abstract
Alzheimer's disease is characterized by the presence of extraneuronal amyloid plaques composed of amyloid-beta (Aβ) fibrillar aggregates in the brains of patients. In mouse models, it has previously been shown that atorvastatin (Ator), a cholesterol-lowering drug, has some reducing effect on the production of cerebral Aβ. A meta-analysis on humans showed moderate effects in the short term but no improvement in the Alzheimer's Disease Assessment Scale—Cognitive Subscale behavioral test. Here, we explore a potential direct effect of Ator on Aβ42 aggregation. Using NMR-based monomer consumption assays and CD spectroscopy, we observed a promoting effect of Ator in its original form (Ator-calcium) on Aβ42 aggregation, as expected because of the presence of calcium ions. The effect was reversed when applying a CaCO3-based calcium ion scavenging method, which was validated by the aforementioned methods as well as thioflavin-T fluorescence assays and transmission electron microscopy. We found that the aggregation was inhibited significantly when the concentration of calcium-free Ator exceeded that of Aβ by at least a factor of 2. The 1H–15N heteronuclear single quantum correlation and saturation-transfer difference NMR data suggest that calcium-free Ator exerts its effect through interaction with the 16KLVF19 binding site on the Aβ peptide via its aromatic rings as well as hydroxyl and methyl groups. On the other hand, molecular dynamics simulations confirmed that the increasing concentration of Ator is necessary for the inhibition of the conformational transition of Aβ from an α-helix-dominant to a β-sheet-dominant structure.
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Affiliation(s)
- Hadi Nedaei
- Department of Biophysics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Nasrollah Rezaei-Ghaleh
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Institute of Physical Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Karin Giller
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Stefan Becker
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Leila Karami
- Department of Cell and Molecular Biology, Kharazmi University, Tehran, Iran
| | - Ali Akbar Moosavi-Movahedi
- Department of Biophysics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Christian Griesinger
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
| | - Ali Akbar Saboury
- Department of Biophysics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.
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5
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Nguyen PH, Derreumaux P. Computer Simulations Aimed at Exploring Protein Aggregation and Dissociation. Methods Mol Biol 2022; 2340:175-196. [PMID: 35167075 DOI: 10.1007/978-1-0716-1546-1_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein aggregation can lead to well-defined structures that are functional, but is also the cause of the death of neuron cells in many neurodegenerative diseases. The complexity of the molecular events involved in the aggregation kinetics of amyloid proteins and the transient and heterogeneous characters of all oligomers prevent high-resolution structural experiments. As a result, computer simulations have been used to determine the atomic structures of amyloid proteins at different association stages as well as to understand fibril dissociation. In this chapter, we first review the current computer simulation methods used for aggregation with some atomistic and coarse-grained results aimed at better characterizing the early formed oligomers and amyloid fibril formation. Then we present the applications of non-equilibrium molecular dynamics simulations to comprehend the dissociation of protein assemblies.
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Affiliation(s)
- Phuong H Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université de Paris, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université de Paris, Paris, France.
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France.
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6
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Nguyen PH, Tufféry P, Derreumaux P. Dynamics of Amyloid Formation from Simplified Representation to Atomistic Simulations. Methods Mol Biol 2022; 2405:95-113. [PMID: 35298810 DOI: 10.1007/978-1-0716-1855-4_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Amyloid fibril formation is an intrinsic property of short peptides, non-disease proteins, and proteins associated with neurodegenerative diseases. Aggregates of the Aβ and tau proteins, the α-synuclein protein, and the prion protein are observed in the brain of Alzheimer's, Parkinson's, and prion disease patients, respectively. Due to the transient short-range and long-range interactions of all species and their high aggregation propensities, the conformational ensemble of these devastating proteins, the exception being for the monomeric prion protein, remains elusive by standard structural biology methods in bulk solution and in lipid membranes. To overcome these limitations, an increasing number of simulations using different sampling methods and protein models have been performed. In this chapter, we first review our main contributions to the field of amyloid protein simulations aimed at understanding the early aggregation steps of short linear amyloid peptides, the conformational ensemble of the Aβ40/42 dimers in bulk solution, and the stability of Aβ aggregates in lipid membrane models. Then we focus on our studies on the interactions of amyloid peptides/inhibitors to prevent aggregation, and long amyloid sequences, including new results on a monomeric tau construct.
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Affiliation(s)
- Phuong Hoang Nguyen
- Laboratoire de Biochimie Théorique, CNRS, Université de Paris, UPR 9080, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Pierre Tufféry
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, RPBS, Paris, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, CNRS, Université de Paris, UPR 9080, Paris, France.
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France.
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7
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An H, Mamuti M, Wang X, Yao H, Wang M, Zhao L, Li L. Rationally designed modular drug delivery platform based on intracellular peptide self‐assembly. EXPLORATION 2021; 1:20210153. [PMCID: PMC10190849 DOI: 10.1002/exp.20210153] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/08/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Hong‐Wei An
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety National Center for Nanoscience and Technology (NCNST) Beijing China
| | - Muhetaerjiang Mamuti
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety National Center for Nanoscience and Technology (NCNST) Beijing China
| | - Xiaofeng Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics Chinese Academy of Sciences (CAS) Beijing China
| | - Haodong Yao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics Chinese Academy of Sciences (CAS) Beijing China
| | - Man‐Di Wang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety National Center for Nanoscience and Technology (NCNST) Beijing China
| | - Lina Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics Chinese Academy of Sciences (CAS) Beijing China
| | - Li‐Li Li
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety National Center for Nanoscience and Technology (NCNST) Beijing China
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8
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Sahoo A, Matysiak S. Effects of applied surface-tension on membrane-assisted Aβ aggregation. Phys Chem Chem Phys 2021; 23:20627-20633. [PMID: 34514475 DOI: 10.1039/d1cp02642a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Accumulation of protein-based (Aβ) aggregates on cellular membranes with varying structural properties is commonly recognized as the key step in Alzheimer's pathogenesis. But experimental and computational challenges have made this biophysical characterization difficult. In particular, studies connecting biological membrane organization and Aβ aggregation are limited. While experiments have suggested that an increased membrane curvature results in faster Aβ peptide aggregation in the context of Alzheimer's disease, a mechanistic explanation for this relation is missing. In this work, we are leveraging molecular simulations with a physics-based coarse grained model to address and understand the relationships between curved cellular membranes and aggregation of a model template peptide Aβ 16-22. In agreement with experimental results, our simulations also suggest a positive correlation between increased peptide aggregation and membrane curvature. More curved membranes have higher lipid packing defects that engage peptide hydrophobic groups and promote faster diffusion leading to peptide fibrillar structures. In addition, we curated the effects of peptide aggregation on the membrane's structure and organization. Interfacial peptide aggregation results in heterogeneous headgroup-peptide interactions and an induced crowding effect at the lipid headgroup region, leading to a more ordered headgroup region and disordered lipid-tails at the membrane core. This work presents a mechanistic and morphological overview of the relationships between the biomembrane local structure and organization, and Aβ peptide aggregation.
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Affiliation(s)
- Abhilash Sahoo
- Biophysics Program, Institute of Physical Science and Technology, University of Maryland, College Park, MD, USA
| | - Silvina Matysiak
- Biophysics Program, Institute of Physical Science and Technology, University of Maryland, College Park, MD, USA.,Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA.
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Illig AM, Strodel B. Performance of Markov State Models and Transition Networks on Characterizing Amyloid Aggregation Pathways from MD Data. J Chem Theory Comput 2020; 16:7825-7839. [DOI: 10.1021/acs.jctc.0c00727] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alexander-Maurice Illig
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Birgit Strodel
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52428 Jülich, Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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10
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Samantray S, Yin F, Kav B, Strodel B. Different Force Fields Give Rise to Different Amyloid Aggregation Pathways in Molecular Dynamics Simulations. J Chem Inf Model 2020; 60:6462-6475. [DOI: 10.1021/acs.jcim.0c01063] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Suman Samantray
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülch, 52428 Jülich, Germany
- AICES Graduate School, RWTH Aachen University, Schinkelstraße 2, 52062 Aachen, Germany
| | - Feng Yin
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülch, 52428 Jülich, Germany
| | - Batuhan Kav
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülch, 52428 Jülich, Germany
| | - Birgit Strodel
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülch, 52428 Jülich, Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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11
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Xiao WY, Wang Y, An HW, Hou D, Mamuti M, Wang MD, Wang J, Xu W, Hu L, Wang H. Click Reaction-Assisted Peptide Immune Checkpoint Blockade for Solid Tumor Treatment. ACS APPLIED MATERIALS & INTERFACES 2020; 12:40042-40051. [PMID: 32805827 DOI: 10.1021/acsami.0c10166] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
One of the major challenges of immune checkpoint blockade (ICB) is the poor penetration of antibody for solid tumor treatment. Herein, peptides with deeper penetration capability are used to develop a click reaction-assisted peptide immune checkpoint blockade (CRICB) strategy that could in situ construct assemblies, enabling enhanced accumulation and prolonged PD-L1 occupancy, ultimately realizing high-performance tumor inhibition. First, the free DBCO-modified targeting peptide (TP) efficiently recognizes and binds PD-L1 in a deep solid tumor. Upon a reagent-free click reaction with a subsequently introduced azide-tethered assembled peptide (AP), the click reaction results in spontaneous self-aggregation in situ with enhanced accumulation and prolonged occupancy. In addition, the penetration of TP-AP (121.2 ± 15.5 μm) is significantly enhanced compared with that of an antibody (19.9 ± 5.6 μm) in a solid tumor tissue. More importantly, significant immunotherapy effects and negligible side effects are observed in 4T1 and CT26 tumor-bearing mice models treated with TP-AP, suggesting the high-performance tumor inhibition attributed to the CRICB strategy. In summary, this CRICB strategy manifest the preferable effects of immune checkpoint blockade, thereby extending the biomedical application of assembling peptides.
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Affiliation(s)
- Wu-Yi Xiao
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China
| | - Yi Wang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
| | - Hong-Wei An
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
| | - Dayong Hou
- Department of Urology, Heilongjiang Key Laboratory of Scientific Research in Urology, The Fourth Hospital of Harbin Medical University, Harbin 150001, China
| | - Muhetaerjiang Mamuti
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
| | - Man-Di Wang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
| | - Jie Wang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
| | - Wanhai Xu
- Department of Urology, Heilongjiang Key Laboratory of Scientific Research in Urology, The Fourth Hospital of Harbin Medical University, Harbin 150001, China
| | - Liming Hu
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China
| | - Hao Wang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
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12
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Theoretical and computational advances in protein misfolding. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 118:1-31. [PMID: 31928722 DOI: 10.1016/bs.apcsb.2019.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Misfolded proteins escape the cellular quality control mechanism and fail to fold properly or remain correctly folded leading to a loss in their functional specificity. Thus misfolding of proteins cause a large number of very different diseases ranging from errors in metabolism to various types of complex neurodegenerative diseases. A theoretical and computational perspective of protein misfolding is presented with a special emphasis on its salient features, mechanism and consequences. These insights quantitatively analyze different determinants of misfolding, that may be applied to design disease specific molecular targets.
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13
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Nguyen PH, Sterpone F, Derreumaux P. Aggregation of disease-related peptides. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 170:435-460. [PMID: 32145950 DOI: 10.1016/bs.pmbts.2019.12.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein misfolding and aggregation of amyloid proteins is the fundamental cause of more than 20 diseases. Molecular mechanisms of the self-assembly and the formation of the toxic aggregates are still elusive. Computer simulations have been intensively used to study the aggregation of amyloid peptides of various amino acid lengths related to neurodegenerative diseases. We review atomistic and coarse-grained simulations of short amyloid peptides aimed at determining their transient oligomeric structures and the early and late aggregation steps.
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Affiliation(s)
- Phuong H Nguyen
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France; Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Fabio Sterpone
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France; Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Philippe Derreumaux
- Laboratory of Theoretical Chemistry, Ton Duc Thang University, Ho Chi Minh City, Vietnam; Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam.
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14
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A tumour-selective cascade activatable self-detained system for drug delivery and cancer imaging. Nat Commun 2019; 10:4861. [PMID: 31649241 PMCID: PMC6813295 DOI: 10.1038/s41467-019-12848-5] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 09/26/2019] [Indexed: 12/20/2022] Open
Abstract
Achieving the activation of drugs within cellular systems may provide targeted therapies. Here we construct a tumour-selective cascade activatable self-detained system (TCASS) and incorporate imaging probes and therapeutics. We show in different mouse models that the TCASS system accumulates in solid tumours. The molecules show enhanced accumulation in tumour regions via the effect of recognition induced self-assembly. Analysis of the molecular penetration in tumour tissue shows that in vivo self-assembly increases the penetration capability compared to typical soft or hard nanomaterials. Importantly, the in vivo self-assembled molecules exhibit a comparable clearance pathway to that of small molecules, which are excreted from organs of the reticuloendothelial system (liver and kidney), while are relatively slowly eliminated from tumour tissues. Finally, this system, combined with the NIR probe, shows high specificity and sensitivity for detecting bladder cancer in isolated intact patient bladders. The activation of drugs within cellular systems may provide targeted therapies for cancer. Here, the authors make a drug delivery system that is activated within the cell and exploits XIAP expression to cleave a linker region, resulting in the self-assembly of the system and drug release within cancer cells.
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15
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Wang Z, An HW, Hou D, Wang M, Zeng X, Zheng R, Wang L, Wang K, Wang H, Xu W. Addressable Peptide Self-Assembly on the Cancer Cell Membrane for Sensitizing Chemotherapy of Renal Cell Carcinoma. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1807175. [PMID: 30663139 DOI: 10.1002/adma.201807175] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/02/2019] [Indexed: 05/06/2023]
Abstract
Chemotherapy has been validated unavailable for treatment of renal cell carcinoma (RCC) in clinic due to its intrinsic drug resistance. Sensitization of chemo-drug response plays a crucial role in RCC treatment and increase of patient survival. Herein, a recognition-reaction-aggregation (RRA) cascaded strategy is utilized to in situ construct peptide-based superstructures on the renal cancer cell membrane, enabling specifically perturbing the permeability of cell membranes and enhancing chemo-drug sensitivity in vitro and in vivo. First, P1-DBCO can specifically recognize renal cancer cells by targeting carbonic anhydrase IX. Subsequently, P2-N3 is introduced and efficiently reacts with P1-DBCO to form a peptide P3, which exhibits enhanced hydrophobicity and simultaneously aggregates into a superstructure. Interestingly, the superstructure retains on the cell membrane and perturbs its integrity/permeability, allowing more doxorubicin (DOX) uptaken by renal cancer cells. Owing to this increased influx, the IC50 is significantly reduced by nearly 3.5-fold compared with that treated with free DOX. Finally, RRA strategy significantly inhibits the tumor growth of xenografted mice with a 3.2-fold enhanced inhibition rate compared with that treated with free DOX. In summary, this newly developed RRA strategy will open a new avenue for chemically engineering cell membranes with diverse biomedical applications.
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Affiliation(s)
- Ziqi Wang
- Department of Urology, The Fourth Hospital of Harbin Medical University, Heilongjiang Key Laboratory of Scientific Research in Urology, Harbin, 150001, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
| | - Hong-Wei An
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Yuquan Road, Beijing, 100049, China
| | - Dayong Hou
- Department of Urology, The Fourth Hospital of Harbin Medical University, Heilongjiang Key Laboratory of Scientific Research in Urology, Harbin, 150001, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
| | - Mandi Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
| | - Xiangzhong Zeng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
| | - Rui Zheng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
| | - Lu Wang
- Department of Urology, The Fourth Hospital of Harbin Medical University, Heilongjiang Key Laboratory of Scientific Research in Urology, Harbin, 150001, China
| | - Keliang Wang
- Department of Urology, The Fourth Hospital of Harbin Medical University, Heilongjiang Key Laboratory of Scientific Research in Urology, Harbin, 150001, China
| | - Hao Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wanhai Xu
- Department of Urology, The Fourth Hospital of Harbin Medical University, Heilongjiang Key Laboratory of Scientific Research in Urology, Harbin, 150001, China
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16
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Man VH, He X, Derreumaux P, Ji B, Xie XQ, Nguyen PH, Wang J. Effects of All-Atom Molecular Mechanics Force Fields on Amyloid Peptide Assembly: The Case of Aβ 16-22 Dimer. J Chem Theory Comput 2019; 15:1440-1452. [PMID: 30633867 PMCID: PMC6745714 DOI: 10.1021/acs.jctc.8b01107] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We investigated the effects of 17 widely used atomistic molecular mechanics force fields (MMFFs) on the structures and kinetics of amyloid peptide assembly. To this end, we performed large-scale all-atom molecular dynamics simulations in explicit water on the dimer of the seven-residue fragment of the Alzheimer's amyloid-β peptide, Aβ16-22, for a total time of 0.34 ms. We compared the effects of these MMFFs by analyzing various global reaction coordinates, secondary structure contents, the fibril population, the in-register and out-of-register architectures, and the fibril formation time at 310 K. While the AMBER94, AMBER99, and AMBER12SB force fields do not predict any β-sheets, the seven force fields, AMBER96, GROMOS45a3, GROMOS53a5, GROMOS53a6, GROMOS43a1, GROMOS43a2, and GROMOS54a7, form β-sheets rapidly. In contrast, the following five force fields, AMBER99-ILDN, AMBER14SB, CHARMM22*, CHARMM36, and CHARMM36m, are the best candidates for studying amyloid peptide assembly, as they provide good balances in terms of structures and kinetics. We also investigated the assembly mechanisms of dimeric Aβ16-22 and found that the fibril formation rate is predominantly controlled by the total β-strand content.
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Affiliation(s)
- Viet Hoang Man
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Xibing He
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité, IBPC, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Beihong Ji
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Phuong H. Nguyen
- Laboratoire de Biochimie Théorique UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité, IBPC, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Junmei Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Corresponding Author:
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17
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Li X, Lei J, Qi R, Xie L, Wei G. Mechanistic insight into E22Q-mutation-induced antiparallel-to-parallel β-sheet transition of Aβ16−22fibrils: an all-atom simulation study. Phys Chem Chem Phys 2019; 21:15686-15694. [DOI: 10.1039/c9cp02561h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
E22Q mutation of Aβ16−22fibrils facilitates parallel β-sheet formation by enhancing Q22–Q22 hydrogen-bonding interaction and A21–A21, F20–F20, F19–F19 and V18–V18 hydrophobic interaction.
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Affiliation(s)
- Xuhua Li
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics
- Fudan University
- Shanghai
- China
| | - Jiangtao Lei
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics
- Fudan University
- Shanghai
- China
| | - Ruxi Qi
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics
- Fudan University
- Shanghai
- China
| | - Luogang Xie
- College of Physics and Electronic Engineering
- Zhengzhou University of Light Industry
- Zhengzhou 453002
- People's Republic of China
| | - Guanghong Wei
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics
- Fudan University
- Shanghai
- China
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18
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Sahoo A, Xu H, Matysiak S. Pathways of amyloid-beta absorption and aggregation in a membranous environment. Phys Chem Chem Phys 2019; 21:8559-8568. [PMID: 30964132 DOI: 10.1039/c9cp00040b] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Aggregation of misfolded oligomeric amyloid-beta (Aβ) peptides on lipid membranes has been identified as a primary event in Alzheimer's pathogenesis. However, the structural and dynamical features of this membrane assisted Aβ aggregation have not been well characterized. The microscopic characterization of dynamic molecular-level interactions in peptide aggregation pathways has been challenging both computationally and experimentally. In this work, we explore differential patterns of membrane-induced Aβ 16-22 (K-L-V-F-F-A-E) aggregation from the microscopic perspective of molecular interactions. Physics-based coarse-grained molecular dynamics (CG-MD) simulations were employed to investigate the effect of lipid headgroup charge - zwitterionic (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine: POPC) and anionic (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine: POPS) - on Aβ 16-22 peptide aggregation. Our analyses present an extensive overview of multiple pathways for peptide absorption and biomechanical forces governing peptide folding and aggregation. In agreement with experimental observations, anionic POPS molecules promote extended configurations in Aβ peptides that contribute towards faster emergence of ordered β-sheet-rich peptide assemblies compared to POPC, suggesting faster fibrillation. In addition, lower cumulative rates of peptide aggregation in POPS due to higher peptide-lipid interactions and slower lipid diffusion result in multiple distinct ordered peptide aggregates that can serve as nucleation seeds for subsequent Aβ aggregation. This study provides an in-silico assessment of experimentally observed aggregation patterns, presents new morphological insights and highlights the importance of lipid headgroup chemistry in modulating the peptide absorption and aggregation process.
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Affiliation(s)
- Abhilash Sahoo
- Biophysics Program, Institute of Physical Science and Technology, University of Maryland, College Park, MD, USA.
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19
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Wilson CJ, Bommarius AS, Champion JA, Chernoff YO, Lynn DG, Paravastu AK, Liang C, Hsieh MC, Heemstra JM. Biomolecular Assemblies: Moving from Observation to Predictive Design. Chem Rev 2018; 118:11519-11574. [PMID: 30281290 PMCID: PMC6650774 DOI: 10.1021/acs.chemrev.8b00038] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Biomolecular assembly is a key driving force in nearly all life processes, providing structure, information storage, and communication within cells and at the whole organism level. These assembly processes rely on precise interactions between functional groups on nucleic acids, proteins, carbohydrates, and small molecules, and can be fine-tuned to span a range of time, length, and complexity scales. Recognizing the power of these motifs, researchers have sought to emulate and engineer biomolecular assemblies in the laboratory, with goals ranging from modulating cellular function to the creation of new polymeric materials. In most cases, engineering efforts are inspired or informed by understanding the structure and properties of naturally occurring assemblies, which has in turn fueled the development of predictive models that enable computational design of novel assemblies. This Review will focus on selected examples of protein assemblies, highlighting the story arc from initial discovery of an assembly, through initial engineering attempts, toward the ultimate goal of predictive design. The aim of this Review is to highlight areas where significant progress has been made, as well as to outline remaining challenges, as solving these challenges will be the key that unlocks the full power of biomolecules for advances in technology and medicine.
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Affiliation(s)
- Corey J. Wilson
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Andreas S. Bommarius
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Julie A. Champion
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Yury O. Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Laboratory of Amyloid Biology & Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia
| | - David G. Lynn
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Anant K. Paravastu
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Chen Liang
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Ming-Chien Hsieh
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Jennifer M. Heemstra
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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20
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Rodriguez RA, Chen LY, Plascencia-Villa G, Perry G. Thermodynamics of Amyloid-β Fibril Elongation: Atomistic Details of the Transition State. ACS Chem Neurosci 2018; 9:783-789. [PMID: 29239603 PMCID: PMC5911799 DOI: 10.1021/acschemneuro.7b00409] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
![]()
Amyloid-β
(Aβ) fibrils and plaques are one of the hallmarks
of Alzheimer’s disease. While the kinetics of fibrillar growth
of Aβ have been extensively studied, several vital questions
remain. In particular, the atomistic origins of the Arrhenius barrier
observed in experiments have not been elucidated. Employing the familiar
thermodynamic integration method, we have directly simulated the dissociation
of an Aβ(15–40) (D23N mutant) peptide from
the surface of a filament along its most probable path (MPP) using
all-atom molecular dynamics. This allows for a direct calculation
of the free energy profile along the MPP, revealing a multipeak energetic
barrier between the free peptide state and the aggregated state. By
definition of the MPP, this simulated unbinding process represents
the reverse of the physical elongation pathway, allowing us to draw
biophysically relevant conclusions from the simulation data. Analyzing
the detailed atomistic interactions along the MPP, we identify the
atomistic origins of these peaks as resulting from the dock-lock mechanism
of filament elongation. Careful analysis of the dynamics of filament
elongation could prove key to the development of novel therapeutic
strategies for amyloid-related diseases.
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Affiliation(s)
- Roberto A. Rodriguez
- Department of Physics and Astronomy, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Liao Y. Chen
- Department of Physics and Astronomy, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Germán Plascencia-Villa
- Department of Physics and Astronomy, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - George Perry
- Department of Biology and Neurosciences Institute, University of Texas at San Antonio, San Antonio, Texas 78249, United States
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21
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Sun Y, Wang B, Ge X, Ding F. Distinct oligomerization and fibrillization dynamics of amyloid core sequences of amyloid-beta and islet amyloid polypeptide. Phys Chem Chem Phys 2017; 19:28414-28423. [PMID: 29038815 PMCID: PMC5657190 DOI: 10.1039/c7cp05695h] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A direct observation of amyloid aggregation from isolated peptides to cross-β fibrils is crucial for understanding the nucleation-dependence process, but the corresponding macroscopic timescales impose a major computational challenge. Using rapid all-atom discrete molecular dynamics simulations, we capture the oligomerization and fibrillization dynamics of the amyloid core sequences of amyloid-β (Aβ) in Alzheimer's disease and islet amyloid polypeptide (IAPP) in type-2 diabetes, namely Aβ16-22 and IAPP22-28. Both peptides and their mixture spontaneously assemble into cross-β aggregates in silico, but follow distinct pathways. Aβ16-22 is highly aggregation-prone with a funneled free energy basin toward multi-layer β-sheet aggregates. IAPP22-28, on the other hand, features the accumulation of unstructured oligomers before the nucleation of β-sheets and growth into double-layer β-sheet aggregates. In the presence of Aβ16-22, the aggregation of IAPP22-28 is promoted by forming co-aggregated multi-layer β-sheets. Our study offers a detailed molecular insight to the long-postulated oligomerization-nucleation process in the amyloid aggregations.
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Affiliation(s)
- Yunxiang Sun
- Department of Physics and Astronomy, Clemson University, Clemson, SC, USA.
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22
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Abstract
Living systems contain remarkable functional capability built within sophisticated self-organizing frameworks. Defining the assembly codes that coordinate these systems could greatly extend nanobiotechnology. To that end, we have highlighted the self-assembling architecture of the chlorosome antenna arrays and report the emulation and extension of their features for the development of cell-compatible photoredox materials. We specifically review work on amyloid peptide scaffolds able to (1) organize light-harvesting chromophores, (2) break peptide bilayer symmetry for directional energy and electron transfer, and (3) incorporate redox active metal ions at high density for energy storage.
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Affiliation(s)
- Rolando F Rengifo
- Emory University, Departments of Biology and Chemistry, 1515 Dickey Dr. NE, Atlanta, GA 30322, USA.
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23
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Dorosh L, Stepanova M. Probing oligomerization of amyloid beta peptide in silico. MOLECULAR BIOSYSTEMS 2017; 13:165-182. [PMID: 27844078 DOI: 10.1039/c6mb00441e] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Aggregation of amyloid β (Aβ) peptide is implicated in fatal Alzheimer's disease, for which no cure is available. Understanding the mechanisms responsible for this aggregation is required in order for therapies to be developed. In an effort to better understand the molecular mechanisms involved in spontaneous aggregation of Aβ peptide, extensive molecular dynamics simulations are reported, and the results are analyzed through a combination of structural biology tools and a novel essential collective dynamics method. Several model systems composed of ten or twelve Aβ17-42 chains in water are investigated, and the influence of metal ions is probed. The results suggest that Aβ monomers tend to aggregate into stable globular-like oligomers with 13-23% of β-sheet content. Two stages of oligomer formation have been identified: quick collapse within the first 40 ns of the simulation, characterized by a decrease in inter-chain separation and build-up of β-sheets, and the subsequent slow relaxation of the oligomer structure. The resulting oligomers comprise a stable, coherently moving sub-aggregate of 6-9 strongly inter-correlated chains. Cu2+ and Fe2+ ions have been found to develop coordination bonds with carboxylate groups of E22, D23 and A42, which remain stable during 200 ns simulations. The presence of Fe2+, and particularly Cu2+ ions, in negatively charged cavities has been found to cause significant changes in the structure and dynamics of the oligomers. The results indicate, in particular, that formation of non-fibrillar oligomers might be involved in early template-free aggregation of Aβ17-42 monomers, with charged species such as Cu2+ or Fe2+ ions playing an important role.
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Affiliation(s)
- L Dorosh
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada. and National Research Council of Canada, Edmonton, Alberta, Canada
| | - M Stepanova
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada. and National Research Council of Canada, Edmonton, Alberta, Canada and Department of Physics, Astronomy, and Materials Science, Missouri State University, Springfield, MO, USA
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24
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Tran TT, Nguyen PH, Derreumaux P. Lattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer's peptides. J Chem Phys 2017; 144:205103. [PMID: 27250331 DOI: 10.1063/1.4951739] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Coarse-grained protein lattice models approximate atomistic details and keep the essential interactions. They are, therefore, suitable for capturing generic features of protein folding and amyloid formation at low computational cost. As our aim is to study the critical nucleus sizes of two experimentally well-characterized peptide fragments Aβ16-22 and Aβ37-42 of the full length Aβ1-42 Alzheimer's peptide, it is important that simulations with the lattice model reproduce all-atom simulations. In this study, we present a comprehensive force field parameterization based on the OPEP (Optimized Potential for Efficient protein structure Prediction) force field for an on-lattice protein model, which incorporates explicitly the formation of hydrogen bonds and directions of side-chains. Our bottom-up approach starts with the determination of the best lattice force parameters for the Aβ16-22 dimer by fitting its equilibrium parallel and anti-parallel β-sheet populations to all-atom simulation results. Surprisingly, the calibrated force field is transferable to the trimer of Aβ16-22 and the dimer and trimer of Aβ37-42. Encouraged by this finding, we characterized the free energy landscapes of the two decamers. The dominant structure of the Aβ16-22 decamer matches the microcrystal structure. Pushing the simulations for aggregates between 4-mer and 12-mer suggests a nucleus size for fibril formation of 10 chains. In contrast, the Aβ37-42 decamer is largely disordered with mixed by parallel and antiparallel chains, suggesting that the nucleus size is >10 peptides. Our refined force field coupled to this on-lattice model should provide useful insights into the critical nucleation number associated with neurodegenerative diseases.
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Affiliation(s)
- Thanh Thuy Tran
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Phuong H Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
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25
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Chiricotto M, Tran TT, Nguyen PH, Melchionna S, Sterpone F, Derreumaux P. Coarse-grained and All-atom Simulations towards the Early and Late Steps of Amyloid Fibril Formation. Isr J Chem 2016. [DOI: 10.1002/ijch.201600048] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Mara Chiricotto
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS; Université Paris Diderot, Sorbonne Paris Cité, IBPC; 13 Rue Pierre et Marie Curie 75005 Paris France
| | - Thanh Thuy Tran
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS; Université Paris Diderot, Sorbonne Paris Cité, IBPC; 13 Rue Pierre et Marie Curie 75005 Paris France
| | - Phuong H. Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS; Université Paris Diderot, Sorbonne Paris Cité, IBPC; 13 Rue Pierre et Marie Curie 75005 Paris France
| | - Simone Melchionna
- Istituto Sistemi Complessi; Consiglio Nazionale delle Ricerche; P. le A. Moro 2 00185 Rome Italy
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS; Université Paris Diderot, Sorbonne Paris Cité, IBPC; 13 Rue Pierre et Marie Curie 75005 Paris France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS; Université Paris Diderot, Sorbonne Paris Cité, IBPC; 13 Rue Pierre et Marie Curie 75005 Paris France
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26
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Schwierz N, Frost CV, Geissler PL, Zacharias M. Dynamics of Seeded Aβ40-Fibril Growth from Atomistic Molecular Dynamics Simulations: Kinetic Trapping and Reduced Water Mobility in the Locking Step. J Am Chem Soc 2016; 138:527-39. [PMID: 26694883 DOI: 10.1021/jacs.5b08717] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Filamentous β-amyloid aggregates are crucial for the pathology of Alzheimer's disease. Despite the tremendous biomedical importance, the molecular pathway of growth propagation is not completely understood and remains challenging to investigate by simulations due to the long time scales involved. Here, we apply extensive all-atom molecular dynamics simulations in explicit water to obtain free energy profiles and kinetic information from position-dependent diffusion profiles for three different Aβ9-40-growth processes: fibril elongation by single monomers at the structurally unequal filament tips and association of larger filament fragments. Our approach provides insight into the molecular steps of the kinetic pathway and allows close agreement with experimental binding free energies and macroscopic growth rates. Water plays a decisive role, and solvent entropy is identified as the main driving force for assembly. Fibril growth is disfavored energetically due to cancellation of direct peptide-peptide interactions and solvation effects. The kinetics of growth is consistent with the characteristic dock/lock mechanism, and docking is at least 2 orders of magnitude faster. During initial docking, interactions are mediated by transient non-native hydrogen bonds, which efficiently catch the incoming monomer or fragment already at separations of about 3 nm. In subsequent locking, the dynamics is much slower due to formation of kinetically trapped conformations caused by long-lived non-native hydrogen bonds. Fibril growth additionally requires collective motion of water molecules to create a dry binding interface. Fibril growth is further retarded due to reduced mobility of the involved hydration water, evident from a 2-fold reduction of the diffusion coefficient.
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Affiliation(s)
- Nadine Schwierz
- Chemistry Department, University of California , Berkeley, California 94720, United States
| | - Christina V Frost
- Physik Department, Technische Universität München , 85748 Garching, Germany
| | - Phillip L Geissler
- Chemistry Department, University of California , Berkeley, California 94720, United States
| | - Martin Zacharias
- Physik Department, Technische Universität München , 85748 Garching, Germany
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27
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Martinez AV, Małolepsza E, Rivera E, Lu Q, Straub JE. Exploring the role of hydration and confinement in the aggregation of amyloidogenic peptides Aβ(16-22) and Sup35(7-13) in AOT reverse micelles. J Chem Phys 2015; 141:22D530. [PMID: 25494801 DOI: 10.1063/1.4902550] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Knowledge of how intermolecular interactions of amyloid-forming proteins cause protein aggregation and how those interactions are affected by sequence and solution conditions is essential to our understanding of the onset of many degenerative diseases. Of particular interest is the aggregation of the amyloid-β (Aβ) peptide, linked to Alzheimer's disease, and the aggregation of the Sup35 yeast prion peptide, which resembles the mammalian prion protein linked to spongiform encephalopathies. To facilitate the study of these important peptides, experimentalists have identified small peptide congeners of the full-length proteins that exhibit amyloidogenic behavior, including the KLVFFAE sub-sequence, Aβ16-22, and the GNNQQNY subsequence, Sup357-13. In this study, molecular dynamics simulations were used to examine these peptide fragments encapsulated in reverse micelles (RMs) in order to identify the fundamental principles that govern how sequence and solution environment influence peptide aggregation. Aβ16-22 and Sup357-13 are observed to organize into anti-parallel and parallel β-sheet arrangements. Confinement in the sodium bis(2-ethylhexyl) sulfosuccinate (AOT) reverse micelles is shown to stabilize extended peptide conformations and enhance peptide aggregation. Substantial fluctuations in the reverse micelle shape are observed, in agreement with earlier studies. Shape fluctuations are found to facilitate peptide solvation through interactions between the peptide and AOT surfactant, including direct interaction between non-polar peptide residues and the aliphatic surfactant tails. Computed amide I IR spectra are compared with experimental spectra and found to reflect changes in the peptide structures induced by confinement in the RM environment. Furthermore, examination of the rotational anisotropy decay of water in the RM demonstrates that the water dynamics are sensitive to the presence of peptide as well as the peptide sequence. Overall, our results demonstrate that the RM is a complex confining environment where substantial direct interaction between the surfactant and peptides plays an important role in determining the resulting ensemble of peptide conformations. By extension the results suggest that similarly complex sequence-dependent interactions may determine conformational ensembles of amyloid-forming peptides in a cellular environment.
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Affiliation(s)
| | - Edyta Małolepsza
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Eva Rivera
- Department of Chemistry and Biochemistry, Queens College, City University of New York (CUNY), Flushing, New York 11791, USA
| | - Qing Lu
- Division of Materials Science and Engineering, Boston University, Brookline, Massachusetts 02446, USA
| | - John E Straub
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
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28
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Zhang T, Nguyen PH, Nasica-Labouze J, Mu Y, Derreumaux P. Folding Atomistic Proteins in Explicit Solvent Using Simulated Tempering. J Phys Chem B 2015; 119:6941-51. [PMID: 25985144 DOI: 10.1021/acs.jpcb.5b03381] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Following a previous report on a coarse-grained protein model in implicit solvent, we applied simulated tempering (ST) with on-the-fly Helmholtz free energy (weight factors) determination to the folding or aggregation of seven proteins with the CHARMM, OPLS, and AMBER protein, and the SPC and TIP3P water force fields. For efficiency and reliability, we also performed replica exchange molecular dynamics (REMD) simulations on the alanine di- and deca-peptide, and the dimer of the Aβ16-22 Alzheimer's fragment, and used experimental data and previous simulation results on the chignolin, beta3s, Trp-cage, and WW domain peptides of 10-37 amino acids. The sampling with ST is found to be more efficient than with REMD for a much lower CPU cost. Starting from unfolded or extended conformations, the WW domain and the Trp-cage peptide fold to their NMR structures with a backbone RMSD of 2.0 and 1 Å. Remarkably, the ST simulation explores transient non-native topologies for Trp-cage that have been rarely discussed by other simulations. Our ST simulations also show that the CHARMM22* force field has limitations in describing accurately the beta3s peptide. Taken together, these results open the door to the study of the configurations of single proteins, protein aggregates, and any molecular systems at atomic details in explicit solvent using a single normal CPU. They also demonstrate that our ST scheme can be used with any force field ranging from quantum mechanics to coarse-grain and atomistic.
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Affiliation(s)
- Tong Zhang
- †Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Denis Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France.,‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Phuong H Nguyen
- †Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Denis Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Jessica Nasica-Labouze
- †Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Denis Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France.,§International School of Advanced Studies (SISSA), Via Bonomea, 265, 34126 Trieste, Italy
| | - Yuguang Mu
- ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Philippe Derreumaux
- †Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Denis Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France.,∥Institut Universitaire de France, 103 Boulevard Saint-Michel, 75005 Paris, France
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29
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Nasica-Labouze J, Nguyen PH, Sterpone F, Berthoumieu O, Buchete NV, Coté S, De Simone A, Doig AJ, Faller P, Garcia A, Laio A, Li MS, Melchionna S, Mousseau N, Mu Y, Paravastu A, Pasquali S, Rosenman DJ, Strodel B, Tarus B, Viles JH, Zhang T, Wang C, Derreumaux P. Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies. Chem Rev 2015; 115:3518-63. [PMID: 25789869 DOI: 10.1021/cr500638n] [Citation(s) in RCA: 474] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jessica Nasica-Labouze
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Phuong H Nguyen
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Fabio Sterpone
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Olivia Berthoumieu
- ‡LCC (Laboratoire de Chimie de Coordination), CNRS, Université de Toulouse, Université Paul Sabatier (UPS), Institut National Polytechnique de Toulouse (INPT), 205 route de Narbonne, BP 44099, Toulouse F-31077 Cedex 4, France
| | | | - Sébastien Coté
- ∥Département de Physique and Groupe de recherche sur les protéines membranaires (GEPROM), Université de Montréal, C.P. 6128, succursale Centre-ville, Montréal, Québec H3C 3T5, Canada
| | - Alfonso De Simone
- ⊥Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Andrew J Doig
- #Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Peter Faller
- ‡LCC (Laboratoire de Chimie de Coordination), CNRS, Université de Toulouse, Université Paul Sabatier (UPS), Institut National Polytechnique de Toulouse (INPT), 205 route de Narbonne, BP 44099, Toulouse F-31077 Cedex 4, France
| | | | - Alessandro Laio
- ○The International School for Advanced Studies (SISSA), Via Bonomea 265, 34136 Trieste, Italy
| | - Mai Suan Li
- ◆Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland.,¶Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Simone Melchionna
- ⬠Instituto Processi Chimico-Fisici, CNR-IPCF, Consiglio Nazionale delle Ricerche, 00185 Roma, Italy
| | | | - Yuguang Mu
- ▲School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Anant Paravastu
- ⊕National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Samuela Pasquali
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | | | - Birgit Strodel
- △Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Bogdan Tarus
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - John H Viles
- ▼School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Tong Zhang
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.,▲School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | | | - Philippe Derreumaux
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.,□Institut Universitaire de France, 75005 Paris, France
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30
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Paleček E, Tkáč J, Bartošík M, Bertók T, Ostatná V, Paleček J. Electrochemistry of nonconjugated proteins and glycoproteins. Toward sensors for biomedicine and glycomics. Chem Rev 2015; 115:2045-108. [PMID: 25659975 PMCID: PMC4360380 DOI: 10.1021/cr500279h] [Citation(s) in RCA: 214] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Indexed: 02/07/2023]
Affiliation(s)
- Emil Paleček
- Institute
of Biophysics Academy of Science of the Czech Republic, v.v.i., Královopolská
135, 612 65 Brno, Czech Republic
| | - Jan Tkáč
- Institute
of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
| | - Martin Bartošík
- Regional
Centre for Applied Molecular Oncology, Masaryk
Memorial Cancer Institute, Žlutý kopec 7, 656 53 Brno, Czech Republic
| | - Tomáš Bertók
- Institute
of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
| | - Veronika Ostatná
- Institute
of Biophysics Academy of Science of the Czech Republic, v.v.i., Královopolská
135, 612 65 Brno, Czech Republic
| | - Jan Paleček
- Central
European Institute of Technology, Masaryk
University, Kamenice
5, 625 00 Brno, Czech Republic
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31
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Liang C, Ni R, Smith JE, Childers WS, Mehta AK, Lynn DG. Kinetic Intermediates in Amyloid Assembly. J Am Chem Soc 2014; 136:15146-9. [DOI: 10.1021/ja508621b] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Chen Liang
- Departments of Chemistry
and Biology, Emory University, Atlanta, Georgia 30322, United States
| | - Rong Ni
- Departments of Chemistry
and Biology, Emory University, Atlanta, Georgia 30322, United States
| | - Jillian E. Smith
- Departments of Chemistry
and Biology, Emory University, Atlanta, Georgia 30322, United States
| | - W. Seth Childers
- Departments of Chemistry
and Biology, Emory University, Atlanta, Georgia 30322, United States
| | - Anil K. Mehta
- Departments of Chemistry
and Biology, Emory University, Atlanta, Georgia 30322, United States
| | - David G. Lynn
- Departments of Chemistry
and Biology, Emory University, Atlanta, Georgia 30322, United States
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32
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Tsigelny IF, Sharikov Y, Kouznetsova VL, Greenberg JP, Wrasidlo W, Gonzalez T, Desplats P, Michael SE, Trejo-Morales M, Overk CR, Masliah E. Structural diversity of Alzheimer's disease amyloid-β dimers and their role in oligomerization and fibril formation. J Alzheimers Dis 2014; 39:583-600. [PMID: 24240640 DOI: 10.3233/jad-131589] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Alzheimer's disease (AD) is associated with the formation of toxic amyloid-β (Aβ)42 oligomers, and recent evidence supports a role for Aβ dimers as building blocks for oligomers. Molecular dynamics simulation studies have identified clans for the dominant conformations of Aβ42 forming dimers; however, it is unclear if a larger spectrum of dimers is involved and which set(s) of dimers might evolve to oligomers verse fibrils. Therefore, for this study we generated multiple structural conformations of Aβ42, using explicit all-atom molecular dynamics, and then clustering the different structures based on key conformational similarities. Those matching a selection threshold were then used to model a process of oligomerization. Remarkably, we showed a greater diversity in Aβ dimers than previously described. Depending on the clan family, different types of Aβ dimers were obtained. While some had the tendency to evolve into oligomeric rings, others formed fibrils of diverse characteristics. Then we selected the dimers that would evolve to membranephilic annular oligomers. Nearly one third of the 28 evaluated annular oligomers had the dimer interfaces between the neighboring Aβ42 monomers with possible salt bridges between the residue K28 from one side and either residue E22 or D23 on the other. Based on these results, key amino acids were identified for point mutations that either enhanced or suppressed the formation and toxicity of oligomer rings. Our studies suggest a greater diversity of Aβ dimers. Understanding the structure of Aβ dimers might be important for the rationale design of small molecules that block formation of toxic oligomers.
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Affiliation(s)
- Igor F Tsigelny
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Yuriy Sharikov
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Valentina L Kouznetsova
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Jerry P Greenberg
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA
| | - Wolfgang Wrasidlo
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Tania Gonzalez
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Paula Desplats
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Sarah E Michael
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | | | - Cassia R Overk
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Eliezer Masliah
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA Department of Pathology, University of California, San Diego, La Jolla, CA, USA
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33
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Han W, Schulten K. Fibril elongation by Aβ(17-42): kinetic network analysis of hybrid-resolution molecular dynamics simulations. J Am Chem Soc 2014; 136:12450-60. [PMID: 25134066 PMCID: PMC4156860 DOI: 10.1021/ja507002p] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
A critical step of β-amyloid
fibril formation is fibril elongation
in which amyloid-β monomers undergo structural transitions to
fibrillar structures upon their binding to fibril tips. The atomic
detail of the structural transitions remains poorly understood. Computational
characterization of the structural transitions is limited so far to
short Aβ segments (5–10 aa) owing to the long time scale
of Aβ fibril elongation. To overcome the computational time
scale limit, we combined a hybrid-resolution model with umbrella sampling
and replica exchange molecular dynamics and performed altogether ∼1.3
ms of molecular dynamics simulations of fibril elongation for Aβ17–42. Kinetic network analysis of biased simulations
resulted in a kinetic model that encompasses all Aβ segments
essential for fibril formation. The model not only reproduces key
properties of fibril elongation measured in experiments, including
Aβ binding affinity, activation enthalpy of Aβ structural
transitions and a large time scale gap (τlock/τdock = 103–104) between Aβ
binding and its structural transitions, but also reveals detailed
pathways involving structural transitions not seen before, namely,
fibril formation both in hydrophobic regions L17-A21 and G37-A42 preceding
fibril formation in hydrophilic region E22-A30. Moreover, the model
identifies as important kinetic intermediates strand–loop–strand
(SLS) structures of Aβ monomers, long suspected to be related
to fibril elongation. The kinetic model suggests further that fibril
elongation arises faster at the fibril tip with exposed L17-A21, rather
than at the other tip, explaining thereby unidirectional fibril growth
observed previously in experiments.
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Affiliation(s)
- Wei Han
- Beckman Institute, ‡Center for Biophysics and Computational Biology, and §Department of Physics, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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34
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Xu L, Chen Y, Wang X. Assembly of Amyloid β Peptides in the Presence of Fibril Seeds: One-Pot Coarse-Grained Molecular Dynamics Simulations. J Phys Chem B 2014; 118:9238-46. [DOI: 10.1021/jp505551m] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Liang Xu
- School of Chemistry, ‡Network and Information Center, and §School of Chemical Machinery, Dalian University of Technology, Dalian, China
| | - Yonggang Chen
- School of Chemistry, ‡Network and Information Center, and §School of Chemical Machinery, Dalian University of Technology, Dalian, China
| | - Xiaojuan Wang
- School of Chemistry, ‡Network and Information Center, and §School of Chemical Machinery, Dalian University of Technology, Dalian, China
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35
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Sterpone F, Melchionna S, Tuffery P, Pasquali S, Mousseau N, Cragnolini T, Chebaro Y, St-Pierre JF, Kalimeri M, Barducci A, Laurin Y, Tek A, Baaden M, Nguyen PH, Derreumaux P. The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems. Chem Soc Rev 2014; 43:4871-93. [PMID: 24759934 PMCID: PMC4426487 DOI: 10.1039/c4cs00048j] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The OPEP coarse-grained protein model has been applied to a wide range of applications since its first release 15 years ago. The model, which combines energetic and structural accuracy and chemical specificity, allows the study of single protein properties, DNA-RNA complexes, amyloid fibril formation and protein suspensions in a crowded environment. Here we first review the current state of the model and the most exciting applications using advanced conformational sampling methods. We then present the current limitations and a perspective on the ongoing developments.
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Affiliation(s)
- Fabio Sterpone
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005, Paris, France.
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36
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Lin D, Luo Y, Wu S, Ma Q, Wei G, Yang X. Investigation of the aggregation process of amyloid-β-(16-22) peptides and the dissolution of intermediate aggregates. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:3170-3175. [PMID: 24588450 DOI: 10.1021/la4048165] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The aggregation processes of amyloid-β-(16-22) peptides (Aβ16-22) are investigated by atomic force microscopy (AFM). It is found that Aβ16-22 peptides quickly aggregate from monomers to oligomers and flakelike structures and finally to fibrils. In particular, unusual morphology change is observed in an early stage of aggregation; that is, the originally formed flakelike structures would disappear in the following aggregation processes. To determine the evolution of the flakelike structures, in situ AFM imaging is carried out in liquid to reveal the real-time morphology change of Aβ16-22. The results provide clear evidence that the flakelike structures are in an unstable intermediate state, which would be dissolved into oligomers or short protofibrils for reorganization. Further fluorescence and attenuated total reflectance Fourier transform infrared (ATR-FTIR) experiments on thioflavin T(ThT) suggest that those flakelike structures contain β-sheet components.
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Affiliation(s)
- Dongdong Lin
- State Key Laboratory of Surface Physics, Fudan University , 220 Handan Road, Shanghai 200433, PR China
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37
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Ning L, Guo J, Bai Q, Jin N, Liu H, Yao X. Structural diversity and initial oligomerization of PrP106-126 studied by replica-exchange and conventional molecular dynamics simulations. PLoS One 2014; 9:e87266. [PMID: 24586266 PMCID: PMC3929351 DOI: 10.1371/journal.pone.0087266] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 12/24/2013] [Indexed: 12/15/2022] Open
Abstract
Prion diseases are marked by cerebral accumulation of the abnormal isoform of the prion protein. A fragment of prion protein composed of residues 106–126 (PrP106–126) exhibits similar properties to full length prion and plays a key role in the conformational conversion from cellular prion to its pathogenic pattern. Soluble oligomers of PrP106–126 have been proposed to be responsible for neurotoxicity. However, the monomeric conformational space and initial oligomerization of PrP106–126 are still obscure, which are very important for understanding the conformational conversion of PrP106–126. In this study, replica exchange molecular dynamics simulations were performed to investigate monomeric and dimeric states of PrP106–126 in implicit solvent. The structural diversity of PrP106–126 was observed and this peptide did not acquire stable structure. The dimeric PrP106–126 also displayed structural diversity and hydrophobic interaction drove the dimerization. To further study initial oligomerization of PrP106–126, 1 µs conventional molecular dynamics simulations of trimer and tetramer formation were carried out in implicit solvent. We have observed the spontaneous formation of several basic oligomers and stable oligomers with high β-sheet contents were sampled in the simulations of trimer and tetramer formation. The β-hairpin formed in hydrophobic tail of PrP106–126 with residues 118–120 in turn may stabilize these oligomers and seed the formation oligomers. This study can provide insight into the detailed information about the structure of PrP106–126 and the dynamics of aggregation of monomeric PrP106–126 into oligomers in atomic level.
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Affiliation(s)
- Lulu Ning
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | - Jingjing Guo
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Qifeng Bai
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | | | - Huanxiang Liu
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
- School of Pharmacy, Lanzhou University, Lanzhou, China
- * E-mail: (HL); (XY)
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
- State Key Lab for Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
- * E-mail: (HL); (XY)
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38
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Nguyen P, Derreumaux P. Understanding amyloid fibril nucleation and aβ oligomer/drug interactions from computer simulations. Acc Chem Res 2014; 47:603-11. [PMID: 24368046 DOI: 10.1021/ar4002075] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Evolution has fine-tuned proteins to accomplish a variety of tasks. Yet, with aging, some proteins assemble into harmful amyloid aggregates associated with neurodegenerative diseases, such as Alzheimer's disease (AD), which presents a complex and costly challenge to our society. Thus, far, drug after drug has failed to slow the progression of AD, characterized by the self-assembly of the 39-43 amino acid β-amyloid (Aβ) protein into extracellular senile plaques that form a cross-β structure. While there is experimental evidence that the Aβ small oligomers are the primary toxic species, standard tools of biology have failed to provide structures of these transient, inhomogeneous assemblies. Despite extensive experimental studies, researchers have not successfully characterized the nucleus ensemble, the starting point for rapid fibril formation. Similarly scientists do not have atomic data to show how the compounds that reduce both fibril formation and toxicity in cells bind to Aβ42 oligomers. In this context, computer simulations are important tools for gaining insights into the self-assembly of amyloid peptides and the molecular mechanism of inhibitors. This Account reviews what analytical models and simulations at different time and length scales tell us about the dynamics, kinetics, and thermodynamics of amyloid fibril formation and, notably, the nucleation process. Though coarse-grained and mesoscopic protein models approximate atomistic details by averaging out unimportant degrees of freedom, they provide generic features of amyloid formation and insights into mechanistic details of the self-assembly process. The thermodynamics and kinetics vary from linear peptides adopting straight β-strands in fibrils to longer peptides adopting in parallel U shaped conformations in fibrils. In addition, these properties change with the balance between electrostatic and hydrophobic interactions and the intrinsic disorder of the system. However, simulations suggest that the critical nucleus size might be on the order of 20 chains under physiological conditions. The transition state might be characterized by a simultaneous change from mixed antiparallel/parallel β-strands with random side-chain packing to the final antiparallel or parallel states with the steric zipper packing of the side chains. Second, we review our current computer-based knowledge of the 3D structures of inhibitors with Aβ42 monomer and oligomers, a prerequisite for developing new drugs against AD. Recent extensive all-atom simulations of Aβ42 dimers with known inhibitors such as the green tea compound epigallocatechin-3-gallate and 1,4-naphthoquinon-2-yl-l-tryptophan provide a spectrum of initial Aβ42/inhibitor structures useful for screening and drug design. We conclude by discussing future directions that may offer opportunities to fully understand nucleation and further AD drug development.
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Affiliation(s)
- Phuong Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
- Institut Universitaire de France, IUF, 103 Boulevard Saint-Michel, 75005 Paris, France
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39
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Liu J, Wang W, Zhang Q, Zhang S, Yuan Z. Study on the Efficiency and Interaction Mechanism of a Decapeptide Inhibitor of β-Amyloid Aggregation. Biomacromolecules 2014; 15:931-9. [DOI: 10.1021/bm401795e] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Jing Liu
- Key Laboratory
of Functional
Polymer Materials of Ministry of Education, and Institute of Polymer
Chemistry, Nankai University, and Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300071, China
| | - Wei Wang
- Key Laboratory
of Functional
Polymer Materials of Ministry of Education, and Institute of Polymer
Chemistry, Nankai University, and Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300071, China
| | - Qian Zhang
- Key Laboratory
of Functional
Polymer Materials of Ministry of Education, and Institute of Polymer
Chemistry, Nankai University, and Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300071, China
| | - Saihui Zhang
- Key Laboratory
of Functional
Polymer Materials of Ministry of Education, and Institute of Polymer
Chemistry, Nankai University, and Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300071, China
| | - Zhi Yuan
- Key Laboratory
of Functional
Polymer Materials of Ministry of Education, and Institute of Polymer
Chemistry, Nankai University, and Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300071, China
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40
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Gill AC. β-hairpin-mediated formation of structurally distinct multimers of neurotoxic prion peptides. PLoS One 2014; 9:e87354. [PMID: 24498083 PMCID: PMC3909104 DOI: 10.1371/journal.pone.0087354] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 12/19/2013] [Indexed: 01/09/2023] Open
Abstract
Protein misfolding disorders are associated with conformational changes in specific proteins, leading to the formation of potentially neurotoxic amyloid fibrils. During pathogenesis of prion disease, the prion protein misfolds into β-sheet rich, protease-resistant isoforms. A key, hydrophobic domain within the prion protein, comprising residues 109-122, recapitulates many properties of the full protein, such as helix-to-sheet structural transition, formation of fibrils and cytotoxicity of the misfolded isoform. Using all-atom, molecular simulations, it is demonstrated that the monomeric 109-122 peptide has a preference for α-helical conformations, but that this peptide can also form β-hairpin structures resulting from turns around specific glycine residues of the peptide. Altering a single amino acid within the 109-122 peptide (A117V, associated with familial prion disease) increases the prevalence of β-hairpin formation and these observations are replicated in a longer peptide, comprising residues 106-126. Multi-molecule simulations of aggregation yield different assemblies of peptide molecules composed of conformationally-distinct monomer units. Small molecular assemblies, consistent with oligomers, comprise peptide monomers in a β-hairpin-like conformation and in many simulations appear to exist only transiently. Conversely, larger assemblies are comprised of extended peptides in predominately antiparallel β-sheets and are stable relative to the length of the simulations. These larger assemblies are consistent with amyloid fibrils, show cross-β structure and can form through elongation of monomer units within pre-existing oligomers. In some simulations, assemblies containing both β-hairpin and linear peptides are evident. Thus, in this work oligomers are on pathway to fibril formation and a preference for β-hairpin structure should enhance oligomer formation whilst inhibiting maturation into fibrils. These simulations provide an important new atomic-level model for the formation of oligomers and fibrils of the prion protein and suggest that stabilization of β-hairpin structure may enhance cellular toxicity by altering the balance between oligomeric and fibrillar protein assemblies.
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Affiliation(s)
- Andrew C. Gill
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush Campus, University of Edinburgh, Roslin, Edinburgh, United Kingdom
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41
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Nguyen PH, Tarus B, Derreumaux P. Familial Alzheimer A2 V Mutation Reduces the Intrinsic Disorder and Completely Changes the Free Energy Landscape of the Aβ1–28 Monomer. J Phys Chem B 2014; 118:501-10. [DOI: 10.1021/jp4115404] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Phuong H. Nguyen
- Laboratoire
de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Bogdan Tarus
- Laboratoire
de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- Laboratoire
de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
- Institut Universitaire de France, IUF, 103 Boulevard Saint-Michel, 75005 Paris, France
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42
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Spiga E, Degiacomi MT, Dal Peraro M. New Strategies for Integrative Dynamic Modeling of Macromolecular Assembly. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 96:77-111. [DOI: 10.1016/bs.apcsb.2014.06.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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43
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Nguyen PH, Derreumaux P. Conformational ensemble and polymorphism of the all-atom Alzheimer's Aβ(37-42) amyloid peptide oligomers. J Phys Chem B 2013; 117:5831-40. [PMID: 23581814 DOI: 10.1021/jp401563n] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Although the Aβ(37-42) peptide has two opposite terminal charges, counterintuitively its current fibril amyloid structure reveals in register parallel β-strands, as formed by the full length Aβ peptide. In this study, we carried out a replica exchange molecular dynamics simulation of 16 all-atom Aβ(37-42) peptides in explicit water starting from randomized and dispersed chains. The extensive conformational sampling (48 replicas, 460 ns/replica) with a total simulation time of 23 μs allows us to obtain a full picture on the equilibrium conformational distribution of oligomers and β-sheet sizes and gain some insights into the oligomerization process at 300 K. At the peptide concentration of 12 mM, self-assembly is described by the condensation-polymerization mechanism with conversion from micelle-like to high β-sheet structures. At equilibrium, the oligomer distribution consists of large aggregates and free monomers, representing 70% and 25% of all species, respectively. Though the formation/dissociation of β-strand is high, the population of 4-5 fully parallel β-strands, consistent with the arrangement in the current fibril, is marginal and that of 4-5 fully antiparallel β-strands, consistent with amyloid polymorphism, is non-negligible. However, the system adopts essentially mixed parallel/antiparallel β-strands. This indicates that a system of 16 Aβ(37-42) chains in explicit solvent still does not form more stable species that will irreversibly grow to a fibril, independently of polymorphism. Our results also suggest that the Aβ(37-42) fibril may display packing polymorphism with antiparallel β-strands, in addition to the experimentally observed in register parallel β-strands.
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Affiliation(s)
- Phuong H Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France.
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44
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Ni B, Baumketner A. Reduced atomic pair-interaction design (RAPID) model for simulations of proteins. J Chem Phys 2013; 138:064102. [PMID: 23425456 PMCID: PMC3579890 DOI: 10.1063/1.4790160] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 01/18/2013] [Indexed: 12/15/2022] Open
Abstract
Increasingly, theoretical studies of proteins focus on large systems. This trend demands the development of computational models that are fast, to overcome the growing complexity, and accurate, to capture the physically relevant features. To address this demand, we introduce a protein model that uses all-atom architecture to ensure the highest level of chemical detail while employing effective pair potentials to represent the effect of solvent to achieve the maximum speed. The effective potentials are derived for amino acid residues based on the condition that the solvent-free model matches the relevant pair-distribution functions observed in explicit solvent simulations. As a test, the model is applied to alanine polypeptides. For the chain with 10 amino acid residues, the model is found to reproduce properly the native state and its population. Small discrepancies are observed for other folding properties and can be attributed to the approximations inherent in the model. The transferability of the generated effective potentials is investigated in simulations of a longer peptide with 25 residues. A minimal set of potentials is identified that leads to qualitatively correct results in comparison with the explicit solvent simulations. Further tests, conducted for multiple peptide chains, show that the transferable model correctly reproduces the experimentally observed tendency of polyalanines to aggregate into β-sheets more strongly with the growing length of the peptide chain. Taken together, the reported results suggest that the proposed model could be used to succesfully simulate folding and aggregation of small peptides in atomic detail. Further tests are needed to assess the strengths and limitations of the model more thoroughly.
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Affiliation(s)
- Boris Ni
- Department of Physics and Optical Science, University of North Carolina Charlotte, 9201 University City Blvd., Charlotte, North Carolina 28262, USA
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45
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Abstract
Coarse-grained models for protein folding and aggregation are used to explore large dimension scales and timescales that are inaccessible to all-atom models in explicit aqueous solution. Combined with enhanced configuration search methods, these simplified models with various levels of granularity offer the possibility to determine equilibrium structures, compare folding kinetics and thermodynamics with experiments for single proteins and understand the dynamic assembly of amyloid proteins leading to neurodegenerative diseases. I shall describe recent progress in developing such models, and discuss their potentials and limitations in probing the folding and misfolding of proteins with computer simulations.
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46
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Lu Y, Wei G, Derreumaux P. Structural, thermodynamical, and dynamical properties of oligomers formed by the amyloid NNQQ peptide: insights from coarse-grained simulations. J Chem Phys 2012; 137:025101. [PMID: 22803563 DOI: 10.1063/1.4732761] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Characterizing the early formed oligomeric intermediates of amyloid peptides is of particular interest due to their links with neurodegenerative diseases. Here we study the NNQQ peptide, known to display parallel β-strands in amyloid fibrils by x-ray microcrystallography, and investigate the structural, thermodynamical, and dynamical properties of 20 NNQQ peptides using molecular dynamics and replica exchange molecular dynamics simulations coupled to a coarse-grained force field. All simulations are initiated from randomized and fully dispersed monomeric conformations. Our simulations reveal that the phase transition is characterized by a change in the oligomer and β-sheet size distributions and the percentage of mixed parallel/antiparallel β-strands when the sheets are formed. At all temperatures, however, the fraction of parallel β-strands remains low, though there are many association/fragmentation events. This work and a growing body of computational studies provide strong evidence that the critical nucleus goes beyond 20 chains and reordering of the β-strands occurs in larger oligomers.
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Affiliation(s)
- Yan Lu
- State Key Laboratory of Surface Physics, and Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China
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47
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Chebaro Y, Pasquali S, Derreumaux P. The Coarse-Grained OPEP Force Field for Non-Amyloid and Amyloid Proteins. J Phys Chem B 2012; 116:8741-52. [DOI: 10.1021/jp301665f] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yassmine Chebaro
- Laboratoire de Biochimie Théorique,
CNRS UPR 9080, Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique,
13 rue Pierre et Marie Curie, 75005 Paris
| | - Samuela Pasquali
- Laboratoire de Biochimie Théorique,
CNRS UPR 9080, Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique,
13 rue Pierre et Marie Curie, 75005 Paris
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique,
CNRS UPR 9080, Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique,
13 rue Pierre et Marie Curie, 75005 Paris
- Institut Universitaire de France, 103 Bvd Saint-Michel, Paris 75005, France
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48
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Waldauer SA, Hassan S, Paoli B, Donaldson PM, Pfister R, Hamm P, Caflisch A, Pellarin R. Photocontrol of Reversible Amyloid Formation with a Minimal-Design Peptide. J Phys Chem B 2012; 116:8961-73. [DOI: 10.1021/jp305311z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Steven A. Waldauer
- Institute
of Physical Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057
Zurich, Switzerland
| | - Shabir Hassan
- Institute
of Physical Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057
Zurich, Switzerland
| | - Beatrice Paoli
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057
Zurich, Switzerland
| | - Paul M. Donaldson
- Institute
of Physical Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057
Zurich, Switzerland
| | - Rolf Pfister
- Institute
of Physical Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057
Zurich, Switzerland
| | - Peter Hamm
- Institute
of Physical Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057
Zurich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057
Zurich, Switzerland
| | - Riccardo Pellarin
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057
Zurich, Switzerland
- Department
of Bioengineering and
Therapeutic Sciences, University of California in San Francisco, 1700 Fourth Street, San Francisco, California
94158, United States
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49
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Childers WS, Anthony NR, Mehta AK, Berland KM, Lynn DG. Phase networks of cross-β peptide assemblies. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:6386-6395. [PMID: 22439620 DOI: 10.1021/la300143j] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Recent evidence suggests that simple peptides can access diverse amphiphilic phases, and that these structures underlie the robust and widely distributed assemblies implicated in nearly 40 protein misfolding diseases. Here we exploit a minimal nucleating core of the Aβ peptide of Alzheimer's disease to map its morphologically accessible phases that include stable intermolecular molten particles, fibers, twisted and helical ribbons, and nanotubes. Analyses with both fluorescence lifetime imaging microscopy (FLIM) and transmission electron microscopy provide evidence for liquid-liquid phase separations, similar to the coexisting dilute and dense protein-rich liquid phases so critical for the liquid-solid transition in protein crystallization. We show that the observed particles are critical for transitions to the more ordered cross-β peptide phases, which are prevalent in all amyloid assemblies, and identify specific conditions that arrest assembly at the phase boundaries. We have identified a size dependence of the particles in order to transition to the para-crystalline phase and a width of the cross-β assemblies that defines the transition between twisted fibers and helically coiled ribbons. These experimental results reveal an interconnected network of increasing molecularly ordered cross-β transitions, greatly extending the initial computational models for cross-β assemblies.
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Affiliation(s)
- W Seth Childers
- Center for Fundamental and Applied Molecular Evolution, NSF/NASA Center for Chemical Evolution, Departments of Chemistry and Biology, Atlanta, Georgia 30322, USA
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50
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Chebaro Y, Jiang P, Zang T, Mu Y, Nguyen PH, Mousseau N, Derreumaux P. Structures of Aβ17-42 trimers in isolation and with five small-molecule drugs using a hierarchical computational procedure. J Phys Chem B 2012; 116:8412-22. [PMID: 22283547 DOI: 10.1021/jp2118778] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The amyloid-β protein (Aβ) oligomers are believed to be the main culprits in the cytoxicity of Alzheimer's disease (AD) and p3 peptides (Aβ17-42 fragments) are present in AD amyloid plaques. Many small-molecule or peptide-based inhibitors are known to slow down Aβ aggregation and reduce the toxicity in vitro, but their exact modes of action remain to be determined since there has been no atomic level of Aβ(p3)-drug oligomers. In this study, we have determined the structure of Aβ17-42 trimers both in aqueous solution and in the presence of five small-molecule inhibitors using a multiscale computational study. These inhibitors include 2002-H20, curcumin, EGCG, Nqtrp, and resveratrol. First, we used replica exchange molecular dynamics simulations coupled to the coarse-grained (CG) OPEP force field. These CG simulations reveal that the conformational ensemble of Aβ17-42 trimer can be described by 14 clusters with each peptide essentially adopting turn/random coil configurations, although the most populated cluster is characterized by one peptide with a β-hairpin at Phe19-Leu31. Second, these 14 dominant clusters and the less-frequent fibril-like state with parallel register of the peptides were subjected to atomistic Autodock simulations. Our analysis reveals that the drugs have multiple binding modes with different binding affinities for trimeric Aβ17-42 although they interact preferentially with the CHC region (residues 17-21). The compounds 2002-H20 and Nqtrp are found to be the worst and best binders, respectively, suggesting that the drugs may interfere at different stages of Aβ oligomerization. Finally, explicit solvent molecular dynamics of two predicted Nqtrp-Aβ17-42 conformations describe at atomic level some possible modes of action for Nqtrp.
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Affiliation(s)
- Yassmine Chebaro
- Laboratoire de Biochimie Théorique, UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
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