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Ermakova E, Makshakova O, Kurbanov R, Ibraev I, Zuev Y, Sedov I. Aggregation of Amyloidogenic Peptide Uperin-Molecular Dynamics Simulations. Molecules 2023; 28:molecules28104070. [PMID: 37241811 DOI: 10.3390/molecules28104070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/05/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Uperin 3.5 is a remarkable natural peptide obtained from the skin of toadlets comprised of 17 amino acids which exhibits both antimicrobial and amyloidogenic properties. Molecular dynamics simulations were performed to study the β-aggregation process of uperin 3.5 as well as two of its mutants, in which the positively charged residues Arg7 and Lys8 have been replaced by alanine. All three peptides rapidly underwent spontaneous aggregation and conformational transition from random coils to beta-rich structures. The simulations reveal that the initial and essential step of the aggregation process involves peptide dimerization and the formation of small beta-sheets. A decrease in positive charge and an increase in the number of hydrophobic residues in the mutant peptides lead to an increase in the rate of their aggregation.
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Affiliation(s)
- Elena Ermakova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, Kazan 420111, Russia
| | - Olga Makshakova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, Kazan 420111, Russia
| | - Rauf Kurbanov
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, Kazan 420111, Russia
| | - Ilya Ibraev
- Chemical Institute, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
| | - Yuriy Zuev
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, Kazan 420111, Russia
| | - Igor Sedov
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, Kazan 420111, Russia
- Chemical Institute, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
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2
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Zeng J, Tang Y, Dong X, Li F, Wei G. Influence of ALS-linked M337V mutation on the conformational ensembles of TDP-43 321-340 peptide monomer and dimer. Proteins 2023. [PMID: 36841957 DOI: 10.1002/prot.26482] [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: 01/09/2023] [Revised: 02/12/2023] [Accepted: 02/19/2023] [Indexed: 02/27/2023]
Abstract
The transactive response (TAR) DNA/RNA-binding protein 43 (TDP-43) can self-assemble into both functional stress granules via liquid-liquid phase separation (LLPS) and pathogenic amyloid fibrillary aggregates that are closely linked to amyotrophic lateral sclerosis. Previous experimental studies reported that the low complexity domain (LCD) of TDP-43 plays an essential role in the LLPS and aggregation of the full-length protein, and it alone can also undergo LLPS to form liquid droplets mainly via intermolecular interactions in the 321-340 region. And the ALS-associated M337V mutation impairs LCD's LLPS and facilitates liquid-solid phase transition. However, the underlying atomistic mechanism is not well understood. Herein, as a first step to understand the M337V-caused LLPS disruption of TDP-43 LCD mediated by the 321-340 region and the fibrillization enhancement, we investigated the conformational properties of monomer/dimer of TDP-43321-340 peptide and its M337V mutant by performing extensive all-atom explicit-solvent replica exchange molecular dynamic simulations. Our simulations demonstrate that M337V mutation alters the residue regions with high helix/β-structure propensities and thus affects the conformational ensembles of both monomer and dimer. M337V mutation inhibits helix formation in the N-terminal Ala-rich region and the C-terminal mutation site region, while facilitating their long β-sheet formation, albeit with a minor impact on the average probability of both helix structure and β-structure. Further analysis of dimer system shows that M337V mutation disrupts inter-molecular helix-helix interactions and W334-W334 π-π stacking interactions which were reported to be important for the LLPS of TDP-43 LCD, whereas enhances the overall peptide residue-residue interactions and weakens peptide-water interactions, which is conducive to peptide fibrillization. This study provides mechanistic insights into the M337V-mutation-induced impairment of phase separation and facilitation of fibril formation of TDP-43 LCD.
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Affiliation(s)
- Jiyuan Zeng
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai, China
| | - Yiming Tang
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai, China
| | - Xuewei Dong
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Fangying Li
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai, China
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai, China
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3
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Lin TY, Ma YW, Tsai MY. Early-Stage Oligomerization of Prion-like Polypeptides Reveals the Molecular Mechanism of Amyloid-Disrupting Capacity by Proline Residues. J Phys Chem B 2023; 127:1074-1088. [PMID: 36705662 PMCID: PMC9924260 DOI: 10.1021/acs.jpcb.2c05463] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 12/09/2022] [Indexed: 01/28/2023]
Abstract
Proline cis/trans isomerization governs protein local conformational changes via its local mechanical rigidity. The amyloid-disrupting capacity of proline is widely acknowledged; however, the molecular mechanism is still not clear. To understand how proline residues in polypeptide chains influence amyloid propensity, we study several truncated sequences of the TDP-43 C-terminal region (287-322) and their triple proline variants (308PPP310). We use coarse-grained molecular simulation to study the time evolution of the process of aggregation in the early stages in an effective high-concentration condition (∼25 mM). This ensures the long time scales for protein association at laboratory concentrations. We use several experimentally determined structure templates as initial structures of monomer conformations. We carry out oligomer size analysis and cluster analysis, along with several structural measures, to characterize the size distributions of oligomers and their morphological/structural properties. We show that average oligomer size is not a good indicator of amyloid propensity. Structural order and/or morphological properties are better alternatives. We show that proline variants can efficiently maintain the formation of large "ordered" oligomers of shorter truncated sequences, i.e., 307-322. This "order" maintenance is weakened when using longer truncated sequences (i.e., 287-322), leading to the formation of "disordered" oligomers. From an energy trade-off perspective, if the entropic effect is weak (short sequence length), the shape-complementarity of proline variants effectively guides the oligomerization process to form "ordered" oligomer intermediates. This leads to a distinct aggregation pathway that promotes amyloid formation (on-pathway). Strong entropic effects (long sequence length), however, would cause the formation of "disordered" oligomers. This in turn will suppress amyloid formation (off-pathway). The proline shape-complementary effects provide a guided morphological restraint to facilitate the pathways of amyloid formation. Our study supports the importance of structure-based kinetic heterogeneity of prion-like sequence fragments in driving different aggregation pathways. This work sheds light on the role of morphological and structural order of early-stage oligomeric species in regulating amyloid-disrupting capacity by prolines.
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Affiliation(s)
- Tong-You Lin
- Department of Chemistry, Tamkang
University, New Taipei
City, Taiwan251301
| | - Yuan-Wei Ma
- Department of Chemistry, Tamkang
University, New Taipei
City, Taiwan251301
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4
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Schäffler M, Khaled M, Strodel B. ATRANET – Automated generation of transition networks for the structural characterization of intrinsically disordered proteins. Methods 2022; 206:18-26. [DOI: 10.1016/j.ymeth.2022.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 10/16/2022] Open
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5
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Puławski W, Dzwolak W. Virtual Quasi-2D Intermediates as Building Blocks for Plausible Structural Models of Amyloid Fibrils from Proteins with Complex Topologies: A Case Study of Insulin. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:7024-7034. [PMID: 35617668 PMCID: PMC9178918 DOI: 10.1021/acs.langmuir.2c00699] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/08/2022] [Indexed: 06/15/2023]
Abstract
Conformational transitions of globular proteins into amyloid fibrils are complex multistage processes exceedingly challenging to simulate using molecular dynamics (MD). Slow monomer diffusion rates and rugged free energy landscapes disfavor swift self-assembly of orderly amyloid architectures within timescales accessible to all-atom MD. Here, we conduct a multiscale MD study of the amyloidogenic self-assembly of insulin: a small protein with a complex topology defined by two polypeptide chains interlinked by three disulfide bonds. To avoid kinetic traps, unconventional preplanarized insulin conformations are used as amyloid building blocks. These starting conformers generated through uniaxial compression of the native monomer in various spatial directions represent 6 distinct (out of 16 conceivable) two-dimensional (2D) topological classes varying in N-/C-terminal segments of insulin's A- and B-chains being placed inside or outside of the central loop constituted by the middle sections of both chains and Cys7A-Cys7B/Cys19B-Cys20A disulfide bonds. Simulations of the fibrillar self-assembly are initiated through a biased in-register alignment of two, three, or four layers of flat conformers belonging to a single topological class. The various starting topologies are conserved throughout the self-assembly process resulting in polymorphic amyloid fibrils varying in structural features such as helical twist, presence of cavities, and overall stability. Some of the protofilament structures obtained in this work are highly compatible with the earlier biophysical studies on insulin amyloid and high-resolution studies on insulin-derived amyloidogenic peptide models postulating the presence of steric zippers. Our approach provides in silico means to study amyloidogenic tendencies and viable amyloid architectures of larger disulfide-constrained proteins with complex topologies.
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Affiliation(s)
- Wojciech Puławski
- Institute
of High Pressure Physics, Polish Academy
of Sciences, 29/37 Sokołowska
Str., 01-142 Warsaw, Poland
| | - Wojciech Dzwolak
- Institute
of High Pressure Physics, Polish Academy
of Sciences, 29/37 Sokołowska
Str., 01-142 Warsaw, Poland
- Faculty
of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Str., 02-093 Warsaw, Poland
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6
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Li L, Liu J, Li X, Tang Y, Shi C, Zhang X, Cui Y, Wang L, Xu W. Influencing factors and characterization methods of nanoparticles regulating amyloid aggregation. SOFT MATTER 2022; 18:3278-3290. [PMID: 35437550 DOI: 10.1039/d1sm01704g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Human disorders associated with amyloid aggregation, such as Alzheimer's disease and Parkinson's disease, afflict the lives of millions worldwide. When peptides and proteins in the body are converted to amyloids, which have a tendency to aggregate, the toxic oligomers produced during the aggregation process can trigger a range of diseases. Nanoparticles (NPs) have been found to possess surface effects that can modulate the amyloid aggregation process and they have potential application value in the treatment of diseases related to amyloid aggregation and fibrillary tangles. In this review, we discuss recent progress relating to studies of nanoparticles that regulate amyloid aggregation. The review focuses on the factors influencing this regulation, which are important as guidelines for the future design of NPs for the treatment of amyloid aggregation. We describe the characterization methods that have been utilized so far in such studies. This review provides research information and characterization methods for the rational design of NPs, which should result in therapeutic strategies for amyloid diseases.
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Affiliation(s)
- Lingyi Li
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China.
| | - Jianhui Liu
- Yantai Center of Ecology and Environment Monitoring of Shandong Province, Yantai 264025, China
| | - Xinyue Li
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China.
| | - Yuanhan Tang
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China.
| | - Changxin Shi
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China.
| | - Xin Zhang
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China.
| | - Yuming Cui
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China.
| | - Linlin Wang
- State Key Laboratory of Long-Acting and Targeting Drug Delivery System, Shandong Luye Pharmaceutical Co., Ltd, Yantai 264000, China.
| | - Wenlong Xu
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China.
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7
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Ma YW, Lin TY, Tsai MY. Fibril Surface-Dependent Amyloid Precursors Revealed by Coarse-Grained Molecular Dynamics Simulation. Front Mol Biosci 2021; 8:719320. [PMID: 34422910 PMCID: PMC8378332 DOI: 10.3389/fmolb.2021.719320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/26/2021] [Indexed: 01/05/2023] Open
Abstract
Amyloid peptides are known to self-assemble into larger aggregates that are linked to the pathogenesis of many neurodegenerative disorders. In contrast to primary nucleation, recent experimental and theoretical studies have shown that many toxic oligomeric species are generated through secondary processes on a pre-existing fibrillar surface. Nucleation, for example, can also occur along the surface of a pre-existing fibril—secondary nucleation—as opposed to the primary one. However, explicit pathways are still not clear. In this study, we use molecular dynamics simulation to explore the free energy landscape of a free Abeta monomer binding to an existing fibrillar surface. We specifically look into several potential Abeta structural precursors that might precede some secondary events, including elongation and secondary nucleation. We find that the overall process of surface-dependent events can be described at least by the following three stages: 1. Free diffusion 2. Downhill guiding 3. Dock and lock. And we show that the outcome of adding a new monomer onto a pre-existing fibril is pathway-dependent, which leads to different secondary processes. To understand structural details, we have identified several monomeric amyloid precursors over the fibrillar surfaces and characterize their heterogeneity using a probability contact map analysis. Using the frustration analysis (a bioinformatics tool), we show that surface heterogeneity correlates with the energy frustration of specific local residues that form binding sites on the fibrillar structure. We further investigate the helical twisting of protofilaments of different sizes and observe a length dependence on the filament twisting. This work presents a comprehensive survey over the properties of fibril growth using a combination of several openMM-based platforms, including the GPU-enabled openAWSEM package for coarse-grained modeling, MDTraj for trajectory analysis, and pyEMMA for free energy calculation. This combined approach makes long-timescale simulation for aggregation systems as well as all-in-one analysis feasible. We show that this protocol allows us to explore fibril stability, surface binding affinity/heterogeneity, as well as fibrillar twisting. All these properties are important for understanding the molecular mechanism of surface-catalyzed secondary processes of fibril growth.
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Affiliation(s)
- Yuan-Wei Ma
- Department of Chemistry, Tamkang University, New Taipei City, Taiwan
| | - Tong-You Lin
- Department of Chemistry, Tamkang University, New Taipei City, Taiwan
| | - Min-Yeh Tsai
- Department of Chemistry, Tamkang University, New Taipei City, Taiwan
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8
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On the Emergence of Orientational Order in Folded Proteins with Implications for Allostery. Symmetry (Basel) 2021. [DOI: 10.3390/sym13050770] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The beautiful structures of single- and multi-domain proteins are clearly ordered in some fashion but cannot be readily classified using group theory methods that are successfully used to describe periodic crystals. For this reason, protein structures are considered to be aperiodic, and may have evolved this way for functional purposes, especially in instances that require a combination of softness and rigidity within the same molecule. By analyzing the solved protein structures, we show that orientational symmetry is broken in the aperiodic arrangement of the secondary structure elements (SSEs), which we deduce by calculating the nematic order parameter, P2. We find that the folded structures are nematic droplets with a broad distribution of P2. We argue that a non-zero value of P2, leads to an arrangement of the SSEs that can resist external forces, which is a requirement for allosteric proteins. Such proteins, which resist mechanical forces in some regions while being flexible in others, transmit signals from one region of the protein to another (action at a distance) in response to binding of ligands (oxygen, ATP, or other small molecules).
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9
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Rahman MU, Rehman AU, Arshad T, Chen HF. Disaggregation mechanism of prion amyloid for tweezer inhibitor. Int J Biol Macromol 2021; 176:510-519. [PMID: 33607137 DOI: 10.1016/j.ijbiomac.2021.02.094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/08/2021] [Accepted: 02/13/2021] [Indexed: 02/07/2023]
Abstract
The aggregation of amyloid has been an important event in the pathology of amyloidogenicity. A number of small molecules have been designed for Amyloidosis treatment. Molecular tweezer CLR01, a potential drug for misfolded β-amyloids inhibition, was reportedly bind directly to Lysine residues and interrupt oligomerization. However, the disaggregation mechanism of amyloid for this inhibitor is unclear. Here we used long timescale of molecular dynamic simulation to reveal the mechanism of disaggregation for pentamer prion amyloid. Molecular docking and molecular dynamics simulation demonstrate that CLR01 is attached with Lysine222 nitrogen by π-cation interaction of its nine aromatic rings and formation of salt bridge/hydrogen bond of one of the two rotatable peripheral anionic phosphate groups. Upon CLR01 binding, we found a major shifting occurs in initial conformation of the oligomer and stretch out the N-terminal chain A from the rest of the amyloid which seems to be the first stage of disaggregated the fibrils slowly yet efficiently. Moreover, the CLR01 remodelled the pentamer Prion220-272 into a compact structure which might be the resistant conformation for further oligomerization. Our work will contribute to better understand the interaction and deterioration mechanism of molecular tweezer for prions and similar amyloids, and offer significant insights into therapeutic development for Amyloidosis treatment.
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Affiliation(s)
- Mueed Ur Rahman
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ashfaq Ur Rehman
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Taaha Arshad
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai Center for Bioinformation Technology, Shanghai 200235, China.
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10
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Szała-Mendyk B, Molski A. Clustering and Fibril Formation during GNNQQNY Aggregation: A Molecular Dynamics Study. Biomolecules 2020; 10:biom10101362. [PMID: 32987720 PMCID: PMC7598727 DOI: 10.3390/biom10101362] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 12/02/2022] Open
Abstract
The precise kinetic pathways of peptide clustering and fibril formation are not fully understood. Here we study the initial clustering kinetics and transient cluster morphologies during aggregation of the heptapeptide fragment GNNQQNY from the yeast prion protein Sup35. We use a mid-resolution coarse-grained molecular dynamics model of Bereau and Deserno to explore the aggregation pathways from the initial random distribution of free monomers to the formation of large clusters. By increasing the system size to 72 peptides we could follow directly the molecular events leading to the formation of stable fibril-like structures. To quantify those structures we developed a new cluster helicity parameter. We found that the formation of fibril-like structures is a cooperative processes that requires a critical number of monomers, M⋆≈25, in a cluster. The terminal tyrosine residue is the structural determinant in the formation of helical fibril-like structures. This work supports and quantifies the two-step aggregation model where the initially formed amorphous clusters grow and, when they are large enough, rearrange into mature twisted structures. However, in addition to the nucleated fibrillation, growing aggregates undergo further internal reorganization, which leads to more compact structures of large aggregates.
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11
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Charest N, Tro M, Bowers MT, Shea JE. Latent Models of Molecular Dynamics Data: Automatic Order Parameter Generation for Peptide Fibrillization. J Phys Chem B 2020; 124:8012-8022. [PMID: 32790375 DOI: 10.1021/acs.jpcb.0c05763] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Variational autoencoders are artificial neural networks with the capability to reduce highly dimensional sets of data to smaller dimensional, latent representations. In this work, these models are applied to molecular dynamics simulations of the self-assembly of coarse-grained peptides to obtain a singled-valued order parameter for amyloid aggregation. This automatically learned order parameter is constructed by time-averaging the latent parametrizations of internal coordinate representations and compared to the nematic order parameter which is commonly used to study ordering of similar systems in literature. It is found that the latent space value provides more tailored insight into the aggregation mechanism's details, correctly identifying fibril formation in instances where the nematic order parameter fails to do so. A means is provided by which the latent space value can be analyzed so that the major contributing internal coordinates are identified, allowing for a direct interpretation of the latent space order parameter in terms of the behavior of the system. The latent model is found to be an effective and convenient way of representing the data from the dynamic ensemble and provides a means of reducing the dimensionality of a system whose scale exceeds molecular systems so-far considered with similar tools. This bypasses a need for researcher speculation on what elements of a system best contribute to summarizing major transitions and suggests latent models are effective and insightful when applied to large systems with a diversity of complex behaviors.
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Affiliation(s)
- Nathaniel Charest
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106-9510, United States
| | - Michael Tro
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106-9510, United States
| | - Michael T Bowers
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106-9510, United States
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106-9510, United States
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12
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Kokotidou C, Jonnalagadda SVR, Orr AA, Vrentzos G, Kretsovali A, Tamamis P, Mitraki A. Designer Amyloid Cell-Penetrating Peptides for Potential Use as Gene Transfer Vehicles. Biomolecules 2019; 10:E7. [PMID: 31861408 PMCID: PMC7023140 DOI: 10.3390/biom10010007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/15/2019] [Accepted: 12/16/2019] [Indexed: 12/24/2022] Open
Abstract
Cell-penetrating peptides are used extensively to deliver molecules into cells due to their unique characteristics such as rapid internalization, charge, and non-cytotoxicity. Amyloid fibril biomaterials were reported as gene transfer or retroviral infection enhancers; no cell internalization of the peptides themselves is reported so far. In this study, we focus on two rationally and computationally designed peptides comprised of β-sheet cores derived from naturally occurring protein sequences and designed positively charged and aromatic residues exposed at key residue positions. The β-sheet cores bestow the designed peptides with the ability to self-assemble into amyloid fibrils. The introduction of positively charged and aromatic residues additionally promotes DNA condensation and cell internalization by the self-assembled material formed by the designed peptides. Our results demonstrate that these designer peptide fibrils can efficiently enter mammalian cells while carrying packaged luciferase-encoding plasmid DNA, and they can act as a protein expression enhancer. Interestingly, the peptides additionally exhibited strong antimicrobial activity against the enterobacterium Escherichia coli.
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Affiliation(s)
- Chrysoula Kokotidou
- Department of Materials Science and Technology, University of Crete, 70013 Heraklion, Grete, Greece;
- Institute of Electronic Structure and Laser (IESL) FORTH, 70013 Heraklion, Crete, Greece
| | - Sai Vamshi R. Jonnalagadda
- Artie McFerrin Department of Chemical Engineering, Texas A&M University College Station, TX 77843-3251, USA; (S.V.R.J.); (A.A.O.)
| | - Asuka A. Orr
- Artie McFerrin Department of Chemical Engineering, Texas A&M University College Station, TX 77843-3251, USA; (S.V.R.J.); (A.A.O.)
| | - George Vrentzos
- Institute of Molecular Biology and Biotechnology (IMBB) FORTH, 70013 Heraklion, Crete, Greece; (G.V.); (A.K.)
| | - Androniki Kretsovali
- Institute of Molecular Biology and Biotechnology (IMBB) FORTH, 70013 Heraklion, Crete, Greece; (G.V.); (A.K.)
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University College Station, TX 77843-3251, USA; (S.V.R.J.); (A.A.O.)
| | - Anna Mitraki
- Department of Materials Science and Technology, University of Crete, 70013 Heraklion, Grete, Greece;
- Institute of Electronic Structure and Laser (IESL) FORTH, 70013 Heraklion, Crete, Greece
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13
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Yang Y, Liu Y, Ning L, Wang L, Mu Y, Li W. Binding Process and Free Energy Characteristics of Cellulose Chain into the Catalytic Domain of Cellobiohydrolase TrCel7A. J Phys Chem B 2019; 123:8853-8860. [PMID: 31557037 DOI: 10.1021/acs.jpcb.9b05023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
It was observed in experiments that the catalytic domain (CD) of Trichoderma reesei Cel7A (TrCel7A) hydrolyzes crystalline cellulose in a processive manner, but the underlying binding mechanism is still unknown. Here, through replica-exchange molecular dynamics simulations, we find that the loading and sucking-in process of the cellulose chain into CD is entropy-driven and enthalpy-unfavorable, which firmly relate to the desolvation of the binding channel of CD. During the loading process, hydrophobic interactions play a dominant role because several aromatic residues have been identified to guide the cellulose chain processing. At the active site, a transition from enthalpy- to entropy-driven is detected for the driving force. Such a finding reveals the indispensability of the catalytic reaction of the glycosidic bond to provide the energy to drive the movements of the cellulose chain. Our study reveals the interaction pictures between the cellulose chain and TrCel7A at the atomic level, which helps better understand the catalytic mechanism of TrCel7A.
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Affiliation(s)
- Yanmei Yang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education , Shandong Normal University , Jinan 250014 , China
| | | | - Lulu Ning
- School of Biological Sciences , Nanyang Technological University , 637551 Singapore
| | | | - Yuguang Mu
- School of Biological Sciences , Nanyang Technological University , 637551 Singapore
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14
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Ahn SH, Grate JW. Foldamer Architectures of Triazine-Based Sequence-Defined Polymers Investigated with Molecular Dynamics Simulations and Enhanced Sampling Methods. J Phys Chem B 2019; 123:9364-9377. [DOI: 10.1021/acs.jpcb.9b06067] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Surl-Hee Ahn
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Jay W. Grate
- Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
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15
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Lao Z, Chen Y, Tang Y, Wei G. Molecular Dynamics Simulations Reveal the Inhibitory Mechanism of Dopamine against Human Islet Amyloid Polypeptide (hIAPP) Aggregation and Its Destabilization Effect on hIAPP Protofibrils. ACS Chem Neurosci 2019; 10:4151-4159. [PMID: 31436406 DOI: 10.1021/acschemneuro.9b00393] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The aberrant self-assembly of human islet amyloid polypeptide (hIAPP) into toxic oligomers, protofibrils, and mature fibrils is associated with the pathogenesis of type 2 diabetes (T2D). Inhibition of hIAPP aggregation and destabilization of preformed hIAPP fibrils are considered as two major therapeutic strategies for treating T2D. Previous experimental studies reported that dopamine prevented the formation of hIAPP oligomers and fibrils. However, the underlying inhibitory mechanism at the atomic level remains elusive. Herein we investigated the conformational ensembles of hIAPP dimer with and without dopamine using replica-exchange molecular dynamics simulations. The simulations demonstrated that dopamine preferentially bound to R11, L12, F15, H18, F23, I26, L27, and Y37 residues, inhibited the formation of β-sheets in the amyloidogenic regions spanning residues 11RLANFLVH18, 22NFGAIL27, and 30TNVGSNT36, and resulted in more disordered hIAPP dimers, thus hindering the amyloid formation of hIAPP. Protonated and deprotonated dopamine molecules displayed distinct binding capabilities but bound to similar residue sites on hIAPP. Additional microsecond molecular dynamics simulations showed that dopamine mainly bound to the β1 and turn regions of hIAPP protofibril and destabilized the protofibril structure. This study not only revealed the molecular mechanism of dopamine toward the inhibition of hIAPP aggregation but also demonstrated the protofibril-destabilizing effects of dopamine, which may be helpful for the design of drug candidates to treat T2D.
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Affiliation(s)
- Zenghui Lao
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
| | - Yujie Chen
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
| | - Yiming Tang
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
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16
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Turchi M, Cai Q, Lian G. In Silico Prediction of the Thermodynamic Equilibrium of Solute Partition in Multiphase Complex Fluids: A Case Study of Oil-Water Microemulsion. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:10855-10865. [PMID: 31335154 DOI: 10.1021/acs.langmuir.9b01513] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Multiphase complex fluids such as micelles, microemulsions, and dispersions are ubiquitous in product formulations of foods, pharmaceuticals, cosmetics, and fine chemicals. Quantifying how active solutes partition in the microstructure of such multiphase fluids is necessary for designing formulations that can optimally deliver the benefits of functional actives. In this paper, we at first predict the structure of a heptane/butanol/sodium dodecyl sulfate droplet in water that self-assembled to form a microemulsion through the molecular dynamics (MD) simulation and subsequently investigate the thermodynamic equilibrium of solute partitioning using COSMOmic. To our knowledge, this is the first time that the MD/COSMOmic approach is used for predicting solute partitioning in a microemulsion. The predicted partition coefficients are compared to experimental values derived from retention measurements of the same microemulsion. We show that the experimental data of droplet-water partition coefficients (Kdroplet/w) can be reliably predicted by the method that combines MD simulations with COSMOmic.
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Affiliation(s)
- Mattia Turchi
- Unilever Research Colworth , Colworth Park , Sharnbrook, Bedfordshire MK44 1LQ , U.K
- Department of Chemical and Process Engineering , University of Surrey , Guildford GU2 7XH , U.K
| | - Qiong Cai
- Department of Chemical and Process Engineering , University of Surrey , Guildford GU2 7XH , U.K
| | - Guoping Lian
- Unilever Research Colworth , Colworth Park , Sharnbrook, Bedfordshire MK44 1LQ , U.K
- Department of Chemical and Process Engineering , University of Surrey , Guildford GU2 7XH , U.K
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17
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Szała B, Molski A. Aggregation kinetics of short peptides: All-atom and coarse-grained molecular dynamics study. Biophys Chem 2019; 253:106219. [PMID: 31301554 DOI: 10.1016/j.bpc.2019.106219] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/14/2019] [Accepted: 07/03/2019] [Indexed: 11/30/2022]
Abstract
Peptides can aggregate into ordered structures with different morphologies. The aggregation mechanism and evolving structures are the subject of intense research. In this paper we have used molecular dynamics to examine the sequence-dependence of aggregation kinetics for three short peptides: octaalanine (Ala8), octaasparagine (Asn8), and the heptapeptide GNNQQNY (abbreviated as GNN). First, we compared the aggregation of 20 randomly distributed peptides using the coarse-grained MARTINI force field and the atomistic OPLS-AA force field. We found that the MARTINI and OPLS-AA aggregation kinetics are similar for Ala8, Asn8, and GNN. Second, we used the MARTINI force field to study the early stages of aggregation kinetics for a larger system with 72 peptides. In the initial stage of aggregation small clusters grow by monomer addition. In the second stage, when the free monomers are depleted, the dominant cluster growth path is cluster-cluster coalescence. We quantified the aggregation kinetics in terms of rate equations. Our study shows that the initial aggregation kinetics are similar for Ala8, Asn8, and GNN but the molecular details can be different, especially for MARTINI Ala8. We hypothesize that peptide aggregation proceed in two steps. In the first step amorphous aggregates are formed, and then, in the second step, they reorganize into ordered structures. We conclude that sequence-specific differences show up in the second step of aggregation.
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Affiliation(s)
- Beata Szała
- Adam Mickiewicz University in Poznań, Faculty of Chemistry, Umultowska 89b, 61-614 Poznań, Poland.
| | - Andrzej Molski
- Adam Mickiewicz University in Poznań, Faculty of Chemistry, Umultowska 89b, 61-614 Poznań, Poland.
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18
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Ray S, Holden S, Martin LL, Panwar AS. Mechanistic insight into the early stages of amyloid formation using an anuran peptide. Pept Sci (Hoboken) 2019. [DOI: 10.1002/pep2.24120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Sourav Ray
- IITB‐Monash Research AcademyIndian Institute of Technology Bombay Powai Mumbai India
- School of ChemistryMonash University Clayton Victoria Australia
- Department of Metallurgical Engineering and Materials ScienceIndian Institute of Technology Bombay Powai Mumbai India
| | | | | | - Ajay Singh Panwar
- Department of Metallurgical Engineering and Materials ScienceIndian Institute of Technology Bombay Powai Mumbai India
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19
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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: 74] [Impact Index Per Article: 14.8] [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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20
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A Biomphalaria glabrata peptide that stimulates significant behaviour modifications in aquatic free-living Schistosoma mansoni miracidia. PLoS Negl Trop Dis 2019; 13:e0006948. [PMID: 30668561 PMCID: PMC6358113 DOI: 10.1371/journal.pntd.0006948] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 02/01/2019] [Accepted: 10/26/2018] [Indexed: 12/25/2022] Open
Abstract
The human disease schistosomiasis (or bilharzia) is caused by the helminth blood fluke parasite Schistosoma mansoni, which requires an intermediate host, the freshwater gastropod snail Biomphalaria glabrata (the most common intermediate host). The free-swimming parasite miracidia utilise an excellent chemosensory sense to detect and locate an appropriate host. This study investigated the biomolecules released by the snail that stimulate changes in the behaviour of the aquatic S. mansoni miracidia. To achieve this, we have performed an integrated analysis of the snail-conditioned water, through chromatography and bioassay-guided behaviour observations, followed by mass spectrometry. A single fraction containing multiple putative peptides could stimulate extreme swimming behaviour modifications (e.g. velocity, angular variation) similar to those observed in response to crude snail mucus. One peptide (P12;—R-DITSGLDPEVADD-KR—) could replicate the stimulation of miracidia behaviour changes. P12 is derived from a larger precursor protein with a signal peptide and multiple dibasic cleavage sites, which is synthesised in various tissues of the snail, including the central nervous system and foot. P12 consists of an alpha helix secondary structure as indicated by circular dichroism spectroscopy. This information will be helpful for the development of approaches to manipulate this parasites life cycle, and opens up new avenues for exploring other parasitic diseases which have an aquatic phase using methods detailed in this investigation. In aquatic environments, where the vast majority of animals live in darkness, key relationships are often formed and maintained by chemical communication (including smell and taste). Parasites with an aquatic life phase rely on an exquisite sense of chemosensation to detect host biomolecules (kairomones), allowing them to locate and infect their host. Our study identifies the first kairomone released by the freshwater gastropod snail Biomphalaria glabrata, an intermediate host for the helminth blood fluke parasite Schistosoma mansoni. This is a key aspect of the S. mansoni life-cycle that ultimately leads to human infection, causing the disease schistosomiasis (or bilharzia), which is considered the most devastating human helminth infection in terms of global morbidity and mortality. The kairomone we identify is a peptide that does not appear to share any similarity with any other known animal peptide. This information will be helpful as we explore methods to interrupt parasite infection, and therefore break the cycle of infection that causes a major human disease.
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21
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Röder K, Joseph JA, Husic BE, Wales DJ. Energy Landscapes for Proteins: From Single Funnels to Multifunctional Systems. ADVANCED THEORY AND SIMULATIONS 2019. [DOI: 10.1002/adts.201800175] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Konstantin Röder
- Department of ChemistryUniversity of CambridgeLensfield Road CB2 1EW Cambridge UK
| | - Jerelle A. Joseph
- Department of ChemistryUniversity of CambridgeLensfield Road CB2 1EW Cambridge UK
| | - Brooke E. Husic
- Department of ChemistryUniversity of CambridgeLensfield Road CB2 1EW Cambridge UK
| | - David J. Wales
- Department of ChemistryUniversity of CambridgeLensfield Road CB2 1EW Cambridge UK
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22
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Entropic forces drive clustering and spatial localization of influenza A M2 during viral budding. Proc Natl Acad Sci U S A 2018; 115:E8595-E8603. [PMID: 30150411 DOI: 10.1073/pnas.1805443115] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The influenza A matrix 2 (M2) transmembrane protein facilitates virion release from the infected host cell. In particular, M2 plays a role in the induction of membrane curvature and/or in the scission process whereby the envelope is cut upon virion release. Here we show using coarse-grained computer simulations that various M2 assembly geometries emerge due to an entropic driving force, resulting in compact clusters or linearly extended aggregates as a direct consequence of the lateral membrane stresses. Conditions under which these protein assemblies will cause the lipid membrane to curve are explored, and we predict that a critical cluster size is required for this to happen. We go on to demonstrate that under the stress conditions taking place in the cellular membrane as it undergoes large-scale membrane remodeling, the M2 protein will, in principle, be able to both contribute to curvature induction and sense curvature to line up in manifolds where local membrane line tension is high. M2 is found to exhibit linactant behavior in liquid-disordered-liquid-ordered phase-separated lipid mixtures and to be excluded from the liquid-ordered phase, in near-quantitative agreement with experimental observations. Our findings support a role for M2 in membrane remodeling during influenza viral budding both as an inducer and a sensor of membrane curvature, and they suggest a mechanism by which localization of M2 can occur as the virion assembles and releases from the host cell, independent of how the membrane curvature is produced.
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23
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Kokotidou C, Jonnalagadda SVR, Orr AA, Seoane-Blanco M, Apostolidou CP, van Raaij MJ, Kotzabasaki M, Chatzoudis A, Jakubowski JM, Mossou E, Forsyth VT, Mitchell EP, Bowler MW, Llamas-Saiz AL, Tamamis P, Mitraki A. A novel amyloid designable scaffold and potential inhibitor inspired by GAIIG of amyloid beta and the HIV-1 V3 loop. FEBS Lett 2018; 592:1777-1788. [PMID: 29772603 DOI: 10.1002/1873-3468.13096] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 05/02/2018] [Indexed: 12/11/2022]
Abstract
The GAIIG sequence, common to the amyloid beta peptide (residues 29-33) and to the HIV-1 gp120 (residues 24-28 in a typical V3 loop), self-assembles into amyloid fibrils, as suggested by theory and the experiments presented here. The longer YATGAIIGNII sequence from the V3 loop also self-assembles into amyloid fibrils, of which the first three and the last two residues are outside the amyloid GAIIG core. We postulate that this sequence, with suitably selected modifications at the flexible positions, can serve as a designable scaffold for novel amyloid-based materials. Moreover, we report the single crystal X-ray structure of the beta-breaker peptide GAIPIG at 1.05 Å resolution. The structural information provided in this study could serve as the basis for structure-based design of potential inhibitors of amyloid formation.
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Affiliation(s)
- Chrysoula Kokotidou
- Department of Materials Science and Technology, University of Crete, Heraklion, Greece.,Institute of Electronic Structure and Laser (IESL), FORTH, Heraklion, Greece
| | | | - Asuka A Orr
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Mateo Seoane-Blanco
- Departamento de Estructura de Macromoleculas, Centro Nacional de Biotecnologia (CSIC), Madrid, Spain
| | - Chrysanthi Pinelopi Apostolidou
- Department of Materials Science and Technology, University of Crete, Heraklion, Greece.,Institute of Electronic Structure and Laser (IESL), FORTH, Heraklion, Greece
| | - Mark J van Raaij
- Departamento de Estructura de Macromoleculas, Centro Nacional de Biotecnologia (CSIC), Madrid, Spain
| | - Marianna Kotzabasaki
- Department of Materials Science and Technology, University of Crete, Heraklion, Greece
| | - Apostolos Chatzoudis
- Department of Materials Science and Technology, University of Crete, Heraklion, Greece
| | - Joseph M Jakubowski
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Estelle Mossou
- Institut Laue Langevin, Grenoble Cedex 9, France.,Faculty of Natural Sciences/Institute for Science and Technology in Medicine, Keele University, Staffordshire, UK
| | - V Trevor Forsyth
- Institut Laue Langevin, Grenoble Cedex 9, France.,Faculty of Natural Sciences/Institute for Science and Technology in Medicine, Keele University, Staffordshire, UK
| | - Edward P Mitchell
- Faculty of Natural Sciences/Institute for Science and Technology in Medicine, Keele University, Staffordshire, UK.,European Synchrotron Radiation Facility, Grenoble Cedex 9, France
| | - Matthew W Bowler
- European Molecular Biology Laboratory, Grenoble, France.,Unit for Virus Host Cell Interactions, University Grenoble Alpes-EMBL-CNRS, Grenoble, France
| | - Antonio L Llamas-Saiz
- X-Ray Unit, RIAIDT, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Anna Mitraki
- Department of Materials Science and Technology, University of Crete, Heraklion, Greece.,Institute of Electronic Structure and Laser (IESL), FORTH, Heraklion, Greece
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24
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Khan MV, Zakariya SM, Khan RH. Protein folding, misfolding and aggregation: A tale of constructive to destructive assembly. Int J Biol Macromol 2018; 112:217-229. [DOI: 10.1016/j.ijbiomac.2018.01.099] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/04/2018] [Accepted: 01/14/2018] [Indexed: 12/20/2022]
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25
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Iglesias J, Saen‐oon S, Soliva R, Guallar V. Computational structure‐based drug design: Predicting target flexibility. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1367] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
| | | | | | - Victor Guallar
- Life Science DepartmentBarcelonaSpain
- ICREA, Passeig Lluís Companys 23BarcelonaSpain
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26
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Katyal N, Deep S. Inhibition of GNNQQNY prion peptide aggregation by trehalose: a mechanistic view. Phys Chem Chem Phys 2018; 19:19120-19138. [PMID: 28702592 DOI: 10.1039/c7cp02912h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Deposition of amyloid fibrils is the seminal event in the pathogenesis of numerous neurodegenerative diseases. The formation of this amyloid assembly is the manifestation of a cascade of structural transitions including toxic oligomer formation in the early stages of aggregation. Thus a viable therapeutic strategy involves the use of small molecular ligands to interfere with this assembly. In this perspective, we have explored the kinetics of aggregate formation of the fibril forming GNNQQNY peptide fragment from the yeast prion protein SUP35 using multiple all atom MD simulations with explicit solvent and provided mechanistic insights into the way trehalose, an experimentally known aggregation inhibitor, modulates the aggregation pathway. The results suggest that the assimilation process is impeded by different barriers at smaller and larger oligomeric sizes: the initial one being easily surpassed at higher temperatures and peptide concentrations. The kinetic profile demonstrates that trehalose delays the aggregation process by increasing both these activation barriers, specifically the latter one. It increases the sampling of small-sized aggregates that lack the beta sheet conformation. Analysis reveals that the barrier in the growth of larger stable oligomers causes the formation of multiple stable small oligomers which then fuse together bimolecularly. The PCA of 26 properties was carried out to deconvolute the events within the temporary lag phases, which suggested dynamism in lags involving an increase in interchain contacts and burial of SASA. The predominant growth route is monomer addition, which changes to condensation on account of a large number of depolymerisation events in the presence of trehalose. The favourable interaction of trehalose specifically with the sidechain of the peptide promotes crowding of trehalose molecules in its vicinity - the combination of both these factors imparts the observed behaviour. Furthermore, increasing trehalose concentration leads to faster expulsion of water molecules than interpeptide interactions. These expelled water molecules have larger translational movement, suggesting an entropy factor to favor the assembly process. Different conformations observed under this condition suggest the role of water molecules in guiding the morphology of the aggregates as well. A similar scenario exists on increasing peptide concentration.
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Affiliation(s)
- Nidhi Katyal
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauzkhas, New Delhi, India.
| | - Shashank Deep
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauzkhas, New Delhi, India.
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27
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Coskuner-Weber O, Uversky VN. Insights into the Molecular Mechanisms of Alzheimer's and Parkinson's Diseases with Molecular Simulations: Understanding the Roles of Artificial and Pathological Missense Mutations in Intrinsically Disordered Proteins Related to Pathology. Int J Mol Sci 2018; 19:E336. [PMID: 29364151 PMCID: PMC5855558 DOI: 10.3390/ijms19020336] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 01/14/2018] [Accepted: 01/16/2018] [Indexed: 12/18/2022] Open
Abstract
Amyloid-β and α-synuclein are intrinsically disordered proteins (IDPs), which are at the center of Alzheimer's and Parkinson's disease pathologies, respectively. These IDPs are extremely flexible and do not adopt stable structures. Furthermore, both amyloid-β and α-synuclein can form toxic oligomers, amyloid fibrils and other type of aggregates in Alzheimer's and Parkinson's diseases. Experimentalists face challenges in investigating the structures and thermodynamic properties of these IDPs in their monomeric and oligomeric forms due to the rapid conformational changes, fast aggregation processes and strong solvent effects. Classical molecular dynamics simulations complement experiments and provide structural information at the atomic level with dynamics without facing the same experimental limitations. Artificial missense mutations are employed experimentally and computationally for providing insights into the structure-function relationships of amyloid-β and α-synuclein in relation to the pathologies of Alzheimer's and Parkinson's diseases. Furthermore, there are several natural genetic variations that play a role in the pathogenesis of familial cases of Alzheimer's and Parkinson's diseases, which are related to specific genetic defects inherited in dominant or recessive patterns. The present review summarizes the current understanding of monomeric and oligomeric forms of amyloid-β and α-synuclein, as well as the impacts of artificial and pathological missense mutations on the structural ensembles of these IDPs using molecular dynamics simulations. We also emphasize the recent investigations on residual secondary structure formation in dynamic conformational ensembles of amyloid-β and α-synuclein, such as β-structure linked to the oligomerization and fibrillation mechanisms related to the pathologies of Alzheimer's and Parkinson's diseases. This information represents an important foundation for the successful and efficient drug design studies.
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Affiliation(s)
- Orkid Coskuner-Weber
- Türkisch-Deutsche Universität, Theoretical and Computational Biophysics Group, Molecular Biotechnology, Sahinkaya Caddesi, No. 86, Beykoz, Istanbul 34820, Turkey.
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia.
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28
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Watts CR, Gregory A, Frisbie C, Lovas S. Effects of force fields on the conformational and dynamic properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations. Proteins 2017; 86:279-300. [PMID: 29235155 DOI: 10.1002/prot.25439] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 12/10/2017] [Indexed: 12/14/2022]
Abstract
The conformational space and structural ensembles of amyloid beta (Aβ) peptides and their oligomers in solution are inherently disordered and proven to be challenging to study. Optimum force field selection for molecular dynamics (MD) simulations and the biophysical relevance of results are still unknown. We compared the conformational space of the Aβ(1-40) dimers by 300 ns replica exchange MD simulations at physiological temperature (310 K) using: the AMBER-ff99sb-ILDN, AMBER-ff99sb*-ILDN, AMBER-ff99sb-NMR, and CHARMM22* force fields. Statistical comparisons of simulation results to experimental data and previously published simulations utilizing the CHARMM22* and CHARMM36 force fields were performed. All force fields yield sampled ensembles of conformations with collision cross sectional areas for the dimer that are statistically significantly larger than experimental results. All force fields, with the exception of AMBER-ff99sb-ILDN (8.8 ± 6.4%) and CHARMM36 (2.7 ± 4.2%), tend to overestimate the α-helical content compared to experimental CD (5.3 ± 5.2%). Using the AMBER-ff99sb-NMR force field resulted in the greatest degree of variance (41.3 ± 12.9%). Except for the AMBER-ff99sb-NMR force field, the others tended to under estimate the expected amount of β-sheet and over estimate the amount of turn/bend/random coil conformations. All force fields, with the exception AMBER-ff99sb-NMR, reproduce a theoretically expected β-sheet-turn-β-sheet conformational motif, however, only the CHARMM22* and CHARMM36 force fields yield results compatible with collapse of the central and C-terminal hydrophobic cores from residues 17-21 and 30-36. Although analyses of essential subspace sampling showed only minor variations between force fields, secondary structures of lowest energy conformers are different.
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Affiliation(s)
- Charles R Watts
- Department of Neurosurgery, Mayo Clinic, College of Medicine, Rochester, Minnesota.,Department of Neurosurgery, Mayo Clinic Health System, La Crosse, Wisconsin
| | - Andrew Gregory
- Department of Neurosurgery, Mayo Clinic Health System, La Crosse, Wisconsin
| | - Cole Frisbie
- Department of Neurosurgery, Mayo Clinic Health System, La Crosse, Wisconsin.,Department of Biomedical Sciences, Creighton University, Omaha, Nebraska
| | - Sándor Lovas
- Department of Biomedical Sciences, Creighton University, Omaha, Nebraska
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29
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Watts CR, Gregory AJ, Frisbie CP, Lovas S. Structural properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations. Proteins 2017; 85:1024-1045. [PMID: 28241387 DOI: 10.1002/prot.25270] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 01/25/2017] [Accepted: 02/12/2017] [Indexed: 12/17/2022]
Abstract
Replica exchange molecular dynamics simulations (300 ns) were used to study the dimerization of amyloid β(1-40) (Aβ(1-40)) polypeptide. Configurational entropy calculations revealed that at physiological temperature (310 K, 37°C) dynamic dimers are formed by randomly docked monomers. Free energy of binding of the two chains to each other was -93.56 ± 6.341 kJ mol-1 . Prevalence of random coil conformations was found for both chains with the exceptions of increased β-sheet content from residues 16-21 and 29-32 of chain A and residues 15-21 and 30-33 of chain B with β-turn/β-bend conformations in both chains from residues 1-16, 21-29 of chain A, 1-16, and 21-29 of chain B. There is a mixed β-turn/β-sheet region from residues 33-38 of both chains. Analysis of intra- and interchain residue distances shows that, although the individual chains are highly flexible, the dimer system stays in a loosely packed antiparallel β-sheet configuration with contacts between residues 17-21 of chain A with residues 17-21 and 31-36 of chain B as well as residues 31-36 of chain A with residues 17-21 and 31-36 of chain B. Based on dihedral principal component analysis, the antiparallel β-sheet-loop-β-sheet conformational motif is favored for many low energy sampled conformations. Our results show that Aβ(1-40) can form dynamic dimers in aqueous solution that have significant conformational flexibility and are stabilized by collapse of the central and C-terminal hydrophobic cores with the expected β-sheet-loop-β-sheet conformational motif. Proteins 2017; 85:1024-1045. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Charles R Watts
- Department of Neurosurgery, Mayo Clinic, College of Medicine, Rochester, Minnesota, 55905.,Department of Neurosurgery, Mayo Clinic Health System, La Crosse, Wisconsin, 54601
| | - Andrew J Gregory
- Department of Neurosurgery, Mayo Clinic Health System, La Crosse, Wisconsin, 54601
| | - Cole P Frisbie
- Department of Neurosurgery, Mayo Clinic Health System, La Crosse, Wisconsin, 54601.,Department of Biomedical Sciences, Creighton University, Omaha, Nebraska, 61718
| | - Sándor Lovas
- Department of Biomedical Sciences, Creighton University, Omaha, Nebraska, 61718
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30
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Schwierz N, Frost CV, Geissler PL, Zacharias M. From Aβ Filament to Fibril: Molecular Mechanism of Surface-Activated Secondary Nucleation from All-Atom MD Simulations. J Phys Chem B 2017; 121:671-682. [DOI: 10.1021/acs.jpcb.6b10189] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nadine Schwierz
- Department
of Theoretical Biophysics, Max Planck Institute for Biophysics, 60438 Frankfurt am Main, Germany
| | - 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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31
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Deidda G, Jonnalagadda SVR, Spies JW, Ranella A, Mossou E, Forsyth VT, Mitchell EP, Bowler MW, Tamamis P, Mitraki A. Self-Assembled Amyloid Peptides with Arg-Gly-Asp (RGD) Motifs As Scaffolds for Tissue Engineering. ACS Biomater Sci Eng 2016; 3:1404-1416. [DOI: 10.1021/acsbiomaterials.6b00570] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Graziano Deidda
- Department of Materials Science and Technology, University of Crete, Heraklion 70013, Greece
- Institute
of Electronic Structure and Laser (IESL), Foundation for Research and Technology−Hellas (FORTH), Heraklion 70013, Greece
| | - Sai Vamshi R. Jonnalagadda
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
| | - Jacob W. Spies
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
| | - Anthi Ranella
- Institute
of Electronic Structure and Laser (IESL), Foundation for Research and Technology−Hellas (FORTH), Heraklion 70013, Greece
| | - Estelle Mossou
- Institut Laue Langevin, 6 rue
Jules Horowitz, 38042 Grenoble Cedex 9, France
- Faculty of
Natural Sciences/Institute for Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, United Kingdom
| | - V. Trevor Forsyth
- Institut Laue Langevin, 6 rue
Jules Horowitz, 38042 Grenoble Cedex 9, France
- Faculty of
Natural Sciences/Institute for Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, United Kingdom
| | - Edward P. Mitchell
- Faculty of
Natural Sciences/Institute for Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, United Kingdom
- European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043 Grenoble Cedex 9, France
| | - Matthew W. Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, CS 90181, F-38042 Grenoble, France
- Unit
for Virus Host Cell Interactions, Université Grenoble Alpes−EMBL-CNRS, 71 avenue des Martyrs, CS 90181, F-38042 Grenoble, France
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
| | - Anna Mitraki
- Department of Materials Science and Technology, University of Crete, Heraklion 70013, Greece
- Institute
of Electronic Structure and Laser (IESL), Foundation for Research and Technology−Hellas (FORTH), Heraklion 70013, Greece
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32
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Kayode O, Wang R, Pendlebury DF, Cohen I, Henin RD, Hockla A, Soares AS, Papo N, Caulfield TR, Radisky ES. An Acrobatic Substrate Metamorphosis Reveals a Requirement for Substrate Conformational Dynamics in Trypsin Proteolysis. J Biol Chem 2016; 291:26304-26319. [PMID: 27810896 DOI: 10.1074/jbc.m116.758417] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/01/2016] [Indexed: 01/13/2023] Open
Abstract
The molecular basis of enzyme catalytic power and specificity derives from dynamic interactions between enzyme and substrate during catalysis. Although considerable effort has been devoted to understanding how conformational dynamics within enzymes affect catalysis, the role of conformational dynamics within protein substrates has not been addressed. Here, we examine the importance of substrate dynamics in the cleavage of Kunitz-bovine pancreatic trypsin inhibitor protease inhibitors by mesotrypsin, finding that the varied conformational dynamics of structurally similar substrates can profoundly impact the rate of catalysis. A 1.4-Å crystal structure of a mesotrypsin-product complex formed with a rapidly cleaved substrate reveals a dramatic conformational change in the substrate upon proteolysis. By using long all-atom molecular dynamics simulations of acyl-enzyme intermediates with proteolysis rates spanning 3 orders of magnitude, we identify global and local dynamic features of substrates on the nanosecond-microsecond time scale that correlate with enzymatic rates and explain differential susceptibility to proteolysis. By integrating multiple enhanced sampling methods for molecular dynamics, we model a viable conformational pathway between substrate-like and product-like states, linking substrate dynamics on the nanosecond-microsecond time scale with large collective substrate motions on the much slower time scale of catalysis. Our findings implicate substrate flexibility as a critical determinant of catalysis.
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Affiliation(s)
| | | | | | - Itay Cohen
- the Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel, and
| | | | | | - Alexei S Soares
- the Photon Sciences Directorate, Brookhaven National Laboratory, Upton, New York 11973
| | - Niv Papo
- the Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel, and
| | - Thomas R Caulfield
- Neuroscience, Mayo Clinic College of Medicine, Jacksonville, Florida 32224,
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33
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Ranganathan S, Maji SK, Padinhateeri R. Defining a Physical Basis for Diversity in Protein Self-Assemblies Using a Minimal Model. J Am Chem Soc 2016; 138:13911-13922. [DOI: 10.1021/jacs.6b06433] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Srivastav Ranganathan
- Department of Biosciences
and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Samir K. Maji
- Department of Biosciences
and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Ranjith Padinhateeri
- Department of Biosciences
and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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34
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Madsen JJ, Fristrup P, Peters GH. Theoretical Assessment of Fluorinated Phospholipids in the Design of Liposomal Drug-Delivery Systems. J Phys Chem B 2016; 120:9661-71. [DOI: 10.1021/acs.jpcb.6b07206] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Jesper J. Madsen
- Department of Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Peter Fristrup
- Department of Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Günther H. Peters
- Department of Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
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35
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Chua KP, Chew LY, Mu Y. Replica exchange molecular dynamics simulation of cross-fibrillation of IAPP and PrP106-126. Proteins 2016; 84:1134-46. [DOI: 10.1002/prot.25060] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 04/14/2016] [Accepted: 04/28/2016] [Indexed: 12/24/2022]
Affiliation(s)
- Khi Pin Chua
- Interdisciplinary Graduate School; Nanyang Technological University; 637551 Singapore
- Complexity Institute, Nanyang Technological University; 637551 Singapore
| | - Lock Yue Chew
- Interdisciplinary Graduate School; Nanyang Technological University; 637551 Singapore
- Complexity Institute, Nanyang Technological University; 637551 Singapore
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences; Nanyang Technological University; 637551 Singapore
| | - Yuguang Mu
- School of Biological Sciences; Nanyang Technological University; 637551 Singapore
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36
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Luiken JA, Bolhuis PG. Prediction of a stable associated liquid of short amyloidogenic peptides. Phys Chem Chem Phys 2016; 17:10556-67. [PMID: 25804723 DOI: 10.1039/c5cp00284b] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Amyloid fibril formation is believed to be a nucleation-controlled process. Depending on the nature of peptide sequence, fibril nucleation can occur in one step, straight from a dilute solution, or in multiple steps via oligomers or disordered aggregates. What determines this process is poorly understood. Since the fibril formation kinetics is driven by thermodynamic forces, knowledge of the phase behavior is crucial. Here, we investigated the phase behavior of three short peptide sequences of varying side-chain hydrophobicity. Replica exchange molecular dynamics simulations of a mid-resolution model indicate that the weakly hydrophobic peptide forms fibrils directly from solution, whereas the most hydrophobic peptide forms a dense liquid phase before crystallizing into ordered fibrils at low temperatures. For the medium hydrophobic peptide we found evidence of a novel additional transition to a liquid phase consisting of clusters of aligned peptides, implying a three-step nucleation process. We tested the robustness of this prediction by applying Wertheim's theory and statistical associating fluid theory to a hard-sphere model dressed with isotropic and anisotropic attractions. We found that the ratio of interaction strengths strongly affects the phase behavior, and under certain conditions indeed gives rise to a stable polymerized liquid phase. The peptide clusters in the associated liquid tend to be slow and long-lived, which may give the oligomer droplet more time to act as a toxic oligomer, before turning into a fibril.
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Affiliation(s)
- Jurriaan A Luiken
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
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37
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Kouza M, Co NT, Nguyen PH, Kolinski A, Li MS. Preformed template fluctuations promote fibril formation: insights from lattice and all-atom models. J Chem Phys 2016; 142:145104. [PMID: 25877597 DOI: 10.1063/1.4917073] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in slowing down fibril elongation in vivo.
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Affiliation(s)
- Maksim Kouza
- Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warszaw, Poland
| | - Nguyen Truong Co
- Department of Physics, Institute of Technology, National University of HCM City, 268 Ly Thuong Kiet Street, District 10, Ho Chi Minh City, Viet Nam
| | - Phuong H Nguyen
- Laboratoire de Biochimie Theorique, UPR 9080 CNRS, IBPC, Universite Paris 7, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Andrzej Kolinski
- Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warszaw, Poland
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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38
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Protective V127 prion variant prevents prion disease by interrupting the formation of dimer and fibril from molecular dynamics simulations. Sci Rep 2016; 6:21804. [PMID: 26906032 PMCID: PMC4764842 DOI: 10.1038/srep21804] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/01/2016] [Indexed: 12/12/2022] Open
Abstract
Recent studies uncovered a novel protective prion protein variant: V127 variant, which was reported intrinsically resistant to prion conversion and propagation. However, the structural basis of its protective effect is still unknown. To uncover the origin of the protective role of V127 variant, molecular dynamics simulations were performed to explore the influence of G127V mutation on two key processes of prion propagation: dimerization and fibril formation. The simulation results indicate V127 variant is unfavorable to form dimer by reducing the main-chain H-bond interactions. The simulations of formed fibrils consisting of β1 strand prove V127 variant will make the formed fibril become unstable and disorder. The weaker interaction energies between layers and reduced H-bonds number for V127 variant reveal this mutation is unfavorable to the formation of stable fibril. Consequently, we find V127 variant is not only unfavorable to the formation of dimer but also unfavorable to the formation of stable core and fibril, which can explain the mechanism on the protective role of V127 variant from the molecular level. Our findings can deepen the understanding of prion disease and may guide the design of peptide mimetics or small molecule to mimic the protective effect of V127 variant.
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39
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Ranganathan S, Ghosh D, Maji SK, Padinhateeri R. A minimal conformational switching-dependent model for amyloid self-assembly. Sci Rep 2016; 6:21103. [PMID: 26883720 PMCID: PMC4756677 DOI: 10.1038/srep21103] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/19/2016] [Indexed: 11/14/2022] Open
Abstract
Amyloid formation is associated with various pathophysiological conditions like Alzheimer’s and Parkinson’s diseases as well as many useful functions. The hallmark of amyloid assemblies is a conformational transition of the constituent proteins into a β - sheet rich filament. Accounting for this conformational transition in amyloidogenic proteins, we develop an analytically solvable model that can probe the dynamics of an ensemble of single filaments. Using the theory and Monte Carlo simulations, we show the presence of two kinetic regimes for the growth of a self-assembling filament – switching-dependent and –independent growth regimes. We observe a saturation in fibril elongation velocities at higher concentrations in the first regime, providing a novel explanation to the concentration-independence of growth velocities observed experimentally. We also compute the length fluctuation of the filaments to characterize aggregate heterogeneity. From the early velocities and length fluctuation, we propose a novel way of estimating the conformational switching rate. Our theory predicts a kinetic phase diagram that has three distinct phases – short oligomers/monomers, disordered aggregates and β -rich filaments. The model also predicts the force generation potential and the intermittent growth of amyloid fibrils evident from single molecular experiments. Our model could contribute significantly to the physical understanding of amyloid aggregation.
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Affiliation(s)
| | - Dhiman Ghosh
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, India
| | - Samir K Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, India
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40
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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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41
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Ganesan SJ, Matysiak S. Interplay between the hydrophobic effect and dipole interactions in peptide aggregation at interfaces. Phys Chem Chem Phys 2016; 18:2449-58. [DOI: 10.1039/c5cp05867h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Amphipathic octapeptide aggregation at hydrophobic–hydrophilic interfaces is largely driven by backbone dipole interactions in peptide aggregation at interfaces.
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Affiliation(s)
- Sai J. Ganesan
- Fischell Department of Bioengineering
- University of Maryland
- College Park
- USA
| | - Silvina Matysiak
- Fischell Department of Bioengineering and Biophysics Program
- University of Maryland
- College Park
- USA
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42
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Kulesza A, Daly S, Choi CM, Simon AL, Chirot F, MacAleese L, Antoine R, Dugourd P. The structure of chromophore-grafted amyloid-β12–28 dimers in the gas-phase: FRET-experiment guided modelling. Phys Chem Chem Phys 2016; 18:9061-9. [DOI: 10.1039/c6cp00263c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Theoretical modelling, ion mobility spectrometry and action-FRET experiments are combined to an experiment guided approach and used to elucidate the structure of chromophore-grafted amyloid-β12–28 dimers in the gas-phase.
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Affiliation(s)
| | - Steven Daly
- Université de Lyon
- F-69622 Lyon
- France
- Institut Lumière Matière
- UMR5306
| | - Chang Min Choi
- Université de Lyon
- F-69622 Lyon
- France
- Institut Lumière Matière
- UMR5306
| | - Anne-Laure Simon
- Université de Lyon
- F-69622 Lyon
- France
- Institut Lumière Matière
- UMR5306
| | - Fabien Chirot
- Université de Lyon
- F-69622 Lyon
- France
- Institut des Sciences Analytiques
- UMR5280
| | - Luke MacAleese
- Université de Lyon
- F-69622 Lyon
- France
- Institut Lumière Matière
- UMR5306
| | - Rodolphe Antoine
- Université de Lyon
- F-69622 Lyon
- France
- Institut Lumière Matière
- UMR5306
| | - Philippe Dugourd
- Université de Lyon
- F-69622 Lyon
- France
- Institut Lumière Matière
- UMR5306
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43
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Denschlag R, Lingenheil M, Tavan P, Mathias G. Simulated Solute Tempering. J Chem Theory Comput 2015; 5:2847-57. [PMID: 26631796 DOI: 10.1021/ct900274n] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
For the enhanced conformational sampling in molecular dynamics (MD) simulations, we present "simulated solute tempering" (SST) which is an easy to implement variant of simulated tempering. SST extends conventional simulated tempering (CST) by key concepts of "replica exchange with solute tempering" (REST, Liu et al. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 13749). We have applied SST, CST, and REST to molecular dynamics (MD) simulations of an alanine octapeptide in explicit water. The weight parameters required for CST and SST are determined by two different formulas whose performance is compared. For SST only one of them yields a uniform sampling of the temperature space. Compared to CST and REST, SST provides the highest exchange probabilities between neighboring rungs in the temperature ladder. Concomitantly, SST leads to the fastest diffusion of the simulation system through the temperature space, in particular, if the "even-odd" exchange scheme is employed in SST. As a result, SST exhibits the highest sampling speed of the investigated tempering methods.
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Affiliation(s)
- Robert Denschlag
- Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians-Universität, Oettingenstrasse 67, 80538 München, Germany
| | - Martin Lingenheil
- Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians-Universität, Oettingenstrasse 67, 80538 München, Germany
| | - Paul Tavan
- Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians-Universität, Oettingenstrasse 67, 80538 München, Germany
| | - Gerald Mathias
- Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians-Universität, Oettingenstrasse 67, 80538 München, Germany
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44
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Srivastava A, Balaji PV. Molecular events during the early stages of aggregation of GNNQQNY: An all atom MD simulation study of randomly dispersed peptides. J Struct Biol 2015; 192:376-391. [DOI: 10.1016/j.jsb.2015.09.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 09/26/2015] [Accepted: 09/30/2015] [Indexed: 12/11/2022]
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45
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Madsen JJ, Ohkubo YZ, Peters GH, Faber JH, Tajkhorshid E, Olsen OH. Membrane Interaction of the Factor VIIIa Discoidin Domains in Atomistic Detail. Biochemistry 2015; 54:6123-31. [PMID: 26346528 DOI: 10.1021/acs.biochem.5b00417] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A recently developed membrane-mimetic model was applied to study membrane interaction and binding of the two anchoring C2-like discoidin domains of human coagulation factor VIIIa (FVIIIa), the C1 and C2 domains. Both individual domains, FVIII C1 and FVIII C2, were observed to bind the phospholipid membrane by partial or full insertion of their extruding loops (the spikes). However, the two domains adopted different molecular orientations in their membrane-bound states; FVIII C2 roughly was positioned normal to the membrane plane, while FVIII C1 displayed a multitude of tilted orientations. The results indicate that FVIII C1 may be important in modulating the orientation of the FVIIIa molecule to optimize the interaction with FIXa, which is anchored to the membrane via its γ-carboxyglutamic acid-rich (Gla) domain. Additionally, a structural change was observed in FVIII C1 in the coiled main chain leading the first spike. A tight interaction with one lipid per domain, similar to what has been suggested for the homologous FVa C2, is characterized. Finally, we rationalize known FVIII antibody epitopes and the scarcity of documented hemophilic missense mutations related to improper membrane binding of FVIIIa, based on the prevalent nonspecificity of ionic interactions in the simulated membrane-bound states of FVIII C1 and FVIII C2.
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Affiliation(s)
- Jesper J Madsen
- Global Research, Novo Nordisk A/S , DK-2760 Måløv, Denmark.,Department of Chemistry, Technical University of Denmark , DK-2800 Kgs. Lyngby, Denmark
| | | | - Günther H Peters
- Department of Chemistry, Technical University of Denmark , DK-2800 Kgs. Lyngby, Denmark
| | - Johan H Faber
- Global Research, Novo Nordisk A/S , DK-2760 Måløv, Denmark
| | | | - Ole H Olsen
- Global Research, Novo Nordisk A/S , DK-2760 Måløv, Denmark
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Luiken JA, Bolhuis PG. Primary Nucleation Kinetics of Short Fibril-Forming Amyloidogenic Peptides. J Phys Chem B 2015; 119:12568-79. [DOI: 10.1021/acs.jpcb.5b05799] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jurriaan A. Luiken
- van ’t
Hoff Institute
for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, Netherlands
| | - Peter G. Bolhuis
- van ’t
Hoff Institute
for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, Netherlands
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Lockhart C, O'Connor J, Armentrout S, Klimov DK. Greedy replica exchange algorithm for heterogeneous computing grids. J Mol Model 2015; 21:243. [PMID: 26311229 PMCID: PMC10955456 DOI: 10.1007/s00894-015-2763-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 07/13/2015] [Indexed: 12/12/2022]
Abstract
Replica exchange molecular dynamics (REMD) has become a valuable tool in studying complex biomolecular systems. However, its application on distributed computing grids is limited by the heterogeneity of this environment. In this study, we propose a REMD implementation referred to as greedy REMD (gREMD) suitable for computations on heterogeneous grids. To decentralize replica management, gREMD utilizes a precomputed schedule of exchange attempts between temperatures. Our comparison of gREMD against standard REMD suggests four main conclusions. First, gREMD accelerates grid REMD simulations by as much as 40 %. Second, gREMD increases CPU utilization rates in grid REMD by up to 60 %. Third, we argue that gREMD is expected to maintain approximately constant CPU utilization rates and simulation wall-clock times with the increase in the number of replicas. Finally, we show that gREMD correctly implements the REMD algorithm and reproduces the conformational ensemble of a short peptide sampled in our previous standard REMD simulations. We believe that gREMD can find its place in large-scale REMD simulations on heterogeneous computing grids.
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Abstract
INTRODUCTION Molecular docking has become a popular method for virtual screening. Docking small molecules to a rigid biological receptor is fast but could produce many false negatives and identify less diverse compounds. Flexible receptor docking has alleviated this problem. AREAS COVERED This article focuses on reviewing ensemble docking as an approximate but inexpensive method to incorporate receptor flexibility in molecular docking. It outlines key features and recent advances of this method and points out problem areas that need to be addressed to make it even more useful in drug discovery. EXPERT OPINION Among the different methods introduced for flexible receptor docking, ensemble docking represents one of the most popular approaches, especially for high-throughput virtual screening. One can generate structural ensembles by using experimental structures, by structural modeling and by various types of molecular simulations. In building a structural ensemble, a judicious choice of the structures to be included can improve performance. Furthermore, reducing the size of the structural ensemble can cut computational costs, and removing the structures that can bind few ligands well could enrich the number of true actives identified by ensemble docking. The ability of ensemble docking to identify more true positives at the top of a rank-ordered list also depends on the choice of the methods to score and rank compounds, an area that needs further research.
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Affiliation(s)
- Chung F Wong
- a University of Missouri-St. Louis, Department of Chemistry and Biochemistry , 1 University Boulevard, St. Louis, MO 63121, USA +1 31 4516 5318 ;
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Luitz M, Bomblies R, Ostermeir K, Zacharias M. Exploring biomolecular dynamics and interactions using advanced sampling methods. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:323101. [PMID: 26194626 DOI: 10.1088/0953-8984/27/32/323101] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Molecular dynamics (MD) and Monte Carlo (MC) simulations have emerged as a valuable tool to investigate statistical mechanics and kinetics of biomolecules and synthetic soft matter materials. However, major limitations for routine applications are due to the accuracy of the molecular mechanics force field and due to the maximum simulation time that can be achieved in current simulations studies. For improving the sampling a number of advanced sampling approaches have been designed in recent years. In particular, variants of the parallel tempering replica-exchange methodology are widely used in many simulation studies. Recent methodological advancements and a discussion of specific aims and advantages are given. This includes improved free energy simulation approaches and conformational search applications.
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Affiliation(s)
- Manuel Luitz
- Physik-Department T38, Technische Universität München, James Franck Str. 1, 85748 Garching, Germany
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50
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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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