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Ilitchev AI, Giammona MJ, Olivas C, Claud SL, Lazar Cantrell KL, Wu C, Buratto SK, Bowers MT. Hetero-oligomeric Amyloid Assembly and Mechanism: Prion Fragment PrP(106-126) Catalyzes the Islet Amyloid Polypeptide β-Hairpin. J Am Chem Soc 2018; 140:9685-9695. [PMID: 29989407 DOI: 10.1021/jacs.8b05925] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein aggregation is typically attributed to the association of homologous amino acid sequences between monomers of the same protein. Coaggregation of heterogeneous peptide species can occur, however, and is implicated in the proliferation of seemingly unrelated protein diseases in the body. The prion protein fragment (PrP106-126) and human islet amyloid polypeptide (hIAPP) serve as an interesting model of nonhomologous protein assembly as they coaggregate, despite a lack of sequence homology. We have applied ion-mobility mass spectrometry, atomic force microscopy, circular dichroism, and high-level molecular modeling to elucidate this important assembly process. We found that the prion fragment not only forms pervasive hetero-oligomeric aggregates with hIAPP but also promotes the transition of hIAPP into its amyloidogenic β-hairpin conformation. Further, when PrP106-126 was combined with non-amyloidogenic rIAPP, the two formed nearly identical hetero-oligomers to those seen with hIAPP, despite rIAPP containing β-sheet breaking proline substitutions. Additionally, while rIAPP does not natively form the amyloidogenic β-hairpin structure, it did so in the presence of PrP106-126 and underwent a conformational transition to β-sheet in solution. We also find that PrP106-126 forms hetero-oligomers with the IAPP8-20 fragment but not with the "aggregation hot spot" IAPP20-29 fragment. PrP106-126 apparently induces IAPP into a β-hairpin structure within the PrP:IAPP heterodimer complex and then, through ligand exchange, catalytically creates the amyloidogenic β-hairpin dimer of IAPP in significantly greater abundance than IAPP does on its own. This is a new mechanistic model that provides a critical foundation for the detailed study of hetero-oligomerization and prion-like proliferation in amyloid systems.
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Affiliation(s)
- Alexandre I Ilitchev
- Department of Chemistry and Biochemistry , University of California , Santa Barbara , California 93106 , United States
| | - Maxwell J Giammona
- Department of Chemistry and Biochemistry , University of California , Santa Barbara , California 93106 , United States
| | - Carina Olivas
- Department of Chemistry and Biochemistry , Rowan University , Glassboro , New Jersey 08028 , United States
| | - Sarah L Claud
- Department of Chemistry , Westmont College , Santa Barbara , California 93108 , United States
| | - Kristi L Lazar Cantrell
- Department of Chemistry , Westmont College , Santa Barbara , California 93108 , United States
| | - Chun Wu
- Department of Chemistry and Biochemistry , Rowan University , Glassboro , New Jersey 08028 , United States
| | - Steven K Buratto
- Department of Chemistry and Biochemistry , University of California , Santa Barbara , California 93106 , United States
| | - Michael T Bowers
- Department of Chemistry and Biochemistry , University of California , Santa Barbara , California 93106 , United States
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2
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Kato K, Nakayoshi T, Fukuyoshi S, Kurimoto E, Oda A. Validation of Molecular Dynamics Simulations for Prediction of Three-Dimensional Structures of Small Proteins. Molecules 2017; 22:molecules22101716. [PMID: 29023395 PMCID: PMC6151455 DOI: 10.3390/molecules22101716] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 10/05/2017] [Accepted: 10/10/2017] [Indexed: 12/14/2022] Open
Abstract
Although various higher-order protein structure prediction methods have been developed, almost all of them were developed based on the three-dimensional (3D) structure information of known proteins. Here we predicted the short protein structures by molecular dynamics (MD) simulations in which only Newton’s equations of motion were used and 3D structural information of known proteins was not required. To evaluate the ability of MD simulationto predict protein structures, we calculated seven short test protein (10–46 residues) in the denatured state and compared their predicted and experimental structures. The predicted structure for Trp-cage (20 residues) was close to the experimental structure by 200-ns MD simulation. For proteins shorter or longer than Trp-cage, root-mean square deviation values were larger than those for Trp-cage. However, secondary structures could be reproduced by MD simulations for proteins with 10–34 residues. Simulations by replica exchange MD were performed, but the results were similar to those from normal MD simulations. These results suggest that normal MD simulations can roughly predict short protein structures and 200-ns simulations are frequently sufficient for estimating the secondary structures of protein (approximately 20 residues). Structural prediction method using only fundamental physical laws are useful for investigating non-natural proteins, such as primitive proteins and artificial proteins for peptide-based drug delivery systems.
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Affiliation(s)
- Koichi Kato
- Graduate School of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Јapan.
- Department of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan.
| | - Tomoki Nakayoshi
- Graduate School of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Јapan.
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan.
| | - Shuichi Fukuyoshi
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan.
| | - Eiji Kurimoto
- Graduate School of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Јapan.
| | - Akifumi Oda
- Graduate School of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Јapan.
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan.
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Lee J, Lee IH, Joung I, Lee J, Brooks BR. Finding multiple reaction pathways via global optimization of action. Nat Commun 2017; 8:15443. [PMID: 28548089 PMCID: PMC5458546 DOI: 10.1038/ncomms15443] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/24/2017] [Indexed: 12/25/2022] Open
Abstract
Global searching for reaction pathways is a long-standing challenge in computational chemistry and biology. Most existing approaches perform only local searches due to computational complexity. Here we present a computational approach, Action-CSA, to find multiple diverse reaction pathways connecting fixed initial and final states through global optimization of the Onsager-Machlup action using the conformational space annealing (CSA) method. Action-CSA successfully overcomes large energy barriers via crossovers and mutations of pathways and finds all possible pathways of small systems without initial guesses on pathways. The rank order and the transition time distribution of multiple pathways are in good agreement with those of long Langevin dynamics simulations. The lowest action folding pathway of FSD-1 is consistent with recent experiments. The results show that Action-CSA is an efficient and robust computational approach to study the multiple pathways of complex reactions and large-scale conformational changes.
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Affiliation(s)
- Juyong Lee
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - In-Ho Lee
- Center for Materials Genome, Korea Research Institute of Standards and Science, Daejeon 34113, Republic of Korea
- Center for In Silico Protein Science, School of Computational Science, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
| | - InSuk Joung
- Center for In Silico Protein Science, School of Computational Science, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
| | - Jooyoung Lee
- Center for In Silico Protein Science, School of Computational Science, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
| | - Bernard R. Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
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Meuzelaar H, Panman MR, van Dijk CN, Woutersen S. Folding of a Zinc-Finger ββα-Motif Investigated Using Two-Dimensional and Time-Resolved Vibrational Spectroscopy. J Phys Chem B 2016; 120:11151-11158. [PMID: 27723346 DOI: 10.1021/acs.jpcb.6b08883] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Small proteins provide good model systems for studying the fundamental forces that control protein folding. Here, we investigate the folding dynamics of the 28-residue zinc-finger mutant FSD-1, which is designed to form a metal-independent folded ββα-motif, and which provides a testing ground for proteins containing a mixed α/β fold. Although the folding of FSD-1 has been actively studied, the folding mechanism remains largely unclear. In particular, it is unclear in what stage of folding the α-helix is formed. To address this issue we investigate the folding mechanism of FSD-1 using a combination of temperature-dependent UV circular dichroism (UV-CD), Fourier transform infrared (FTIR) spectroscopy, two-dimensional infrared (2D-IR) spectroscopy, and temperature-jump (T-jump) transient-IR spectroscopy. Our UV-CD and FTIR data show different thermal melting transitions, indicating multistate folding behavior. Temperature-dependent 2D-IR spectra indicate that the α-helix is the most stable structural element of FSD-1. To investigate the folding/unfolding re-equilibration dynamics of FSD-1, the conformational changes induced by a nanosecond T-jump are probed with transient-IR and transient dispersed-pump-probe (DPP) IR spectroscopy. We observe biexponential T-jump relaxation kinetics (with time constants of 80 ± 13 ns and 1300 ± 100 ns at 322 K), confirming that the folding involves an intermediate state. The IR and dispersed-pump-probe IR spectra associated with the two kinetic components suggest that the folding of FSD-1 involves early formation of the α-helix, followed by the formation of the β-hairpin and hydrophobic contacts.
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Affiliation(s)
- Heleen Meuzelaar
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Matthijs R Panman
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Chris N van Dijk
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Sander Woutersen
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam , Science Park 904, 1098 XH Amsterdam, The Netherlands
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5
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The Folding of de Novo Designed Protein DS119 via Molecular Dynamics Simulations. Int J Mol Sci 2016; 17:ijms17050612. [PMID: 27128902 PMCID: PMC4881441 DOI: 10.3390/ijms17050612] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 04/13/2016] [Accepted: 04/13/2016] [Indexed: 02/01/2023] Open
Abstract
As they are not subjected to natural selection process, de novo designed proteins usually fold in a manner different from natural proteins. Recently, a de novo designed mini-protein DS119, with a βαβ motif and 36 amino acids, has folded unusually slowly in experiments, and transient dimers have been detected in the folding process. Here, by means of all-atom replica exchange molecular dynamics (REMD) simulations, several comparably stable intermediate states were observed on the folding free-energy landscape of DS119. Conventional molecular dynamics (CMD) simulations showed that when two unfolded DS119 proteins bound together, most binding sites of dimeric aggregates were located at the N-terminal segment, especially residues 5-10, which were supposed to form β-sheet with its own C-terminal segment. Furthermore, a large percentage of individual proteins in the dimeric aggregates adopted conformations similar to those in the intermediate states observed in REMD simulations. These results indicate that, during the folding process, DS119 can easily become trapped in intermediate states. Then, with diffusion, a transient dimer would be formed and stabilized with the binding interface located at N-terminals. This means that it could not quickly fold to the native structure. The complicated folding manner of DS119 implies the important influence of natural selection on protein-folding kinetics, and more improvement should be achieved in rational protein design.
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6
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Lei J, Qi R, Wei G, Nussinov R, Ma B. Self-aggregation and coaggregation of the p53 core fragment with its aggregation gatekeeper variant. Phys Chem Chem Phys 2016; 18:8098-107. [PMID: 26923710 PMCID: PMC6456058 DOI: 10.1039/c5cp06538k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Recent studies suggested that p53 aggregation can lead to loss-of-function (LoF), dominant-negative (DN) and gain-of-function (GoF) effects, with adverse cancer consequences. The p53 aggregation-nucleating (251)ILTIITL(257) fragment is a key segment in wild-type p53 aggregation; however, an I254R mutation can prevent it. It was suggested that self-assembly of wild-type p53 and its cross-interaction with mutants differ from the classical amyloid nucleation-growth mechanism. Here, using replica exchange molecular dynamics (REMD) simulations, we studied the cross-interactions of this p53 core fragment and its aggregation rescue I254R mutant. We found that the core fragment displays strong aggregation propensity, whereas the gatekeeper I254R mutant tends to be disordered, consistent with experiments. Our cross-interaction results reveal that the wild-type p53 fragment promotes β-sheet formation of the I254R mutant by shifting the disordered mutant peptides into aggregating states. As a result, the system has similar oligomeric structures, inter-peptide interactions and free energy landscape as the wild type fragment does, revealing a prion-like process. We also found that in the cross-interaction system, the wild-type species has higher tendency to interact with the mutant than with itself. This phenomenon illustrates synergistic effects between the p53 (251)ILTIITL(257) fragment and the mutant resembling prion cross-species propagation, cautioning against exploiting it in drug discovery.
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Affiliation(s)
- Jiangtao Lei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University, Shanghai, P. R. China.
| | - Ruxi Qi
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University, Shanghai, P. R. China.
| | - Guanghong Wei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University, Shanghai, P. R. China.
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, USA. and Sackler Inst. of Molecular Medicine Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, USA.
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7
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Zhang M, Hu R, Chen H, Chang Y, Ma J, Liang G, Mi J, Wang Y, Zheng J. Polymorphic cross-seeding amyloid assemblies of amyloid-β and human islet amyloid polypeptide. Phys Chem Chem Phys 2015; 17:23245-56. [PMID: 26283068 DOI: 10.1039/c5cp03329b] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Epidemiological studies have shown that the development of Alzheimer's disease (AD) is associated with type 2 diabetes (T2D), but it still remains unclear how AD and T2D are connected. Heterologous cross-seeding between the causative peptides of Aβ and hIAPP may represent a molecular link between AD and T2D. Here, we computationally modeled and simulated a series of cross-seeding double-layer assemblies formed by Aβ and hIAPP peptides using all-atom and coarse-gained molecular dynamics (MD) simulations. The cross-seeding Aβ-hIAPP assemblies showed a wide range of polymorphic structures via a combination of four β-sheet-to-β-sheet interfaces and two packing orientations, focusing on a comparison of different matches of β-sheet layers. Two cross-seeding Aβ-hIAPP assemblies with different interfacial β-sheet packings exhibited high structural stability and favorable interfacial interactions in both oligomeric and fibrillar states. Both Aβ-hIAPP assemblies displayed interfacial dehydration to different extents, which in turn promoted Aβ-hIAPP association depending on interfacial polarity and geometry. Furthermore, computational mutagenesis studies revealed that disruption of interfacial salt bridges largely disfavor the β-sheet-to-β-sheet association, highlighting the importance of salt bridges in the formation of cross-seeding assemblies. This work provides atomic-level information on the cross-seeding interactions between Aβ and hIAPP, which may be involved in the interplay between these two disorders.
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Affiliation(s)
- Mingzhen Zhang
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, USA.
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8
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Susa AC, Wu C, Bernstein SL, Dupuis NF, Wang H, Raleigh DP, Shea JE, Bowers MT. Defining the molecular basis of amyloid inhibitors: human islet amyloid polypeptide-insulin interactions. J Am Chem Soc 2014; 136:12912-9. [PMID: 25144879 PMCID: PMC4183647 DOI: 10.1021/ja504031d] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Indexed: 11/28/2022]
Abstract
Human islet amyloid polypeptide (hIAPP or Amylin) is a 37 residue hormone that is cosecreted with insulin from the pancreatic islets. The aggregation of hIAPP plays a role in the progression of type 2 diabetes and contributes to the failure of islet cell grafts. Despite considerable effort, little is known about the mode of action of IAPP amyloid inhibitors, and this has limited rational drug design. Insulin is one of the most potent inhibitors of hIAPP fibril formation, but its inhibition mechanism is not understood. In this study, the aggregation of mixtures of hIAPP with insulin, as well as with the separate A and B chains of insulin, were characterized using ion mobility spectrometry-based mass spectrometry and atomic force microscopy. Insulin and the insulin B chain target the hIAPP monomer in its compact isoform and shift the equilibrium away from its extended isoform, an aggregation-prone conformation, and thus inhibit hIAPP from forming β-sheets and subsequently amyloid fibrils. All-atom molecular modeling supports these conclusions.
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Affiliation(s)
- Anna C. Susa
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, California 93106, United States
| | - Chun Wu
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, California 93106, United States
| | - Summer L. Bernstein
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, California 93106, United States
| | - Nicholas F. Dupuis
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, California 93106, United States
| | - Hui Wang
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Daniel P. Raleigh
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Joan-Emma Shea
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, California 93106, United States
| | - Michael T. Bowers
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, California 93106, United States
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Yang C, Kim E, Pak Y. Probing α/β Balances in Modified Amber Force Fields from a Molecular Dynamics Study on a ββα Model Protein (1FSD). B KOREAN CHEM SOC 2014. [DOI: 10.5012/bkcs.2014.35.6.1713] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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10
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Structural similarities and differences between amyloidogenic and non-amyloidogenic islet amyloid polypeptide (IAPP) sequences and implications for the dual physiological and pathological activities of these peptides. PLoS Comput Biol 2013; 9:e1003211. [PMID: 24009497 PMCID: PMC3757079 DOI: 10.1371/journal.pcbi.1003211] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 07/20/2013] [Indexed: 12/22/2022] Open
Abstract
IAPP, a 37 amino-acid peptide hormone belonging to the calcitonin family, is an intrinsically disordered protein that is coexpressed and cosecreted along with insulin by pancreatic islet β-cells in response to meals. IAPP plays a physiological role in glucose regulation; however, in certain species, IAPP can aggregate and this process is linked to β-cell death and Type II Diabetes. Using replica exchange molecular dynamics with extensive sampling (16 replicas per sequence and 600 ns per replica), we investigate the structure of the monomeric state of two species of aggregating peptides (human and cat IAPP) and two species of non-aggregating peptides (pig and rat IAPP). Our simulations reveal that the pig and rat conformations are very similar, and consist of helix-coil and helix-hairpin conformations. The aggregating sequences, on the other hand, populate the same helix-coil and helix-hairpin conformations as the non-aggregating sequence, but, in addition, populate a hairpin structure. Our exhaustive simulations, coupled with available peptide-activity data, leads us to a structure-activity relationship (SAR) in which we propose that the functional role of IAPP is carried out by the helix-coil conformation, a structure common to both aggregating and non-aggregating species. The pathological role of this peptide may have multiple origins, including the interaction of the helical elements with membranes. Nonetheless, our simulations suggest that the hairpin structure, only observed in the aggregating species, might be linked to the pathological role of this peptide, either as a direct precursor to amyloid fibrils, or as part of a cylindrin type of toxic oligomer. We further propose that the helix-hairpin fold is also a possible aggregation prone conformation that would lead normally non-aggregating variants of IAPP to form fibrils under conditions where an external perturbation is applied. The SAR relationship is used to suggest the rational design of therapeutics for treating diabetes. IAPP, a 37 amino-acid peptide hormone belonging to the calcitonin family, is an intrinsically disordered peptide produced along with insulin by pancreatic islet β-cells in response to meals. In its functional form, IAPP acts as a synergic partner of insulin to reduce blood glucose. IAPP can, however, also play a pathological role, contributing to Type II diabetes (T2D). Knowledge of the structural nature of the physiological and pathological forms of IAPP will facilitate the rational design of novel drugs for therapeutic treatment of T2D. However, because IAPP does not fold to a single structure, but rather co-exists between multiple functional (and toxic) structures, it is extremely challenging for experimental methods to gain detailed structural information. Using a computational approach, we were able to obtain detailed structures of four IAPP variants and propose a novel structural hypothesis for the two opposing roles of this peptide.
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Abstract
We have carried out all-atom action-derived molecular dynamics (ADMD) folding simulations of the full-size FSD-1. FSD-1 is a designed mini-protein of 28 residues containing both α and β secondary structure elements. Multiple folding pathways are found for FSD-1, which is consistent with existing computational studies. Hydrophobic collapse is observed first, and then subsequent folding events proceeds by forming either α-helix or β-hairpin. Concurrent formation of the full tertiary structure and the secondary structure elements of α-helix and β-hairpin is observed. The folding pathway of FSD-1 elucidated by ADMD simulations does not follow the scenario of the framework model. ADMD simulations provide significant insights for the general mechanisms of protein folding and conformational changes.
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Affiliation(s)
- In-Ho Lee
- Korea Research Institute of Standards and Science, Daejeon 305-340, Korea
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12
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Tang JL, Wu PJ, Wang SC, Lee CI. Insights into Structural Properties of Denatured Human Prion 121-230 at Melting Temperature Studied by Replica Exchange Molecular Dynamics. J Phys Chem B 2012; 116:3305-12. [DOI: 10.1021/jp208433w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jaw-Luen Tang
- Department
of Physics, ‡Department of Life Science, National Chung Cheng University, Ming-Hsiung Chia-Yi, Taiwan 62102,
ROC
| | - Po-Jen Wu
- Department
of Physics, ‡Department of Life Science, National Chung Cheng University, Ming-Hsiung Chia-Yi, Taiwan 62102,
ROC
| | - Shing-Chuen Wang
- Department
of Physics, ‡Department of Life Science, National Chung Cheng University, Ming-Hsiung Chia-Yi, Taiwan 62102,
ROC
| | - Cheng-I Lee
- Department
of Physics, ‡Department of Life Science, National Chung Cheng University, Ming-Hsiung Chia-Yi, Taiwan 62102,
ROC
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13
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Danilkovich AV, Lipkin VM, Udovichenko IP. Classification of self-organizing peptides. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011; 37:780-5. [DOI: 10.1134/s1068162011060069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Dupuis NF, Wu C, Shea JE, Bowers MT. The amyloid formation mechanism in human IAPP: dimers have β-strand monomer-monomer interfaces. J Am Chem Soc 2011; 133:7240-3. [PMID: 21517093 DOI: 10.1021/ja1081537] [Citation(s) in RCA: 184] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Early oligomerization of human IAPP (hIAPP) is responsible for β-cell death in the pancreas and is increasingly considered a primary pathological process linked to Type II Diabetes (T2D). Yet, the assembly mechanism remains poorly understood, largely due to the inability of conventional techniques to probe distributions or detailed structures of early oligomeric species. Here, we describe the first experimental data on the isolated and unmodified dimers of human (hIAPP) and nonamyloidogenic rat IAPP (rIAPP). The experiments reveal that the human IAPP dimers are more extended than those formed by rat IAPP and likely descend from extended monomers. Independent all-atom molecular dynamics simulations show that rIAPP forms compact helix and coil rich dimers, whereas hIAPP forms β-strand rich dimers that are generally more extended. Also, the simulations reveal that the monomer-monomer interfaces of the hIAPP dimers are dominated by β-strands and that β-strands can recruit coil or helix structured regions during the dimerization process. Our β-rich interface contrasts with an N-terminal helix-to-helix interface proposed in the literature but is consistent with existing experimental data on the self-interaction pattern of hIAPP, mutation effects, and inhibition effects of the N-methylation in the mutation region.
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Affiliation(s)
- Nicholas F Dupuis
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, USA
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