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Huang F, Huang J, Yan J, Liu Y, Lian J, Sun Q, Ding F, Sun Y. Molecular Insights into the Effects of F16L and F19L Substitutions on the Conformation and Aggregation Dynamics of Human Calcitonin. J Chem Inf Model 2024; 64:4500-4510. [PMID: 38745385 DOI: 10.1021/acs.jcim.4c00553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Human calcitonin (hCT) regulates calcium-phosphorus metabolism, but its amyloid aggregation disrupts physiological activity, increases thyroid carcinoma risk, and hampers its clinical use for bone-related diseases like osteoporosis and Paget's disease. Improving hCT with targeted modifications to mitigate amyloid formation while maintaining its function holds promise as a strategy. Understanding how each residue in hCT's amyloidogenic core affects its structure and aggregation dynamics is crucial for designing effective analogues. Mutants F16L-hCT and F19L-hCT, where Phe residues in the core are replaced with Leu as in nonamyloidogenic salmon calcitonin, showed different aggregation kinetics. However, the molecular effects of these substitutions in hCT are still unclear. Here, we systematically investigated the folding and self-assembly conformational dynamics of hCT, F16L-hCT, and F19L-hCT through multiple long-time scale independent atomistic discrete molecular dynamics (DMD) simulations. Our results indicated that the hCT monomer primarily assumed unstructured conformations with dynamic helices around residues 4-12 and 14-21. During self-assembly, the amyloidogenic core of hCT14-21 converted from dynamic helices to β-sheets. However, substituting F16L did not induce significant conformational changes, as F16L-hCT exhibited characteristics similar to those of wild-type hCT in both monomeric and oligomeric states. In contrast, F19L-hCT exhibited substantially more helices and fewer β-sheets than did hCT, irrespective of their monomers or oligomers. The substitution of F19L significantly enhanced the stability of the helical conformation for hCT14-21, thereby suppressing the helix-to-β-sheet conformational conversion. Overall, our findings elucidate the molecular mechanisms underlying hCT aggregation and the effects of F16L and F19L substitutions on the conformational dynamics of hCT, highlighting the critical role of F19 as an important target in the design of amyloid-resistant hCT analogs for future clinical applications.
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Affiliation(s)
- Fengjuan Huang
- Ningbo Institute of Innovation for Combined Medicine and Engineering, Lihuili Hospital Affiliated to Ningbo University, Ningbo University, Ningbo 315211, China
- School of Medicine, Ningbo University, Ningbo 315211, China
| | - Jiahui Huang
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Jiajia Yan
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Yuying Liu
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Jiangfang Lian
- Ningbo Institute of Innovation for Combined Medicine and Engineering, Lihuili Hospital Affiliated to Ningbo University, Ningbo University, Ningbo 315211, China
| | - Qinxue Sun
- Ningbo Institute of Innovation for Combined Medicine and Engineering, Lihuili Hospital Affiliated to Ningbo University, Ningbo University, Ningbo 315211, China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States
| | - Yunxiang Sun
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States
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Mandour AA, Elkaeed EB, Hagras M, Refaat HM, Ismail NS. Virtual screening approach for the discovery of selective 5α-reductase type II inhibitors for benign prostatic hyperplasia treatment. Future Med Chem 2023; 15:2149-2163. [PMID: 37955117 DOI: 10.4155/fmc-2023-0065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 10/24/2023] [Indexed: 11/14/2023] Open
Abstract
Background: 5α-Reductase type II (5αR2) inhibition is a promising strategy for benign prostatic hyperplasia treatment. A computational approach including virtual screening, ligand-based 3D pharmacophore modeling, 2D quantitative structure-activity relationship and molecular docking simulations were adopted to develop novel inhibitors. Results: Hits were first filtered via the validated pharmacophore and 2D quantitative structure-activity relationship models. Docking on the recently determined cocrystallized structure of 5αR2 showed three promising hits. Visual inspection results were compared with finasteride ligand and dihydrotestosterone as reference, to explain the role of binding to Glu57 and Tyr91 for 5αR2 selective inhibition. Conclusion: Alignment between Hit 2 and finasteride in the binding pocket showed similar binding modes. The biological activity prediction showed antitumor and androgen targeting activity of the new hits.
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Affiliation(s)
- Asmaa A Mandour
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Future University in Egypt (FUE), Cairo, 11835, Egypt
| | - Eslam B Elkaeed
- Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Riyadh, 13713, Saudi Arabia
| | - Mohamed Hagras
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Hanan M Refaat
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Future University in Egypt (FUE), Cairo, 11835, Egypt
| | - Nasser Sm Ismail
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Future University in Egypt (FUE), Cairo, 11835, Egypt
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3
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Khan A, Nayeem SM. Effect of TMAO and Urea on Dimers and Tetramers of Amyloidogenic Heptapeptides ( 23FGAILSS 29). ACS OMEGA 2020; 5:26986-26998. [PMID: 33134659 PMCID: PMC7593999 DOI: 10.1021/acsomega.0c01031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 09/08/2020] [Indexed: 06/11/2023]
Abstract
Human islet amyloid polypeptide (hIAPP) (1-37) is an intrinsically disordered protein that is released with insulin by β-cells found in the pancreas. Under certain environmental conditions, hIAPP can aggregate, which leads to β-cell death. FGAILSS (23-29) residues of the hIAPP protein form β sheets, which may be toxic species in type 2 diabetes (T2D) patients. All-atom molecular dynamics (MD) simulations have been used to analyze the effect of two distinct types of osmolytes trimethylamine N-oxide (TMAO) and urea on two and four FGAILSS heptapeptides. TMAO leads the individual peptide toward an extended conformation with a higher radius of gyration and favors the formation of antiparallel β-sheets with an increase in its concentration. However, urea mostly shows compaction of individual peptides except at 4.0 M in the case of a tetramer but does not show aggregation behavior as a whole. TMAO leads both the dimer and tetramer toward the native state with an increase in its concentration. Moreover, both the dimer and tetramer show irregular behavior in urea. The tetramer in 4.0 M urea shows the maximum fraction of native contacts due to the formation of antiparallel β-sheets. This formation of antiparallel β-sheets favors the aggregation of peptides. TMAO forms a smaller number of hydrogen bonds with peptides as compared to urea as the exclusion of TMAO and accumulation of urea around the peptides have occurred in the first solvation shell (FSS). Principal component analysis (PCA) results suggest that the minima in the free energy landscape (FEL) plot are homogeneous for a particular conformation in TMAO with smaller basins, while in urea, the dimer shows minima mostly for extended conformations. For a 4.0 M urea concentration, the tetramer shows the minimum for antiparallel β-sheets, which indicates the aggregation behavior of the tetramer, and for a higher concentration, it shows minima with wider basins of extended conformations.
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Patel S, Sasidhar YU, Chary KVR. Mechanism of Initiation, Association, and Formation of Amyloid Fibrils Modeled with the N-Terminal Peptide Fragment, IKYLEFIS, of Myoglobin G-Helix. J Phys Chem B 2017; 121:7536-7549. [PMID: 28707888 DOI: 10.1021/acs.jpcb.7b02205] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Some peptides and proteins undergo self-aggregation under certain conditions, leading to amyloid fibrils formation, which is related to many disease conditions. It is important to understand such amyloid fibrils formation to provide mechanistic detail that governs the process. A predominantly α-helical myoglobin has been reported recently to readily form amyloid fibrils at a higher temperature, similar to its G-helix segment. Here, we have investigated the mechanism of amyloid fibrils formation by performing multiple long molecular dynamics simulations (27 μs) on the N-terminal segment of the G-helix of myoglobin. These simulations resulted in the formation of a single-layered tetrameric β-sheet with mixed parallel and antiparallel β-strands and this is the most common event irrespective of many different starting structures. Formation of the single-layered tetrameric β-sheet takes place following three distinctive pathways. The process of fibril initiation is dependent on temperature. Further, this study provides mechanistic insights into the formation of multilayered fibrilar structure, which could be applicable to a wider variety of peptides or proteins to understand the amyloidogenesis.
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Affiliation(s)
- Sunita Patel
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences , Hyderabad 500075, India.,UM-DAE Centre for Excellence in Basic Sciences , Mumbai University Campus, Mumbai 400098, India
| | - Yellamraju U Sasidhar
- Department of Chemistry, Indian Institute of Technology Bombay , Mumbai 400076, India
| | - Kandala V R Chary
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences , Hyderabad 500075, India.,Tata Institute of Fundamental Research , Mumbai 400005, India
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5
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Rigoldi F, Metrangolo P, Redaelli A, Gautieri A. Nanostructure and stability of calcitonin amyloids. J Biol Chem 2017; 292:7348-7357. [PMID: 28283568 PMCID: PMC5418037 DOI: 10.1074/jbc.m116.770271] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/24/2017] [Indexed: 12/03/2022] Open
Abstract
Calcitonin is a 32-amino acid thyroid hormone that can form amyloid fibrils. The structural basis of the fibril formation and stabilization is still debated and poorly understood. The reason is that NMR data strongly suggest antiparallel β-sheet calcitonin assembly, whereas modeling studies on the short DFNKF peptide (corresponding to the sequence from Asp15 to Phe19 of human calcitonin and reported as the minimal amyloidogenic module) show that it assembles with parallel β-sheets. In this work, we first predict the structure of human calcitonin through two complementary molecular dynamics (MD) methods, finding that human calcitonin forms an α-helix. We use extensive MD simulations to compare previously proposed calcitonin fibril structures. We find that two conformations, the parallel arrangement and one of the possible antiparallel structures (with Asp15 and Phe19 aligned), are highly stable and ordered. Nonetheless, fibrils with parallel molecules show bulky loops formed by residues 1 to 7 located on the same side, which could limit or prevent the formation of larger amyloids. We investigate fibrils formed by the DFNKF peptide by simulating different arrangements of this amyloidogenic core sequence. We show that DFNKF fibrils are highly stable when assembled in parallel β-sheets, whereas they quickly unfold in antiparallel conformation. Our results indicate that the DFNKF peptide represents only partially the full-length calcitonin behavior. Contrary to the full-length polypeptide, in fact, the DFNKF sequence is not stable in antiparallel conformation, suggesting that the residue flanking the amyloidogenic peptide contributes to the stabilization of the experimentally observed antiparallel β-sheet packing.
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Affiliation(s)
- Federica Rigoldi
- From the Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Pierangelo Metrangolo
- the Dipartimento di Chimica, Materiali e Ingegneria Chimica "Giulio Natta," Politecnico di Milano, Via L. Mancinelli 7, 20131 Milano, Italy, and.,the VTT - Tecnical Research Centre of Finland, Biologinkuja 7, 02150 Espoo, Finland
| | - Alberto Redaelli
- From the Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Alfonso Gautieri
- From the Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy,
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6
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Bertolani A, Pizzi A, Pirrie L, Gazzera L, Morra G, Meli M, Colombo G, Genoni A, Cavallo G, Terraneo G, Metrangolo P. Crystal Structure of the DFNKF Segment of Human Calcitonin Unveils Aromatic Interactions between Phenylalanines. Chemistry 2017; 23:2051-2058. [PMID: 27806188 PMCID: PMC5573999 DOI: 10.1002/chem.201604639] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Indexed: 12/24/2022]
Abstract
Although intensively studied, the high-resolution crystal structure of the peptide DFNKF, the core-segment of human calcitonin, has never been described. Here we report how the use of iodination as a strategy to promote crystallisation and facilitate phase determination, allowed us to solve, for the first time, the single-crystal X-ray structure of a DFNKF derivative. Computational studies suggest that both the iodinated and the wild-type peptides populate very similar conformations. Furthermore, the conformer found in the solid-state structure is one of the most populated in solution, making the crystal structure a reliable model for the peptide in solution. The crystal structure of DFNKF(I) confirms the overall features of the amyloid cross-β spine and highlights how aromatic-aromatic interactions are important structural factors in the self-assembly of this peptide. A detailed analysis of such interactions is reported.
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Affiliation(s)
- Arianna Bertolani
- Laboratory of Nanostructured Fluorinated Materials (NFMLab)Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
| | - Andrea Pizzi
- Laboratory of Nanostructured Fluorinated Materials (NFMLab)Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
| | - Lisa Pirrie
- Laboratory of Nanostructured Fluorinated Materials (NFMLab)Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
| | - Lara Gazzera
- Laboratory of Nanostructured Fluorinated Materials (NFMLab)Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
| | - Giulia Morra
- Istituto di Chimica del Riconoscimento MolecolareCNRVia Mario Bianco 920131MilanoItaly
| | - Massimiliano Meli
- Istituto di Chimica del Riconoscimento MolecolareCNRVia Mario Bianco 920131MilanoItaly
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento MolecolareCNRVia Mario Bianco 920131MilanoItaly
| | - Alessandro Genoni
- Laboratoire SRSMC, UMR 7565CNRSVandoeuvre-lès-Nancy54506France
- Laboratoire SRSMC, UMR 7565Université de LorraineVandoeuvre-lès-Nancy54506France
| | - Gabriella Cavallo
- Laboratory of Nanostructured Fluorinated Materials (NFMLab)Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
| | - Giancarlo Terraneo
- Laboratory of Nanostructured Fluorinated Materials (NFMLab)Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
| | - Pierangelo Metrangolo
- Laboratory of Nanostructured Fluorinated Materials (NFMLab)Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
- Istituto di Chimica del Riconoscimento MolecolareCNRVia Mario Bianco 920131MilanoItaly
- HYBER Centre of ExcellenceDepartment of Applied PhysicsAalto University, P.O. Box 1510002150EspooFinland
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7
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Kamgar-Parsi K, Tolchard J, Habenstein B, Loquet A, Naito A, Ramamoorthy A. Structural Biology of Calcitonin: From Aqueous Therapeutic Properties to Amyloid Aggregation. Isr J Chem 2016. [DOI: 10.1002/ijch.201600096] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kian Kamgar-Parsi
- Applied Physics Program; University of Michigan; Ann Arbor MI 48109-1040 USA
| | - James Tolchard
- Institute of Chemistry and Biology of Membranes and Nanoobjects, CNRS, CBMN, UMR 5248; University of Bordeaux; 33600 Pessac France
| | - Birgit Habenstein
- Institute of Chemistry and Biology of Membranes and Nanoobjects, CNRS, CBMN, UMR 5248; University of Bordeaux; 33600 Pessac France
| | - Antoine Loquet
- Institute of Chemistry and Biology of Membranes and Nanoobjects, CNRS, CBMN, UMR 5248; University of Bordeaux; 33600 Pessac France
| | - Akira Naito
- Graduate School of Engineering; Yokohama National University; 79-5 Tokiwadai Hodogaya-ku Yokohama 240-8501 Japan
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry and Biophysics Program; University of Michigan; 930 North University Avenue Ann Arbor MI 48109-1055 USA
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8
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Fichman G, Guterman T, Adler-Abramovich L, Gazit E. The Use of the Calcitonin Minimal Recognition Module for the Design of DOPA-Containing Fibrillar Assemblies. NANOMATERIALS 2014; 4:726-740. [PMID: 28344244 PMCID: PMC5304689 DOI: 10.3390/nano4030726] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/28/2014] [Accepted: 08/08/2014] [Indexed: 11/20/2022]
Abstract
Amyloid deposits are insoluble fibrous protein aggregates, identified in numerous diseases, which self-assemble through molecular recognition. This process is facilitated by short amino acid sequences, identified as minimal modules. Peptides corresponding to these motifs can be used for the formation of amyloid-like fibrillar assemblies in vitro. Such assemblies hold broad appeal in nanobiotechnology due to their ordered structure and to their ability to be functionalized. The catechol functional group, present in the non-coded L-3,4-dihydroxyphenylalanine (DOPA) amino acid, can take part in diverse chemical interactions. Moreover, DOPA-incorporated polymers have demonstrated adhesive properties and redox activity. In this work, amyloid-like fibrillar assemblies were formed through the self-assembly of a pentapeptide containing DOPA residues, Asp-DOPA-Asn-Lys-DOPA. The design of this peptide was based on the minimal amyloidogenic recognition motif of the human calcitonin hormone, Asp-Phe-Asn-Lys-Phe, the first amyloidogenic pentapeptide identified. By substituting phenylalanine with DOPA, we obtained DOPA-functionalized amyloid-like assemblies in water. Electron microscopy revealed elongated, linear fibril-like nanometric assemblies. Secondary structure analysis indicated the presence of amyloid-characteristic β-sheet structures as well as random coil structures. Deposition of silver on the DOPA-incorporated assemblies suggested redox activity and demonstrated the applicative potential of this novel nanobiomaterial.
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Affiliation(s)
- Galit Fichman
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel.
| | - Tom Guterman
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel.
| | - Lihi Adler-Abramovich
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel.
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel.
- Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel.
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9
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Srivastava A, Balaji PV. Interplay of sequence, topology and termini charge in determining the stability of the aggregates of GNNQQNY mutants: a molecular dynamics study. PLoS One 2014; 9:e96660. [PMID: 24817093 PMCID: PMC4015988 DOI: 10.1371/journal.pone.0096660] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 04/11/2014] [Indexed: 01/16/2023] Open
Abstract
This study explores the stabilities of single sheet parallel systems of three sequence variants of 1GNNQQNY7, N2D, N2S and N6D, with variations in aggregate size (5–8) and termini charge (charged or neutral). The aggregates were simulated at 300 and 330 K. These mutations decrease amyloid formation in the yeast prion protein Sup35. The present study finds that these mutations cause instability even in the peptide context. The protonation status of termini is found to be a key determinant of stabilities; other determinants are sequence, position of mutation and aggregate size. All systems with charged termini are unstable, whereas both stable and unstable systems are found when the termini are neutral. When termini are charged, the largest stable aggregate for the N2S and N6D systems has 3 to 4 peptides whereas N2D mutation supports oligomers of larger size (5-and 6-mers) as well. Mutation at 2nd position (N2S and N2D) results in fewer H-bonds at the mutated as well as neighboring (Gly1/Gln4) positions. However, no such effect is found if mutation is at 6th position (N6D). The effect of Asn→Asp mutation depends on the position and termini charge: it is more destabilizing at the 2nd position than at the 6th in case of neutral termini, however, the opposite is true in case of charged termini. Appearance of twist in stable systems and in smaller aggregates formed in unstable systems suggests that twist is integral to amyloid arrangement. Disorder, dissociation or rearrangement of peptides, disintegration or collapse of aggregates and formation of amorphous aggregates observed in these simulations are likely to occur during the early stages of aggregation also. The smaller aggregates formed due to such events have a variety of arrangements of peptides. This suggests polymorphic nature of oligomers and presence of a heterogeneous mixture of oligomers during early stages of aggregation.
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Affiliation(s)
- Alka Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Petety V. Balaji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
- * E-mail:
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10
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Zhou ZL, Ho Y, Liu HL, Elumalai P, Chen WH. Computer-aided discovery of novel non-peptide inhibitors against amyloid-beta (Aβ) peptide aggregation for treating Alzheimer's disease. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.910600] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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11
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Wang JL, Liu HL, Zhou ZL, Chen WH, Ho Y. Discovery of novel 5α-reductase type II inhibitors by pharmacophore modelling, virtual screening, molecular docking and molecular dynamics simulations. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2013.878865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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12
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Molecular Dynamics Studies on Amyloidogenic Proteins. COMPUTATIONAL METHODS TO STUDY THE STRUCTURE AND DYNAMICS OF BIOMOLECULES AND BIOMOLECULAR PROCESSES 2014. [DOI: 10.1007/978-3-642-28554-7_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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13
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Zhou ZL, Liu HL, Wu JW, Tsao CW, Chen WH, Liu KT, Ho Y. Combining Structure-Based Pharmacophore andIn SilicoApproaches to Discover Novel Selective Serotonin Reuptake Inhibitors. Chem Biol Drug Des 2013; 82:705-17. [DOI: 10.1111/cbdd.12192] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Revised: 06/20/2013] [Accepted: 07/09/2013] [Indexed: 01/04/2023]
Affiliation(s)
- Zheng-Li Zhou
- Institute of Biochemical and Biomedical Engineering; National Taipei University of Technology; 1 Sec. 3 ZhongXiao E. Road Taipei 10608 Taiwan
| | - Hsuan-Liang Liu
- Institute of Biochemical and Biomedical Engineering; National Taipei University of Technology; 1 Sec. 3 ZhongXiao E. Road Taipei 10608 Taiwan
- Department of Chemical Engineering and Biotechnology; National Taipei University of Technology; 1 Sec. 3 ZhongXiao E. Road Taipei 10608 Taiwan
| | - Josephine W. Wu
- Department of Optometry; Central Taiwan University of Science and Technology; 666 Buzih Road Taichung 40601 Taiwan
| | - Cheng-Wen Tsao
- Department of Applied Cosmetology; Taoyuan Innovation Institute of Technology; 414 Sec. 3, Jhongshan E. Road Jhongli City Taoyuan County 32091 Taiwan
| | - Wei-Hsi Chen
- Chemistry Division; Institute of Nuclear Energy Research; 1000 Wunhua Road Longtan Township Taoyuan County 32546 Taiwan
| | - Kung-Tien Liu
- Everlight Chemical Industrial Corporation; 6th Fl, 77, Tun Hua South Road, Sec.2 Taipei 106 Taiwan
| | - Yih Ho
- School of Pharmacy; Taipei Medical University; 250 Wu-Hsing Street Taipei 110 Taiwan
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14
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Srivastava A, Balaji PV. Size, orientation and organization of oligomers that nucleate amyloid fibrils: Clues from MD simulations of pre-formed aggregates. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:963-73. [DOI: 10.1016/j.bbapap.2012.05.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 04/27/2012] [Accepted: 05/04/2012] [Indexed: 11/30/2022]
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15
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Huang R, Vivekanandan S, Brender JR, Abe Y, Naito A, Ramamoorthy A. NMR characterization of monomeric and oligomeric conformations of human calcitonin and its interaction with EGCG. J Mol Biol 2011; 416:108-20. [PMID: 22200484 DOI: 10.1016/j.jmb.2011.12.023] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 12/05/2011] [Accepted: 12/10/2011] [Indexed: 11/17/2022]
Abstract
Calcitonin is a 32-residue peptide hormone known for its hypocalcemic effect and its inhibition of bone resorption. While calcitonin has been used in therapy for osteoporosis and Paget's disease for decades, human calcitonin (hCT) forms fibrils in aqueous solution that limit its therapeutic application. The molecular mechanism of fiber formation by calcitonin is not well understood. Here, high-resolution structures of hCT at concentrations of 0.3 mM and 1 mM have been investigated using NMR spectroscopy. Comparing the structures of hCT at different concentrations, we discovered that the peptide undergoes a conformational transition from an extended to a β-hairpin structure in the process of molecular association. This conformational transition locates the aromatic side chains of Tyr12 and Phe16 in a favorable way for intermolecular π-π stacking, which is proposed to be a crucial interaction for peptide association and fibrillation. One-dimensional (1)H NMR experiments confirm that oligomerization of hCT accompanies the conformational transition at 1 mM concentration. The effect of the polyphenol epigallocatechin 3-gallate (EGCG) on hCT fibrillation was also investigated by NMR and electron microscopy, which show that EGCG efficiently inhibits fibril formation of hCT by preventing the initial association of hCT before fiber formation. The NMR experiments also indicate that the interaction between aromatic rings of EGCG and the aromatic side chains of the peptide may play an important role in inhibiting fibril formation of hCT.
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Affiliation(s)
- Rui Huang
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
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Jain A, Sankararamakrishnan R. Dynamics of Noncovalent Interactions in All-α and All-β Class Proteins: Implications for the Stability of Amyloid Aggregates. J Chem Inf Model 2011; 51:3208-16. [DOI: 10.1021/ci200302q] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Alok Jain
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur −208016, India
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Lin YF, Zhao JH, Liu HL, Wu JW, Chuang CK, Liu KT, Lin HY, Tsai WB, Ho Y. Insights into the structural stability and possible aggregation pathways of the LYQLEN peptides derived from human insulin. J Taiwan Inst Chem Eng 2011. [DOI: 10.1016/j.jtice.2010.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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18
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Zhou ZL, Zhao JH, Liu HL, Wu JW, Liu KT, Chuang CK, Tsai WB, Ho Y. The Possible Structural Models for Polyglutamine Aggregation: A Molecular Dynamics Simulations Study. J Biomol Struct Dyn 2011; 28:743-58. [DOI: 10.1080/07391102.2011.10508603] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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19
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Zhao JH, Liu HL, Chuang CK, Liu KT, Tsai WB, Ho Y. Molecular dynamics simulations to investigate the stability and aggregation behaviour of the amyloid-forming peptide VQIVYK from tau protein. MOLECULAR SIMULATION 2010. [DOI: 10.1080/08927022.2010.499147] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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20
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Chang LK, Zhao JH, Liu HL, Wu JW, Chuang CK, Liu KT, Chen JT, Tsai WB, Ho Y. The Importance of Steric Zipper on the Aggregation of the MVGGVV Peptide Derived from the Amyloid β Peptide. J Biomol Struct Dyn 2010; 28:39-50. [DOI: 10.1080/07391102.2010.10507342] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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21
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Pizzanelli S, Forte C, Monti S, Zandomeneghi G, Hagarman A, Measey TJ, Schweitzer-Stenner R. Conformations of phenylalanine in the tripeptides AFA and GFG probed by combining MD simulations with NMR, FTIR, polarized Raman, and VCD spectroscopy. J Phys Chem B 2010; 114:3965-78. [PMID: 20184301 DOI: 10.1021/jp907502n] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Conformational properties of small, flexible peptides are a matter of ongoing interest since they can be considered as models for unfolded proteins. However, the investigation of the conformations of small peptides is challenging as they are ensembles of rapidly interconverting conformers; moreover, the different methods used are prone to different approximations and errors. In order to obtain more reliable results, it is prudent to combine different techniques; here, molecular dynamics (MD) simulations together with nuclear magnetic resonance (NMR), Fourier transform IR (FTIR), polarized Raman, and vibrational circular dichroism (VCD) measurements were used to study the conformational propensity of phenylalanine in the tripeptides AFA and GFG, motivated by the relevance of phenylalanine for the self-aggregation of peptides. The results of this analysis indicate that the F residue predominantly populates the beta-strand (beta) and polyproline II (PPII) conformations in both AFA and GFG. However, while phenylalanine exhibits a propensity for beta-strand conformations in GFG (0.40 < or = beta population < or = 0.69 and 0.29 < or = PPII population < or = 0.42), the substitution of terminal glycines with alanine residues induces a higher population of PPII (0.31 < or = beta population < or = 0.50 and 0.37 < or = PPII population < or = 0.57).
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Affiliation(s)
- Silvia Pizzanelli
- Istituto per i Processi Chimico Fisici, Consiglio Nazionale delle Ricerche, Area della Ricerca di Pisa, via G. Moruzzi, 1 56124 Pisa, Italy.
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22
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Shtainfeld A, Sheynis T, Jelinek R. Specific Mutations Alter Fibrillation Kinetics, Fiber Morphologies, and Membrane Interactions of Pentapeptides Derived from Human Calcitonin. Biochemistry 2010; 49:5299-307. [DOI: 10.1021/bi1002713] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Amit Shtainfeld
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Tania Sheynis
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Raz Jelinek
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
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23
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Kang M, Smith PE. A Pairwise Preferential Interaction Model for Understanding Peptide Aggregation. INTERNATIONAL JOURNAL OF THERMOPHYSICS 2010; 31:793-804. [PMID: 20694045 PMCID: PMC2914330 DOI: 10.1007/s10765-009-0694-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
A pairwise preferential interaction model (PPIM), based on Kirkwood-Buff integrals, is developed to quantify and characterize the interactions between some of the functional groups commonly observed in peptides. The existing experimental data are analyzed to determine the preferential interaction (PI) parameters for different amino acid and small peptide systems in aqueous solutions. The PIs between the different functional groups present in the peptides are then isolated and quantified by assuming simple pairwise additivity. The PPIM approach provides consistent estimates for the pair interactions between the same functional groups obtained from different solute molecules. Furthermore, these interactions appear to be chemically intuitive. It is argued that this type of approach can provide valuable information concerning specific functional group correlations which could give rise to peptide aggregation.
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24
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Tsai HHG, Lee JB, Tseng SS, Pan XA, Shih YC. Folding and membrane insertion of amyloid-beta (25-35) peptide and its mutants: Implications for aggregation and neurotoxicity. Proteins 2010; 78:1909-25. [DOI: 10.1002/prot.22705] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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25
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26
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Lin YF, Zhao JH, Liu HL, Liu KT, Chen JT, Tsai WB, Ho Y. Structural stability and aggregation behavior of the VEALYL peptide derived from human insulin: A molecular dynamics simulation study. Biopolymers 2009; 94:269-78. [DOI: 10.1002/bip.21322] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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27
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Chang LK, Zhao JH, Liu HL, Liu KT, Chen JT, Tsai WB, Ho Y. Molecular Dynamics Simulations to Investigate the Structural Stability and Aggregation Behavior of the GGVVIA Oligomers Derived from Amyloid β Peptide. J Biomol Struct Dyn 2009; 26:731-40. [DOI: 10.1080/07391102.2009.10507285] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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28
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Fang PS, Zhao JH, Liu HL, Liu KT, Chen JT, Lin HY, Huang CH, Fang HW. Molecular Dynamics Simulations to Gain Insights into the Stability and Morphologies of K3 Oligomers from β2-microglobulin. J Biomol Struct Dyn 2009; 26:549-59. [DOI: 10.1080/07391102.2009.10507270] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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29
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Noy K, Kalisman N, Keasar C. Prediction of structural stability of short beta-hairpin peptides by molecular dynamics and knowledge-based potentials. BMC STRUCTURAL BIOLOGY 2008; 8:27. [PMID: 18510728 PMCID: PMC2427033 DOI: 10.1186/1472-6807-8-27] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2007] [Accepted: 05/29/2008] [Indexed: 11/10/2022]
Abstract
BACKGROUND The structural stability of peptides in solution strongly affects their binding affinities and specificities. Thus, in peptide biotechnology, an increase in the structural stability is often desirable. The present work combines two orthogonal computational techniques, Molecular Dynamics and a knowledge-based potential, for the prediction of structural stability of short peptides (< 20 residues) in solution. RESULTS We tested the new approach on four families of short beta-hairpin peptides: TrpZip, MBH, bhpW and EPO, whose structural stabilities have been experimentally measured in previous studies. For all four families, both computational techniques show considerable correlation (r > 0.65) with the experimentally measured stabilities. The consensus of the two techniques shows higher correlation (r > 0.82). CONCLUSION Our results suggest a prediction scheme that can be used to estimate the relative structural stability within a peptide family. We discuss the applicability of this predictive approach for in-silico screening of combinatorial peptide libraries.
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Affiliation(s)
- Karin Noy
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva, Israel.
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30
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Zheng J, Ma B, Chang Y, Nussinov R. Molecular dynamics simulations of Alzheimer Abeta40 elongation and lateral association. FRONT BIOSCI-LANDMRK 2008; 13:3919-30. [PMID: 18508486 DOI: 10.2741/2980] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Amyloid-beta (Abeta) peptides can elongate in the fibril axis and associate in the lateral direction. We present detailed atomic Abeta models with different in-register intermolecular beta-sheet-beta-sheet associations. We probe structural stability, conformational dynamics, and association force of Abeta oligomers with various sizes and structures for both wild-type and mutated sequences using molecular dynamics (MD) simulations. MD simulations show that an Abeta oligomer that is laterally associated through the C-terminal-C-terminal interface is energetically more favorable than other oligomers with the N-terminal-N-terminal and C-terminal-N-terminal interfaces. We further develop a simple numerical model to describe the kinetics of Abeta aggregation process by considering fibril elongation and lateral association using a Monte Carlo algorithm. Kinetic data suggest that fibril elongation and lateral association are mutually competitive. Single-point mutations of Glu22 or Met35 at the interfaces have profound negative effects on intermolecular beta-sheet-beta-sheet association. These disease-related mutants (E22K, E22Q, and M35O) display more flexible structures, weaker lateral association, and stronger elongation tendencies than the wild type, suggesting that amyloid oligomerization and neurotoxicity might be linked to fibril longitudinal growth.
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Affiliation(s)
- Jie Zheng
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, USA.
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31
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32
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Melquiond A, Boucher G, Mousseau N, Derreumaux P. Following the aggregation of amyloid-forming peptides by computer simulations. J Chem Phys 2007; 122:174904. [PMID: 15910066 DOI: 10.1063/1.1886725] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
There is experimental evidence suggesting that the toxicity of neurodegenerative diseases such as Alzheimer's disease may result from the soluble intermediate oligomers. It is therefore important to characterize extensively the early steps of oligomer formation at atomic level. As these structures are metastable and short lived, experimental data are difficult to obtain and they must be complemented with numerical simulations. In this work, we use the activation-relaxation technique coupled with a coarse-grained energy model to study in detail the mechanisms of aggregation of four lys-phe-phe-glu (KFFE) peptides. This is the shortest peptide known to form amyloid fibrils in vitro. Our simulations indicate that four KFFE peptides adopt a variety of oligomeric states (tetramers, trimers, and dimers) with various orientations of the chains in rapid equilibrium. This conformational distribution is consistent with all-atom molecular-dynamics simulations in explicit solvent and is sequence dependent; as seen experimentally, the lys-pro-gly-glu (KPGE) peptides adopt disordered structures in solution. Our unbiased simulations also indicate that the assembly process is much more complex than previously thought and point to intermediate structures which likely are kinetic traps for longer chains.
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Affiliation(s)
- Adrien Melquiond
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico-Chimique et Université Paris 7, France
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33
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Flöck D, Rossetti G, Daidone I, Amadei A, Di Nola A. Aggregation of small peptides studied by molecular dynamics simulations. Proteins 2006; 65:914-21. [PMID: 16981204 DOI: 10.1002/prot.21168] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Peptides and proteins tend to aggregate under appropriate conditions. The amyloid fibrils that are ubiquitously found among these structures are associated with major human diseases like Alzheimer's disease, type II diabetes, and various prion diseases. Lately, it has been observed that even very short peptides like tetra and pentapeptides can form ordered amyloid structures. Here, we present aggregation studies of three such small polypeptide systems, namely, the two amyloidogenic peptides DFNKF and FF, and a control (nonamyloidogenic) one, the AGAIL. The respective aggregation process is studied by all-atom Molecular Dynamics simulations, which allow to shed light on the fine details of the association and aggregation process. Our analysis suggests that naturally aggregating systems exhibit significantly diverse overall cluster shape properties and specific intermolecular interactions. Additional analysis was also performed on the previously studied NFGAIL system.
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Affiliation(s)
- Dagmar Flöck
- Department of Chemistry, University of Rome La Sapienza, Rome 00185, Italy.
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34
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Röhrig UF, Laio A, Tantalo N, Parrinello M, Petronzio R. Stability and structure of oligomers of the Alzheimer peptide Abeta16-22: from the dimer to the 32-mer. Biophys J 2006; 91:3217-29. [PMID: 16920832 PMCID: PMC1614475 DOI: 10.1529/biophysj.106.088542] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Several neurodegenerative diseases such as Alzheimer's, Parkinson's, and Huntington's diseases are associated with amyloid fibrils formed by different polypeptides. We probe the structure and stability of oligomers of different sizes of the fragment Abeta(16-22) of the Alzheimer beta-amyloid peptide using atomic-detail molecular dynamics simulations with explicit solvent. We find that only large oligomers form a stable beta-sheet aggregate, the minimum nucleus size being of the order of 8-16 peptides. This effect is attributed to better hydrophobic contacts and a better shielding of backbone-backbone hydrogen bonds from the solvent in bigger assemblies. Moreover, the observed stability of beta-sheet aggregates with a different number of layers can be explained on the basis of their solvent-accessible surface area. Depending on the stacking interface between the sheets, we observe straight or twisted structures, which could be linked to the experimentally observed polymorphism of amyloid fibrils. To compare our 32-mer structure to experimental data, we calculate its x-ray diffraction pattern. Good agreement is found between experimentally and theoretically determined reflections, suggesting that our model indeed closely resembles the structures found in vitro.
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Affiliation(s)
- Ute F Röhrig
- Centro Studi e Ricerche Enrico Fermi, Compendio Viminale, Rome, Italy.
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35
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Tsai HHG, Gunasekaran K, Nussinov R. Sequence and structure analysis of parallel beta helices: implication for constructing amyloid structural models. Structure 2006; 14:1059-72. [PMID: 16765899 DOI: 10.1016/j.str.2006.03.015] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2005] [Revised: 02/13/2006] [Accepted: 03/25/2006] [Indexed: 11/18/2022]
Abstract
Increasing evidence suggests that amyloids and parallel beta helices may share similar motifs. A systemic analysis of beta helices is performed to examine their sequence and structural characteristics. Ile prefers to occur in beta strands. In contrast, Pro is disfavored, compatible with the underlying assumption in Pro-scanning mutagenesis. Cys, Asn, and Phe form significant homostacking (identical amino acid interactions). Asn is highly conserved in the high-energy, left-handed alpha-helical conformation, where it frequently forms amide stacking. Based on the observed prominent stacking of chemically similar residues in parallel beta helices, we propose that within the "cross-beta" framework, amyloids with longer peptide chains may have common structural features of in-register, parallel alignment, with the side chains forming identical amino acid ladders. The requirement of ladder formation limits the combinations of side chain interactions. Such a limit combined with environmental conditions (e.g., pH, concentration) could be a major reason for the ability of most polypeptides to form amyloids.
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Affiliation(s)
- Hui-Hsu Gavin Tsai
- Department of Chemistry, National Central University, Chung-Li 32001, Taiwan.
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36
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Zheng J, Ma B, Tsai CJ, Nussinov R. Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35. Biophys J 2006; 91:824-33. [PMID: 16679374 PMCID: PMC1563778 DOI: 10.1529/biophysj.106.083246] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A seven amino acid yeast prion sup-35 fragment (GNNQQNY) forms amyloid fibrils. The availability of its detailed atomic oligomeric structure makes it a good model for studying the early stage of aggregation. Here we perform long all-atom explicit solvent molecular simulations of various sizes and arrangements of oligomer seeds of the wild-type and its mutants to study its stability and dynamics. Previous studies have suggested that the early stage rate-limiting step of oligomer formation occurs in high-order oligomers. Our simulations show that with the increase in the number of strands even from a dimer to a trimer, oligomer stability increases dramatically. This suggests that the minimal nucleus seed for GNNQQNY fibril formation could be small and is likely three or four peptides, in agreement with experiment, and that higher-order oligomers do not dissociate quickly since they have small diffusion coefficients and thus slow kinetics. Further, for the hydrophilic polar GNNQQNY, there are no hydrogen bonds and no hydrophobic interactions between adjacent beta-sheets. Simulations suggest that within the sheet, the driving forces to associate and stabilize are interstrand backbone-backbone and side chain-side chain hydrogen bonds, whereas between the sheets, shape-complementary by the dry polar steric zipper via the side chains of Asn-2, Gln-4, and Asn-6 holds the sheets together, as proposed in an earlier study. Since the polar side chains of Asn-2, Gln-4, and Asn-6 act as a hook to bind two neighboring sheets together, these geometric restraints reduce the conformational search for the correct side chain packing to a two-dimensional problem of intersheet side chain interactions. Mutant simulations show that substitution of Asn-2, Gln-4, or Asn-6 by Ala would disrupt this steric zipper, leading to unstable oligomers.
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Affiliation(s)
- Jie Zheng
- Basic Research Program, SAIC-Frederick, Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, Maryland 21702, USA
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37
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Zanuy D, Nussinov R, Alemán C. From peptide-based material science to protein fibrils: discipline convergence in nanobiology. Phys Biol 2006; 3:S80-90. [PMID: 16582467 DOI: 10.1088/1478-3975/3/1/s08] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This paper illustrates the merits of convergence in nanobiology of two seemingly disparate fields, material science and computational biology. Traditionally, material science has been a discipline involving design and fabrication of synthetic polymers consisting of repeating units. Collaboration with synthetic organic chemists allowed design of new polymers, with a range of altered conformations. Yet, naturally occurring proteins are also materials. Their varied sequences and structures should enrich material science providing more complex shapes, scaffolds and chemical properties. For material scientists, the enhanced coverage of chemical space obtained by integrating proteins and synthetic organic chemistry through the introduction of non-natural residues allows a range of new useful potential applications.
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Affiliation(s)
- David Zanuy
- Departament d'Enginyeria Química, ETS d'Enginyeria Industrial de Barcelona, Universitat Politécnica de Catalunya, Diagonal 647, Barcelona E-08028, Spain
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38
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López de la Paz M, de Mori GMS, Serrano L, Colombo G. Sequence Dependence of Amyloid Fibril Formation: Insights from Molecular Dynamics Simulations. J Mol Biol 2005; 349:583-96. [PMID: 15882870 DOI: 10.1016/j.jmb.2005.03.081] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2004] [Revised: 03/23/2005] [Accepted: 03/29/2005] [Indexed: 11/19/2022]
Abstract
The clarification of the physico-chemical determinants underlying amyloid deposition is critical for our understanding of misfolding diseases. With this purpose we have performed a systematic all-atom molecular dynamics (MD) study of a series of single point mutants of the de novo designed amyloidogenic peptide STVIIE. Sixteen different 50ns long simulations using explicit solvent have been carried out starting from four different conformations of a polymeric six-stranded beta-sheet. The simulations have provided evidence for the influence of a small number of site-specific hydrophobic interactions on the packing and stabilization of nascent aggregates, as well as the interplay between side-chain interactions and the net charge of the molecule on the strand arrangement of polymeric beta-sheets. This MD analysis has also shed light into the origin of the position dependence on mutation of beta-sheet polymerization that was found experimentally for this model system. Our results suggest that MD can be applied to detect critical positions for beta-sheet aggregation within a given amyloidogenic stretch. Studies similar to the one presented here can guide site-directed mutations or the design of drugs that specifically disrupt the key stabilizing interactions of beta-sheet aggregates.
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39
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Tsai HHG, Reches M, Tsai CJ, Gunasekaran K, Gazit E, Nussinov R. Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: significant role of Asn ladder. Proc Natl Acad Sci U S A 2005; 102:8174-9. [PMID: 15923262 PMCID: PMC1149403 DOI: 10.1073/pnas.0408653102] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent evidence suggests that amyloidogenic oligomers may be the toxic species in cell cultures. Thus, it is crucial to understand their structure and oligomerization mechanism in atomistic detail. By employing tens of fast central processing units and an advanced phase-space sampling algorithm, parallel-tempering molecular dynamics, we have explored the energy landscape of amyloidogenic peptide oligomerization in explicit water. A pentapeptide, DFNKF, derived from human calcitonin and its mutant, DFAKF, was simulated with a total simulation time of approximately 500 ns. The detailed oligomerization process of a DFNKF parallel beta-sheet formation at 300 K has been characterized. The assembly of a parallel beta-sheet from the amorphous state mainly occurs via a "bottleneck" channel where the interstrand Asn-Asn stacking is the major interaction. The interactions of Asn-Asn stacking include both backbone and side-chain hydrogen bonds. The Asn-Asn interactions work like "glue" by sticking the DFNKF strands together and assist the "on-pathway" oligomerization. The Asn-Asn stacking observed here is similar to the Asn ladder commonly found in globular beta-helix proteins. A control run shows that when Asn is mutated to Ala, the stability and population of the DFAKF parallel beta-sheet is decreased. Furthermore, our in vitro mutagenesis experiments show that the ability of DFAKF peptides to form amyloid fibrils is significantly reduced, in agreement with the simulations. Knowledge of the energy landscape of oligomerization may provide hints for rational drug design, preventing amyloid-associated diseases.
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Affiliation(s)
- Hui-Hsu Gavin Tsai
- Basic Research Program, SAIC-Frederick, Inc., Laboratory of Experimental and Computational Biology, National Cancer Institute, Building 469, Room 145, Frederick, MD 21702, USA.
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40
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Haspel N, Zanuy D, Ma B, Wolfson H, Nussinov R. A Comparative Study of Amyloid Fibril Formation by Residues 15–19 of the Human Calcitonin Hormone: A Single β-Sheet Model with a Small Hydrophobic Core. J Mol Biol 2005; 345:1213-27. [PMID: 15644216 DOI: 10.1016/j.jmb.2004.11.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2003] [Revised: 05/19/2004] [Accepted: 11/01/2004] [Indexed: 11/30/2022]
Abstract
Experimentally, the human calcitonin hormone (hCT) can form highly stable amyloid protofibrils. Further, a peptide consisting of hCT residues 15-19, DFNKF, was shown to create highly ordered fibrils, similar to those formed by the entire hormone sequence. However, there are limited experimental data regarding the detailed 3D arrangement of either of these fibrils. We have modeled the DFNKF protofibril, using molecular dynamics simulations. We tested the stabilities of single sheet and of various multi sheet models. Remarkably, our most ordered and stable model consists of a parallel-stranded, single beta-sheet with a relatively insignificant hydrophobic core. We investigate the chemical and physical interactions responsible for the high structural organization of this single beta-sheet amyloid fibril. We observe that the most important chemical interactions contributing to the stability of the DFNKF organization are electrostatic, specifically between the Lys and the C terminus, between the Asp and N terminus, and a hydrogen bond network between the Asn side-chains of adjacent strands. Additionally, we observe hydrophobic and aromatic pi stacking interactions. We further simulated truncated filaments, FNKF and DFNK. Our tetra-peptide mutant simulations assume models similar to the penta-peptide. Experimentally, the FNKF does not create fibrils while DFNK does, albeit short and less ordered than DFNKF. In the simulations, the FNKF system was less stable than the DFNK and DFNKF. DFNK also lost many of its original interactions becoming less organized, however, many contacts were maintained. Thus, our results emphasize the role played by specific amino acid interactions. To further study specific interactions, we have mutated the penta-peptide, simulating DANKF, DFNKA and EFNKF. Here we describe the model, its relationship to experiment and its implications to amyloid organization.
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Affiliation(s)
- Nurit Haspel
- School of Computer Science, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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41
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Oakley MT, Garibaldi JM, Hirst JD. Lattice models of peptide aggregation: Evaluation of conformational search algorithms. J Comput Chem 2005; 26:1638-46. [PMID: 16170797 DOI: 10.1002/jcc.20306] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We present a series of conformational search calculations on the aggregation of short peptide fragments that form fibrils similar to those seen in many protein mis-folding diseases. The proteins were represented by a face-centered cubic lattice model with the conformational energies calculated using the Miyazawa-Jernigan potential. The searches were performed using algorithms based on the Metropolis Monte Carlo method, including simulated annealing and replica exchange. We also present the results of searches using the tabu search method, an algorithm that has been used for many optimization problems, but has rarely been used in protein conformational searches. The replica exchange algorithm consistently found more stable structures then the other algorithms, and was particularly effective for the octamers and larger systems.
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Affiliation(s)
- Mark T Oakley
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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