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Iscen A, Kaygisiz K, Synatschke CV, Weil T, Kremer K. Multiscale Simulations of Self-Assembling Peptides: Surface and Core Hydrophobicity Determine Fibril Stability and Amyloid Aggregation. Biomacromolecules 2024; 25:3063-3075. [PMID: 38652055 PMCID: PMC11094720 DOI: 10.1021/acs.biomac.4c00151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/25/2024]
Abstract
Assemblies of peptides and proteins through specific intermolecular interactions set the basis for macroscopic materials found in nature. Peptides provide easily tunable hydrogen-bonding interactions, which can lead to the formation of ordered structures such as highly stable β-sheets that can form amyloid-like supramolecular peptide nanofibrils (PNFs). PNFs are of special interest, as they could be considered as mimics of various fibrillar structures found in nature. In their ability to serve as supramolecular scaffolds, they could mimic certain features of the extracellular matrix to provide stability, interact with pathogens such as virions, and transduce signals between the outside and inside of cells. Many PNFs have been reported that reveal rich bioactivities. PNFs supporting neuronal cell growth or lentiviral gene transduction have been studied systematically, and their material properties were correlated to bioactivities. However, the impact of the structure of PNFs, their dynamics, and stabilities on their unique functions is still elusive. Herein, we provide a microscopic view of the self-assembled PNFs to unravel how the amino acid sequence of self-assembling peptides affects their secondary structure and dynamic properties of the peptides within supramolecular fibrils. Based on sequence truncation, amino acid substitution, and sequence reordering, we demonstrate that peptide-peptide aggregation propensity is critical to form bioactive β-sheet-rich structures. In contrast to previous studies, a very high peptide aggregation propensity reduces bioactivity due to intermolecular misalignment and instabilities that emerge when fibrils are in close proximity to other fibrils in solution. Our multiscale simulation approach correlates changes in biological activity back to single amino acid modifications. Understanding these relationships could lead to future material discoveries where the molecular sequence predictably determines the macroscopic properties and biological activity. In addition, our studies may provide new insights into naturally occurring amyloid fibrils in neurodegenerative diseases.
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Affiliation(s)
- Aysenur Iscen
- Department
of Polymer Theory, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Kübra Kaygisiz
- Department
of Synthesis of Macromolecules, Max Planck
Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Christopher V. Synatschke
- Department
of Synthesis of Macromolecules, Max Planck
Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Tanja Weil
- Department
of Synthesis of Macromolecules, Max Planck
Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Kurt Kremer
- Department
of Polymer Theory, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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2
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Niehaus TA, Prost E, Loriot V, Lépine F, Bergé L, Skupin S. THz to far-infrared spectra of the known crystal polymorphs of phenylalanine. Phys Chem Chem Phys 2024; 26:7329-7334. [PMID: 38353103 DOI: 10.1039/d3cp05805k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
There is renewed interest in the structure of the essential amino acid phenylalanine in the solid state. Three new polymorphs were found in the years 2012 to 2014. Here, we investigate the structure, stability, and energetical ordering of these phases using first-principles simulations at the level of density functional theory incorporating van der Waals interactions. Two of the distinct crystal forms are found to be structurally similar and energetically very close after vibrational free energy corrections have been taken into account. Infrared absorption spectra are likewise calculated and compared to experimental measurements. By combining measurements obtained with a commercial Fourier transform infra-red spectrometer and a homemade air-photonics-based THz time domain spectrometer, we could carry out this comparison in the vibrational frequency region from 1 to 40 THz. The excellent agreement of the line positions and the established energy ranking allow us to identify the most stable polymorph of phenylalanine.
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Affiliation(s)
- Thomas A Niehaus
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France.
| | - Emilien Prost
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France.
| | - Vincent Loriot
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France.
| | - Franck Lépine
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France.
| | - Luc Bergé
- Centre Lasers Intenses et Applications, Université de Bordeaux-CNRS-CEA, 33405 Talence Cedex, France
| | - Stefan Skupin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France.
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3
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Tiwari OS, Gazit E. Characterization of amyloid-like metal-amino acid assemblies with remarkable catalytic activity. Methods Enzymol 2024; 697:181-209. [PMID: 38816123 DOI: 10.1016/bs.mie.2024.01.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
While enzymes are potentially useful in various applications, their limited operational stability and production costs have led to an extensive search for stable catalytic agents that will retain the efficiency, specificity, and environmental-friendliness of natural enzymes. Despite extensive efforts, there is still an unmet need for improved enzyme mimics and novel concepts to discover and optimize such agents. Inspired by the catalytic activity of amyloids and the formation of amyloid-like assemblies by metabolites, our group pioneered the development of novel metabolite-metal co-assemblies (bio-nanozymes) that produce nanomaterials mimicking the catalytic function of common metalloenzymes that are being used for various technological applications. In addition to their notable activity, bio-nanozymes are remarkably safe as they are purely composed of amino acids and minerals that are harmless to the environment. The bio-nanozymes exhibit high efficiency and exceptional robustness, even under extreme conditions of temperature, pH, and salinity that are impractical for enzymes. Our group has recently also demonstrated the formation of ordered amino acid co-assemblies showing selective and preferential interactions comparable to the organization of residues in folded proteins. The identified bio-nanozymes can be used in various applications including environmental remediation, synthesis of new materials, and green energy.
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Affiliation(s)
- Om Shanker Tiwari
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ehud Gazit
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel; Department of Materials Science and Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
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4
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Yang L, Wang Y, Zhang W, Ma G. New Insight into the Structural Nature of Diphenylalanine Nanotube through Comparison with Amyloid Assemblies. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:1046-1057. [PMID: 38153333 DOI: 10.1021/acs.langmuir.3c03270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Diphenylalanine (FF) nanotubes are a star material in the field of peptide self-assembly and have demonstrated numerous intriguing applications. Due to its resemblance to amyloid assembly, the FF nanotube is widely regarded as a simplified mimic of amyloids. Yet, whether FF nanotube truly possesses amyloid structure remains an open question. To better understand the structural nature of FF nanotube, we herein performed a comparative structural investigation between FF nanotube and typical amyloid systems by Aβ1-40, Aβ1-42, Aβ16-22, Aβ13-23, α-synuclein, and lysozyme using Fourier transform infrared spectroscopy. Through this comparative investigation, we obtained clear evidence to support that the FF nanotube does not possess a β-sheet structure, a key structural characteristic of amyloid assembly, thus revealing the non-amyloid structural nature of the FF nanotube. At last, in light of our new finding, we further discussed the unique self-assembly behaviors of FF during nanotube formation and the implications of our work for FF nanotube related applications.
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Affiliation(s)
- Lujuan Yang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Key Laboratory of Analytical Science and Technology of Hebei Province, State Key Laboratory of New Pharmaceutical Preparations and Excipients, College of Chemistry and Materials Science, Hebei University, Baoding 071002, China
| | - Yao Wang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Key Laboratory of Analytical Science and Technology of Hebei Province, State Key Laboratory of New Pharmaceutical Preparations and Excipients, College of Chemistry and Materials Science, Hebei University, Baoding 071002, China
| | - Wenkai Zhang
- Department of Physics, Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China
| | - Gang Ma
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Key Laboratory of Analytical Science and Technology of Hebei Province, State Key Laboratory of New Pharmaceutical Preparations and Excipients, College of Chemistry and Materials Science, Hebei University, Baoding 071002, China
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5
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Kuila S, Dey S, Singh P, Shrivastava A, Nanda J. Phenylalanine-based fibrillar systems. Chem Commun (Camb) 2023; 59:14509-14523. [PMID: 37987167 DOI: 10.1039/d3cc04138g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Phenylketonuria (PKU) is an inborn metabolic disorder characterized by excess accumulation of phenylalanine (Phe) and its fibril formation, resulting in progressive intellectual disability. Several research groups have approached from various directions to understand the formation of toxic amyloid fibrils from the essential amino acid Phe. Different parameters like the nature of the solvent, pH, Phe concentration, temperature, etc. influence the fibril formation kinetics. In this article, we have summarized all major findings regarding the formation of Phe-based fibrils in aqueous and organic media and discussed how non-covalent interactions are involved in the self-assembly process using spectroscopic and microscopic techniques. The toxicity of Phe-based fibrils is compared with other neurodegenerative peptides. It is noted that the Phe-based fibrils can also induce various globular proteins into toxic fibrils. Later, we discuss the different approaches to inhibit fibril formation and reduce its toxicity. The presence of polyphenolic compounds, drugs, amino acids, nanoparticles, metal ions, crown ethers, and others showed a remarkable inhibitory effect on fibril formation. To the best of our knowledge, this is the first-ever etymological analysis of the Phe-fibrillar system and its inhibition to create a strong database against PKU.
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Affiliation(s)
- Soumen Kuila
- Department of Chemistry, University of North Bengal, Raja Rammohanpur, Siliguri 734013, West Bengal, India.
| | - Sukantha Dey
- Department of Chemistry, University of North Bengal, Raja Rammohanpur, Siliguri 734013, West Bengal, India.
| | - Pijush Singh
- Department of Chemistry, University of North Bengal, Raja Rammohanpur, Siliguri 734013, West Bengal, India.
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741235, West Bengal, India
| | - Akash Shrivastava
- Department of Chemistry, University of North Bengal, Raja Rammohanpur, Siliguri 734013, West Bengal, India.
| | - Jayanta Nanda
- Department of Chemistry, University of North Bengal, Raja Rammohanpur, Siliguri 734013, West Bengal, India.
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Kaygisiz K, Rauch-Wirth L, Dutta A, Yu X, Nagata Y, Bereau T, Münch J, Synatschke CV, Weil T. Data-mining unveils structure-property-activity correlation of viral infectivity enhancing self-assembling peptides. Nat Commun 2023; 14:5121. [PMID: 37612273 PMCID: PMC10447463 DOI: 10.1038/s41467-023-40663-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 08/01/2023] [Indexed: 08/25/2023] Open
Abstract
Gene therapy via retroviral vectors holds great promise for treating a variety of serious diseases. It requires the use of additives to boost infectivity. Amyloid-like peptide nanofibers (PNFs) were shown to efficiently enhance retroviral gene transfer. However, the underlying mode of action of these peptides remains largely unknown. Data-mining is an efficient method to systematically study structure-function relationship and unveil patterns in a database. This data-mining study elucidates the multi-scale structure-property-activity relationship of transduction enhancing peptides for retroviral gene transfer. In contrast to previous reports, we find that not the amyloid fibrils themselves, but rather µm-sized β-sheet rich aggregates enhance infectivity. Specifically, microscopic aggregation of β-sheet rich amyloid structures with a hydrophobic surface pattern and positive surface charge are identified as key material properties. We validate the reliability of the amphiphilic sequence pattern and the general applicability of the key properties by rationally creating new active sequences and identifying short amyloidal peptides from various pathogenic and functional origin. Data-mining-even for small datasets-enables the development of new efficient retroviral transduction enhancers and provides important insights into the diverse bioactivity of the functional material class of amyloids.
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Affiliation(s)
- Kübra Kaygisiz
- Department Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Lena Rauch-Wirth
- Institute of Molecular Virology, Ulm University Medical Center, Meyerhofstraße 1, 89081, Ulm, Germany
| | - Arghya Dutta
- Department Polymer Theory, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Xiaoqing Yu
- Department Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Yuki Nagata
- Department Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Tristan Bereau
- Department Polymer Theory, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
- Institute for Theoretical Physics, Heidelberg University, Philosophenweg 19, 69120, Heidelberg, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Meyerhofstraße 1, 89081, Ulm, Germany
| | - Christopher V Synatschke
- Department Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.
| | - Tanja Weil
- Department Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.
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7
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Supramolecule self-assembly synthesis of amyloid phenylalanine-Cu fibrils with laccase-like activity and their application for dopamine determination. Mikrochim Acta 2022; 189:98. [PMID: 35147785 DOI: 10.1007/s00604-022-05194-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 01/17/2022] [Indexed: 10/19/2022]
Abstract
Laccases are multicopper proteins for dioxygen-involved oxidation of a broad spectrum of organic compounds. I Novel amyloid-like phenylalanine-Cu (F-Cu(II)) fibrils were developed, which were obtained via supramolecular self-assembly of Cu2+ and phenylalanine (F) under basic condition. The obtained amyloid-like fibrils represented highly periodic structure, of which the lattice unit was constructed via alternating hydrophobic (aromatic environment) and hydrophilic (both hydrogen bonding and Cu(II) coordination) interactions. Relative to natural laccases, the amyloid-like F-Cu(II) architecture exhibited comparable substrate affinity (Michaelis constant, Km = 0.75 mM) and higher catalytic efficiency (kcat/Km = 773.33 × 10-3 g-1 min-1L). Moreover, it exhibited remarkable tolerances in pH (4 ~ 10), temperature (room temperature ~ 200 ℃), organic solvent, and long-term storage (> 15 days). These stabilities were superior among the reported nature and artificial laccases, presenting a more promising candidate in various chemo- or bio-applications. In addition, F-Cu(II) fibrils could catalyze the oxidation of dopamine (DA) to a brown product, in which a new absorption band at 470 nm was observed. Based on this, a simple colorimetric assay for the detection of DA could be performed. We reported a novel amyloid-like phenylalanine-Cu fibrils, in which F-Cu+ complex can mimick the T1 site of natural laccase to oxidize the substrates. Then electrons transferred to F-Cu2+ complex via N-H···O=C hydrogen binding pathway. Finally, the dioxygen was transformed to water though radical reaction.
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8
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Erimban S, Daschakraborty S. How does excess phenylalanine affect the packing density and fluidity of a lipid membrane? Phys Chem Chem Phys 2021; 23:27294-27303. [PMID: 34850794 DOI: 10.1039/d1cp05004d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phenylketonuria (PKU) is an autosomal recessive error of phenylalanine (Phe) metabolism, where untreated Phe becomes cytotoxic. Previous experiments found that excess Phe decreases the packing density and increases the fluidity and permeability of a lipid membrane. It was proposed that Phe forms cytotoxic nanoscopic amyloid-like fibrils. In another study, the Phe fibrils were not visible near the lipid membrane. So, what leads to the deleterious effect of Phe on the lipid membrane? We put forward a molecular mechanism for the observed effect of excess Phe on the lipid membrane using all-atom molecular dynamics simulation. This study suggests that Phe monomers spontaneously intercalate into the membrane and form small hydrogen-bonded clusters, some of which locally perturb the membrane. These local effects result in an overall reduction in the membrane packing density, enhancement of membrane fluidity, and an increase of water permeability, observed in experiments. The present study does not observe any effect of the nanoscopic fibrillar structure of Phe on the membrane. This study, therefore, provides alternative insights into the excess Phe cytotoxicity in PKU disease.
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Affiliation(s)
- Shakkira Erimban
- Department of Chemistry, Indian Institute of Technology Patna, Bihar, 801106, India.
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9
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Zaguri D, Zimmermann MR, Meisl G, Levin A, Rencus-Lazar S, Knowles TPJ, Gazit E. Kinetic and Thermodynamic Driving Factors in the Assembly of Phenylalanine-Based Modules. ACS NANO 2021; 15:18305-18311. [PMID: 34694771 DOI: 10.1021/acsnano.1c07537] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The formation of ordered protein and peptide assemblies is a phenomenon related to a wide range of human diseases. However, the mechanism of assembly at the molecular level remains largely unknown. Minimal models enable the exploration of the underlying interactions that are at the core of such self-assembly processes. In particular, the ability of phenylalanine, a single aromatic amino acid, to form an amyloid-like structure has challenged the previous dogma viewing a peptide backbone as a prerequisite for assembly. The driving forces controlling the nucleation and assembly in the absence of a peptide backbone remain to be identified. Here, aiming to unravel these forces, we explored the kinetics and thermodynamics of three phenylalanine-containing molecules during their assembly process: the amino acid phenylalanine, which accumulates in phenylketonuria patients, the diphenylalanine core-motif of the amyloid β peptide related to Alzheimer's disease, and the extended triphenylalanine peptide which forms a range of distinct nanostructures in vitro. We found that the aggregation propensity, regarding the critical monomer concentration, strongly increases with size, with triphenylalanine being the most aggregation-prone species under our experimental conditions. In the context of classical nucleation theory, this increase in aggregation propensity can be attributed to the larger free energy decrease upon aggregation of larger peptides and is not due to the presence/absence of a peptide bond per se. Taken together, this work provides insights into the aggregation processes of chemically simple systems and suggests that both backbone-containing peptides and backbone-lacking amino acids assemble through a similar mechanism, thus supporting the classification of amino acids in the continuum of amyloid-forming building blocks.
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Affiliation(s)
- Dor Zaguri
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Manuela R Zimmermann
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Georg Meisl
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Aviad Levin
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Sigal Rencus-Lazar
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Ehud Gazit
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 6997801, Israel
- BLAVATNIK CENTER for Drug Discovery for Drug Discovery, Tel Aviv University, Tel Aviv 6997801, Israel
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10
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Anand BG, Prajapati KP, Ansari M, Yadav DK, Temgire M, Kar K. Genesis of Neurotoxic Hybrid Nanofibers from the Coassembly of Aromatic Amino Acids. ACS APPLIED MATERIALS & INTERFACES 2021; 13:36722-36736. [PMID: 34327979 DOI: 10.1021/acsami.1c04161] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Considering the relevance of accumulation and self-assembly of metabolites and aftermath of biological consequences, it is important to know whether they undergo coassembly and what properties the resultant hybrid higher-order structures would exhibit. This work reveals the inherent tendency of aromatic amino acids to undergo a spontaneous coassembly process under physiologically mimicked conditions, which yields neurotoxic hybrid nanofibers. Resultant hybrid nanostructures resembled the β-structured conformers stabilized by H-bonds and π-π stacking interactions, which were highly toxic to human neuroblastoma cells. The hybrid nanofibers also showed strong cross-seeding potential that triggered in vitro aggregation of diverse globular proteins and brain extract components, converting the native structures into cross-β-rich amyloid aggregates. The heterogenic nature of the hybrid nanofibers seems crucial for their higher toxicity and faster cross-seeding potential as compared to the homogeneous amino acid nanofibers. Our findings reveal the importance of aromaticity-driven optimized intermolecular arrangements for the coassembly of aromatic amino acids, and the results may provide important clues to the fundamental understanding of metabolite accumulation-related complications.
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Affiliation(s)
- Bibin Gnanadhason Anand
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Kailash Prasad Prajapati
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Masihuzzaman Ansari
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Deepak Kumar Yadav
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Mayur Temgire
- Department of Chemical Engineering, Indian Institution of Technology Bombay, Powai, Mumbai 400076, India
| | - Karunakar Kar
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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11
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Rehak P, Král P. Hybridization of Biomolecular Crystals and Low-Dimensional Materials. ACS NANO 2021; 15:6678-6683. [PMID: 33818078 DOI: 10.1021/acsnano.0c10027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In cellular environments, metabolites, peptides, proteins, and other biomolecules can self-assemble into planar and fibrilar molecular crystals. We use atomistic molecular dynamics simulations to show that such biomolecular crystals coupled with low-dimensional materials can form stable hybrid superstructures. We discuss enantiopure and racemic TRP and PHE amino acid crystals adsorbed on or intercalated between graphene, phosphorene, and carbon nanotubes. While racemic biomolecular crystals tend to stay straight in solutions and when adsorbed on flat and cylindrical nanosurfaces, enantiopure crystals undergo twisting. Mixed material properties of these hybrid superstructures can be attractive in many applications.
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Affiliation(s)
- Pavel Rehak
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Petr Král
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
- Departments of Physics, Pharmaceutical Sciences, and Chemical Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
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12
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Balasco N, Diaferia C, Morelli G, Vitagliano L, Accardo A. Amyloid-Like Aggregation in Diseases and Biomaterials: Osmosis of Structural Information. Front Bioeng Biotechnol 2021; 9:641372. [PMID: 33748087 PMCID: PMC7966729 DOI: 10.3389/fbioe.2021.641372] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/05/2021] [Indexed: 11/13/2022] Open
Abstract
The discovery that the polypeptide chain has a remarkable and intrinsic propensity to form amyloid-like aggregates endowed with an extraordinary stability is one of the most relevant breakthroughs of the last decades in both protein/peptide chemistry and structural biology. This observation has fundamental implications, as the formation of these assemblies is systematically associated with the insurgence of severe neurodegenerative diseases. Although the ability of proteins to form aggregates rich in cross-β structure has been highlighted by recent studies of structural biology, the determination of the underlying atomic models has required immense efforts and inventiveness. Interestingly, the progressive molecular and structural characterization of these assemblies has opened new perspectives in apparently unrelated fields. Indeed, the self-assembling through the cross-β structure has been exploited to generate innovative biomaterials endowed with promising mechanical and spectroscopic properties. Therefore, this structural motif has become the fil rouge connecting these diversified research areas. In the present review, we report a chronological recapitulation, also performing a survey of the structural content of the Protein Data Bank, of the milestones achieved over the years in the characterization of cross-β assemblies involved in the insurgence of neurodegenerative diseases. A particular emphasis is given to the very recent successful elucidation of amyloid-like aggregates characterized by remarkable molecular and structural complexities. We also review the state of the art of the structural characterization of cross-β based biomaterials by highlighting the benefits of the osmosis of information between these two research areas. Finally, we underline the new promising perspectives that recent successful characterizations of disease-related amyloid-like assemblies can open in the biomaterial field.
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Affiliation(s)
- Nicole Balasco
- Institute of Biostructures and Bioimaging (IBB), CNR, Naples, Italy
| | - Carlo Diaferia
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples “Federico II”, Naples, Italy
| | - Giancarlo Morelli
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples “Federico II”, Naples, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging (IBB), CNR, Naples, Italy
| | - Antonella Accardo
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples “Federico II”, Naples, Italy
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13
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Yamaguchi R, Tanaka R, Maetani M, Tabe H, Yamada Y. Efficient capturing of hydrogen peroxide in dilute aqueous solution by co-crystallization with amino acids. CrystEngComm 2021. [DOI: 10.1039/d1ce00688f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
X-ray structure analyses of co-crystals of H2O2 and l-Phe, dl-Phe, or dl-Asp prepared in a dilute aqueous solution (30 wt%) indicated that multi-layer motifs including water molecule is important for highly efficient H2O2 capture in dilute solutions.
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Affiliation(s)
- Ryota Yamaguchi
- Department of Applied Chemistry and Bioengineering, Graduate School of Engineering, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
| | - Rika Tanaka
- Department of Applied Chemistry and Bioengineering, Graduate School of Engineering, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
- Analytical Center of Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
| | - Mayu Maetani
- Department of Applied Chemistry and Bioengineering, Graduate School of Engineering, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
| | - Hiroyasu Tabe
- Department of Applied Chemistry and Bioengineering, Graduate School of Engineering, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
- Research Center for Artificial Photosynthesis (ReCAP), Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
| | - Yusuke Yamada
- Department of Applied Chemistry and Bioengineering, Graduate School of Engineering, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
- Research Center for Artificial Photosynthesis (ReCAP), Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
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14
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Banerjee P, Rajak K, Nandi PK, Pal S, Ghosh M, Mishra S, Sarkar N. Aging-Dependent Morphological Crystallinity Determines Membrane Activity of l-Phenylalanine Self-Assembles. J Phys Chem Lett 2020; 11:8585-8591. [PMID: 32931285 DOI: 10.1021/acs.jpclett.0c01831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Amyloid polymorphism has emerged as an important topic of research in recent years to identify the particular species responsible for several neurodegenerative disorders, whereas the concept is overlooked in the case of the simplest building block, that is, l-phenylalanine (l-Phe) self-assembly. Here, we report the first evidence of l-Phe polymorphism and the conversion of metastable helical fibrillar to thermodynamically stable rodlike crystalline morphologies with increasing time and temperature. Furthermore, only the fibrillar l-Phe polymorph shows a significant modulation of the model membrane. In addition, the l-Phe molecules prefer to arrange in a multilayered rodlike fashion than in a lateral arrangement, which reduces the membrane binding ability of the l-Phe polymorph due to the decrease in the partial charge of the N-terminal of l-Phe units. The present work exemplifies a different approach to understanding l-Phe self-assembly and provides an effective strategy for the therapy of phenylketonuria by scrutinizing the discrete membrane activity of different l-Phe polymorphs.
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Affiliation(s)
- Pavel Banerjee
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, WB, India
| | - Karunamoy Rajak
- Centre for Theoretical Studies, Indian Institute of Technology Kharagpur, Kharagpur 721302, WB, India
| | - Pratyush Kiran Nandi
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, WB, India
| | - Siddhartha Pal
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, WB, India
| | - Meghna Ghosh
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, WB, India
| | - Sabyashachi Mishra
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, WB, India
- Centre for Computational and Data Sciences, Indian Institute of Technology Kharagpur, Kharagpur 721302, WB, India
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, WB, India
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15
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Ke PC, Zhou R, Serpell LC, Riek R, Knowles TPJ, Lashuel HA, Gazit E, Hamley IW, Davis TP, Fändrich M, Otzen DE, Chapman MR, Dobson CM, Eisenberg DS, Mezzenga R. Half a century of amyloids: past, present and future. Chem Soc Rev 2020; 49:5473-5509. [PMID: 32632432 PMCID: PMC7445747 DOI: 10.1039/c9cs00199a] [Citation(s) in RCA: 290] [Impact Index Per Article: 72.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Amyloid diseases are global epidemics with profound health, social and economic implications and yet remain without a cure. This dire situation calls for research into the origin and pathological manifestations of amyloidosis to stimulate continued development of new therapeutics. In basic science and engineering, the cross-β architecture has been a constant thread underlying the structural characteristics of pathological and functional amyloids, and realizing that amyloid structures can be both pathological and functional in nature has fuelled innovations in artificial amyloids, whose use today ranges from water purification to 3D printing. At the conclusion of a half century since Eanes and Glenner's seminal study of amyloids in humans, this review commemorates the occasion by documenting the major milestones in amyloid research to date, from the perspectives of structural biology, biophysics, medicine, microbiology, engineering and nanotechnology. We also discuss new challenges and opportunities to drive this interdisciplinary field moving forward.
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Affiliation(s)
- Pu Chun Ke
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Zhongshan Hospital, Fudan University, 111 Yixueyuan Rd, Xuhui District, Shanghai, China
| | - Ruhong Zhou
- Institute of Quantitative Biology, Zhejiang University, Hangzhou 310058, China; Department of Chemistry, Columbia University, New York, New York, 10027, USA
| | - Louise C. Serpell
- School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK
| | - Roland Riek
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Wolfgang-Pauli-Str. 10, 8093 Zurich, Switzerland
| | - Tuomas P. J. Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Cavendish Laboratory, University of Cambridge, J J Thomson Avenue, CB3 0HE, Cambridge, UK
| | - Hilal A. Lashuel
- Laboratory of Molecular Neurobiology and Neuroproteomics, Brain Mind Institute, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences; Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Ian W. Hamley
- School of Chemistry, Food Biosciences and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - Thomas P. Davis
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane Qld 4072, Australia
| | - Marcus Fändrich
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany
| | - Daniel Erik Otzen
- Department of Molecular Biology, Center for Insoluble Protein Structures (inSPIN), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Matthew R. Chapman
- Department of Molecular, Cellular and Developmental Biology, Centre for Microbial Research, University of Michigan, Ann Arbor, MI 48109-1048, USA
| | - Christopher M. Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - David S. Eisenberg
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute and Howard Hughes Medical Institute, UCLA, Los Angeles, CA, USA
| | - Raffaele Mezzenga
- Department of Health Science & Technology, ETH Zurich, Schmelzbergstrasse 9, LFO, E23, 8092 Zurich, Switzerland
- Department of Materials, ETH Zurich, Wolfgang Pauli Strasse 10, 8093 Zurich, Switzerland
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16
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Singh P, Misra S, Sepay N, Mondal S, Ray D, Aswal VK, Nanda J. Self-assembling behaviour of a modified aromatic amino acid in competitive medium. SOFT MATTER 2020; 16:6599-6607. [PMID: 32608458 DOI: 10.1039/d0sm00584c] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Aromatic amino acid, specifically phenylalanine (Phe), is one of the most studied building blocks in peptide synthesis due to its importance in biology. It is reported in the literature that Phe-containing peptides have a high tendency to form different self-assembled materials due to efficient aromatic-aromatic interactions. In this article, we have tuned the supramolecular interactions of phenylalanine by making it electron-deficient upon introduction of the nitro group in the ring. The presence of the nitro group has a profound influence on the self-assembly process. It has been observed that 4-nitrophenylalanine (4NP) is a highly efficient gelator compared with the native phenylalanine in DMSO solvent in terms of minimum gelation concentration and it forms hydrogen bonding mediated crystals in water. The change of self-assembling patterns of 4NP in these solvents was studied using X-ray diffraction, UV-Vis spectroscopy, FE-SEM and other techniques. With the help of different experimental data and density functional theory (DFT), we have simulated the theoretical structure of 4NP in DMSO. The theoretical structure of 4NP in DMSO is different compared with that of crystals in water. We then studied the self-assembly process of 4NP in the mixed solvent of DMSO (polar aprotic) and water (polar protic). Different competitive non-covalent interactions of solvents as well as the ratio of the solvent mixture guide the final self-assembly state of 4NP.
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Affiliation(s)
- Pijush Singh
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur, P.O. Botanic Garden, Howrah-711103, West Bengal, India.
| | - Souvik Misra
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur, P.O. Botanic Garden, Howrah-711103, West Bengal, India.
| | - Nayim Sepay
- Department of Chemistry, Jadavpur University, Jadavpur, Kolkata-700032, India
| | - Sanjoy Mondal
- Polymer Science Unit, Indian association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Debes Ray
- Solid State Physics Division, Bhabha Atomic Research Centre Trombay, Mumbai, 400085, India
| | - Vinod K Aswal
- Solid State Physics Division, Bhabha Atomic Research Centre Trombay, Mumbai, 400085, India
| | - Jayanta Nanda
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur, P.O. Botanic Garden, Howrah-711103, West Bengal, India.
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17
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Gupta S, Singh I, Sharma AK, Kumar P. Ultrashort Peptide Self-Assembly: Front-Runners to Transport Drug and Gene Cargos. Front Bioeng Biotechnol 2020; 8:504. [PMID: 32548101 PMCID: PMC7273840 DOI: 10.3389/fbioe.2020.00504] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/29/2020] [Indexed: 12/18/2022] Open
Abstract
The translational therapies to promote interaction between cell and signal come with stringent eligibility criteria. The chemically defined, hierarchically organized, and simpler yet blessed with robust intermolecular association, the peptides, are privileged to make the cut-off for sensing the cell-signal for biologics delivery and tissue engineering. The signature service and insoluble network formation of the peptide self-assemblies as hydrogels have drawn a spell of research activity among the scientists all around the globe in the past decades. The therapeutic peptide market players are anticipating promising growth opportunities due to the ample technological advancements in this field. The presence of the other organic moieties, enzyme substrates and well-established protecting groups like Fmoc and Boc etc., bring the best of both worlds. Since the large sequences of peptides severely limit the purification and their isolation, this article reviews the account of last 5 years' efforts on novel approaches for formulation and development of single molecule amino acids, ultra-short peptide self-assemblies (di- and tri- peptides only) and their derivatives as drug/gene carriers and tissue-engineering systems.
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Affiliation(s)
- Seema Gupta
- Chemistry Department, Acharya Narendra Dev College, University of Delhi, New Delhi, India
| | - Indu Singh
- Chemistry Department, Acharya Narendra Dev College, University of Delhi, New Delhi, India
- Nucleic Acids Research Laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Ashwani K. Sharma
- Nucleic Acids Research Laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Pradeep Kumar
- Nucleic Acids Research Laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
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18
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Banerjee P, Pyne A, Sarkar N. Understanding the Self-Assembling Behavior of Biological Building Block Molecules: A Spectroscopic and Microscopic Approach. J Phys Chem B 2020; 124:2065-2080. [PMID: 32081003 DOI: 10.1021/acs.jpcb.9b09123] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
"Mother nature" utilizes molecular self-assembly as an efficient tool to design several fascinating supramolecular architectures from simple building blocks like amino acids, peptides, and nucleobases. The self-assembling behavior of various biologically important molecules, morphological outcomes, molecular mechanism of association, and finally their applications in the real world draw broad interest from chemical and biological point of views. In this present Feature Article, the amyloid hypothesis is extended to include nonproteinaceous single metabolites that invoke a new paradigm for the pathology of inborn metabolic disorders. In this scenario, we dedicate this paper to understanding the morphological consequences and mechanistic insight of the self-assembly of some important amino acids (e.g., l-phenylalanine, l-tyrosine, glycine, etc.) and nucleobases (adenine and eight uracil moiety derivatives). Using proper spectroscopic and microscopic tools, distinct assembling mechanisms of different amino acids and nucleobases have been established. Again, lanthanides, polyphenolic compounds such as crown ethers, and a worldwide drink, beer, are elegantly employed as inhibitors of the resulting fibrillar aggregated structures. As a consequence, this study will cover literally a vast region in the self-assembling outcomes of single biologically important molecules, and therefore, we expect that a detailed understanding of such morphological outcomes using spectroscopic and microscopic approaches may open a new paradigm in this burgeoning field.
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Affiliation(s)
- Pavel Banerjee
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302 WB, India
| | - Arghajit Pyne
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302 WB, India
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302 WB, India
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19
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Pérez-Mellor A, Le Barbu-Debus K, Zehnacker A. Solid-state synthesis of cyclo LD-diphenylalanine: A chiral phase built from achiral subunits. Chirality 2020; 32:693-703. [PMID: 32078197 DOI: 10.1002/chir.23195] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 12/21/2022]
Abstract
The solid-state structure of LL/DD or LD/DL diphenylalanine diluted in KBr pellets is studied by infrared (IR) absorption and vibrational circular dichroism (VCD) spectroscopy. The structure depends on the absolute configuration of the residues. The natural LL diphenylalanine exists as a mixture of neutral and zwitterionic structures, depending on the humidity of the sample, while mostly the zwitterion is observed for LD diphenylalanine whatever the experimental conditions. The system undergoes spontaneous cyclization upon heating at 125°C, resulting to the formation of a diketopiperazine (DKP) dipeptide as the only product. The reaction is faster for LD than for LL diphenylalanine. As expected, LL and DD diphenylalanine react to form the LL and DD enantiomers of cyclo diphenylalanine. Interestingly, the DKP dipeptides formed from the LD or DL diphenylalanine show unexpected optical activity, with opposite VCD spectra for the products formed from the LD and DL reagents. This is explained in terms of chirality synchronization between the monomers within the crystal, which retain the symmetry of the reagent, resulting to the formation of a new chiral phase made from transiently chiral molecules.
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Affiliation(s)
- Ariel Pérez-Mellor
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, University Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Katia Le Barbu-Debus
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, University Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, University Paris-Sud, Université Paris-Saclay, Orsay, France
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20
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Makam P, Yamijala SSRKC, Tao K, Shimon LJW, Eisenberg DS, Sawaya MR, Wong BM, Gazit E. Non-proteinaceous hydrolase comprised of a phenylalanine metallo-supramolecular amyloid-like structure. Nat Catal 2019; 2:977-985. [PMID: 31742246 PMCID: PMC6861134 DOI: 10.1038/s41929-019-0348-x] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 08/09/2019] [Indexed: 12/20/2022]
Abstract
Enzymatic activity is crucial for various technological applications, yet the complex structures and limited stability of enzymes often hinder their use. Hence, de novo design of robust biocatalysts that are much simpler than their natural counterparts and possess enhanced catalytic activity has long been a goal in biotechnology. Here, we present evidence for the ability of a single amino acid to self-assemble into a potent and stable catalytic structural entity. Spontaneously, phenylalanine (F) molecules coordinate with zinc ions to form a robust, layered, supramolecular amyloid-like ordered architecture (F-Zn(ii)) and exhibit remarkable carbonic anhydrase-like catalytic activity. Notably, amongst the reported artificial biomolecular hydrolases, F-Zn(ii) displays the lowest molecular mass and highest catalytic efficiency, in addition to reusability, thermal stability, substrate specificity, stereoselectivity and rapid catalytic CO2 hydration ability. Thus, this report provides a rational path towards future de novo design of minimalistic biocatalysts for biotechnological and industrial applications.
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Affiliation(s)
- Pandeeswar Makam
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | | | - Kai Tao
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Linda J. W. Shimon
- Chemical Research Support, The Weizmann Institute of Science, Rehovot, Israel
| | - David S. Eisenberg
- Department of Biological Chemistry and Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, UCLA–DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA, USA
| | - Michael R. Sawaya
- Department of Biological Chemistry and Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, UCLA–DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA, USA
| | - Bryan M. Wong
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
- Department of Physics and Astronomy, and Materials Science and Engineering Program, University of California, Riverside, CA, USA
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel
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21
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Anand BG, Prajapati KP, Dubey K, Ahamad N, Shekhawat DS, Rath PC, Joseph GK, Kar K. Self-Assembly of Artificial Sweetener Aspartame Yields Amyloid-like Cytotoxic Nanostructures. ACS NANO 2019; 13:6033-6049. [PMID: 31021591 DOI: 10.1021/acsnano.9b02284] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Recent reports have revealed the intrinsic propensity of single aromatic metabolites to undergo self-assembly and form nanostructures of amyloid nature. Hence, identifying whether aspartame, a universally consumed artificial sweetener, is inherently aggregation prone becomes an important area of investigation. Although the reports on aspartame-linked side effects describe a multitude of metabolic disorders, the mechanistic understanding of such destructive effects is largely mysterious. Since aromaticity, an aggregation-promoting factor, is intrinsic to aspartame's chemistry, it is important to know whether aspartame can undergo self-association and if such a property can predispose any cytotoxicity to biological systems. Our study finds that aspartame molecules, under mimicked physiological conditions, undergo a spontaneous self-assembly process yielding regular β-sheet-like cytotoxic nanofibrils of amyloid nature. The resultant aspartame fibrils were found to trigger amyloid cross-seeding and become a toxic aggregation trap for globular proteins, Aβ peptides, and aromatic metabolites that convert native structures to β-sheet-like fibrils. Aspartame fibrils were also found to induce hemolysis, causing DNA damage resulting in both apoptosis and necrosis-mediated cell death. Specific spatial arrangement between aspartame molecules is predicted to form a regular amyloid-like architecture with a sticky exterior that is capable of promoting viable H-bonds, electrostatic interactions, and hydrophobic contacts with biomolecules, leading to the onset of protein aggregation and cell death. Results reveal that the aspartame molecule is inherently amyloidogenic, and the self-assembly of aspartame becomes a toxic trap for proteins and cells, exposing the bitter side of such a ubiquitously used artificial sweetener.
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Affiliation(s)
- Bibin Gnanadhason Anand
- Department of Bioscience and Bioengineering , Indian Institute of Technology Jodhpur , Jodhpur 342037 , India
| | | | - Kriti Dubey
- School of Life Sciences , Jawaharlal Nehru University , New Delhi 110067 , India
| | - Naseem Ahamad
- School of Life Sciences , Jawaharlal Nehru University , New Delhi 110067 , India
| | - Dolat Singh Shekhawat
- Department of Bioscience and Bioengineering , Indian Institute of Technology Jodhpur , Jodhpur 342037 , India
| | - Pramod Chandra Rath
- School of Life Sciences , Jawaharlal Nehru University , New Delhi 110067 , India
| | - George Kodimattam Joseph
- Department of Bioscience and Bioengineering , Indian Institute of Technology Jodhpur , Jodhpur 342037 , India
| | - Karunakar Kar
- School of Life Sciences , Jawaharlal Nehru University , New Delhi 110067 , India
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22
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Cuppen HM, Smets MMH, Krieger AM, van den Ende JA, Meekes H, van Eck ERH, Görbitz CH. The Rich Solid-State Phase Behavior of l-Phenylalanine: Disappearing Polymorphs and High Temperature Forms. CRYSTAL GROWTH & DESIGN 2019; 19:1709-1719. [PMID: 30872978 PMCID: PMC6410616 DOI: 10.1021/acs.cgd.8b01655] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/13/2018] [Indexed: 06/02/2023]
Abstract
After years of controversy over the solid state structure of the essential amino acid l-phenylalanine, four different polymorphic forms were published recently. The common form I has symmetry P21 with four molecules in the asymmetric unit (Z' = 4), similar to form III, but with a different arrangement of molecular bilayers. Form II, obtained from the hydrate at very low humidity, is unrelated to forms I and III, as is the high-density form IV. The present investigation demonstrates that this prototype aromatic amino acid has two additional high-temperature phases Ih and IIIh obtained from form I and form III above 458 and 440 K, respectively, when flipping between two alternative side-chain conformations becomes dynamic and causes pairs of molecules, initially crystallographically independent, to become equivalent above a sharp transition temperature. These abrupt and reversible phase changes occur with a reduction of Z' from 4 (low T) to 2 (high T) and modified crystal symmetry. We furthermore experienced an example of disappearing polymorph for form I which after growing form III in one of our laboratories could no longer be crystallized at room temperature. In contrast, form III crystals may be irreversibly converted to form I crystals as a result of sliding of molecular bilayers in the crystal at elevated temperature. No conversions between the high-temperature forms Ih and IIIh were found. The remarkable crystallographic results are here corroborated by Molecular Dynamics and metadynamics simulations of the form I - form III system.
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Affiliation(s)
- Herma M. Cuppen
- Radboud
University Nijmegen, Institute for Molecules
and Materials, Heyendaalseweg
135, 6525 AJ Nijmegen, The Netherlands
| | - Mireille M. H. Smets
- Radboud
University Nijmegen, Institute for Molecules
and Materials, Heyendaalseweg
135, 6525 AJ Nijmegen, The Netherlands
| | - Annika M. Krieger
- Radboud
University Nijmegen, Institute for Molecules
and Materials, Heyendaalseweg
135, 6525 AJ Nijmegen, The Netherlands
| | - Joost A. van den Ende
- Radboud
University Nijmegen, Institute for Molecules
and Materials, Heyendaalseweg
135, 6525 AJ Nijmegen, The Netherlands
| | - Hugo Meekes
- Radboud
University Nijmegen, Institute for Molecules
and Materials, Heyendaalseweg
135, 6525 AJ Nijmegen, The Netherlands
| | - Ernst R. H. van Eck
- Radboud
University Nijmegen, Institute for Molecules
and Materials, Heyendaalseweg
135, 6525 AJ Nijmegen, The Netherlands
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23
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Ziaunys M, Smirnovas V. Emergence of visible light optical properties of L-phenylalanine aggregates. PeerJ 2019; 7:e6518. [PMID: 30828498 PMCID: PMC6394350 DOI: 10.7717/peerj.6518] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 01/26/2019] [Indexed: 01/09/2023] Open
Abstract
The ability of phenylalanine to form fibrillar nanostructures was demonstrated on multiple occasions, and such an oligomerization reaction could be the cause of cytotoxicity in patients with phenylketonuria. These findings were supported by claims that L-phenylalanine (Phe) fibrils have amyloid properties and can be detected using thioflavin T fluorescence assay. However, a part of Phe aggregation studies reported the opposite data, suggesting no amyloid structures to be formed. Due to the contradicting reports, the amyloid nature of Phe aggregates remains uncertain. In this work we tested Phe aggregation under conditions where amyloid formation was previously reported. We show the emergence of Phe aggregates with visible light optical properties that overlap with the spectra of dyes used in amyloid fibril assays, which could lead to false-positive identifications.
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Affiliation(s)
- Mantas Ziaunys
- Vilnius University, Life Sciences Center, Institute of Biotechnology, Vilnius, Lithuania
| | - Vytautas Smirnovas
- Vilnius University, Life Sciences Center, Institute of Biotechnology, Vilnius, Lithuania
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24
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Hess D, Mayer P. The crystal structures of benzylammonium phenylacetate and its hydrate. Acta Crystallogr E Crystallogr Commun 2019; 75:194-201. [PMID: 30800450 PMCID: PMC6362638 DOI: 10.1107/s2056989019000288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 01/07/2019] [Indexed: 11/10/2022]
Abstract
The crystal packing of benzylammonium phenylacetate (1) and its hydrate (2) is governed by hydrogen bonds formed between the ammonium and acetate groups and the water molecule of crystallization (in 2 only). The benzyl moieties for hydrophobic layers with the aromatic rings adopting edge-to-face arrangements. The title compounds benzylammonium phenylacetate, C7H10N+·C8H7O2− (1), and its monohydrate, C7H10N+·C8H7O2−·H2O (2), can be obtained by evaporating methanolic solutions containing equimolar amounts of benzylamine and phenylacetic acid in the absence and presence of water, respectively. N—H⋯O hydrogen bonds in the crystal structure of 1 lead to the formation of hydrophilic channels running along the b-axis direction. The hydrogen-bonding system is best described by fused R34(10) ring patterns, often observed in ammonium carboxylate salts. In 2, the presence of the crystal water leads to the formation of a two-dimensional hydrogen-bonding network. The benzyl moieties in 1 and 2 form hydrophobic layers in the crystal structures with the aromatic rings adopting edge-to-face arrangements.
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25
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Pal S, Banerjee P, Mondal D, Sarkar N. Light-induced morphological transition between unconjugated bilirubin photoisomers. SOFT MATTER 2018; 14:8325-8332. [PMID: 30289141 DOI: 10.1039/c8sm01801d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Morphology switching by an external stimulus creates the possibility to detect and control the activity and functionality of bio-molecules. Unconjugated bilirubin (UCB), a waste product resulting from heme catabolism, is highly sensitive towards blue light induced configurational conversion from (4Z,15Z) to (4Z,15E)-bilirubin. UCB has a distinct elongated nanostructure which is readily photoswitchable to spherical by external blue light (470 nm) irradiation. Herein, the morphology alteration by blue light was nicely correlated with the photoisomerisation of UCB, using different microscopic and spectroscopic techniques. To restrict the other photo-incidents during phototreatment on UCB, a suitable time frame was calibrated by monitoring the absorption, HPLC, lifetime distribution and 1H NMR studies. Furthermore, by the help of this morphological transition as a marker, UCB early stage photoisomerisation has also been triggered by two-photon irradiation (940 nm).
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Affiliation(s)
- Siddhartha Pal
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, West Bengal, India.
| | - Pavel Banerjee
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, West Bengal, India.
| | - Dipankar Mondal
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, West Bengal, India.
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, West Bengal, India.
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Kundu N, Banik D, Sarkar N. Self-Assembly of Amphiphiles into Vesicles and Fibrils: Investigation of Structure and Dynamics Using Spectroscopy and Microscopy Techniques. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:11637-11654. [PMID: 29544249 DOI: 10.1021/acs.langmuir.7b04355] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Amphiphiles are a class of molecules which are known to assemble into a variety of nanostructures. The understanding and applications of self-assembled systems are based on what has been learned from biology. Among the vast number of self-assemblies, in this article, we have described the formation, characterization, and dynamics of two important biologically inspired assemblies: vesicles and fibrils. Vesicles, which can be classified into several categories depending on the sizes and components, are of great interest due to their potential applications in drug delivery and as nanoscale reactors. The structure and dynamics of vesicles can also mimic the complex geometry of the cell membrane. On the other hand, the self-assembly of proteins, peptides, and even single amino acids leads to a number of degenerative disorders. Thus, a complete understanding of these self-assembled systems is necessary. In this article, we discuss recent work on vesicular aggregates composed of phospholipids, fatty acids, and ionic as well as nonionic surfactants and single amino acid-based fibrils such as phenylalanine and tyrosine. Beside the characterization, we also emphasize the excited-state dynamics inside the aggregates for a proper understanding of the organization, reactivity, and heterogeneity of the aggregates.
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Affiliation(s)
- Niloy Kundu
- Department of Chemistry , Indian Institute of Technology , Kharagpur 721302 , WB India
| | - Debasis Banik
- Department of Chemistry , Indian Institute of Technology , Kharagpur 721302 , WB India
| | - Nilmoni Sarkar
- Department of Chemistry , Indian Institute of Technology , Kharagpur 721302 , WB India
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Bera S, Mondal S, Rencus-Lazar S, Gazit E. Organization of Amino Acids into Layered Supramolecular Secondary Structures. Acc Chem Res 2018; 51:2187-2197. [PMID: 30095247 DOI: 10.1021/acs.accounts.8b00131] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The unique physiochemical properties and multiscale organization of layered materials draw the attention of researchers across a wide range of scientific disciplines. Layered structures are commonly found in diverse biological systems where they fulfill various functions. A prominent example of layered biological materials is the organization of proteins and polypeptides into the archetypal aggregated amyloidal structures. While the organization of proteins into amyloid structures was initially associated with various degenerative disorders, it was later revealed that proteins not related to any disease could also form identical layered assemblies. Thus, it appears that the ability of peptides and proteins to produce amyloid-like aggregates represents a generic property of polyamides to assemble into higher order fibrillar structures. In the aggregated state, the peptide backbone forms β-sheet structures which are further organized into layered arrangements. We have recently extended the identified amyloidogenic building blocks to include not only peptides or proteins, but also single amino acids and other metabolites. High resolution spectroscopy and crystallography analyses confirm the clear potential of amino acids and other metabolites to form layered amyloid-like aggregates showing biophysical and biochemical properties similar to protein amyloids. Therefore, the generic propensity of peptides and proteins backbones to assemble into layered organizations may emanate from their basic building block, the amino acid. In this Account, we aim to introduce the concept of supramolecular β-sheet organization of single amino acids and to present an analysis of their layered-structure organization based on single crystal structures. We demonstrate that, despite the different side-chains that considerably vary in their chemical properties, all coded amino acids display a layer-like assembly stabilized by α-amine to α-carboxyl H-bonds, resembling supramolecular β-sheet structures, while the side-chains determine the higher order organization of the layers. Our work presents the first analysis of the β-sheet propensity of single amino acids in their unbound form, indicating an evolutionary predisposition. We classify the amino acids β-sheet propensity on the basis of the interlayer separation distance in the crystal packing, which correlates well with previously reported classifications based on various criteria, such as hydrophobicity, steric bulkiness, and folding. In addition, we demonstrate that the relative direction of α-amine to α-carboxyl H-bonding pattern provides critical insights regarding the stabilization of parallel versus antiparallel β-sheet structures by the various amino acids. Taken together, our analysis of amino acid crystals provides substantial information regarding protein folding and dynamics and could serve as basic rules set for the design of potential building blocks for molecular self-assembly to produce functional materials of tunable properties, an important objective of bottom-up nanotechnology.
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Affiliation(s)
- Santu Bera
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Sudipta Mondal
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Sigal Rencus-Lazar
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
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28
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Au ion-mediated self-assembled tyrosine-rich peptide nanostructure embedded with gold nanoparticle satellites. J IND ENG CHEM 2018. [DOI: 10.1016/j.jiec.2018.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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29
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Chakraborty P, Gazit E. Amino Acid Based Self-assembled Nanostructures: Complex Structures from Remarkably Simple Building Blocks. CHEMNANOMAT : CHEMISTRY OF NANOMATERIALS FOR ENERGY, BIOLOGY AND MORE 2018; 4:730-740. [PMID: 30713827 PMCID: PMC6352958 DOI: 10.1002/cnma.201800147] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Amino acids are the simplest biological building blocks capable of forming discreet nanostructures by supramolecular self-assembly. The understanding of the process of organization of amino acid nanostructures is of fundamental importance for the study of metabolic diseases as well as for materials science applications. Although peptide self-assembled structures have been the topic of many review articles, much less attention has been devoted to the ability of amino acid building blocks, both natural and synthetic, to form ordered assemblies with defined architectures and notable physical properties, by the process of self-association. Herein, we try to shed light on amino acid based nanostructures, their fabrication and implications. We discuss self-assembled nanostructures, including hydrogels with nanoscale order, obtained from both modified and unmodified single amino acids. We also envision some future prospects in this emerging field.
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Affiliation(s)
- Priyadarshi Chakraborty
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
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30
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Self-assembling behavior of pyrimidine analogues: Unveiling the factors behind morphological diversity. J Colloid Interface Sci 2018; 522:63-73. [DOI: 10.1016/j.jcis.2018.03.058] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/15/2018] [Accepted: 03/16/2018] [Indexed: 11/22/2022]
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31
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Differential inhibition of metabolite amyloid formation by generic fibrillation-modifying polyphenols. Commun Chem 2018. [DOI: 10.1038/s42004-018-0025-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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32
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Sögütoglu LC, Lutz M, Meekes H, de Gelder R, Vlieg E. Polymorphism and Modulation of Para-Substituted l-Phenylalanine. CRYSTAL GROWTH & DESIGN 2017; 17:6231-6238. [PMID: 29234239 PMCID: PMC5721337 DOI: 10.1021/acs.cgd.7b00747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 09/21/2017] [Indexed: 06/07/2023]
Abstract
The crystal structure of para-methyl-l-phenylalanine at 230 K resembles that of the para-fluorinated analogue from the literature but is commensurately modulated with seven molecules in the asymmetric unit (Z' = 7). At 100 K, the superstructure loses its modulation, leading to a unit cell with Z' = 1, with clear disorder in the phenyl ring orientations. The methyl-substituent in para-methyl-l-phenylalanine has, in contrast to fluorine, no polar interactions with protons of neighboring molecules, which might allow for the well-defined modulation of the crystal structure at 230 K.
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Affiliation(s)
- Leyla-Cann Sögütoglu
- Radboud
University, Institute for Molecules and
Materials, Heyendaalseweg
135, 6525 AJ, Nijmegen, The Netherlands
| | - Martin Lutz
- Crystal
and Structural Chemistry, Bijvoet Center for Biomolecular Research,
Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Hugo Meekes
- Radboud
University, Institute for Molecules and
Materials, Heyendaalseweg
135, 6525 AJ, Nijmegen, The Netherlands
| | - René de Gelder
- Radboud
University, Institute for Molecules and
Materials, Heyendaalseweg
135, 6525 AJ, Nijmegen, The Netherlands
| | - Elias Vlieg
- Radboud
University, Institute for Molecules and
Materials, Heyendaalseweg
135, 6525 AJ, Nijmegen, The Netherlands
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33
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He T, Misuraca JC, Musah RA. "Carboranyl-cysteine"-Synthesis, Structure and Self-Assembly Behavior of a Novel α-Amino Acid. Sci Rep 2017; 7:16995. [PMID: 29209068 PMCID: PMC5717241 DOI: 10.1038/s41598-017-16926-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/20/2017] [Indexed: 11/09/2022] Open
Abstract
Substitution of the thiol proton in cysteine with m-carborane furnished 2-amino-3-(1,7-dicarba-closo-dodecacarboranyl-1-thio)propanoic acid (3), a boron cluster amino acid that exhibits self-assembly to form micron-sized constructs. Field emission scanning electron microscopy revealed that ethanol solutions of 3 form floret-shaped constructs, while fibrillar architectures are formed in water. Furthermore, slow evaporation of methanol solutions of 3 produced crystals whose structure was revealed by X-ray crystallography. The crystal structure shows that the hydrogen bonding interactions between pairs of 3 result in the formation of bilayers of 174 Å in length. The orientation of the clusters is not random in the crystal structure, such that the side-by-side aligned polyhedra are offset by 158 degrees. The material was characterized by FT-IR, NMR, high resolution mass spectrometry and dynamic light scattering. Circular dichroism studies indicated that self-assembly occurs at concentrations as low as 0.01 μM. This represents the first demonstration of self-assembly of a carborane-based molecule in the absence of metals. The amino acid motif provides opportunities for the controlled synthesis of extended multimeric units with tunable properties and the potential for applications in biology, medicine and materials chemistry.
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Affiliation(s)
- Tianyu He
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | | | - Rabi A Musah
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA.
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34
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Banik D, Banerjee P, Sabeehuddin G, Sarkar N. Effects of a common worldwide drink (Beer) on l-Phenylalanine and l-Tyrosine fibrillar assemblies. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.08.066] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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35
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Intrinsic property of phenylalanine to trigger protein aggregation and hemolysis has a direct relevance to phenylketonuria. Sci Rep 2017; 7:11146. [PMID: 28894147 PMCID: PMC5593866 DOI: 10.1038/s41598-017-10911-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/15/2017] [Indexed: 01/31/2023] Open
Abstract
Excess accumulation of phenylalanine is the characteristic of untreated Phenylketonuria (PKU), a well-known genetic abnormality, which triggers several neurological, physical and developmental severities. However, the fundamental mechanism behind the origin of such diverse health problems, particularly the issue of how they are related to the build-up of phenylalanine molecules in the body, is largely unknown. Here, we show cross-seeding ability of phenylalanine fibrils that can effectively initiate an aggregation process in proteins under physiological conditions, converting native protein structures to β-sheet assembly. The resultant fibrils were found to cause severe hemolysis, yielding a plethora of deformed erythrocytes that is highly relevant to phenylketonuria. Unique arrangement of zwitterionic phenylalanine molecules in their amyloid-like higher order entities is predicted to promote both hydrophobic and electrostatic interaction, sufficient enough to trap proteins and to preferentially interact with the membrane components of RBCs. Since the prevalence of hemolysis and amyloid related psychoneurological severities are mostly observed in PKU patients, we propose that the inherent property of phenylalanine fibrils to trigger hemolysis and to induce protein aggregation may have direct relevance to the disease mechanism of PKU.
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36
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Ramalhete SM, Foster JS, Green HR, Nartowski KP, Heinrich M, Martin PC, Khimyak YZ, Lloyd GO. Halogen effects on the solid-state packing of phenylalanine derivatives and the resultant gelation properties. Faraday Discuss 2017; 203:423-439. [DOI: 10.1039/c7fd00108h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Phenylalanine is an important amino acid both biologically, essential to human health, and industrially, as a building block of artificial sweeteners. Our interest in this particular amino acid and its derivatives lies with its ability to form gels in a number of solvents. We present here the studies of the influence of halogen addition to the aromatic ring on the gelation properties and we analyse the crystal structures of a number of these materials to elucidate the trends in their behaviour based on the halogen addition to the aromatic group and the interactions that result.
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Affiliation(s)
| | - Jamie S. Foster
- Institute of Chemical Sciences
- School of Engineering and Physical Sciences
- Heriot-Watt University
- Edinburgh
- UK
| | - Hayley R. Green
- Institute of Chemical Sciences
- School of Engineering and Physical Sciences
- Heriot-Watt University
- Edinburgh
- UK
| | - Karol P. Nartowski
- School of Pharmacy
- University of East Anglia
- Norwich
- UK
- Department of Drug Form Technology
| | - Margaux Heinrich
- Institute of Chemical Sciences
- School of Engineering and Physical Sciences
- Heriot-Watt University
- Edinburgh
- UK
| | | | | | - Gareth O. Lloyd
- Institute of Chemical Sciences
- School of Engineering and Physical Sciences
- Heriot-Watt University
- Edinburgh
- UK
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37
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Shaham-Niv S, Rehak P, Vuković L, Adler-Abramovich L, Král P, Gazit E. Formation of Apoptosis-Inducing Amyloid Fibrils by Tryptophan. Isr J Chem 2016. [DOI: 10.1002/ijch.201600076] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Shira Shaham-Niv
- Department of Molecular Microbiology and Biotechnology; George S. Wise Faculty of Life Sciences; Tel Aviv University; Tel Aviv 69978 Israel
| | - Pavel Rehak
- Department of Chemistry; University of Illinois at Chicago; Chicago USA
| | - Lela Vuković
- Department of Chemistry; University of Texas at El Paso; El Paso USA
| | - Lihi Adler-Abramovich
- Department of Oral Biology; The Goldschleger School of Dental Medicine; Tel Aviv University; Tel Aviv 69978 Israel
| | - Petr Král
- Department of Chemistry; University of Illinois at Chicago; Chicago USA
- Department of Physics; University of Illinois at Chicago; Chicago USA
- Department of Biopharmaceutical Sciences; University of Illinois at Chicago; Chicago USA
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology; George S. Wise Faculty of Life Sciences; Tel Aviv University; Tel Aviv 69978 Israel
- Department of Materials Science and Engineering; Iby and Aladar Fleischman Faculty of Engineering; Tel Aviv University; Tel Aviv 69978 Israel
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38
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Lee M, Kwon J, Na S. Mechanical behavior comparison of spider and silkworm silks using molecular dynamics at atomic scale. Phys Chem Chem Phys 2016; 18:4814-21. [PMID: 26806791 DOI: 10.1039/c5cp06809f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Spider and silkworm silk proteins have received much attention owing to their inherent structural stability, biodegradability, and biocompatibility. These silk protein materials have various mechanical characteristics such as elastic modulus, ultimate strength and fracture toughness. While the considerable mechanical characteristics of the core crystalline regions of spider silk proteins at the atomistic scale have been investigated through several experimental techniques and computational studies, there is a lack of comparison between spider and silkworm fibroins in the atomistic scale. In this study, we investigated the differences between the mechanical characteristics of spider and silkworm fibroin structures by applying molecular dynamics and steered molecular dynamics. We found that serine amino acids in silkworm fibroins not only increased the number of hydrogen bonds, but also altered their structural characteristics and mechanical properties.
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Affiliation(s)
- Myeongsang Lee
- Department of Mechanical Engineering Korea University, Seoul 02841, Republic of Korea.
| | - Junpyo Kwon
- Department of Mechanical Engineering Korea University, Seoul 02841, Republic of Korea.
| | - Sungsoo Na
- Department of Mechanical Engineering Korea University, Seoul 02841, Republic of Korea.
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39
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Görbitz CH, Karen P, Dušek M, Petříček V. An exceptional series of phase transitions in hydrophobic amino acids with linear side chains. IUCRJ 2016; 3:341-353. [PMID: 28461895 PMCID: PMC5391856 DOI: 10.1107/s2052252516010472] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 06/28/2016] [Indexed: 05/06/2023]
Abstract
The solid-state phase transitions and intermediate structures of S-2-amino-butanoic acid (l-2-aminobutyric acid), S-2-aminopentanoic acid (l-norvaline), S-2-aminohexanoic acid (l-norleucine) and l-methionine between 100 and 470 K, identified by differential scanning calorimetry, have been characterized in a comprehensive single-crystal X-ray diffraction investigation. Unlike other enantiomeric amino acids investigated until now, this group featuring linear side chains displays up to five distinct phases. The multiple transitions between them involve a number of different processes: alteration of the hydrogen-bond pattern, to our knowledge the first example of this observed for an amino acid, sliding of molecular bilayers, seen previously only for racemates and quasiracemates, concerted side-chain rearrangements and abrupt as well as gradual modifications of the side-chain disorder. Ordering of l-norleucine upon cooling even proceeds via an incommensurately modulated structure. l-Methionine has previously been described as being fully ordered at room temperature. An accurate refinement now reveals extensive disorder for both molecules in the asymmetric unit, while two previously unknown phases occur above room temperature.
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Affiliation(s)
| | - Pavel Karen
- Department of Chemistry, University of Oslo, N-0315 Oslo, Norway
| | - Michal Dušek
- Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, 182 21 Praha 8, Czech Republic
| | - Václav Petříček
- Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, 182 21 Praha 8, Czech Republic
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40
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Gazit E. Metabolite amyloids: a new paradigm for inborn error of metabolism disorders. J Inherit Metab Dis 2016; 39:483-8. [PMID: 27271695 DOI: 10.1007/s10545-016-9946-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 05/02/2016] [Accepted: 05/04/2016] [Indexed: 01/09/2023]
Abstract
The formation of ordered amyloid assemblies is associated with major human degenerative disorders, including Alzheimer's disease, Parkinson's disease, and type 2 diabetes. Amyloid fibrils are elongated nanoscale structures that bind to specific dyes (including thioflavin T and Congo red). Amyloid fibrillar assemblies or their early intermediates are known to induce apoptotic cytotoxic effect. Until recently, amyloid fiber formation was observed only with proteins and peptides. We reported in 2012 that a single amino acid, phenylalanine, could also form typical amyloid fibrils with the same morphology, dye-binding specificity, and electron diffraction pattern as protein amyloids. X-ray crystallography demonstrated the formation of supramolecular β-sheet-like organization by phenylalanine at its zwitterionic form. Metabolite amyloids had pronounced cytotoxicity that could be depleted by treatment with antibodies raised against the phenylalanine structures. We suggested that the observed amyloid formation could explain some of the symptoms observed in phenylketonuria (PKU) upon the accumulation of phenylalanine. Follow-up studies by other groups revealed the ability of phenylalanine amyloids to bind to membranes, as observed with protein amyloids. Furthermore, the doxycycline amyloid formation inhibitor was shown to also affect the formation of phenylalanine amyloids. In 2015, it was reported that other metabolites involved in metabolic disorders, including adenine, uracil, tyrosine, and orotic acid, could form amyloid-like assemblies. It was further demonstrated that the assemblies induce apoptotic cell death. Taken together, we suggest a new hypothesis to understand the etiology of degenerative processes observed in inborn error of metabolism disorders and indicate new avenues for treatment.
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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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41
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Badawi HM, Khan I. A comparative study of the vibrational spectra of the anticancer drug melphalan and its fundamental molecules 3-phenylpropionic acid and l-phenylalanine. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.01.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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42
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Doxycycline hinders phenylalanine fibril assemblies revealing a potential novel therapeutic approach in phenylketonuria. Sci Rep 2015; 5:15902. [PMID: 26510963 PMCID: PMC4625134 DOI: 10.1038/srep15902] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/06/2015] [Indexed: 12/16/2022] Open
Abstract
A new paradigm for the aetiopathology of phenylketonuria suggests the presence of amyloid-like assemblies in the brains of transgenic mouse models and patients with phenylketonuria, possibly shedding light on the selective cognitive deficit associated with this disease. Paralleling the amyloidogenic route that identifies different stages of peptide aggregation, corresponding to different levels of toxicity, we experimentally address for the first time, the physico-chemical properties of phenylalanine aggregates via Small Angle, Wide Angle X-ray Scattering and Atomic Force Microscopy. Results are consistent with the presence of well-structured, aligned fibres generated by milliMolar concentrations of phenylalanine. Moreover, the amyloid-modulating doxycycline agent affects the local structure of phenylalanine aggregates, preventing the formation of well-ordered crystalline structures. Phenylalanine assemblies prove toxic in vitro to immortalized cell lines and primary neuronal cells. Furthermore, these assemblies also cause dendritic sprouting alterations and synaptic protein impairment in neurons. Doxycycline counteracts these toxic effects, suggesting an approach for the development of future innovative non-dietary preventive therapies.
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Shaham-Niv S, Adler-Abramovich L, Schnaider L, Gazit E. Extension of the generic amyloid hypothesis to nonproteinaceous metabolite assemblies. SCIENCE ADVANCES 2015; 1:e1500137. [PMID: 26601224 PMCID: PMC4643800 DOI: 10.1126/sciadv.1500137] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 06/25/2015] [Indexed: 05/26/2023]
Abstract
The accumulation of amyloid fibrils is the hallmark of several major human diseases. Although the formation of these supramolecular entities has previously been associated with proteins and peptides, it was later demonstrated that even phenylalanine, a single amino acid, can form fibrils that have amyloid-like biophysical, biochemical, and cytotoxic properties. Moreover, the generation of antibodies against these assemblies in phenylketonuria patients and the correlating mice model suggested a pathological role for the assemblies. We determine that several other metabolites that accumulate in metabolic disorders form ordered amyloid-like ultrastructures, which induce apoptotic cell death, as observed for amyloid structures. The formation of amyloid-like assemblies by metabolites implies a general phenomenon of amyloid formation, not limited to proteins and peptides, and offers a new paradigm for metabolic diseases.
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Affiliation(s)
- Shira Shaham-Niv
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Lihi Adler-Abramovich
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Tel Aviv Univeristy, Tel Aviv 69978, Israel
| | - Lee Schnaider
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
- Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel
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44
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Arnon Z, Adler-Abramovich L, Levin A, Gazit E. Solvent-Induced Self-Assembly of Highly Hydrophobic Tetra- and Pentaphenylalanine Peptides. Isr J Chem 2015. [DOI: 10.1002/ijch.201400184] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Williams PA, Hughes CE, Harris KDM. L-Lysine: Exploiting Powder X-ray Diffraction to Complete the Set of Crystal Structures of the 20 Directly Encoded Proteinogenic Amino Acids. Angew Chem Int Ed Engl 2015; 54:3973-7. [DOI: 10.1002/anie.201411520] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Indexed: 11/07/2022]
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Williams PA, Hughes CE, Harris KDM. L-Lysine: Exploiting Powder X-ray Diffraction to Complete the Set of Crystal Structures of the 20 Directly Encoded Proteinogenic Amino Acids. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201411520] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Hughes CE, Williams PA, Keast VL, Charalampopoulos VG, Edwards-Gau GR, Harris KDM. New in situ solid-state NMR techniques for probing the evolution of crystallization processes: pre-nucleation, nucleation and growth. Faraday Discuss 2015; 179:115-40. [DOI: 10.1039/c4fd00215f] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The application of in situ techniques for investigating crystallization processes promises to yield significant new insights into fundamental aspects of crystallization science. With this motivation, we recently developed a new in situ solid-state NMR technique that exploits the ability of NMR to selectively detect the solid phase in heterogeneous solid–liquid systems (of the type that exist during crystallization from solution), with the liquid phase “invisible” to the measurement. As a consequence, the technique allows the first solid particles produced during crystallization to be observed and identified, and allows the evolution of different solid phases (e.g., polymorphs) present during the crystallization process to be monitored as a function of time. This in situ solid-state NMR strategy has been demonstrated to be a powerful approach for establishing the sequence of solid phases produced during crystallization and for the discovery of new polymorphs. The most recent advance of the in situ NMR methodology has been the development of a strategy (named “CLASSIC NMR”) that allows both solid-state NMR and liquid-state NMR spectra to be measured (essentially simultaneously) during the crystallization process, yielding information on the complementary changes that occur in both the solid and liquid phases as a function of time. In this article, we present new results that highlight the application of our in situ NMR techniques to successfully unravel different aspects of crystallization processes, focusing on: (i) the application of a CLASSIC NMR approach to monitor competitive inclusion processes in solid urea inclusion compounds, (ii) exploiting liquid-state NMR to gain insights into co-crystal formation between benzoic acid and pentafluorobenzoic acid, and (iii) applications of in situ solid-state NMR for the discovery of new solid forms of trimethylphosphine oxide and l-phenylalanine. Finally, the article discusses a number of important fundamental issues relating to practical aspects, the interpretation of results and the future scope of these techniques, including: (i) an assessment of the smallest size of solid particle that can be detected in in situ solid-state NMR studies of crystallization, (ii) an appraisal of whether the rapid sample spinning required by the NMR measurement technique may actually influence or perturb the crystallization behaviour, and (iii) a discussion of factors that influence the sensitivity and time-resolution of in situ solid-state NMR experiments.
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Ihlefeldt FS, Pettersen FB, von Bonin A, Zawadzka M, Görbitz CH. The polymorphs of L-phenylalanine. Angew Chem Int Ed Engl 2014; 53:13600-4. [PMID: 25336255 DOI: 10.1002/anie.201406886] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 08/26/2014] [Indexed: 11/11/2022]
Abstract
The solid-state structure of the amino acid phenylalanine (Phe) offers a potential key to understanding the behavior of a large class of important aromatic compounds. Obtaining good single crystals is, however, notoriously difficult. The structure of the common polymorph of Phe, form I, was first reported by Weissbuch et al. (as D-Phe) in 1990, but the correctness of the published C2 unit cell with two disordered molecules in the asymmetric unit was later questioned and other space groups suggested. The identity of form I of L-Phe is here established to be P21 with Z'=4, based on data from a well-diffracting single crystal grown from an acetic acid solution of the amino acid. A second new polymorph, form IV, together with the two recently described forms II and III provide unprecedented information on the structural complexity of this essential amino acid. It is furthermore documented that the racemate, dl-Phe, does not grow proper single crystals.
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Ihlefeldt FS, Pettersen FB, von Bonin A, Zawadzka M, Görbitz CH. Die Polymorphe vonL-Phenylalanin. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201406886] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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