1
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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. [PMID: 38745385 DOI: 10.1021/acs.jcim.4c00553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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2
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Chang Y, Pan P, Tu L. Unraveling the underlying mechanisms of reduced amyloidogenic properties in human calcitonin via double mutations. Protein Sci 2024; 33:e4952. [PMID: 38501491 PMCID: PMC10949316 DOI: 10.1002/pro.4952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 02/01/2024] [Accepted: 02/19/2024] [Indexed: 03/20/2024]
Abstract
The therapeutic efficacy of peptide-based drugs is commonly hampered by the intrinsic propensity to aggregation. A notable example is human calcitonin (hCT), a peptide hormone comprising 32 amino acids, which is synthesized and secreted by thyroid gland parafollicular cells (C cells). This hormone plays a vital role in regulating blood calcium levels and upholding bone integrity. Despite its physiological importance, utilizing hCT as a drug is hampered by its inclination to form amyloid. To address this limitation, an alternative is provided by salmon calcitonin (sCT), which possesses a lower aggregation propensity. Although sharing the same disulfide bond at the N terminus as hCT, sCT differs from hCT at a total of 16 amino acid positions. However, due to the dissimilarity in sequences, using sCT as a clinical replacement occasionally results in adverse side effects in patients. Earlier investigations have highlighted the significant roles of Tyr-12 and Asn-17 in inducing the formation of amyloid fibrils. By introducing double mutations at these sites, the ability to hinder aggregation can be significantly augmented. This study delves into the oligomerization and helical structure formation of the hCT double mutant (Y12LN17H hCT, noted as DM hCT), as well as two single mutants (Y12L and N17H), aiming to elucidate the mechanism behind hCT fibrillization. In addition, computational prediction tools were employed again to identify potential substitutes. Although the results yielded were not entirely satisfactory, a comparison between the newly examined and previously found hCT double mutants provides insights into the reduced aggregation propensity of the latter. This research endeavor holds the promise of informing the design of more effective therapeutic peptide drugs in the future.
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Affiliation(s)
- Yu‐Pei Chang
- Department of ChemistryNational Taiwan Normal UniversityTaipeiTaiwan
| | - Pei‐Chun Pan
- Department of ChemistryNational Taiwan Normal UniversityTaipeiTaiwan
| | - Ling‐Hsien Tu
- Department of ChemistryNational Taiwan Normal UniversityTaipeiTaiwan
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3
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Yan J, Wang Y, Fan X, Zou Y, Ding F, Huang F, Sun Y. Deciphering the influence of Y12L and N17H substitutions on the conformation and oligomerization of human calcitonin. SOFT MATTER 2024; 20:693-703. [PMID: 38164981 PMCID: PMC10845004 DOI: 10.1039/d3sm01332d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
The abnormal aggregation of human calcitonin (hCT) hormone peptides impairs their physiological function, leading to harmful immune responses and cytotoxicity, which limits their clinical utility. Interestingly, a representative hCT analog incorporating Y12L and N17H substitutions (DM-hCT) has shown reduced aggregation tendencies while maintaining bioactivity. But the molecular mechanism of Y12L and N17H substitutions on the conformational dynamics of hCT remains unclear. Here, we systematically investigated the folding and self-assembly dynamics of hCT and DM-hCT using atomistic discrete molecular dynamics (DMD) simulations. Our findings revealed that hCT monomers predominantly adopted unstructured conformations with dynamic helices. Oligomerization of hCT resulted in the formation of β-sheet-rich aggregates and β-barrel intermediates. The Y12L and N17H substitutions enhanced helical conformations and suppressed β-sheet formation in both monomers and oligomers. These substitutions stabilized the dynamic helices and disrupted aromatic interactions responsible for β-sheet formation at residue 12. Notably, DM-hCT assemblies still exhibited β-sheets in phenylalanine-rich and C-terminal hydrophobic regions, suggesting that future optimizations should focus on these areas. Our simulations provide insights into the molecular mechanisms underlying hCT aggregation and the amyloid-resistant effects of Y12L and N17H substitutions. These findings have valuable implications for the development of clinical hCT analogs.
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Affiliation(s)
- Jiajia Yan
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China.
- Ningbo Institute of Innovation for Combined Medicine and Engineering (NIIME), Ningbo Medical Center Lihuili Hospital, Ningbo 315211, China.
| | - Ying Wang
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China.
| | - Xinjie Fan
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China.
| | - Yu Zou
- Department of Sport and Exercise Science, Zhejiang University, Hangzhou 310058, China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA.
| | - Fengjuan Huang
- Ningbo Institute of Innovation for Combined Medicine and Engineering (NIIME), Ningbo Medical Center Lihuili Hospital, Ningbo 315211, China.
| | - Yunxiang Sun
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China.
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA.
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4
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Li D, Ma Y, Xia W, Tao Y, Zhang Y, Zhang H, Li D, Dai B, Liu C. Creating an Amyloid 'Kaleidoscope' Using Short Iodinated Peptides. Angew Chem Int Ed Engl 2023; 62:e202310737. [PMID: 37650358 DOI: 10.1002/anie.202310737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/25/2023] [Accepted: 08/30/2023] [Indexed: 09/01/2023]
Abstract
Amyloid fibrils formed by peptides with different sequences exhibit diversified morphologies, material properties and activities, making them valuable for developing functional bionanomaterials. However, the molecular understanding underlying the structural diversity of peptide fibrillar assembly at atomic level is still lacking. In this study, by using cryogenic electron microscopy, we first revealed the structural basis underlying the highly reversible assembly of 1 GFGGNDNFG9 (referred to as hnRAC1) peptide fibril. Furthermore, by installing iodine at different sites of hnRAC1, we generated a collection of peptide fibrils with distinct thermostability. By determining the atomic structures of the iodinated fibrils, we discovered that iodination at different sites of the peptide facilitates the formation of diverse halogen bonds and triggers the assembly of entirely different structures of iodinated fibrils. Finally, based on this structural knowledge, we designed an iodinated peptide that assembles into new atomic structures of fibrils, exhibiting superior thermostability, that aligned with our design. Our work provides an in-depth understanding of the atomic-level processes underlying the formation of diverse peptide fibril structures, and paves the way for creating an amyloid "kaleidoscope" by employing various modifications and peptide sequences to fine-tune the atomic structure and properties of fibrillar nanostructures.
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Affiliation(s)
- Danni Li
- School of Sensing Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yeyang Ma
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China
- University of the Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Wencheng Xia
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China
- University of the Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Youqi Tao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yiling Zhang
- School of Sensing Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hong Zhang
- School of Sensing Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bin Dai
- School of Sensing Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China
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5
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Sori L, Pizzi A, Bergamaschi G, Gori A, Gautieri A, Demitri N, Soncini M, Metrangolo P. Computation meets experiment: identification of highly efficient fibrillating peptides. CrystEngComm 2023; 25:4503-4510. [PMID: 38014394 PMCID: PMC10424810 DOI: 10.1039/d3ce00495c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 07/03/2023] [Indexed: 11/29/2023]
Abstract
Self-assembling peptides are of huge interest for biological, medical and nanotechnological applications. The enormous chemical variety that is available from the 20 amino acids offers potentially unlimited peptide sequences, but it is currently an issue to predict their supramolecular behavior in a reliable and cheap way. Herein we report a computational method to screen and forecast the aqueous self-assembly propensity of amyloidogenic pentapeptides. This method was found also as an interesting tool to predict peptide crystallinity, which may be of interest for the development of peptide based drugs.
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Affiliation(s)
- Lorenzo Sori
- Laboratory of Supramolecular and BioNano Materials (SupraBioNanoLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano Via Luigi Mancinelli 7 20131 Milan Italy
| | - Andrea Pizzi
- Laboratory of Supramolecular and BioNano Materials (SupraBioNanoLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano Via Luigi Mancinelli 7 20131 Milan Italy
| | - Greta Bergamaschi
- Istituto di Scienze e Tecnologie Chimiche - National Research Council of Italy (SCITEC-CNR) 20131 Milan Italy
| | - Alessandro Gori
- Istituto di Scienze e Tecnologie Chimiche - National Research Council of Italy (SCITEC-CNR) 20131 Milan Italy
| | - Alfonso Gautieri
- Department of Electronics, Information and Bioengineering, Politecnico di Milano 20131 Milan Italy
| | - Nicola Demitri
- Elettra - Sincrotrone Trieste S.S. 14 Km 163.5 in Area Science Park 34149 Basovizza - Trieste Italy
| | - Monica Soncini
- Department of Electronics, Information and Bioengineering, Politecnico di Milano 20131 Milan Italy
| | - Pierangelo Metrangolo
- Laboratory of Supramolecular and BioNano Materials (SupraBioNanoLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano Via Luigi Mancinelli 7 20131 Milan Italy
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6
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Liu Y, Wang Y, Zhang Y, Zou Y, Wei G, Ding F, Sun Y. Structural Perturbation of Monomers Determines the Amyloid Aggregation Propensity of Calcitonin Variants. J Chem Inf Model 2023; 63:308-320. [PMID: 36456917 PMCID: PMC9839651 DOI: 10.1021/acs.jcim.2c01202] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Human calcitonin (hCT) is a polypeptide hormone that participates in calcium-phosphorus metabolism. Irreversible aggregation of 32-amino acid hCT into β-sheet-rich amyloid fibrils impairs physiological activity and increases the risk of medullary carcinoma of the thyroid. Amyloid-resistant hCT derivatives substituting critical amyloidogenic residues are of particular interest for clinical applications as therapeutic drugs against bone-related diseases. Uncovering the aggregation mechanism of hCT at the molecular level, therefore, is important for the design of amyloid-resistant hCT analogues. Here, we investigated the aggregation dynamics of hCT, non-amyloidogenic salmon calcitonin (sCT), and two hCT analogues with reduced aggregation tendency─TL-hCT and phCT─using long timescale discrete molecular dynamics simulations. Our results showed that hCT monomers mainly adopted unstructured conformations with dynamically formed helices around the central region. hCT self-assembled into helix-rich oligomers first, followed by a conformational conversion into β-sheet-rich oligomers with β-sheets formed by residues 10-30 and stabilized by aromatic and hydrophobic interactions. Our simulations confirmed that TL-hCT and phCT oligomers featured more helices and fewer β-sheets than hCT. Substitution of central aromatic residues with leucine in TL-hCT and replacing C-terminal hydrophobic residue with hydrophilic amino acid in phCT only locally suppressed β-sheet propensities in the central region and C-terminus, respectively. Having mutations in both central and C-terminal regions, sCT monomers and dynamically formed oligomers predominantly adopted helices, confirming that both central aromatic and C-terminal hydrophobic residues played important roles in the fibrillization of hCT. We also observed the formation of β-barrel intermediates, postulated as the toxic oligomers in amyloidosis, for hCT but not for sCT. Our computational study depicts a complete picture of the aggregation dynamics of hCT and the effects of mutations. The design of next-generation amyloid-resistant hCT analogues should consider the impact on both amyloidogenic regions and also take into account the amplification of transient β-sheet population in monomers upon aggregation.
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Affiliation(s)
- Yuying Liu
- Department of Physics, Ningbo University, Ningbo 315211, China
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai 200433, P. R. China
| | - Ying Wang
- Department of Physics, Ningbo University, Ningbo 315211, China
| | - Yu Zhang
- Department of Physics, Ningbo University, Ningbo 315211, China
| | - Yu Zou
- Department of Sport and Exercise Science, Zhejiang University, Hangzhou 310058, China
| | - Guanghong Wei
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai 200433, P. R. China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Yunxiang Sun
- Department of Physics, Ningbo University, Ningbo 315211, China
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai 200433, P. R. China
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
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7
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Marchetti A, Pizzi A, Bergamaschi G, Demitri N, Stollberg U, Diederichsen U, Pigliacelli C, Metrangolo P. Fibril Structure Demonstrates the Role of Iodine Labelling on a Pentapeptide Self‐Assembly. Chemistry 2022; 28:e202104089. [PMID: 35084787 PMCID: PMC9306938 DOI: 10.1002/chem.202104089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Indexed: 12/16/2022]
Affiliation(s)
- Alessandro Marchetti
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab) Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta” Politecnico di Milano Via L. Mancinelli 7 20131 Milano Italy
| | - Andrea Pizzi
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab) Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta” Politecnico di Milano Via L. Mancinelli 7 20131 Milano Italy
| | - Greta Bergamaschi
- Istituto di Scienze e Tecnologie Chimiche National Research Council of Italy Via M. Bianco 9 20131 Milano Italy
| | - Nicola Demitri
- Elettra – Sincrotrone Trieste S.S. 14 Km 163.5 in Area Science Park 34149 Basovizza Trieste Italy
| | - Ulrike Stollberg
- Institute for Organic and Biomolecular Chemistry Georg-August-University Göttingen Tammannstr. 2 37077 Göttingen Germany
| | - Ulf Diederichsen
- Institute for Organic and Biomolecular Chemistry Georg-August-University Göttingen Tammannstr. 2 37077 Göttingen Germany
| | - Claudia Pigliacelli
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab) Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta” Politecnico di Milano Via L. Mancinelli 7 20131 Milano Italy
| | - Pierangelo Metrangolo
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab) Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta” Politecnico di Milano Via L. Mancinelli 7 20131 Milano Italy
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8
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Bergamaschi G, Musicò A, Frigerio R, Strada A, Pizzi A, Talone B, Ghezzi J, Gautieri A, Chiari M, Metrangolo P, Vanna R, Baldelli Bombelli F, Cretich M, Gori A. Composite Peptide-Agarose Hydrogels for Robust and High-Sensitivity 3D Immunoassays. ACS APPLIED MATERIALS & INTERFACES 2022; 14:4811-4822. [PMID: 35060693 DOI: 10.1021/acsami.1c18466] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Canonical immunoassays rely on highly sensitive and specific capturing of circulating biomarkers by interacting biomolecular baits. In this frame, bioprobe immobilization in spatially discrete three-dimensional (3D) spots onto analytical surfaces by hydrogel encapsulation was shown to provide relevant advantages over conventional two-dimensional (2D) platforms. Yet, the broad application of 3D systems is still hampered by hurdles in matching their straightforward fabrication with optimal functional properties. Herein, we report on a composite hydrogel obtained by combining a self-assembling peptide (namely, Q3 peptide) with low-temperature gelling agarose that is proved to have simple and robust application in the fabrication of microdroplet arrays, overcoming hurdles and limitations commonly associated with 3D hydrogel assays. We demonstrate the real-case scenario feasibility of our 3D system in the profiling of Covid-19 patients' serum IgG immunoreactivity, which showed remarkably improved signal-to-noise ratio over canonical assays in the 2D format and exquisite specificity. Overall, the new two-component hydrogel widens the perspectives of hydrogel-based arrays and represents a step forward towards their routine use in analytical practices.
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Affiliation(s)
- Greta Bergamaschi
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
| | - Angelo Musicò
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
| | - Roberto Frigerio
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
| | - Alessandro Strada
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, 20131 Milan, Italy
| | - Andrea Pizzi
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, 20131 Milan, Italy
| | - Benedetta Talone
- Physics Department, Politecnico di Milano, P.zza Leonardo da Vinci 32, 20133 Milan, Italy
| | - Jacopo Ghezzi
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
- Biomolecular Engineering Lab, Dept. Electronics, Information and Bioengineering, Politecnico di Milano, 20133 Milan, Italy
| | - Alfonso Gautieri
- Biomolecular Engineering Lab, Dept. Electronics, Information and Bioengineering, Politecnico di Milano, 20133 Milan, Italy
| | - Marcella Chiari
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
| | - Pierangelo Metrangolo
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, 20131 Milan, Italy
| | - Renzo Vanna
- Istituto di Fotonica e Nanotecnologie─National Research Council of Italy (IFN-CNR), 20133 Milan, Italy
| | - Francesca Baldelli Bombelli
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, 20131 Milan, Italy
| | - Marina Cretich
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
| | - Alessandro Gori
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
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9
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Renawala HK, Chandrababu KB, Topp EM. Fibrillation of Human Calcitonin and Its Analogs: Effects of Phosphorylation and Disulfide Reduction. Biophys J 2020; 120:86-100. [PMID: 33220304 DOI: 10.1016/j.bpj.2020.11.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/24/2020] [Accepted: 11/10/2020] [Indexed: 11/16/2022] Open
Abstract
Some therapeutic peptides self-assemble in solution to form ordered, insoluble, β-sheet-rich amyloid fibrils. This physical instability can result in reduced potency, cause immunogenic side effects, and limit options for formulation. Understanding the mechanisms of fibrillation is key to developing rational mitigation strategies. Here, amide hydrogen-deuterium exchange with mass spectrometric analysis (HDX-MS) coupled with proteolytic digestion was used to identify the early stage interactions leading to fibrillation of human calcitonin (hCT), a peptide hormone important in calcium metabolism. hCT fibrillation kinetics was sigmoidal, with lag, growth, and plateau phases as shown by thioflavin T and turbidity measurements. HDX-MS of fibrillating hCT (pH 7.4; 25°C) suggested early involvement of the N-terminal (1-11) and central (12-19) fragments in interactions during the lag phase, whereas C-terminal fragments (20-32 and 26-32) showed limited involvement during this period. The residue-level information was used to develop phosphorylated hCT analogs that showed modified fibrillation that depended on phosphorylation site. Phosphorylation in the central region resulted in complete inhibition of fibrillation for the phospho-Thr-13 hCT analog, whereas phosphorylation in the N-terminal and C-terminal regions inhibited but did not prevent fibrillation. Reduction of the Cys1-Cys7 disulfide bond resulted in faster fibrillation with involvement of different hCT residues as indicated by pulsed HDX-MS. Together, the results demonstrate that small structural changes have significant effects on hCT fibrillation and that understanding these effects can inform the rational development of fibrillation-resistant hCT analogs.
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Affiliation(s)
- Harshil K Renawala
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana
| | - Karthik B Chandrababu
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana
| | - Elizabeth M Topp
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana; National Institute for Bioprocessing Research and Training, Dublin, Ireland.
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10
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Prabakaran R, Rawat P, Kumar S, Michael Gromiha M. ANuPP: A Versatile Tool to Predict Aggregation Nucleating Regions in Peptides and Proteins. J Mol Biol 2020; 433:166707. [PMID: 33972019 DOI: 10.1016/j.jmb.2020.11.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/28/2020] [Accepted: 11/05/2020] [Indexed: 12/22/2022]
Abstract
Short aggregation prone sequence motifs can trigger aggregation in peptide and protein sequences. Most algorithms developed so far to identify potential aggregation prone regions (APRs) use amino acid residue composition and/or sequence pattern features. In this work, we have investigated the importance of atomic-level characteristics rather than residue level to understand the initiation of aggregation in proteins and peptides. Using atomic-level features an ensemble-classifier, ANuPP has been developed to predict the aggregation-nucleating regions in peptides and proteins. In a dataset of 1279 hexapeptides, ANuPP achieved an area under the curve (AUC) of 0.831 with 77% accuracy on 10-fold cross-validation and an AUC of 0.883 with 83% accuracy in a blind test dataset of 142 hexapeptides. Further, it showed an average SOV of 48.7% on identifying APR regions in 37 proteins. The performance of ANuPP is better than other methods reported in the literature on both amyloidogenic hexapeptide prediction and APR identification. We have developed a web server for ANuPP and it is available at https://web.iitm.ac.in/bioinfo2/ANuPP/. Insights gained from this work demonstrate the importance of atomic and functional group characteristics towards diversity of atomic level origins as well as mechanisms of protein aggregation.
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Affiliation(s)
- R Prabakaran
- Protein Bioinformatics Lab, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - Puneet Rawat
- Protein Bioinformatics Lab, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - Sandeep Kumar
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA.
| | - M Michael Gromiha
- Protein Bioinformatics Lab, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India; School of Computing, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan.
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11
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Ye H, Li H, Gao Z. Y12 nitration of human calcitonin (hCT): A promising strategy to produce non-aggregation bioactive hCT. Nitric Oxide 2020; 104-105:11-19. [PMID: 32827754 DOI: 10.1016/j.niox.2020.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/25/2020] [Accepted: 08/11/2020] [Indexed: 02/06/2023]
Abstract
Irreversible aggregation can extremely limit the bioavailability and therapeutic activity of peptide-based drugs. There is therefore an urgent demand of effective strategy to control peptide aggregation. Recently, we found that tyrosine nitration at certain sites of peptide can effectively inhibit its aggregation. This minor modification may be an ideal strategy to the rational design of peptide-based drugs with low aggregation propensity yet without loss of bioactivity. Human calcitonin (hCT) is such a peptide hormone known for its hypocalcaemic effect but has limited pharmaceutical potential due to a high tendency to aggregate. In this study, by using multiple techniques including Fluorescence, TEM, Nu-PAGE and CD, we demonstrated that Y12 nitration of hCT would significantly inhibit its self-assembles, and we also found that this modification would not only reduce the cytotoxicity induced by peptide aggregation, but also had little effect on its potency. This finding may provide a novel strategy for clinically application of hCT instead of sCT.
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Affiliation(s)
- Huixian Ye
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China; School of Chemistry and Chemical Engineering, Jinggangshan University, Ji'an, Jiangxi, 343009, China
| | - Hailing Li
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Zhonghong Gao
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China.
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12
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Pizzi A, Pigliacelli C, Bergamaschi G, Gori A, Metrangolo P. Biomimetic engineering of the molecular recognition and self-assembly of peptides and proteins via halogenation. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213242] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Maiolo D, Pizzi A, Gori A, Bergamaschi G, Pigliacelli C, Gazzera L, Consonni A, Baggi F, Moda F, Baldelli Bombelli F, Metrangolo P, Resnati G. Enhanced self-assembly of the 7–12 sequence of amyloid-β peptide by tyrosine bromination. Supramol Chem 2020. [DOI: 10.1080/10610278.2020.1734203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Daniele Maiolo
- Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”, Politecnico Di Milano, Milano, Italy
| | - Andrea Pizzi
- Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”, Politecnico Di Milano, Milano, Italy
| | - Alessandro Gori
- Istituto Di Scienze E Tecnologie Chimiche, National Research Council of Italy, Milano, Italy
| | - Greta Bergamaschi
- Istituto Di Scienze E Tecnologie Chimiche, National Research Council of Italy, Milano, Italy
| | - Claudia Pigliacelli
- Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”, Politecnico Di Milano, Milano, Italy
- Hyber Center of Excellence, Department of Applied Physics, Aalto University, Espoo, Finland
| | - Lara Gazzera
- Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”, Politecnico Di Milano, Milano, Italy
| | | | - Fulvio Baggi
- Fondazione IRCCS Istituto Neurologico “Carlo Besta”, 20133 Milano, Italy
| | - Fabio Moda
- Fondazione IRCCS Istituto Neurologico “Carlo Besta”, 20133 Milano, Italy
| | - Francesca Baldelli Bombelli
- Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”, Politecnico Di Milano, Milano, Italy
| | - Pierangelo Metrangolo
- Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”, Politecnico Di Milano, Milano, Italy
- Hyber Center of Excellence, Department of Applied Physics, Aalto University, Espoo, Finland
| | - Giuseppe Resnati
- Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”, Politecnico Di Milano, Milano, Italy
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14
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Maiolo D, Pizzi A, Gori A, Gazzera L, Demitri N, Genoni A, Baggi F, Moda F, Terraneo G, Baldelli Bombelli F, Metrangolo P, Resnati G. Halogenation of the N-Terminus Tyrosine 10 Promotes Supramolecular Stabilization of the Amyloid-β Sequence 7-12. ChemistryOpen 2020; 9:253-260. [PMID: 32110506 PMCID: PMC7041548 DOI: 10.1002/open.201900350] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/07/2020] [Indexed: 12/16/2022] Open
Abstract
Here, we demonstrate that introduction of halogen atoms at the tyrosine 10 phenol ring of the DSGYEV sequence derived from the flexible amyloid‐β N‐terminus, promotes its self‐assembly in the solid state. In particular, we report the crystal structures of two halogen‐modified sequences, which we found to be stabilized in the solid state by halogen‐mediated interactions. The structural study is corroborated by Non‐Covalent Interaction (NCI) analysis. Our results prove that selective halogenation of an amino acid enhances the supramolecular organization of otherwise unstructured biologically‐relevant sequences. This method may develop as a general strategy for stabilizing highly polymorphic peptide regions.
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Affiliation(s)
- Daniele Maiolo
- Dept. Chem., Mater., and Chem. Eng. "Giulio Natta" Politecnico di Milano Via L. Mancinelli 7 20131 Milano Italy
| | - Andrea Pizzi
- Dept. Chem., Mater., and Chem. Eng. "Giulio Natta" Politecnico di Milano Via L. Mancinelli 7 20131 Milano Italy
| | - Alessandro Gori
- Istituto di Scienze e Tecnologie Chimiche National Research Council of Italy Via M. Bianco 9 20131 Milano Italy
| | - Lara Gazzera
- Dept. Chem., Mater., and Chem. Eng. "Giulio Natta" Politecnico di Milano Via L. Mancinelli 7 20131 Milano Italy
| | - Nicola Demitri
- Elettra - Sincrotrone Trieste S.S. 14 Km 163.5 in Area Science Park 34149 Basovizza - Trieste Italy
| | - Alessandro Genoni
- Laboratoire de Physique et Chimie Théoriques Université de Lorraine and CNRS UMR CNRS 7019 1 Boulevard Arago 57078 Metz France
| | - Fulvio Baggi
- Fondazione IRCCS Istituto Neurologico "Carlo Besta" Via G. Celoria 11 20133 Milan Italy
| | - Fabio Moda
- Fondazione IRCCS Istituto Neurologico "Carlo Besta" Via G. Celoria 11 20133 Milan Italy
| | - Giancarlo Terraneo
- Dept. Chem., Mater., and Chem. Eng. "Giulio Natta" Politecnico di Milano Via L. Mancinelli 7 20131 Milano Italy.,Istituto di Scienze e Tecnologie Chimiche National Research Council of Italy Via M. Bianco 9 20131 Milano Italy
| | - Francesca Baldelli Bombelli
- Dept. Chem., Mater., and Chem. Eng. "Giulio Natta" Politecnico di Milano Via L. Mancinelli 7 20131 Milano Italy
| | - Pierangelo Metrangolo
- Dept. Chem., Mater., and Chem. Eng. "Giulio Natta" Politecnico di Milano Via L. Mancinelli 7 20131 Milano Italy
| | - Giuseppe Resnati
- Dept. Chem., Mater., and Chem. Eng. "Giulio Natta" Politecnico di Milano Via L. Mancinelli 7 20131 Milano Italy
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15
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Kawasaki T, Tsukiyama K, Irizawa A. Dissolution of a fibrous peptide by terahertz free electron laser. Sci Rep 2019; 9:10636. [PMID: 31337794 PMCID: PMC6650392 DOI: 10.1038/s41598-019-47011-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 07/09/2019] [Indexed: 11/09/2022] Open
Abstract
Fibrous peptides such as amyloid fibrils have various roles in biological system, e.g., as causal factor of serious amyloidosis in human and as functional regulator of cell formation in bacteria and eukaryotes. In addition, the fiber-type format is promising as biocompatible scaffold. Therefore, the dissolution method of peptide fibril is potentially useful at many scenes in medical and material fields: as reductive way of pathogenic amyloid, as modification technique of cell structure, and as fabrication tool of biomaterials. However, the fibril structure is generally difficult to be dissociated due to its rigid stacked conformation. Here, we propose a physical engineering technology using terahertz free electron laser (FEL) at far-infrared wavelengths from 70 to 80 μm. Infrared microscopy analysis of the irradiated fibril of calcitonin peptide as a model showed that β-sheet was decreased, and α-helix, turn, and others were increased, compared to those of the fibril before the FEL irradiation. Interestingly, the dissociative effect by the far-infrared laser was remarkable than that by the mid-infrared laser tuned to 6.1 μm that corresponds to amide I. In addition, simple heating at 363 K deformed the fibril state but increased the amount of β-sheet, which was contrast with the action by the FEL, and scanning-electron microscopy and Congo-red staining revealed that the fibril was collapsed power-dependently within a range from 25 to 900 mJ energies supplied with the FEL at 74 μm. It can be considered that irradiation of intense terahertz wave can dissociate fibrous conformation of peptide with little influence of thermal effect.
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Affiliation(s)
- Takayasu Kawasaki
- IR Free Electron Laser Research Center, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan.
| | - Koichi Tsukiyama
- IR Free Electron Laser Research Center, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Akinori Irizawa
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
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16
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Pizzi A, Catalano L, Demitri N, Dichiarante V, Terraneo G, Metrangolo P. Halogen bonding as a key interaction in the self‐assembly of iodinated diphenylalanine peptides. Pept Sci (Hoboken) 2019. [DOI: 10.1002/pep2.24127] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Andrea Pizzi
- Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”Politecnico di Milano Via Luigi Mancinelli 7, 20131 Milano Italy
| | - Luca Catalano
- Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”Politecnico di Milano Via Luigi Mancinelli 7, 20131 Milano Italy
| | - Nicola Demitri
- Elettra‐Sincrotrone Trieste, S.S. 14 Km 163.5 in Area Science Park, 34149 Basovizza Trieste Italy
| | - Valentina Dichiarante
- Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”Politecnico di Milano Via Luigi Mancinelli 7, 20131 Milano Italy
| | - Giancarlo Terraneo
- Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”Politecnico di Milano Via Luigi Mancinelli 7, 20131 Milano Italy
| | - Pierangelo Metrangolo
- Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”Politecnico di Milano Via Luigi Mancinelli 7, 20131 Milano Italy
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17
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Molecular dynamics investigation of halogenated amyloidogenic peptides. J Mol Model 2019; 25:124. [PMID: 31020417 DOI: 10.1007/s00894-019-4012-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 03/29/2019] [Indexed: 12/18/2022]
Abstract
Besides their biomolecular relevance, amyloids, generated by the self-assembly of peptides and proteins, are highly organized structures useful for nanotechnology applications. The introduction of halogen atoms in these peptides, and thus the possible formation of halogen bonds, allows further possibilities to finely tune the amyloid nanostructure. In this work, we performed molecular dynamics simulations on different halogenated derivatives of the β-amyloid peptide core-sequence KLVFF, by using a modified AMBER force field in which the σ-hole located on the halogen atom is modeled with a positively charged extra particle. The analysis of equilibrated structures shows good agreement with crystallographic data and experimental results, in particular concerning the formation of halogen bonds and the stability of the supramolecular structures. The modified force field described here allows describing the atomistic details contributing to peptides aggregation, with particular focus on the role of halogen bonds. This framework can potentially help the design of novel halogenated peptides with desired aggregation propensity. Graphical abstract Molecular dynamics investigation of halogenated amyloidogenic peptides.
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18
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Ye H, Zhou J, Li H, Gao Z. Heme prevents highly amyloidogenic human calcitonin (hCT) aggregation: A potential new strategy for the clinical reuse of hCT. J Inorg Biochem 2019; 196:110686. [PMID: 31003065 DOI: 10.1016/j.jinorgbio.2019.03.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/20/2019] [Accepted: 03/31/2019] [Indexed: 11/26/2022]
Abstract
Irreversible aggregation can extremely limit the bioavailability and therapeutic activity of peptide-based drugs. Thus, peptide fibrillation is an excellent challenge for biotechnological drug development. Human calcitonin (hCT) is such a peptide hormone known for its hypocalcaemic effect but has limited pharmaceutical potential due to a high tendency to aggregate. hCT is therefore not widely used preparation in clinical practice. Nonetheless, hCT seems to be still an ideal target for clinical therapy when fibrillation is effectively inhibited, because the alternatives of hCT can stimulate undesirable immune responses in patients and cause side effects. Interestingly, heme is an essential component for many livings and has been shown a strong inhibitory effect on some amyloidogenic peptides aggregation. Here we demonstrate that it may be a most suitable, safe, biocompatible small molecule inhibitor on hCT aggregation, and thereby improving its activity when guiding the drug peptide in clinical therapeutics. In this work, we found that heme was able to reversibly bind with hCT to form a heme-hCT complex with a moderate binding constant (9.17 × 106 M-1) and significantly suppress the aggregation of hCT probably accomplished by heme binding to it, blocking the β-sheet structure assembly which is essential in hCT fibril aggregation. Meanwhile, the heme-hCT complexes showed enhanced bioactivity compared to hCT itself after a 24 h incubation time in reducing blood calcium levels in mice. This study may develop a new strategy to reuse the wild-type hCT in clinical therapeutics.
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Affiliation(s)
- Huixian Ye
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, School of chemistry and chemical Engineering, Huazhong university of Science and Technology, Wuhan 430074, People's Republic of China
| | - Jun Zhou
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, School of chemistry and chemical Engineering, Huazhong university of Science and Technology, Wuhan 430074, People's Republic of China
| | - Hailing Li
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, School of chemistry and chemical Engineering, Huazhong university of Science and Technology, Wuhan 430074, People's Republic of China.
| | - Zhonghong Gao
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, School of chemistry and chemical Engineering, Huazhong university of Science and Technology, Wuhan 430074, People's Republic of China.
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19
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Abstract
The formation of ordered nanostructures by molecular self-assembly of proteins and peptides represents one of the principal directions in nanotechnology. Indeed, polyamides provide superior features as materials with diverse physical properties. A reductionist approach allowed the identification of extremely short peptide sequences, as short as dipeptides, which could form well-ordered amyloid-like β-sheet-rich assemblies comparable to supramolecular structures made of much larger proteins. Some of the peptide assemblies show remarkable mechanical, optical, and electrical characteristics. Another direction of reductionism utilized a natural noncoded amino acid, α-aminoisobutryic acid, to form short superhelical assemblies. The use of this exceptional helix inducer motif allowed the fabrication of single heptad repeats used in various biointerfaces, including their use as surfactants and DNA-binding agents. Two additional directions of the reductionist approach include the use of peptide nucleic acids (PNAs) and coassembly techniques. The diversified accomplishments of the reductionist approach, as well as the exciting future advances it bears, are discussed.
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Affiliation(s)
- Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, Department of Materials Science and Engineering, Tel Aviv University, Tel Aviv 6997801, Israel;
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20
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Frederix PWJM, Patmanidis I, Marrink SJ. Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments. Chem Soc Rev 2018; 47:3470-3489. [PMID: 29688238 PMCID: PMC5961611 DOI: 10.1039/c8cs00040a] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Indexed: 01/01/2023]
Abstract
In bionanotechnology, the field of creating functional materials consisting of bio-inspired molecules, the function and shape of a nanostructure only appear through the assembly of many small molecules together. The large number of building blocks required to define a nanostructure combined with the many degrees of freedom in packing small molecules has long precluded molecular simulations, but recent advances in computational hardware as well as software have made classical simulations available to this strongly expanding field. Here, we review the state of the art in simulations of self-assembling bio-inspired supramolecular systems. We will first discuss progress in force fields, simulation protocols and enhanced sampling techniques using recent examples. Secondly, we will focus on efforts to enable the comparison of experimentally accessible observables and computational results. Experimental quantities that can be measured by microscopy, spectroscopy and scattering can be linked to simulation output either directly or indirectly, via quantum mechanical or semi-empirical techniques. Overall, we aim to provide an overview of the various computational approaches to understand not only the molecular architecture of nanostructures, but also the mechanism of their formation.
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Affiliation(s)
- Pim W. J. M. Frederix
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Groningen , The Netherlands . ;
| | - Ilias Patmanidis
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Groningen , The Netherlands . ;
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Groningen , The Netherlands . ;
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21
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Pizzi A, Demitri N, Terraneo G, Metrangolo P. Halogen bonding at the wet interfaces of an amyloid peptide structure. CrystEngComm 2018. [DOI: 10.1039/c8ce01205a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Halogenation is a promising tool to stabilize – through halogen bonds – the wet interface of amyloid structures.
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Affiliation(s)
- Andrea Pizzi
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab)
- Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”
- Politecnico di Milano
- Milano I-20131
- Italy
| | - Nicola Demitri
- Elettra – Sincrotrone Trieste
- 34149 Basovizza – Trieste
- Italy
| | - Giancarlo Terraneo
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab)
- Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”
- Politecnico di Milano
- Milano I-20131
- Italy
| | - Pierangelo Metrangolo
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab)
- Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”
- Politecnico di Milano
- Milano I-20131
- Italy
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22
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Pizzi A, Dichiarante V, Terraneo G, Metrangolo P. Crystallographic insights into the self-assembly of KLVFF amyloid-beta peptides. Biopolymers 2017; 110. [PMID: 29178159 DOI: 10.1002/bip.23088] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/23/2017] [Accepted: 10/30/2017] [Indexed: 02/06/2023]
Abstract
Amyloidogenic peptide fragment KLVFF (H2 N-Lys-Leu-Val-Phe-Phe-COOH, Aβ16-20 ), the core-sequence of the polypeptide Aβ40, is a well-studied model for amyloid formation. However, due to its low crystallinity, detailed atomic information of KLVFF structure is lacking. Here we report the high-resolution single-crystal X-ray structure of two monohalogenated KLVFF derivatives, KLVFF(I) and KLVFF(Br). The obtained results highlight how halogenation is a good strategy to promote crystallization and facilitate the phase determination of KLVFF(I) and KLVFF(Br) fragments. Detailed structural studies on the packing features of both monohalogenated derivatives reveal the role of the halogen atoms showing that when they are positioned on the Phe aromatic moiety at the C-terminus they do not form halogen bonds and thus do not produce any extra stabilization of the β-sheet in the self-assembly process. The structural evidences gained from these studies corroborate the various polymorphic nanostructures of the halogenated variants of KLVFF and confirm the possibility to use halogenation as innovative strategy to tune the morphology of this pentapeptide.
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Affiliation(s)
- Andrea Pizzi
- Laboratory of Supramolecular and Bio-Nanomaterials (SupraBioNanoLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, Milano, I-20131, Italy
| | - Valentina Dichiarante
- Laboratory of Supramolecular and Bio-Nanomaterials (SupraBioNanoLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, Milano, I-20131, Italy
| | - Giancarlo Terraneo
- Laboratory of Supramolecular and Bio-Nanomaterials (SupraBioNanoLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, Milano, I-20131, Italy
| | - Pierangelo Metrangolo
- Laboratory of Supramolecular and Bio-Nanomaterials (SupraBioNanoLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, Milano, I-20131, Italy
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23
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Lomont JP, Ostrander JS, Ho JJ, Petti MK, Zanni MT. Not All β-Sheets Are the Same: Amyloid Infrared Spectra, Transition Dipole Strengths, and Couplings Investigated by 2D IR Spectroscopy. J Phys Chem B 2017; 121:8935-8945. [PMID: 28851219 DOI: 10.1021/acs.jpcb.7b06826] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the transition dipole strengths and frequencies of the amyloid β-sheet amide I mode for the aggregated proteins amyloid-β1-40, calcitonin, α-synuclein, and glucagon. According to standard vibrational coupling models for proteins, the frequencies of canonical β-sheets are set by their size and structural and environmental disorder, which determines the delocalization length of the vibrational excitons. The larger the delocalization the lower the frequency of the main infrared-allowed transition, A⊥. The models also predict an accompanying increase in transition dipole strength. For the proteins measured here, we find no correlation between transition dipole strengths and amyloid β-sheet transition frequency. To understand this observation, we have extracted from the protein data bank crystal structures of amyloid peptides from which we calculate the amide I vibrational couplings, and we use these in a model β-sheet Hamiltonian to simulate amyloid vibrational spectra. We find that the variations in amyloid β-sheet structures (e.g., dihedral angles, interstrand distances, and orientations) create significant differences in the average values for interstrand and nearest neighbor couplings, and that those variations encompass the variation in measured A⊥ frequencies. We also find that off-diagonal disorder about the average values explains the range of transition dipole strengths observed experimentally. Thus, we conclude that the lack of correlation between transition dipole-strength and frequency is caused by variations in amyloid β-sheet structure. Taken together, these results indicate that the amide I frequency is very sensitive to amyloid β-sheet structure, the β-sheets of these 4 proteins are not identical, and the assumption that frequency of amyloids scales with β-sheet size cannot be adopted without an accompanying measurement of transition dipole strengths.
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Affiliation(s)
- Justin P Lomont
- Department of Chemistry, University of Wisconsin-Madison , Madison, WI 53706, United States
| | - Joshua S Ostrander
- Department of Chemistry, University of Wisconsin-Madison , Madison, WI 53706, United States
| | - Jia-Jung Ho
- Department of Chemistry, University of Wisconsin-Madison , Madison, WI 53706, United States
| | - Megan K Petti
- Department of Chemistry, University of Wisconsin-Madison , Madison, WI 53706, United States
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison , Madison, WI 53706, United States
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24
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Kamgar-Parsi K, Hong L, Naito A, Brooks CL, Ramamoorthy A. Growth-incompetent monomers of human calcitonin lead to a noncanonical direct relationship between peptide concentration and aggregation lag time. J Biol Chem 2017; 292:14963-14976. [PMID: 28739873 PMCID: PMC5592673 DOI: 10.1074/jbc.m117.791236] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 07/19/2017] [Indexed: 11/06/2022] Open
Abstract
The role of the peptide hormone calcitonin in skeletal protection has led to its use as a therapeutic for osteoporosis. However, calcitonin aggregation into amyloid fibrils limits its therapeutic efficacy, necessitating a modification of calcitonin's aggregation kinetics. Here, we report a direct relationship between human calcitonin (hCT) concentration and aggregation lag time. This kinetic trend was contrary to the conventional understanding of amyloid aggregation and persisted over a range of aggregation conditions, as confirmed by thioflavin-T kinetics assays, CD spectroscopy, and transmission EM. Dynamic light scattering, 1H NMR experiments, and seeded thioflavin-T assay results indicated that differences in initial peptide species contribute to this trend more than variations in the primary nucleus formation rate. On the basis of kinetics modeling results, we propose a mechanism whereby a structural conversion of hCT monomers is needed before incorporation into the fibril. Our kinetic mechanism recapitulates the experimentally observed relationship between peptide concentration and lag time and represents a novel mechanism in amyloid aggregation. Interestingly, hCT at low pH and salmon calcitonin (sCT) exhibited the canonical inverse relationship between concentration and lag time. Comparative studies of hCT and sCT with molecular dynamics simulations and CD indicated an increased α-helical structure in sCT and low-pH hCT monomers compared with neutral-pH hCT, suggesting that α-helical monomers represent a growth-competent species, whereas unstructured random coil monomers represent a growth-incompetent species. Our finding that initial monomer concentration is positively correlated with lag time in hCT aggregation could help inform future efforts for improving therapeutic applications of CT.
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Affiliation(s)
- Kian Kamgar-Parsi
- From the Applied Physics Program, University of Michigan, Ann Arbor, Michigan 48109
| | - Liu Hong
- Zhou Pei-Yuan Center for Applied Mathematics, Tsinghua University, Beijing 100084, China
| | - Akira Naito
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan, and
| | - Charles L Brooks
- Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109-1055
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109-1055
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25
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Pizzi A, Pigliacelli C, Gori A, Ikkala O, Demitri N, Terraneo G, Castelletto V, Hamley IW, Baldelli Bombelli F, Metrangolo P. Halogenation dictates the architecture of amyloid peptide nanostructures. NANOSCALE 2017; 9:9805-9810. [PMID: 28696473 PMCID: PMC5708343 DOI: 10.1039/c7nr03263c] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Amyloid peptides yield a plethora of interesting nanostructures though difficult to control. Here we report that depending on the number, position, and nature of the halogen atoms introduced into either one or both phenylalanine benzene rings of the amyloid β peptide-derived core-sequence KLVFF, four different architectures were obtained in a controlled manner. Our findings demonstrate that halogenation may develop as a general strategy to engineer amyloidal peptide self-assembly and obtain new amyloidal nanostructures.
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Affiliation(s)
- Andrea Pizzi
- Laboratory of Supramolecular and BioNano Materials (SupraBioNanoLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, Milano I-20131, Italy.
| | | | - Alessandro Gori
- Istituto di Chimica del Riconoscimento Molecolare - National Research Council of Italy (ICRM-CNR), Laboratory of Peptide and Protein Chemistry, Via Mario Bianco 9, 20131 Milano, Italy
| | - Olli Ikkala
- Department of Applied Physics, Aalto University, Espoo, FI-02150, Finland
| | - Nicola Demitri
- Elettra - Sincrotrone Trieste, S.S. 14 Km 163.5 in Area Science Park, 34149 Basovizza - Trieste, Italy
| | - Giancarlo Terraneo
- Laboratory of Supramolecular and BioNano Materials (SupraBioNanoLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, Milano I-20131, Italy.
| | - Valeria Castelletto
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK
| | - Ian W Hamley
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK
| | - Francesca Baldelli Bombelli
- Laboratory of Supramolecular and BioNano Materials (SupraBioNanoLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, Milano I-20131, Italy.
| | - Pierangelo Metrangolo
- Laboratory of Supramolecular and BioNano Materials (SupraBioNanoLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, Milano I-20131, Italy. and Department of Applied Physics, Aalto University, Espoo, FI-02150, Finland and Istituto di Chimica del Riconoscimento Molecolare - National Research Council of Italy (ICRM-CNR), Laboratory of Peptide and Protein Chemistry, Via Mario Bianco 9, 20131 Milano, Italy
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26
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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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27
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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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Pizzi A, Lascialfari L, Demitri N, Bertolani A, Maiolo D, Carretti E, Metrangolo P. Halogen bonding modulates hydrogel formation from Fmoc amino acids. CrystEngComm 2017. [DOI: 10.1039/c7ce00031f] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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