1
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Kumar V, Ozguney B, Vlachou A, Chen Y, Gazit E, Tamamis P. Peptide Self-Assembled Nanocarriers for Cancer Drug Delivery. J Phys Chem B 2023; 127:1857-1871. [PMID: 36812392 PMCID: PMC10848270 DOI: 10.1021/acs.jpcb.2c06751] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/24/2022] [Indexed: 02/24/2023]
Abstract
The design of novel cancer drug nanocarriers is critical in the framework of cancer therapeutics. Nanomaterials are gaining increased interest as cancer drug delivery systems. Self-assembling peptides constitute an emerging novel class of highly attractive nanomaterials with highly promising applications in drug delivery, as they can be used to facilitate drug release and/or stability while reducing side effects. Here, we provide a perspective on peptide self-assembled nanocarriers for cancer drug delivery and highlight the aspects of metal coordination, structure stabilization, and cyclization, as well as minimalism. We review particular challenges in nanomedicine design criteria and, finally, provide future perspectives on addressing a portion of the challenges via self-assembling peptide systems. We consider that the intrinsic advantages of such systems, along with the increasing progress in computational and experimental approaches for their study and design, could possibly lead to novel classes of single or multicomponent systems incorporating such materials for cancer drug delivery.
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Affiliation(s)
- Vijay
Bhooshan Kumar
- The
Shmunis School of Biomedicine and Cancer Research, George S. Wise
Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Busra Ozguney
- Artie
McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
| | - Anastasia Vlachou
- Artie
McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
| | - Yu Chen
- The
Shmunis School of Biomedicine and Cancer Research, George S. Wise
Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ehud Gazit
- The
Shmunis School of Biomedicine and Cancer Research, 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
- Sagol
School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Phanourios Tamamis
- Artie
McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
- Department
of Materials Science and Engineering, Texas
A&M University, College
Station, Texas 77843-3003, United States
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2
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Wang BX, Kane C, Nicastro L, King O, Kit-Anan W, Downing B, Deidda G, Couch LS, Pinali C, Mitraki A, MacLeod KT, Terracciano CM. Integrins Increase Sarcoplasmic Reticulum Activity for Excitation-Contraction Coupling in Human Stem Cell-Derived Cardiomyocytes. Int J Mol Sci 2022; 23:10940. [PMID: 36142853 PMCID: PMC9504605 DOI: 10.3390/ijms231810940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/10/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
Engagement of the sarcoplasmic reticulum (SR) Ca2+ stores for excitation-contraction (EC)-coupling is a fundamental feature of cardiac muscle cells. Extracellular matrix (ECM) proteins that form the extracellular scaffolding supporting cardiac contractile activity are thought to play an integral role in the modulation of EC-coupling. At baseline, human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) show poor utilisation of SR Ca2+ stores, leading to inefficient EC-coupling, like developing or human CMs in cardiac diseases such as heart failure. We hypothesised that integrin ligand-receptor interactions between ECM proteins and CMs recruit the SR to Ca2+ cycling during EC-coupling. hiPSC-CM monolayers were cultured on fibronectin-coated glass before 24 h treatment with fibril-forming peptides containing the integrin-binding tripeptide sequence arginine-glycine-aspartic acid (2 mM). Micropipette application of 40 mM caffeine in standard or Na+/Ca2+-free Tyrode's solutions was used to assess the Ca2+ removal mechanisms. Microelectrode recordings were conducted to analyse action potentials in current-clamp. Confocal images of labelled hiPSC-CMs were analysed to investigate hiPSC-CM morphology and ultrastructural arrangements in Ca2+ release units. This study demonstrates that peptides containing the integrin-binding sequence arginine-glycine-aspartic acid (1) abbreviate hiPSC-CM Ca2+ transient and action potential duration, (2) increase co-localisation between L-type Ca2+ channels and ryanodine receptors involved in EC-coupling, and (3) increase the rate of SR-mediated Ca2+ cycling. We conclude that integrin-binding peptides induce recruitment of the SR for Ca2+ cycling in EC-coupling through functional and structural improvements and demonstrate the importance of the ECM in modulating cardiomyocyte function in physiology.
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Affiliation(s)
- Brian X. Wang
- National Heart & Lung Institute, Imperial College London, London SW7 2AZ, UK
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK
| | - Christopher Kane
- National Heart & Lung Institute, Imperial College London, London SW7 2AZ, UK
| | - Laura Nicastro
- National Heart & Lung Institute, Imperial College London, London SW7 2AZ, UK
| | - Oisín King
- National Heart & Lung Institute, Imperial College London, London SW7 2AZ, UK
- Human Safety, Bayer Crop Science, 06903 Sophia-Antipolis, France
| | - Worrapong Kit-Anan
- National Heart & Lung Institute, Imperial College London, London SW7 2AZ, UK
| | - Barrett Downing
- National Heart & Lung Institute, Imperial College London, London SW7 2AZ, UK
| | - Graziano Deidda
- Institute of Electronic Structure and Laser (IESL), Foundation for Research and Technology−Hellas (FORTH), 700 13 Heraklion, Greece
- Department of Materials Science and Technology, University of Crete, 700 13 Heraklion, Greece
| | - Liam S. Couch
- National Heart & Lung Institute, Imperial College London, London SW7 2AZ, UK
| | - Christian Pinali
- Division of Cardiovascular Sciences, University of Manchester, Manchester M13 9NT, UK
| | - Anna Mitraki
- Institute of Electronic Structure and Laser (IESL), Foundation for Research and Technology−Hellas (FORTH), 700 13 Heraklion, Greece
- Department of Materials Science and Technology, University of Crete, 700 13 Heraklion, Greece
| | - Kenneth T. MacLeod
- National Heart & Lung Institute, Imperial College London, London SW7 2AZ, UK
| | - Cesare M. Terracciano
- National Heart & Lung Institute, Imperial College London, London SW7 2AZ, UK
- Laboratory of Myocardial Electrophysiology, 4th Floor, Imperial Centre for Translational and Experimental Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
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3
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Orr AA, Kuhlmann SK, Tamamis P. Computational design of a β-wrapin's N-terminal domain with canonical and non-canonical amino acid modifications mimicking curcumin's proposed inhibitory function. Biophys Chem 2022; 286:106805. [DOI: 10.1016/j.bpc.2022.106805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/14/2022] [Accepted: 03/18/2022] [Indexed: 12/14/2022]
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4
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Aviv M, Cohen-Gerassi D, Orr AA, Misra R, Arnon ZA, Shimon LJW, Shacham-Diamand Y, Tamamis P, Adler-Abramovich L. Modification of a Single Atom Affects the Physical Properties of Double Fluorinated Fmoc-Phe Derivatives. Int J Mol Sci 2021; 22:ijms22179634. [PMID: 34502542 PMCID: PMC8431810 DOI: 10.3390/ijms22179634] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/29/2021] [Accepted: 08/30/2021] [Indexed: 11/16/2022] Open
Abstract
Supramolecular hydrogels formed by the self-assembly of amino-acid based gelators are receiving increasing attention from the fields of biomedicine and material science. Self-assembled systems exhibit well-ordered functional architectures and unique physicochemical properties. However, the control over the kinetics and mechanical properties of the end-products remains puzzling. A minimal alteration of the chemical environment could cause a significant impact. In this context, we report the effects of modifying the position of a single atom on the properties and kinetics of the self-assembly process. A combination of experimental and computational methods, used to investigate double-fluorinated Fmoc-Phe derivatives, Fmoc-3,4F-Phe and Fmoc-3,5F-Phe, reveals the unique effects of modifying the position of a single fluorine on the self-assembly process, and the physical properties of the product. The presence of significant physical and morphological differences between the two derivatives was verified by molecular-dynamics simulations. Analysis of the spontaneous phase-transition of both building blocks, as well as crystal X-ray diffraction to determine the molecular structure of Fmoc-3,4F-Phe, are in good agreement with known changes in the Phe fluorination pattern and highlight the effect of a single atom position on the self-assembly process. These findings prove that fluorination is an effective strategy to influence supramolecular organization on the nanoscale. Moreover, we believe that a deep understanding of the self-assembly process may provide fundamental insights that will facilitate the development of optimal amino-acid-based low-molecular-weight hydrogelators for a wide range of applications.
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Affiliation(s)
- Moran Aviv
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; (M.A.); (D.C.-G.); (R.M.); (Z.A.A.)
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 6997801, Israel
- The Center for the Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
- School of Mechanical Engineering, Afeka Tel Aviv Academic College of Engineering, Tel Aviv 6910717, Israel
| | - Dana Cohen-Gerassi
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; (M.A.); (D.C.-G.); (R.M.); (Z.A.A.)
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 6997801, Israel
- The Center for the Physics and Chemistry of Living Systems, 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;
| | - Asuka A. Orr
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, USA; (A.A.O.); (P.T.)
| | - Rajkumar Misra
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; (M.A.); (D.C.-G.); (R.M.); (Z.A.A.)
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 6997801, Israel
- The Center for the Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Zohar A. Arnon
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; (M.A.); (D.C.-G.); (R.M.); (Z.A.A.)
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 6997801, Israel
- The Center for the Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Linda J. W. Shimon
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 76132701, Israel;
| | - Yosi Shacham-Diamand
- Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel;
- Department of Physical Electronics, School of Electrical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel
- TAU/TiET Food Security Center of Excellence (T2FSCoE), Thapar Institute of Engineering and Technology, Patiala 147004, India
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, USA; (A.A.O.); (P.T.)
- Department of Materials Science and Engineering, Texas A&M University, College Station, TX 77843-3003, USA
| | - Lihi Adler-Abramovich
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; (M.A.); (D.C.-G.); (R.M.); (Z.A.A.)
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 6997801, Israel
- The Center for the Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
- Correspondence:
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5
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Abstract
Self-assembly of proteins and peptides into the amyloid fold is a widespread phenomenon in the natural world. The structural hallmark of self-assembly into amyloid fibrillar assemblies is the cross-beta motif, which conveys distinct morphological and mechanical properties. The amyloid fibril formation has contrasting results depending on the organism, in the sense that it can bestow an organism with the advantages of mechanical strength and improved functionality or, on the contrary, could give rise to pathological states. In this chapter we review the existing information on amyloid-like peptide aggregates, which could either be derived from protein sequences, but also could be rationally or de novo designed in order to self-assemble into amyloid fibrils under physiological conditions. Moreover, the development of self-assembled fibrillar biomaterials that are tailored for the desired properties towards applications in biomedical or environmental areas is extensively analyzed. We also review computational studies predicting the amyloid propensity of the natural amino acid sequences and the structure of amyloids, as well as designing novel functional amyloid materials.
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Affiliation(s)
- C. Kokotidou
- University of Crete, Department of Materials Science and Technology Voutes Campus GR-70013 Heraklion Crete Greece
- FORTH, Institute for Electronic Structure and Laser N. Plastira 100 GR 70013 Heraklion Greece
| | - P. Tamamis
- Texas A&M University, Artie McFerrin Department of Chemical Engineering College Station Texas 77843-3122 USA
| | - A. Mitraki
- University of Crete, Department of Materials Science and Technology Voutes Campus GR-70013 Heraklion Crete Greece
- FORTH, Institute for Electronic Structure and Laser N. Plastira 100 GR 70013 Heraklion Greece
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6
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Insights into the interactions of bisphenol and phthalate compounds with unamended and carnitine-amended montmorillonite clays. Comput Chem Eng 2020; 143. [PMID: 33122868 PMCID: PMC7591107 DOI: 10.1016/j.compchemeng.2020.107063] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Montmorillonite clays could be promising sorbents to mitigate toxic compound exposures. Bisphenols A (BPA) and S (BPS) as well as phthalates, dibutyl phthalate (DBP) and di-2-ethylhexyl phthalate (DEHP), are ubiquitous environmental contaminants linked to adverse health effects. Here, we combined computational and experimental methods to investigate the ability of montmorillonite clays to sorb these compounds. Molecular dynamics simulations predicted that parent, unamended, clay has higher binding propensity for BPA and BPS than for DBP and DEHP; carnitine-amended clay improved BPA and BPS binding, through carnitine simultaneously anchoring to the clay through its quaternary ammonium cation and forming hydrogen bonds with BPA and BPS. Experimental isothermal analysis confirmed that carnitine-amended clay has enhanced BPA binding capacity, affinity and enthalpy. Our studies demonstrate how computational and experimental methods, combined, can characterize clay binding and sorption of toxic compounds, paving the way for future investigation of clays to reduce BPA and BPS exposure.
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7
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Kokotidou C, Jonnalagadda SVR, Orr AA, Vrentzos G, Kretsovali A, Tamamis P, Mitraki A. Designer Amyloid Cell-Penetrating Peptides for Potential Use as Gene Transfer Vehicles. Biomolecules 2019; 10:E7. [PMID: 31861408 PMCID: PMC7023140 DOI: 10.3390/biom10010007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/15/2019] [Accepted: 12/16/2019] [Indexed: 12/24/2022] Open
Abstract
Cell-penetrating peptides are used extensively to deliver molecules into cells due to their unique characteristics such as rapid internalization, charge, and non-cytotoxicity. Amyloid fibril biomaterials were reported as gene transfer or retroviral infection enhancers; no cell internalization of the peptides themselves is reported so far. In this study, we focus on two rationally and computationally designed peptides comprised of β-sheet cores derived from naturally occurring protein sequences and designed positively charged and aromatic residues exposed at key residue positions. The β-sheet cores bestow the designed peptides with the ability to self-assemble into amyloid fibrils. The introduction of positively charged and aromatic residues additionally promotes DNA condensation and cell internalization by the self-assembled material formed by the designed peptides. Our results demonstrate that these designer peptide fibrils can efficiently enter mammalian cells while carrying packaged luciferase-encoding plasmid DNA, and they can act as a protein expression enhancer. Interestingly, the peptides additionally exhibited strong antimicrobial activity against the enterobacterium Escherichia coli.
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Affiliation(s)
- Chrysoula Kokotidou
- Department of Materials Science and Technology, University of Crete, 70013 Heraklion, Grete, Greece;
- Institute of Electronic Structure and Laser (IESL) FORTH, 70013 Heraklion, Crete, Greece
| | - Sai Vamshi R. Jonnalagadda
- Artie McFerrin Department of Chemical Engineering, Texas A&M University College Station, TX 77843-3251, USA; (S.V.R.J.); (A.A.O.)
| | - Asuka A. Orr
- Artie McFerrin Department of Chemical Engineering, Texas A&M University College Station, TX 77843-3251, USA; (S.V.R.J.); (A.A.O.)
| | - George Vrentzos
- Institute of Molecular Biology and Biotechnology (IMBB) FORTH, 70013 Heraklion, Crete, Greece; (G.V.); (A.K.)
| | - Androniki Kretsovali
- Institute of Molecular Biology and Biotechnology (IMBB) FORTH, 70013 Heraklion, Crete, Greece; (G.V.); (A.K.)
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University College Station, TX 77843-3251, USA; (S.V.R.J.); (A.A.O.)
| | - Anna Mitraki
- Department of Materials Science and Technology, University of Crete, 70013 Heraklion, Grete, Greece;
- Institute of Electronic Structure and Laser (IESL) FORTH, 70013 Heraklion, Crete, Greece
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8
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Orr AA, Shaykhalishahi H, Mirecka EA, Jonnalagadda SVR, Hoyer W, Tamamis P. Elucidating the multi-targeted anti-amyloid activity and enhanced islet amyloid polypeptide binding of β-wrapins. Comput Chem Eng 2018; 116:322-332. [PMID: 30405276 PMCID: PMC6217933 DOI: 10.1016/j.compchemeng.2018.02.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
β-wrapins are engineered binding proteins stabilizing the β-hairpin conformations of amyloidogenic proteins islet amyloid polypeptide (IAPP), amyloid-β, and α-synuclein, thus inhibiting their amyloid propensity. Here, we use computational and experimental methods to investigate the molecular recognition of IAPP by β-wrapins. We show that the multi-targeted, IAPP, amyloid-β, and α-synuclein, binding properties of β-wrapins originate mainly from optimized interactions between β-wrapin residues and sets of residues in the three amyloidogenic proteins with similar physicochemical properties. Our results suggest that IAPP is a comparatively promiscuous β-wrapin target, probably due to the low number of charged residues in the IAPP β-hairpin motif. The sub-micromolar affinity of β-wrapin HI18, specifically selected against IAPP, is achieved in part by salt-bridge formation between HI18 residue Glu10 and the IAPP N-terminal residue Lys1, both located in the flexible N-termini of the interacting proteins. Our findings provide insights towards developing novel protein-based single- or multi-targeted therapeutics.
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Affiliation(s)
- Asuka A. Orr
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
| | - Hamed Shaykhalishahi
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf 40204, Germany
| | - Ewa A. Mirecka
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf 40204, Germany
| | - Sai Vamshi R. Jonnalagadda
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf 40204, Germany
- Institute of Structural Biochemistry (ICS-6), Research Centre Jülich, Jülich 52425, Germany
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
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9
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Jonnalagadda SVR, Kokotidou C, Orr AA, Fotopoulou E, Henderson KJ, Choi CH, Lim WT, Choi SJ, Jeong HK, Mitraki A, Tamamis P. Computational Design of Functional Amyloid Materials with Cesium Binding, Deposition, and Capture Properties. J Phys Chem B 2018; 122:7555-7568. [DOI: 10.1021/acs.jpcb.8b04103] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
| | - Chrysoula Kokotidou
- Department of Materials Science and Technology, University of Crete, Heraklion 700 13, Crete, Greece
- Institute of Electronic Structure and Laser (IESL) FORTH, Heraklion 711 10, Crete, Greece
| | | | - Emmanouela Fotopoulou
- Department of Materials Science and Technology, University of Crete, Heraklion 700 13, Crete, Greece
| | | | | | - Woo Taik Lim
- Department of Applied Chemistry, Andong National University, Andong 36729, Republic of Korea
| | - Sang June Choi
- Department of Environmental Engineering, Kyungpook National University, Daegu 41566, Republic of Korea
| | | | - Anna Mitraki
- Department of Materials Science and Technology, University of Crete, Heraklion 700 13, Crete, Greece
- Institute of Electronic Structure and Laser (IESL) FORTH, Heraklion 711 10, Crete, Greece
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10
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Kokotidou C, Jonnalagadda SVR, Orr AA, Seoane-Blanco M, Apostolidou CP, van Raaij MJ, Kotzabasaki M, Chatzoudis A, Jakubowski JM, Mossou E, Forsyth VT, Mitchell EP, Bowler MW, Llamas-Saiz AL, Tamamis P, Mitraki A. A novel amyloid designable scaffold and potential inhibitor inspired by GAIIG of amyloid beta and the HIV-1 V3 loop. FEBS Lett 2018; 592:1777-1788. [PMID: 29772603 DOI: 10.1002/1873-3468.13096] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 05/02/2018] [Indexed: 12/11/2022]
Abstract
The GAIIG sequence, common to the amyloid beta peptide (residues 29-33) and to the HIV-1 gp120 (residues 24-28 in a typical V3 loop), self-assembles into amyloid fibrils, as suggested by theory and the experiments presented here. The longer YATGAIIGNII sequence from the V3 loop also self-assembles into amyloid fibrils, of which the first three and the last two residues are outside the amyloid GAIIG core. We postulate that this sequence, with suitably selected modifications at the flexible positions, can serve as a designable scaffold for novel amyloid-based materials. Moreover, we report the single crystal X-ray structure of the beta-breaker peptide GAIPIG at 1.05 Å resolution. The structural information provided in this study could serve as the basis for structure-based design of potential inhibitors of amyloid formation.
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Affiliation(s)
- Chrysoula Kokotidou
- Department of Materials Science and Technology, University of Crete, Heraklion, Greece.,Institute of Electronic Structure and Laser (IESL), FORTH, Heraklion, Greece
| | | | - Asuka A Orr
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Mateo Seoane-Blanco
- Departamento de Estructura de Macromoleculas, Centro Nacional de Biotecnologia (CSIC), Madrid, Spain
| | - Chrysanthi Pinelopi Apostolidou
- Department of Materials Science and Technology, University of Crete, Heraklion, Greece.,Institute of Electronic Structure and Laser (IESL), FORTH, Heraklion, Greece
| | - Mark J van Raaij
- Departamento de Estructura de Macromoleculas, Centro Nacional de Biotecnologia (CSIC), Madrid, Spain
| | - Marianna Kotzabasaki
- Department of Materials Science and Technology, University of Crete, Heraklion, Greece
| | - Apostolos Chatzoudis
- Department of Materials Science and Technology, University of Crete, Heraklion, Greece
| | - Joseph M Jakubowski
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Estelle Mossou
- Institut Laue Langevin, Grenoble Cedex 9, France.,Faculty of Natural Sciences/Institute for Science and Technology in Medicine, Keele University, Staffordshire, UK
| | - V Trevor Forsyth
- Institut Laue Langevin, Grenoble Cedex 9, France.,Faculty of Natural Sciences/Institute for Science and Technology in Medicine, Keele University, Staffordshire, UK
| | - Edward P Mitchell
- Faculty of Natural Sciences/Institute for Science and Technology in Medicine, Keele University, Staffordshire, UK.,European Synchrotron Radiation Facility, Grenoble Cedex 9, France
| | - Matthew W Bowler
- European Molecular Biology Laboratory, Grenoble, France.,Unit for Virus Host Cell Interactions, University Grenoble Alpes-EMBL-CNRS, Grenoble, France
| | - Antonio L Llamas-Saiz
- X-Ray Unit, RIAIDT, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Anna Mitraki
- Department of Materials Science and Technology, University of Crete, Heraklion, Greece.,Institute of Electronic Structure and Laser (IESL), FORTH, Heraklion, Greece
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11
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Orr AA, Wördehoff MM, Hoyer W, Tamamis P. Uncovering the Binding and Specificity of β-Wrapins for Amyloid-β and α-Synuclein. J Phys Chem B 2016; 120:12781-12794. [DOI: 10.1021/acs.jpcb.6b08485] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Asuka A. Orr
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
| | - Michael M. Wördehoff
- Institut
für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany
| | - Wolfgang Hoyer
- Institut
für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany
- Institute
of Structural Biochemistry (ICS-6), Research Centre Jülich, 52425 Jülich, Germany
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
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12
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Deidda G, Jonnalagadda SVR, Spies JW, Ranella A, Mossou E, Forsyth VT, Mitchell EP, Bowler MW, Tamamis P, Mitraki A. Self-Assembled Amyloid Peptides with Arg-Gly-Asp (RGD) Motifs As Scaffolds for Tissue Engineering. ACS Biomater Sci Eng 2016; 3:1404-1416. [DOI: 10.1021/acsbiomaterials.6b00570] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Graziano Deidda
- Department of Materials Science and Technology, University of Crete, Heraklion 70013, Greece
- Institute
of Electronic Structure and Laser (IESL), Foundation for Research and Technology−Hellas (FORTH), Heraklion 70013, Greece
| | - Sai Vamshi R. Jonnalagadda
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
| | - Jacob W. Spies
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
| | - Anthi Ranella
- Institute
of Electronic Structure and Laser (IESL), Foundation for Research and Technology−Hellas (FORTH), Heraklion 70013, Greece
| | - Estelle Mossou
- Institut Laue Langevin, 6 rue
Jules Horowitz, 38042 Grenoble Cedex 9, France
- Faculty of
Natural Sciences/Institute for Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, United Kingdom
| | - V. Trevor Forsyth
- Institut Laue Langevin, 6 rue
Jules Horowitz, 38042 Grenoble Cedex 9, France
- Faculty of
Natural Sciences/Institute for Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, United Kingdom
| | - Edward P. Mitchell
- Faculty of
Natural Sciences/Institute for Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, United Kingdom
- European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043 Grenoble Cedex 9, France
| | - Matthew W. Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, CS 90181, F-38042 Grenoble, France
- Unit
for Virus Host Cell Interactions, Université Grenoble Alpes−EMBL-CNRS, 71 avenue des Martyrs, CS 90181, F-38042 Grenoble, France
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
| | - Anna Mitraki
- Department of Materials Science and Technology, University of Crete, Heraklion 70013, Greece
- Institute
of Electronic Structure and Laser (IESL), Foundation for Research and Technology−Hellas (FORTH), Heraklion 70013, Greece
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13
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Loo Y, Goktas M, Tekinay AB, Guler MO, Hauser CAE, Mitraki A. Self-Assembled Proteins and Peptides as Scaffolds for Tissue Regeneration. Adv Healthc Mater 2015; 4:2557-86. [PMID: 26461979 DOI: 10.1002/adhm.201500402] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 07/24/2015] [Indexed: 12/15/2022]
Abstract
Self-assembling proteins and peptides are increasingly gaining interest for potential use as scaffolds in tissue engineering applications. They self-organize from basic building blocks under mild conditions into supramolecular structures, mimicking the native extracellular matrix. Their properties can be easily tuned through changes at the sequence level. Moreover, they can be produced in sufficient quantities with chemical synthesis or recombinant technologies to allow them to address homogeneity and standardization issues required for applications. Here. recent advances in self-assembling proteins, peptides, and peptide amphiphiles that form scaffolds suitable for tissue engineering are reviewed. The focus is on a variety of motifs, ranging from minimalistic dipeptides, simplistic ultrashort aliphatic peptides, and peptide amphiphiles to large "recombinamer" proteins. Special emphasis is placed on the rational design of self-assembling motifs and biofunctionalization strategies to influence cell behavior and modulate scaffold stability. Perspectives for combination of these "bottom-up" designer strategies with traditional "top-down" biofabrication techniques for new generations of tissue engineering scaffolds are highlighted.
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Affiliation(s)
- Yihua Loo
- Institute for Bioengineering and Nanotechnology; A* STAR; 31 Biopolis Way The Nanos 138669 Singapore
| | - Melis Goktas
- Institute of Materials Science and Nanotechnology; National Nanotechnology Research Center (UNAM); Bilkent University; Ankara Turkey 06800
| | - Ayse B. Tekinay
- Institute of Materials Science and Nanotechnology; National Nanotechnology Research Center (UNAM); Bilkent University; Ankara Turkey 06800
| | - Mustafa O. Guler
- Institute of Materials Science and Nanotechnology; National Nanotechnology Research Center (UNAM); Bilkent University; Ankara Turkey 06800
| | - Charlotte A. E. Hauser
- Institute for Bioengineering and Nanotechnology; A* STAR; 31 Biopolis Way The Nanos 138669 Singapore
| | - Anna Mitraki
- Department of Materials Science and Technology; University of Crete; Greece 70013
- Institute for Electronic Structure and Lasers (IESL); Foundation for Research and Technology Hellas (FORTH); Vassilika Vouton; Heraklion Crete Greece 70013
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14
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Marchesan S, Vargiu AV, Styan KE. The Phe-Phe Motif for Peptide Self-Assembly in Nanomedicine. Molecules 2015; 20:19775-88. [PMID: 26540034 PMCID: PMC6332413 DOI: 10.3390/molecules201119658] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 10/25/2015] [Accepted: 10/27/2015] [Indexed: 01/19/2023] Open
Abstract
Since its discovery, the Phe-Phe motif has gained in popularity as a minimalist building block to drive the self-assembly of short peptides and their analogues into nanostructures and hydrogels. Molecules based on the Phe-Phe motif have found a range of applications in nanomedicine, from drug delivery and biomaterials to new therapeutic paradigms. Here we discuss the various production methods for this class of compounds, and the characterization, nanomorphologies, and application of their self-assembled nanostructures. We include the most recent findings on their remarkable properties, which hold substantial promise for the creation of the next generation nanomedicines.
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Affiliation(s)
- Silvia Marchesan
- Chemical and Pharmaceutical Sciences Department, University of Trieste, Via L. Giorgieri 1, Trieste 34127, Italy.
| | - Attilio V Vargiu
- Department of Physics, University of Cagliari, Cittadella Universitaria S.P. Monserrato-Sestu Km. 0.700, Monserrato 09042, Italy.
| | - Katie E Styan
- CSIRO Manufacturing, Bayview Ave Clayton, VIC 3168, Australia.
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15
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Elucidating a key anti-HIV-1 and cancer-associated axis: the structure of CCL5 (Rantes) in complex with CCR5. Sci Rep 2014; 4:5447. [PMID: 24965094 PMCID: PMC4894430 DOI: 10.1038/srep05447] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 06/05/2014] [Indexed: 01/01/2023] Open
Abstract
CCL5 (RANTES) is an inflammatory chemokine which binds to chemokine receptor CCR5 and induces signaling. The CCL5:CCR5 associated chemotactic signaling is of critical biological importance and is a potential HIV-1 therapeutic axis. Several studies provided growing evidence for the expression of CCL5 and CCR5 in non-hematological malignancies. Therefore, the delineation of the CCL5:CCR5 complex structure can pave the way for novel CCR5-targeted drugs. We employed a computational protocol which is primarily based on free energy calculations and molecular dynamics simulations, and report, what is to our knowledge, the first computationally derived CCL5:CCR5 complex structure which is in excellent agreement with experimental findings and clarifies the functional role of CCL5 and CCR5 residues which are associated with binding and signaling. A wealth of polar and non-polar interactions contributes to the tight CCL5:CCR5 binding. The structure of an HIV-1 gp120 V3 loop in complex with CCR5 has recently been derived through a similar computational protocol. A comparison between the CCL5 : CCR5 and the HIV-1 gp120 V3 loop : CCR5 complex structures depicts that both the chemokine and the virus primarily interact with the same CCR5 residues. The present work provides insights into the blocking mechanism of HIV-1 by CCL5.
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16
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Tamamis P, Floudas CA. Molecular recognition of CCR5 by an HIV-1 gp120 V3 loop. PLoS One 2014; 9:e95767. [PMID: 24763408 PMCID: PMC3999033 DOI: 10.1371/journal.pone.0095767] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 03/29/2014] [Indexed: 12/04/2022] Open
Abstract
The binding of protein HIV-1 gp120 to coreceptors CCR5 or CXCR4 is a key step of the HIV-1 entry to the host cell, and is predominantly mediated through the V3 loop fragment of HIV-1 gp120. In the present work, we delineate the molecular recognition of chemokine receptor CCR5 by a dual tropic HIV-1 gp120 V3 loop, using a comprehensive set of computational tools predominantly based on molecular dynamics simulations and free energy calculations. We report, what is to our knowledge, the first complete HIV-1 gp120 V3 loop : CCR5 complex structure, which includes the whole V3 loop and the N-terminus of CCR5, and exhibits exceptional agreement with previous experimental findings. The computationally derived structure sheds light into the functional role of HIV-1 gp120 V3 loop and CCR5 residues associated with the HIV-1 coreceptor activity, and provides insights into the HIV-1 coreceptor selectivity and the blocking mechanism of HIV-1 gp120 by maraviroc. By comparing the binding of the specific dual tropic HIV-1 gp120 V3 loop with CCR5 and CXCR4, we observe that the HIV-1 gp120 V3 loop residues 13-21, which include the tip, share nearly identical structural and energetic properties in complex with both coreceptors. This result paves the way for the design of dual CCR5/CXCR4 targeted peptides as novel potential anti-AIDS therapeutics.
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Affiliation(s)
- Phanourios Tamamis
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, United States of America
| | - Christodoulos A. Floudas
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, United States of America
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17
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Molecular recognition of CXCR4 by a dual tropic HIV-1 gp120 V3 loop. Biophys J 2014; 105:1502-14. [PMID: 24048002 DOI: 10.1016/j.bpj.2013.07.049] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 07/16/2013] [Accepted: 07/29/2013] [Indexed: 01/01/2023] Open
Abstract
HIV-1 cell entry is initiated by the interaction of the viral envelope glycoprotein gp120 with CD4, and chemokine coreceptors CXCR4 and CCR5. The molecular recognition of CXCR4 or CCR5 by the HIV-1 gp120 is mediated through the V3 loop, a fragment of gp120. The binding of the V3 loop to CXCR4 or CCR5 determines the cell tropism of HIV-1 and constitutes a key step before HIV-1 cell entry. Thus, elucidating the molecular recognition of CXCR4 by the V3 loop is important for understanding HIV-1 viral infectivity and tropism, and for the design of HIV-1 inhibitors. We employed a comprehensive set of computational tools, predominantly based on free energy calculations and molecular-dynamics simulations, to investigate the molecular recognition of CXCR4 by a dual tropic V3 loop. We report what is, to our knowledge, the first HIV-1 gp120 V3 loop:CXCR4 complex structure. The computationally derived structure reveals an abundance of polar and nonpolar intermolecular interactions contributing to the HIV-1 gp120:CXCR4 binding. Our results are in remarkable agreement with previous experimental findings. Therefore, this work sheds light on the functional role of HIV-1 gp120 V3 loop and CXCR4 residues associated with HIV-1 coreceptor activity.
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18
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Tamamis P, Floudas CA. Elucidating a key component of cancer metastasis: CXCL12 (SDF-1α) binding to CXCR4. J Chem Inf Model 2014; 54:1174-88. [PMID: 24660779 PMCID: PMC4004218 DOI: 10.1021/ci500069y] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
The chemotactic signaling induced
by the binding of chemokine CXCL12
(SDF-1α) to chemokine receptor CXCR4 is of significant biological
importance and is a potential therapeutic axis against HIV-1. However,
as CXCR4 is overexpressed in certain cancer cells, the CXCL12:CXCR4
signaling is involved in tumor metastasis, progression, angiogenesis,
and survival. Motivated by the pivotal role of the CXCL12:CXCR4 axis
in cancer, we employed a comprehensive set of computational tools,
predominantly based on free energy calculations and molecular dynamics
simulations, to obtain insights into the molecular recognition of
CXCR4 by CXCL12. We report, what is to our knowledge, the first computationally
derived CXCL12:CXCR4 complex structure which is in remarkable agreement
with experimental findings and sheds light into the functional role
of CXCL12 and CXCR4 residues which are associated with binding and
signaling. Our results reveal that the CXCL12 N-terminal domain is
firmly bound within the CXCR4 transmembrane domain, and the central
24–50 residue domain of CXCL12 interacts with the upper N-terminal
domain of CXCR4. The stability of the CXCL12:CXCR4 complex structure
is attributed to an abundance of nonpolar and polar intermolecular
interactions, including salt bridges formed between positively charged
CXCL12 residues and negatively charged CXCR4 residues. The success
of the computational protocol can mainly be attributed to the nearly
exhaustive docking conformational search, as well as the heterogeneous
dielectric implicit water-membrane-water model used to simulate and
select the optimum conformations. We also recently utilized this protocol
to elucidate the binding of an HIV-1 gp120 V3 loop in complex with
CXCR4, and a comparison between the molecular recognition of CXCR4
by CXCL12 and the HIV-1 gp120 V3 loop shows that both CXCL12 and the
HIV-1 gp120 V3 loop share the same CXCR4 binding pocket, as they mostly
interact with the same CXCR4 residues.
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Affiliation(s)
- Phanourios Tamamis
- Department of Chemical and Biological Engineering, Princeton University , New Jersey 08544, United States
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19
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Tamamis P, Terzaki K, Kassinopoulos M, Mastrogiannis L, Mossou E, Forsyth VT, Mitchell EP, Mitraki A, Archontis G. Self-Assembly of an Aspartate-Rich Sequence from the Adenovirus Fiber Shaft: Insights from Molecular Dynamics Simulations and Experiments. J Phys Chem B 2014; 118:1765-74. [DOI: 10.1021/jp409988n] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Phanourios Tamamis
- Department
of Physics, University of Cyprus, 75 Kallipoleos Street, CY1678 Nicosia, Cyprus
| | - Konstantina Terzaki
- Department
of Materials Science and Technology, University of Crete, P.O. Box 2208, GR-71003 Heraklion, Crete, Greece
- Institute for Electronic Structure and Laser, FORTH, P.O. Box 1527, GR-71110 Heraklion, Greece
| | - Michalis Kassinopoulos
- Department
of Physics, University of Cyprus, 75 Kallipoleos Street, CY1678 Nicosia, Cyprus
| | - Lefteris Mastrogiannis
- Department
of Materials Science and Technology, University of Crete, P.O. Box 2208, GR-71003 Heraklion, Crete, Greece
- Institute for Electronic Structure and Laser, FORTH, P.O. Box 1527, GR-71110 Heraklion, Greece
| | - Estelle Mossou
- EPSAM/ISTM, Keele University, Keele, Staffordshire ST5
5BG, United Kingdom
- Partnership
for Structural Biology, Institut Laue Langevin, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France
| | - V. Trevor Forsyth
- EPSAM/ISTM, Keele University, Keele, Staffordshire ST5
5BG, United Kingdom
- Partnership
for Structural Biology, Institut Laue Langevin, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France
| | - Edward P. Mitchell
- Partnership
for Structural Biology, Institut Laue Langevin, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France
- European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043 Grenoble Cedex 9, France
| | - Anna Mitraki
- Department
of Materials Science and Technology, University of Crete, P.O. Box 2208, GR-71003 Heraklion, Crete, Greece
- Institute for Electronic Structure and Laser, FORTH, P.O. Box 1527, GR-71110 Heraklion, Greece
| | - Georgios Archontis
- Department
of Physics, University of Cyprus, 75 Kallipoleos Street, CY1678 Nicosia, Cyprus
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20
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Tamamis P, Kasotakis E, Archontis G, Mitraki A. Combination of theoretical and experimental approaches for the design and study of fibril-forming peptides. Methods Mol Biol 2014; 1216:53-70. [PMID: 25213410 DOI: 10.1007/978-1-4939-1486-9_3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Self-assembling peptides that can form supramolecular structures such as fibrils, ribbons, and nanotubes are of particular interest to modern bionanotechnology and materials science. Their ability to form biocompatible nanostructures under mild conditions through non-covalent interactions offers a big biofabrication advantage. Structural motifs extracted from natural proteins are an important source of inspiration for the rational design of such peptides. Examples include designer self-assembling peptides that correspond to natural coiled-coil motifs, amyloid-forming proteins, and natural fibrous proteins. In this chapter, we focus on the exploitation of structural information from beta-structured natural fibers. We review a case study of short peptides that correspond to sequences from the adenovirus fiber shaft. We describe both theoretical methods for the study of their self-assembly potential and basic experimental protocols for the assessment of fibril-forming assembly.
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Affiliation(s)
- Phanourios Tamamis
- Department of Physics, University of Cyprus, 20537, CY1678, Nicosia, Cyprus
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21
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Khoury GA, Tamamis P, Pinnaduwage N, Smadbeck J, Kieslich CA, Floudas CA. Princeton_TIGRESS: protein geometry refinement using simulations and support vector machines. Proteins 2013; 82:794-814. [PMID: 24174311 DOI: 10.1002/prot.24459] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 10/18/2013] [Accepted: 10/22/2013] [Indexed: 12/30/2022]
Abstract
Protein structure refinement aims to perform a set of operations given a predicted structure to improve model quality and accuracy with respect to the native in a blind fashion. Despite the numerous computational approaches to the protein refinement problem reported in the previous three CASPs, an overwhelming majority of methods degrade models rather than improve them. We initially developed a method tested using blind predictions during CASP10 which was officially ranked in 5th place among all methods in the refinement category. Here, we present Princeton_TIGRESS, which when benchmarked on all CASP 7,8,9, and 10 refinement targets, simultaneously increased GDT_TS 76% of the time with an average improvement of 0.83 GDT_TS points per structure. The method was additionally benchmarked on models produced by top performing three-dimensional structure prediction servers during CASP10. The robustness of the Princeton_TIGRESS protocol was also tested for different random seeds. We make the Princeton_TIGRESS refinement protocol freely available as a web server at http://atlas.princeton.edu/refinement. Using this protocol, one can consistently refine a prediction to help bridge the gap between a predicted structure and the actual native structure.
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Affiliation(s)
- George A Khoury
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, 08540
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22
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Terzaki K, Kalloudi E, Mossou E, Mitchell EP, Forsyth VT, Rosseeva E, Simon P, Vamvakaki M, Chatzinikolaidou M, Mitraki A, Farsari M. Mineralized self-assembled peptides on 3D laser-made scaffolds: a new route toward ‘scaffold on scaffold’ hard tissue engineering. Biofabrication 2013; 5:045002. [DOI: 10.1088/1758-5082/5/4/045002] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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23
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Rissanou AN, Georgilis E, Kasotakis E, Mitraki A, Harmandaris V. Effect of solvent on the self-assembly of dialanine and diphenylalanine peptides. J Phys Chem B 2013; 117:3962-75. [PMID: 23510047 DOI: 10.1021/jp311795b] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Diphenylalanine (FF) is a very common peptide with many potential applications, both biological and technological, due to a large number of different nanostructures which it attains. The current work concerns a detailed study of the self-assembled structures of FF in two different solvents, an aqueous (H2O) and an organic (CH3OH) through simulations and experiments. Detailed atomistic molecular dynamics (MD) simulations of FF in both solvents have been performed, using an explicit solvent model. The self-assembling propensity of FF in water is obvious while in methanol a very weak self-assembling propensity is observed. We studied and compared structural properties of FF in the two different solvents and a comparison with a system of dialanine (AA) in the corresponding solvents was also performed. In addition, temperature-dependence studies were carried out. Finally, the simulation predictions were compared to new experimental data, which were produced in the framework of the present work. A very good qualitative agreement between simulation and experimental observations was found.
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Affiliation(s)
- Anastassia N Rissanou
- Department of Applied Mathematics, University of Crete, GR-71409, Heraklion, Crete, Greece.
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24
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Kasotakis E, Mitraki A. Designed self-assembling peptides as templates for the synthesis of metal nanoparticles. Methods Mol Biol 2013; 996:195-202. [PMID: 23504425 DOI: 10.1007/978-1-62703-354-1_11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Self-assembling peptides are water soluble and form biocompatible nanostructures under mild conditions through non-covalent interactions. They form supramolecular structures such as ribbons, nanotubes, and fibrils. Of particular interest is the possibility of using these peptide fibrils as templates for the growth of inorganic materials, such as metallic nanoparticles. The ability to reliably produce metal-coated fibrils with robust binding of metal nanoparticles is a vital first step towards the exploitation of these fibrils as conducting nanowires with applications in nano-circuitry. One promising strategy consists of the rational introduction of metal-binding amino acids (such as cysteine) at the level of the peptide building block. Upon assembly of the building blocks into fibrils, cysteine residues that remain accessible at the outside of the fibril core could serve as nucleation sites for metals. We will review in this chapter a case study of rationally designed cysteine-containing peptides and basic protocols for their metallization with silver, gold, and platinum nanoparticles.
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Affiliation(s)
- Emmanouil Kasotakis
- Department of Materials Science and Technology, and Institute for Electronic Structure and Laser, Foundation for Research and Technology-Hellas, (IESL-FORTH), University of Crete, Vassilika Vouton, Heraklion, Crete, Greece
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25
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Kasotakis E, Mitraki A. Silica biotemplating by self-assembling peptides via serine residues activated by the peptide amino terminal group. Biopolymers 2012. [DOI: 10.1002/bip.22091] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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26
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Polydorides S, Amara N, Aubard C, Plateau P, Simonson T, Archontis G. Computational protein design with a generalized Born solvent model: application to Asparaginyl-tRNA synthetase. Proteins 2011; 79:3448-68. [PMID: 21563215 DOI: 10.1002/prot.23042] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Revised: 02/25/2011] [Accepted: 03/03/2011] [Indexed: 12/13/2022]
Abstract
Computational Protein Design (CPD) is a promising method for high throughput protein and ligand mutagenesis. Recently, we developed a CPD method that used a polar-hydrogen energy function for protein interactions and a Coulomb/Accessible Surface Area (CASA) model for solvent effects. We applied this method to engineer aspartyl-adenylate (AspAMP) specificity into Asparaginyl-tRNA synthetase (AsnRS), whose substrate is asparaginyl-adenylate (AsnAMP). Here, we implement a more accurate function, with an all-atom energy for protein interactions and a residue-pairwise generalized Born model for solvent effects. As a first test, we compute aminoacid affinities for several point mutants of Aspartyl-tRNA synthetase (AspRS) and Tyrosyl-tRNA synthetase and stability changes for three helical peptides and compare with experiment. As a second test, we readdress the problem of AsnRS aminoacid engineering. We compare three design criteria, which optimize the folding free-energy, the absolute AspAMP affinity, and the relative (AspAMP-AsnAMP) affinity. The sequences and conformations are improved with respect to our previous, polar-hydrogen/CASA study: For several designed complexes, the AspAMP carboxylate forms three interactions with a conserved arginine and a designed lysine, as in the active site of the AspRS:AspAMP complex. The conformations and interactions are well maintained in molecular dynamics simulations and the sequences have an inverted specificity, favoring AspAMP over AsnAMP. The method is not fully successful, since experimental measurements with the seven most promising sequences show that they do not catalyze at a detectable level the adenylation of Asp (or Asn) with ATP. This may be due to weak AspAMP binding and/or disruption of transition-state stabilization.
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27
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Viguier B, Zór K, Kasotakis E, Mitraki A, Clausen CH, Svendsen WE, Castillo-León J. Development of an electrochemical metal-ion biosensor using self-assembled peptide nanofibrils. ACS APPLIED MATERIALS & INTERFACES 2011; 3:1594-1600. [PMID: 21443268 DOI: 10.1021/am200149h] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
This article describes the combination of self-assembled peptide nanofibrils with metal electrodes for the development of an electrochemical metal-ion biosensor. The biological nanofibrils were immobilized on gold electrodes and used as biorecognition elements for the complexation with copper ions. These nanofibrils were obtained under aqueous conditions, at room temperature and outside the clean room. The functionalized gold electrode was evaluated by cyclic voltammetry, impedance spectroscopy, energy dispersive X-ray and atomic force microscopy. The obtained results displayed a layer of nanofibrils able to complex with copper ions in solution. The response of the obtained biosensor was linear up to 50 μM copper and presented a sensitivity of 0.68 μA cm⁻² μM⁻¹. Moreover, the fabricated sensor could be regenerated to a copper-free state allowing its reutilization.
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Affiliation(s)
- Bruno Viguier
- Department of Biotechnology, Lund University, Getingevagen 60, P.O. Box 124, S-22100 Lund, Sweden
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28
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Pieridou G, Avgousti-Menelaou C, Tamamis P, Archontis G, Hayes SC. UV resonance Raman study of TTR(105-115) structural evolution as a function of temperature. J Phys Chem B 2011; 115:4088-98. [PMID: 21428385 DOI: 10.1021/jp107519b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
UV resonance Raman spectroscopy was used to probe the temperature dependence of the conformation of TTR(105-115) in solution. Resonance Raman spectra with excitation at 239.5 nm, show an increase in the absolute resonance Raman cross section of Tyr with an increase in temperature. This trend is associated with an increase in the hydrophobicity of the Tyr local environment, suggesting a conformational change at 28 °C. Excitation at ~200 nm is known to enhance scattering due to amide vibrations and provides insights as to the secondary structure of a peptide or protein. UVRR spectra at this excitation suggest that in solution the peptide assumes a disordered conformation with frequent formation of β-turns. Explicit-solvent replica-exchange MD simulations of the isolated peptide in the region 15 to 37 °C suggest that the dominant conformation assumed by the peptide corresponds to a coil with β-turns in the central and C-terminal region. In line with the experiments, an increase in temperature induces structural order in the peptide, reflected by an increase in the probability for the formation of β-turns and hydrophobic side-chain contacts, mainly in the 8-11 moiety, and to a lesser extent in the 4-7 moiety.
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Affiliation(s)
- G Pieridou
- Department of Chemistry, University of Cyprus, P.O. Box 20537, 1678, Nicosia, Cyprus
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Chennamsetty N, Voynov V, Kayser V, Helk B, Trout BL. Prediction of Aggregation Prone Regions of Therapeutic Proteins. J Phys Chem B 2010; 114:6614-24. [DOI: 10.1021/jp911706q] [Citation(s) in RCA: 149] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Naresh Chennamsetty
- Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, and Novartis Pharma AG, CH-4002, Basel, Switzerland
| | - Vladimir Voynov
- Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, and Novartis Pharma AG, CH-4002, Basel, Switzerland
| | - Veysel Kayser
- Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, and Novartis Pharma AG, CH-4002, Basel, Switzerland
| | - Bernhard Helk
- Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, and Novartis Pharma AG, CH-4002, Basel, Switzerland
| | - Bernhardt L. Trout
- Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, and Novartis Pharma AG, CH-4002, Basel, Switzerland
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