51
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Reja A, Afrose SP, Das D. Aldolase Cascade Facilitated by Self‐Assembled Nanotubes from Short Peptide Amphiphiles. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914633] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Antara Reja
- Department of Chemical Sciences & Centre for Advanced Functional MaterialsIndian Institute of Science Education and Research (IISER) Kolkata Mohanpur, West Bengal 741246 India
| | - Syed Pavel Afrose
- Department of Chemical Sciences & Centre for Advanced Functional MaterialsIndian Institute of Science Education and Research (IISER) Kolkata Mohanpur, West Bengal 741246 India
| | - Dibyendu Das
- Department of Chemical Sciences & Centre for Advanced Functional MaterialsIndian Institute of Science Education and Research (IISER) Kolkata Mohanpur, West Bengal 741246 India
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52
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Frenkel-Pinter M, Samanta M, Ashkenasy G, Leman LJ. Prebiotic Peptides: Molecular Hubs in the Origin of Life. Chem Rev 2020; 120:4707-4765. [PMID: 32101414 DOI: 10.1021/acs.chemrev.9b00664] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.
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Affiliation(s)
- Moran Frenkel-Pinter
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mousumi Samanta
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Luke J Leman
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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53
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Sarkhel B, Chatterjee A, Das D. Covalent Catalysis by Cross β Amyloid Nanotubes. J Am Chem Soc 2020; 142:4098-4103. [PMID: 32083482 DOI: 10.1021/jacs.9b13517] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The binding pockets of extant enzymes feature precise positioning of amino acid residues that facilitate multiple complex transformations exploiting covalent and non-covalent interactions. Reversible covalent anchoring is extensively used as an efficient tool by Nature for activating modern enzymes such as esterases and dehydratases and also for proteins like opsins for the complex process of visual phototransduction. Here we construct paracrystalline amyloid surfaces through the self-propagation of short peptides which offer binding pockets exposed with arrays of imidazoles and lysines. As covalent catalysis is utilized by modern-day enzymes, these homogeneous amyloid nanotubes exploit Schiff imine formation via the exposed lysines to efficiently hydrolyze both activated and inactivated esters. Controls where lysines were mutated with charged residues accessed similar morphologies but did not augment the rate. The designed amyloid microphases thus foreshadow the generation of binding pockets of advanced proteins and have the potential to contribute to the development of functional materials.
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Affiliation(s)
- Baishakhi Sarkhel
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - Ayan Chatterjee
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - Dibyendu Das
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
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54
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Reja A, Afrose SP, Das D. Aldolase Cascade Facilitated by Self-Assembled Nanotubes from Short Peptide Amphiphiles. Angew Chem Int Ed Engl 2020; 59:4329-4334. [PMID: 31920004 DOI: 10.1002/anie.201914633] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/17/2019] [Indexed: 12/25/2022]
Abstract
Early evolution benefited from a complex network of reactions involving multiple C-C bond forming and breaking events that were critical for primitive metabolism. Nature gradually chose highly evolved and complex enzymes such as lyases to efficiently facilitate C-C bond formation and cleavage with remarkable substrate selectivity. Reported here is a lipidated short peptide which accesses a homogenous nanotubular morphology to efficiently catalyze C-C bond cleavage and formation. This system shows morphology-dependent catalytic rates, suggesting the formation of a binding pocket and registered enhancements in the presence of the hydrogen-bond donor tyrosine, which is exploited by extant aldolases. These assemblies showed excellent substrate selectivity and templated the formation of a specific adduct from a pool of possible adducts. The ability to catalyze metabolically relevant cascade transformations suggests the importance of such systems in early evolution.
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Affiliation(s)
- Antara Reja
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
| | - Syed Pavel Afrose
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
| | - Dibyendu Das
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
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55
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Bomba R, Rout SK, Bütikofer M, Kwiatkowski W, Riek R, Greenwald J. Carbonyl Sulfide as a Prebiotic Activation Agent for Stereo- and Sequence-Selective, Amyloid-Templated Peptide Elongation. ORIGINS LIFE EVOL B 2019; 49:213-224. [PMID: 31845164 DOI: 10.1007/s11084-019-09586-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 09/26/2019] [Indexed: 01/28/2023]
Abstract
Prebiotic chemical replication is a commonly assumed precursor to and prerequisite for life and as such is the one of the goals of our research. We have previously reported on the role that short peptide amyloids could have played in a template-based chemical elongation. Here we take a step closer to the goal by reproducing amyloid-templated peptide elongation with carbonyl sulfide (COS) in place of the less-prebiotically relevant carbonyldiimidazole (CDI) used in the earlier study. Our investigation shows that the sequence-selectivity and stereoselectivity of the amyloid-templated reaction is similar for both activation chemistries. Notably, the amyloid protects the peptides from some of the side-reactions that take place with the COS-activation.
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Affiliation(s)
- Radoslaw Bomba
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
| | - Saroj K Rout
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
| | - Matthias Bütikofer
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
| | - Witek Kwiatkowski
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland.
| | - Jason Greenwald
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland.
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56
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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: 114] [Impact Index Per Article: 22.8] [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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57
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Symmetry and Dissymmetry in Protein Structure—System-Coding Its Biological Specificity. Symmetry (Basel) 2019. [DOI: 10.3390/sym11101215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The solenoid is a highly ordered structure observed in proteins, characterized by a set of symmetries. A group of enzymes—lyases containing solenoid fragments—was subjected to analysis with focus on their distribution of hydrophobicity/hydrophilicity, applying the fuzzy oil drop model. The model differentiates between a monocentric distribution hydrophobic core (spherical symmetry—mathematically modeled by a 3D Gaussian) and linear propagation of hydrophobicity (symmetry based on translation of structural units, i.e., chains—evident in amyloids). The linearly ordered solenoid carries information that affects the structure of the aqueous solvent in its neighborhood. Progressive disruption of its symmetry (via incorporation of asymmetrical fragments of varying size) appears to facilitate selective interaction with the intended substrate during enzymatic catalysis.
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58
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Orts J, Aulikki Wälti M, Ghosh D, Campioni S, Saupe SJ, Riek R. Rational Structure-Based Design of Fluorescent Probes for Amyloid Folds. Chembiochem 2019; 20:1161-1166. [PMID: 30548150 DOI: 10.1002/cbic.201800664] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Indexed: 11/09/2022]
Abstract
Amyloid fibrils are pathological hallmarks of various human diseases, including Parkinson's, Alzheimer's, amyotrophic lateral sclerosis (ALS or motor neurone disease), and prion diseases. Treatment of the amyloid diseases are hindered, among other factors, by timely detection and therefore, early detection of the amyloid fibrils would be beneficial for treatment against these disorders. Here, a small molecular fluorescent probe is reported that selectively recognize the fibrillar form of amyloid beta(1-42), α-synuclein, and HET-s(218-289) protein over their monomeric conformation. The rational design of the reporters relies on the well-known cross-β-sheet repetition motif, the key structural feature of amyloids.
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Affiliation(s)
- Julien Orts
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Marielle Aulikki Wälti
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Dhiman Ghosh
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Silvia Campioni
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland.,Present address: Cellulose & Wood Materials, Empa-Swiss Federal Laboratories for Materials Science and Technology, Überlandstrasse 129, 8600, Dübendorf, Switzerland
| | - Sven J Saupe
- Institut de Biochimie et Génétique Cellulaires, UMR 5095, Université de Bordeaux, 1, rue Camille Saint Saëns, 33077, Bordeaux, France
| | - Roland Riek
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
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59
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Franchi N, Ballarin L, Peronato A, Cima F, Grimaldi A, Girardello R, de Eguileor M. Functional amyloidogenesis in immunocytes from the colonial ascidian Botryllus schlosseri: Evolutionary perspective. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 90:108-120. [PMID: 30236880 DOI: 10.1016/j.dci.2018.09.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/14/2018] [Accepted: 09/15/2018] [Indexed: 06/08/2023]
Abstract
Cytotoxic morula cells (MCs) and phagocytes are the circulating immunocytes of the colonial ascidian Botryllus schlosseri: Both these cells can synthesise amyloid fibrils, supporting the idea that physiological amyloidogenesis is involved in inflammation and modulation of immune responses. Intriguingly, amyloid of B. schlosseri immunocytes is made of two different proteins. MCs, the first cells to sense non-self and involved in the allorejection reaction between contacting genetically incompatible colonies, use melanin encapsulation as the principal method to fight non-self. They release amyloid fibrils formed by p102 protein that allow the packaging and deposit of melanin and other toxic molecules nearby the invader or in the contact region of incompatible colonies. Phagocytes release amyloid-based extracellular traps when challenged with microbes: their amyloid fibrils harbour BsAPP, an orthologue of the vertebrate amyloidogeneic protein APP. This strategy of immune response, present also in human neutrophils, allows phagocytes to block and engulf bacteria and fungi.
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Affiliation(s)
- Nicola Franchi
- Department of Biology, University of Padova, Padova, Italy
| | | | - Anna Peronato
- Department of Biology, University of Padova, Padova, Italy
| | - Francesca Cima
- Department of Biology, University of Padova, Padova, Italy
| | - Annalisa Grimaldi
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Rossana Girardello
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Magda de Eguileor
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
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60
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Bomba R, Kwiatkowski W, Sánchez-Ferrer A, Riek R, Greenwald J. Cooperative Induction of Ordered Peptide and Fatty Acid Aggregates. Biophys J 2018; 115:2336-2347. [PMID: 30503535 DOI: 10.1016/j.bpj.2018.10.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 10/19/2018] [Accepted: 10/31/2018] [Indexed: 01/18/2023] Open
Abstract
Interactions between biological membranes and disease-associated amyloids are well documented, and their prevalence suggests that an inherent affinity exists between these molecular assemblies. Our interest in the molecular origins of life have led us to investigate the nature of such interactions in the context of their molecular predecessors (i.e., vesicle-forming amphiphiles and small peptides). Under certain conditions, amyloidogenic peptides or fatty acids are each able to form ordered structures on their own; however, we report here on their cooperative assembly into novel, to our knowledge, highly ordered structures. We first examined an amyloidogenic eight-residue peptide, which forms amyloids at pH 11, yet because of its positive electrostatic character remains soluble at a neutral pH. In mixtures with simple fatty acids, this peptide is also able to form novel, to our knowledge, coaggregates at a neutral pH whose structures are sensitive to both the fatty acid concentration and identity. Below the critical vesicle concentration, the mixtures of fatty acid and peptide yield a flocculent precipitate with an underlying β-structure. Above the critical vesicle concentration, the mixtures yield a translucent precipitate that consists of tube-like structures. Small-angle x-ray scattering and fiber diffraction data were used to model their structures as hollow-core two-shell cylinders in which the inner shell is a bilayer of fatty acid and the outer shell alternates between amyloid and bilayers of fatty acid. The further analysis of decanoic acid with a panel of 13 other basic amyloidogenic peptides confirmed the general nature of the observed interactions. The cooperativity within this heterogeneous system is attributed to the structurally repetitive natures of the fatty acid bilayer and the cross-β-sheet motif, providing compatible scaffolds for attractive electrostatic interactions. We show these interactions to be mutually beneficial, expanding the phase space of both peptides and fatty acids while providing a simple yet robust physical connection between two distinct entities relevant for life.
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Affiliation(s)
- Radoslaw Bomba
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Zürich, Switzerland
| | - Witek Kwiatkowski
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Zürich, Switzerland
| | - Antoni Sánchez-Ferrer
- Department of Health Sciences and Technology, Swiss Federal Institute of Technology, IFNH, LFO, Zürich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Zürich, Switzerland.
| | - Jason Greenwald
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Zürich, Switzerland.
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61
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Al-Halifa S, Babych M, Zottig X, Archambault D, Bourgault S. Amyloid self-assembling peptides: Potential applications in nanovaccine engineering and biosensing. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24095] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Soultan Al-Halifa
- Department of Chemistry; Université du Québec à Montréal; Montreal, QC Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO; Québec QC Canada
| | - Margaryta Babych
- Department of Chemistry; Université du Québec à Montréal; Montreal, QC Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO; Québec QC Canada
| | - Ximena Zottig
- Department of Chemistry; Université du Québec à Montréal; Montreal, QC Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO; Québec QC Canada
| | - Denis Archambault
- Department of Biological Sciences; Université du Québec à Montréal; Montreal, QC Canada
- Swine and Poultry Infectious Diseases Research Centre, CRIPA; QC Canada
| | - Steve Bourgault
- Department of Chemistry; Université du Québec à Montréal; Montreal, QC Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO; Québec QC Canada
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62
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Russell MJ. Green Rust: The Simple Organizing 'Seed' of All Life? Life (Basel) 2018; 8:E35. [PMID: 30150570 PMCID: PMC6161180 DOI: 10.3390/life8030035] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 06/28/2018] [Accepted: 08/14/2018] [Indexed: 01/18/2023] Open
Abstract
Korenaga and coworkers presented evidence to suggest that the Earth's mantle was dry and water filled the ocean to twice its present volume 4.3 billion years ago. Carbon dioxide was constantly exhaled during the mafic to ultramafic volcanic activity associated with magmatic plumes that produced the thick, dense, and relatively stable oceanic crust. In that setting, two distinct and major types of sub-marine hydrothermal vents were active: ~400 °C acidic springs, whose effluents bore vast quantities of iron into the ocean, and ~120 °C, highly alkaline, and reduced vents exhaling from the cooler, serpentinizing crust some distance from the heads of the plumes. When encountering the alkaline effluents, the iron from the plume head vents precipitated out, forming mounds likely surrounded by voluminous exhalative deposits similar to the banded iron formations known from the Archean. These mounds and the surrounding sediments, comprised micro or nano-crysts of the variable valence FeII/FeIII oxyhydroxide known as green rust. The precipitation of green rust, along with subsidiary iron sulfides and minor concentrations of nickel, cobalt, and molybdenum in the environment at the alkaline springs, may have established both the key bio-syntonic disequilibria and the means to properly make use of them-the elements needed to effect the essential inanimate-to-animate transitions that launched life. Specifically, in the submarine alkaline vent model for the emergence of life, it is first suggested that the redox-flexible green rust micro- and nano-crysts spontaneously precipitated to form barriers to the complete mixing of carbonic ocean and alkaline hydrothermal fluids. These barriers created and maintained steep ionic disequilibria. Second, the hydrous interlayers of green rust acted as engines that were powered by those ionic disequilibria and drove essential endergonic reactions. There, aided by sulfides and trace elements acting as catalytic promoters and electron transfer agents, nitrate could be reduced to ammonia and carbon dioxide to formate, while methane may have been oxidized to methyl and formyl groups. Acetate and higher carboxylic acids could then have been produced from these C1 molecules and aminated to amino acids, and thence oligomerized to offer peptide nests to phosphate and iron sulfides, and secreted to form primitive amyloid-bounded structures, leading conceivably to protocells.
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Affiliation(s)
- Michael J Russell
- Planetary Chemistry and Astrobiology, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109-8099, USA.
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63
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Wang ZG, Wang H, Liu Q, Duan F, Shi X, Ding B. Designed Self-Assembly of Peptides with G-Quadruplex/Hemin DNAzyme into Nanofibrils Possessing Enzyme-Mimicking Active Sites and Catalytic Functions. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00896] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhen-Gang Wang
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People’s Republic of China
| | - Hui Wang
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People’s Republic of China
| | - Qing Liu
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People’s Republic of China
| | - Fangyuan Duan
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People’s Republic of China
| | - Xinghua Shi
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
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64
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Greenwald J, Kwiatkowski W, Riek R. Peptide Amyloids in the Origin of Life. J Mol Biol 2018; 430:3735-3750. [PMID: 29890117 DOI: 10.1016/j.jmb.2018.05.046] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 05/29/2018] [Accepted: 05/31/2018] [Indexed: 10/14/2022]
Abstract
How life can emerge from non-living matter is one of the fundamental mysteries of the universe. A bottom-up approach to this problem focuses on the potential chemical precursors of life, in particular the nature of the first replicative molecules. Such thinking has led to the currently most popular idea: that an RNA-like molecule played a central role as the first replicative and catalytic molecule. Here, we review an alternative hypothesis that has recently gained experimental support, focusing on the role of amyloidogenic peptides rather than nucleic acids, in what has been by some termed "the amyloid-world" hypothesis. Amyloids are well-ordered peptide aggregates that have a fibrillar morphology due to their underlying structure of a one-dimensional crystal-like array of peptides in a β-strand conformation. While they are notorious for their implication in several neurodegenerative diseases including Alzheimer's disease, amyloids also have many biological functions. In this review, we will elaborate on the following properties of amyloids in relation to their fitness as a prebiotic entity: they can be formed by very short peptides with simple amino acids sequences; as aggregates they are more chemically stable than their isolated component peptides; they can possess diverse catalytic activities; they can form spontaneously during the prebiotic condensation of amino acids; they can act as templates in their own chemical replication; they have a structurally repetitive nature that enables them to interact with other structurally repetitive biopolymers like RNA/DNA and polysaccharides, as well as with structurally repetitive surfaces like amphiphilic membranes and minerals.
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Affiliation(s)
- Jason Greenwald
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Witek Kwiatkowski
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland.
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65
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Abstract
Self-assembly of molecules often results in new emerging properties. Even very short peptides can self-assemble into structures with a variety of physical and structural characteristics. Remarkably, many peptide assemblies show high catalytic activity in model reactions reaching efficiencies comparable to those found in natural enzymes by weight. In this review, we discuss different strategies used to rationally develop self-assembled peptide catalysts with natural and unnatural backbones as well as with metal-containing cofactors.
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Affiliation(s)
- O Zozulia
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA.
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Maury CPJ. Amyloid and the origin of life: self-replicating catalytic amyloids as prebiotic informational and protometabolic entities. Cell Mol Life Sci 2018; 75:1499-1507. [PMID: 29550973 PMCID: PMC5897472 DOI: 10.1007/s00018-018-2797-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 02/19/2018] [Accepted: 03/13/2018] [Indexed: 01/29/2023]
Abstract
A crucial stage in the origin of life was the emergence of the first molecular entity that was able to replicate, transmit information, and evolve on the early Earth. The amyloid world hypothesis posits that in the pre-RNA era, information processing was based on catalytic amyloids. The self-assembly of short peptides into β-sheet amyloid conformers leads to extraordinary structural stability and novel multifunctionality that cannot be achieved by the corresponding nonaggregated peptides. The new functions include self-replication, catalytic activities, and information transfer. The environmentally sensitive template-assisted replication cycles generate a variety of amyloid polymorphs on which evolutive forces can act, and the fibrillar assemblies can serve as scaffolds for the amyloids themselves and for ribonucleotides proteins and lipids. The role of amyloid in the putative transition process from an amyloid world to an amyloid-RNA-protein world is not limited to scaffolding and protection: the interactions between amyloid, RNA, and protein are both complex and cooperative, and the amyloid assemblages can function as protometabolic entities catalyzing the formation of simple metabolite precursors. The emergence of a pristine amyloid-based in-put sensitive, chiroselective, and error correcting information-processing system, and the evolvement of mutualistic networks were, arguably, of essential importance in the dynamic processes that led to increased complexity, organization, compartmentalization, and, eventually, the origin of life.
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67
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Mirkin NG, Krimm S. Milieu-Initiated Inversion of the Aqueous Polyproline II/β Propensity in the Alanine Tripeptide: Aggregation Origin of the Onset of Amyloid Formation. J Phys Chem B 2018; 122:4428-4432. [PMID: 29617133 DOI: 10.1021/acs.jpcb.8b00612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Extending our earlier analogous study of the alanine dipeptide (ADP), we have now analyzed the effect of the external environment on the polyproline II (P) and β relative energies, the P/β propensity, of the alanine tripeptide (ATP). Ab initio calculations of ATP(H2O)19 and ATP(H2O)19(HCl) exhibit the same propensity inversion as in ADP: in the pure water case the PP conformation is favored while the addition of the HCl molecule results in the ββ conformation being of lower energy. A comparison, following an intermediate insertion and departure of an HCl molecule, shows that the energy of a hydrogen-bonded (H2O)19βATP::βATP(H2O)19 structure is lower than that of the sum of two separate PP systems, i.e., that the aggregated state of the peptide is favored. This arises from the basic physical response to their total environmental influences. Questions about quantitative results from molecular dynamics simulations, obviously needed to analyze longer chains and other side chains, are addressed via rigid water calculations. The desirability of basing studies of amyloid formation on our proposed alternative milieu-folding paradigm is discussed.
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Affiliation(s)
- Noemi G Mirkin
- LSA Biophysics , University of Michigan , 930 N. University Avenue , Ann Arbor , Michigan 48109 , United States
| | - Samuel Krimm
- LSA Biophysics , University of Michigan , 930 N. University Avenue , Ann Arbor , Michigan 48109 , United States
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68
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A prebiotic template-directed peptide synthesis based on amyloids. Nat Commun 2018; 9:234. [PMID: 29339755 PMCID: PMC5770463 DOI: 10.1038/s41467-017-02742-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 12/21/2017] [Indexed: 11/24/2022] Open
Abstract
The prebiotic replication of information-coding molecules is a central problem concerning life’s origins. Here, we report that amyloids composed of short peptides can direct the sequence-selective, regioselective and stereoselective condensation of amino acids. The addition of activated DL-arginine and DL-phenylalanine to the peptide RFRFR-NH2 in the presence of the complementary template peptide Ac-FEFEFEFE-NH2 yields the isotactic product FRFRFRFR-NH2, 1 of 64 possible triple addition products, under conditions in which the absence of template yields only single and double additions of mixed stereochemistry. The templating mechanism appears to be general in that a different amyloid formed by (Orn)V(Orn)V(Orn)V(Orn)V-NH2 and Ac-VDVDVDVDV-NH2 is regioselective and stereoselective for N-terminal, L-amino-acid addition while the ornithine-valine peptide alone yields predominantly sidechain condensation products with little stereoselectivity. Furthermore, the templating reaction is stable over a wide range of pH (5.6–8.6), salt concentration (0–4 M NaCl), and temperature (25–90 °C), making the amyloid an attractive model for a prebiotic peptide replicating system. Amyloids may have played an important role in prebiotic molecular evolution but understanding replication of such information-coding molecules is still a problem. Here the authors design a model amyloid substrate and demonstrate sequence regio- and stereoselectivity during template-based replication.
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69
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Freyssin A, Page G, Fauconneau B, Rioux Bilan A. Natural polyphenols effects on protein aggregates in Alzheimer's and Parkinson's prion-like diseases. Neural Regen Res 2018; 13:955-961. [PMID: 29926816 PMCID: PMC6022479 DOI: 10.4103/1673-5374.233432] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Alzheimer's and Parkinson's diseases are the most common neurodegenerative diseases. They are characterized by protein aggregates and so can be considered as prion-like disease. The major components of these deposits are amyloid peptide and tau for Alzheimer's disease, α-synuclein and synphilin-1 for Parkinson's disease. Drugs currently proposed to treat these pathologies do not prevent neurodegenerative processes and are mainly symptomatic therapies. Molecules inducing inhibition of aggregation or disaggregation of these proteins could have beneficial effects, especially if they have other beneficial effects for these diseases. Thus, several natural polyphenols, which have antioxidative, anti-inflammatory and neuroprotective properties, have been largely studied, for their effects on protein aggregates found in these diseases, notably in vitro. In this article, we propose to review the significant papers concerning the role of polyphenols on aggregation and disaggregation of amyloid peptide, tau, α-synuclein, synphilin-1, suggesting that these compounds could be useful in the treatments in Alzheimer's and Parkinson's diseases.
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Affiliation(s)
- Aline Freyssin
- University of Poitiers, EA3808 NEUVACOD (Neurovascular Unit and Cognitive Disorders), Pôle Biologie Santé, Poitiers, France
| | - Guylène Page
- University of Poitiers, EA3808 NEUVACOD (Neurovascular Unit and Cognitive Disorders), Pôle Biologie Santé, Poitiers, France
| | - Bernard Fauconneau
- University of Poitiers, EA3808 NEUVACOD (Neurovascular Unit and Cognitive Disorders), Pôle Biologie Santé, Poitiers, France
| | - Agnès Rioux Bilan
- University of Poitiers, EA3808 NEUVACOD (Neurovascular Unit and Cognitive Disorders), Pôle Biologie Santé, Poitiers, France
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70
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Abstract
Aggregation of proteins into amyloids has long been recognized as one of the major contributors to disease and aging. Amyloids are known to catalyze their own formation but they have been considered the rock-bottom thermodynamic minimum of the protein fold without much functionality. We have recently demonstrated that aggregation of short peptides in the presence of metal ions gives rise to efficient catalytic activity. Here we present a detailed protocol for the synthesis and purification of these peptides and the preparation of amyloid-like fibrils. Then we describe an easy-to-perform, high-throughput assay to measure their hydrolytic activity.
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Affiliation(s)
- Zsofia Lengyel
- Department of Chemistry, Syracuse University, Syracuse, NY, USA
| | - Caroline M Rufo
- Department of Chemistry, Syracuse University, Syracuse, NY, USA
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71
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Jacob RS, Das S, Singh N, Patel K, Datta D, Sen S, Maji SK. Amyloids Are Novel Cell-Adhesive Matrices. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1112:79-97. [PMID: 30637692 DOI: 10.1007/978-981-13-3065-0_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Amyloids are highly ordered peptide/protein aggregates traditionally associated with multiple human diseases including neurodegenerative disorders. However, recent studies suggest that amyloids can also perform several biological functions in organisms varying from bacteria to mammals. In many lower organisms, amyloid fibrils function as adhesives due to their unique surface topography. Recently, amyloid fibrils have been shown to support attachment and spreading of mammalian cells by interacting with the cell membrane and by cell adhesion machinery activation. Moreover, similar to cellular responses on natural extracellular matrices (ECMs), mammalian cells on amyloid surfaces also use integrin machinery for spreading, migration, and differentiation. This has led to the development of biocompatible and implantable amyloid-based hydrogels that could induce lineage-specific differentiation of stem cells. In this chapter, based on adhesion of both lower organisms and mammalian cells on amyloid nanofibrils, we posit that amyloids could have functioned as a primitive extracellular matrix in primordial earth.
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Affiliation(s)
- Reeba S Jacob
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Subhadeep Das
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Namrata Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Komal Patel
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Debalina Datta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Shamik Sen
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Samir K Maji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India.
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72
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Taran O, Chen C, Omosun TO, Hsieh MC, Rha A, Goodwin JT, Mehta AK, Grover MA, Lynn DG. Expanding the informational chemistries of life: peptide/RNA networks. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2017; 375:rsta.2016.0356. [PMID: 29133453 DOI: 10.1098/rsta.2016.0356] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/03/2017] [Indexed: 06/07/2023]
Abstract
The RNA world hypothesis simplifies the complex biopolymer networks underlining the informational and metabolic needs of living systems to a single biopolymer scaffold. This simplification requires abiotic reaction cascades for the construction of RNA, and this chemistry remains the subject of active research. Here, we explore a complementary approach involving the design of dynamic peptide networks capable of amplifying encoded chemical information and setting the stage for mutualistic associations with RNA. Peptide conformational networks are known to be capable of evolution in disease states and of co-opting metal ions, aromatic heterocycles and lipids to extend their emergent behaviours. The coexistence and association of dynamic peptide and RNA networks appear to have driven the emergence of higher-order informational systems in biology that are not available to either scaffold independently, and such mutualistic interdependence poses critical questions regarding the search for life across our Solar System and beyond.This article is part of the themed issue 'Reconceptualizing the origins of life'.
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Affiliation(s)
- Olga Taran
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Chenrui Chen
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Tolulope O Omosun
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Ming-Chien Hsieh
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Allisandra Rha
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Jay T Goodwin
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Anil K Mehta
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Martha A Grover
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - David G Lynn
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
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73
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Seoudi RS, Mechler A. Design Principles of Peptide Based Self-Assembled Nanomaterials. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1030:51-94. [DOI: 10.1007/978-3-319-66095-0_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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74
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Foldability of a Natural De Novo Evolved Protein. Structure 2017; 25:1687-1696.e4. [PMID: 29033289 DOI: 10.1016/j.str.2017.09.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 07/22/2017] [Accepted: 09/15/2017] [Indexed: 12/13/2022]
Abstract
The de novo evolution of protein-coding genes from noncoding DNA is emerging as a source of molecular innovation in biology. Studies of random sequence libraries, however, suggest that young de novo proteins will not fold into compact, specific structures typical of native globular proteins. Here we show that Bsc4, a functional, natural de novo protein encoded by a gene that evolved recently from noncoding DNA in the yeast S. cerevisiae, folds to a partially specific three-dimensional structure. Bsc4 forms soluble, compact oligomers with high β sheet content and a hydrophobic core, and undergoes cooperative, reversible denaturation. Bsc4 lacks a specific quaternary state, however, existing instead as a continuous distribution of oligomer sizes, and binds dyes indicative of amyloid oligomers or molten globules. The combination of native-like and non-native-like properties suggests a rudimentary fold that could potentially act as a functional intermediate in the emergence of new folded proteins de novo.
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75
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The Physiological and Pathological Implications of the Formation of Hydrogels, with a Specific Focus on Amyloid Polypeptides. Biomolecules 2017; 7:biom7040070. [PMID: 28937634 PMCID: PMC5745453 DOI: 10.3390/biom7040070] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 08/30/2017] [Accepted: 09/18/2017] [Indexed: 02/07/2023] Open
Abstract
Hydrogels are water-swollen and viscoelastic three-dimensional cross-linked polymeric network originating from monomer polymerisation. Hydrogel-forming polypeptides are widely found in nature and, at a cellular and organismal level, they provide a wide range of functions for the organism making them. Amyloid structures, arising from polypeptide aggregation, can be damaging or beneficial to different types of organisms. Although the best-known amyloids are those associated with human pathologies, this underlying structure is commonly used by higher eukaryotes to maintain normal cellular activities, and also by microbial communities to promote their survival and growth. Amyloidogenesis occurs by nucleation-dependent polymerisation, which includes several species (monomers, nuclei, oligomers, and fibrils). Oligomers of pathological amyloids are considered the toxic species through cellular membrane perturbation, with the fibrils thought to represent a protective sink for toxic species. However, both functional and disease-associated amyloids use fibril cross-linking to form hydrogels. The properties of amyloid hydrogels can be exploited by organisms to fulfil specific physiological functions. Non-physiological hydrogelation by pathological amyloids may provide additional toxic mechanism(s), outside of membrane toxicity by oligomers, such as physical changes to the intracellular and extracellular environments, with wide-spread consequences for many structural and dynamic processes, and overall effects on cell survival.
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76
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He X, Zhang F, Zhang L, Zhang Q, Fang G, Liu J, Wang S, Zhang S. Probing the structure-activity relationship of a novel artificial cellobiose hydrolase. J Mater Chem B 2017; 5:5225-5233. [PMID: 32264107 DOI: 10.1039/c7tb01426k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The remarkable catalytic properties of enzymes contribute to their unique 3D structures and arrangement of amino acid residues, which provide a blueprint for the design of artificial enzymes. Here, a series of peptide catalysts (PCs) that mimic the unique orientation and function of β-glycosyl hydrolases were designed. Transmission electron microscopy (TEM), fluorescence analysis, circular dichroism spectroscopy, X-ray diffraction and computational modeling were used to investigate and compare the relationship of the fibrinous structure of PCs with its glycoside hydrolysis activity. These results indicated that the catalytic activity of PCs was not only related to their amyloid-like structures, but it can also be influenced by the site, species, molecular arrangement and steric hindrance of the amino acid sequence. What's more, this is the first report on peptide-inspired catalysts that mimic the natural cellobiose hydrolases. All this provided insights into the potential use of peptide nanoenzymes in the generation of efficient artificial enzymes.
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Affiliation(s)
- Xingxing He
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Tianjin University of Science and Technology, Tianjin 300457, China.
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77
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Pohorille A, Wilson MA, Shannon G. Flexible Proteins at the Origin of Life. Life (Basel) 2017; 7:E23. [PMID: 28587235 PMCID: PMC5492145 DOI: 10.3390/life7020023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/10/2017] [Accepted: 05/24/2017] [Indexed: 11/17/2022] Open
Abstract
Almost all modern proteins possess well-defined, relatively rigid scaffolds that provide structural preorganization for desired functions. Such scaffolds require the sufficient length of a polypeptide chain and extensive evolutionary optimization. How ancestral proteins attained functionality, even though they were most likely markedly smaller than their contemporary descendants, remains a major, unresolved question in the origin of life. On the basis of evidence from experiments and computer simulations, we argue that at least some of the earliest water-soluble and membrane proteins were markedly more flexible than their modern counterparts. As an example, we consider a small, evolved in vitro ligase, based on a novel architecture that may be the archetype of primordial enzymes. The protein does not contain a hydrophobic core or conventional elements of the secondary structure characteristic of modern water-soluble proteins, but instead is built of a flexible, catalytic loop supported by a small hydrophilic core containing zinc atoms. It appears that disorder in the polypeptide chain imparts robustness to mutations in the protein core. Simple ion channels, likely the earliest membrane protein assemblies, could also be quite flexible, but still retain their functionality, again in contrast to their modern descendants. This is demonstrated in the example of antiamoebin, which can serve as a useful model of small peptides forming ancestral ion channels. Common features of the earliest, functional protein architectures discussed here include not only their flexibility, but also a low level of evolutionary optimization and heterogeneity in amino acid composition and, possibly, the type of peptide bonds in the protein backbone.
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Affiliation(s)
- Andrew Pohorille
- Exobiology Branch, MS 239-4, NASA Ames Research Center, Moffett Field, CA 94035, USA.
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94132, USA.
| | - Michael A Wilson
- Exobiology Branch, MS 239-4, NASA Ames Research Center, Moffett Field, CA 94035, USA.
- SETI Institute, 189 N Bernardo Ave #200, Mountain View, CA 94043, USA.
| | - Gareth Shannon
- Exobiology Branch, MS 239-4, NASA Ames Research Center, Moffett Field, CA 94035, USA.
- NASA Postdoctoral Program Fellow, NASA Ames Research Center, Moffett Field, CA 94035, USA.
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78
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Abstract
Throughout biology, amyloids are key structures in both functional proteins and the end product of pathologic protein misfolding. Amyloids might also represent an early precursor in the evolution of life because of their small molecular size and their ability to self-purify and catalyze chemical reactions. They also provide attractive backbones for advanced materials. When β-strands of an amyloid are arranged parallel and in register, side chains from the same position of each chain align, facilitating metal chelation when the residues are good ligands such as histidine. High-resolution structures of metalloamyloids are needed to understand the molecular bases of metal-amyloid interactions. Here we combine solid-state NMR and structural bioinformatics to determine the structure of a zinc-bound metalloamyloid that catalyzes ester hydrolysis. The peptide forms amphiphilic parallel β-sheets that assemble into stacked bilayers with alternating hydrophobic and polar interfaces. The hydrophobic interface is stabilized by apolar side chains from adjacent sheets, whereas the hydrated polar interface houses the Zn2+-binding histidines with binding geometries unusual in proteins. Each Zn2+ has two bis-coordinated histidine ligands, which bridge adjacent strands to form an infinite metal-ligand chain along the fibril axis. A third histidine completes the protein ligand environment, leaving a free site on the Zn2+ for water activation. This structure defines a class of materials, which we call metal-peptide frameworks. The structure reveals a delicate interplay through which metal ions stabilize the amyloid structure, which in turn shapes the ligand geometry and catalytic reactivity of Zn2.
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79
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Copani A. The underexplored question of β-amyloid monomers. Eur J Pharmacol 2017; 817:71-75. [PMID: 28577967 DOI: 10.1016/j.ejphar.2017.05.057] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 05/12/2017] [Accepted: 05/30/2017] [Indexed: 01/03/2023]
Abstract
Conceived more than 25 years ago, the amyloid cascade hypothesis of Alzheimer's disease has evolved to accommodate new findings, namely different forms of β-amyloid aggregates and downstream dysfunctions. Yet, the cascade does not mention its very beginning, the β-amyloid monomer. Here, I will discuss the monomer from a functional evolutionary perspective, highlighting the potential advantages of a native unfolded state that, however, involves an amyloidogenic risk. Finally, I will make a summary of what is known about its functional role in the brain and discuss the implications of its conceivable shortage in the development of Alzheimer's disease.
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Affiliation(s)
- Agata Copani
- Department of Drug Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy.
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80
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Jacob RS, Sen S, Maji SK. Adhesion of Human Mesenchymal Stem Cells and Differentiation of SH-SY5Y Cells on Amyloid Fibrils. ACTA ACUST UNITED AC 2016. [DOI: 10.1002/masy.201600071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Reeba S. Jacob
- Department of Biosciences and Bioengineering; Indian Institute of Technology Bombay; Mumbai Maharashtra 400076 India
| | - Shamik Sen
- Department of Biosciences and Bioengineering; Indian Institute of Technology Bombay; Mumbai Maharashtra 400076 India
| | - Samir K. Maji
- Department of Biosciences and Bioengineering; Indian Institute of Technology Bombay; Mumbai Maharashtra 400076 India
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81
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Greenwald J, Friedmann MP, Riek R. Amyloid Aggregates Arise from Amino Acid Condensations under Prebiotic Conditions. Angew Chem Int Ed Engl 2016; 55:11609-13. [DOI: 10.1002/anie.201605321] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/14/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Jason Greenwald
- Laboratory of Physical Chemistry, D-CHAB; ETH Zürich; Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
| | - Michael P. Friedmann
- Laboratory of Physical Chemistry, D-CHAB; ETH Zürich; Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, D-CHAB; ETH Zürich; Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
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82
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Greenwald J, Friedmann MP, Riek R. Amyloid Aggregates Arise from Amino Acid Condensations under Prebiotic Conditions. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605321] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jason Greenwald
- Laboratory of Physical Chemistry, D-CHAB; ETH Zürich; Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
| | - Michael P. Friedmann
- Laboratory of Physical Chemistry, D-CHAB; ETH Zürich; Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, D-CHAB; ETH Zürich; Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
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83
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Makhlynets OV, Gosavi PM, Korendovych IV. Short Self-Assembling Peptides Are Able to Bind to Copper and Activate Oxygen. Angew Chem Int Ed Engl 2016; 55:9017-20. [PMID: 27276534 PMCID: PMC5064842 DOI: 10.1002/anie.201602480] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 04/21/2016] [Indexed: 11/07/2022]
Abstract
We have shown that de novo designed peptides self-assemble in the presence of copper to create supramolecular assemblies capable of carrying out the oxidation of dimethoxyphenol in the presence of dioxygen. Formation of the supramolecular assembly, which is akin to a protein fold, is critical for productive catalysis since peptides possessing the same functional groups but lacking the ability to self-assemble do not catalyze substrate oxidation. The ease with which we have discovered robust and productive oxygen activation catalysts suggests that these prion-like assemblies might have served as intermediates in the evolution of enzymatic function and opens the path for the development of new catalyst nanomaterials.
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Affiliation(s)
- Olga V Makhlynets
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Pallavi M Gosavi
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Ivan V Korendovych
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA.
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84
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Makhlynets OV, Gosavi PM, Korendovych IV. Short Self‐Assembling Peptides Are Able to Bind to Copper and Activate Oxygen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602480] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Olga V. Makhlynets
- Department of Chemistry Syracuse University 111 College Place Syracuse NY 13244 USA
| | - Pallavi M. Gosavi
- Department of Chemistry Syracuse University 111 College Place Syracuse NY 13244 USA
| | - Ivan V. Korendovych
- Department of Chemistry Syracuse University 111 College Place Syracuse NY 13244 USA
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85
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Crystallographic studies on protein misfolding: Domain swapping and amyloid formation in the SH3 domain. Arch Biochem Biophys 2016; 602:116-126. [PMID: 26924596 DOI: 10.1016/j.abb.2016.02.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 02/19/2016] [Accepted: 02/23/2016] [Indexed: 12/18/2022]
Abstract
Oligomerization by 3D domain swapping is found in a variety of proteins of diverse size, fold and function. In the early 1960s this phenomenon was postulated for the oligomers of ribonuclease A, but it was not until the 1990s that X-ray diffraction provided the first experimental evidence of this special manner of oligomerization. Nowadays, structural information has allowed the identification of these swapped oligomers in over one hundred proteins. Although the functional relevance of this phenomenon is not clear, this alternative folding of protomers into intertwined oligomers has been related to amyloid formation. Studies on proteins that develop 3D domain swapping might provide some clues on the early stages of amyloid formation. The SH3 domain is a small modular domain that has been used as a model to study the basis of protein folding. Among SH3 domains, the c-Src-SH3 domain emerges as a helpful model to study 3D domain swapping and amyloid formation.
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86
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Jacob RS, George E, Singh PK, Salot S, Anoop A, Jha NN, Sen S, Maji SK. Cell Adhesion on Amyloid Fibrils Lacking Integrin Recognition Motif. J Biol Chem 2016; 291:5278-98. [PMID: 26742841 DOI: 10.1074/jbc.m115.678177] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Indexed: 12/23/2022] Open
Abstract
Amyloids are highly ordered, cross-β-sheet-rich protein/peptide aggregates associated with both human diseases and native functions. Given the well established ability of amyloids in interacting with cell membranes, we hypothesize that amyloids can serve as universal cell-adhesive substrates. Here, we show that, similar to the extracellular matrix protein collagen, amyloids of various proteins/peptides support attachment and spreading of cells via robust stimulation of integrin expression and formation of integrin-based focal adhesions. Additionally, amyloid fibrils are also capable of immobilizing non-adherent red blood cells through charge-based interactions. Together, our results indicate that both active and passive mechanisms contribute to adhesion on amyloid fibrils. The present data may delineate the functional aspect of cell adhesion on amyloids by various organisms and its involvement in human diseases. Our results also raise the exciting possibility that cell adhesivity might be a generic property of amyloids.
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Affiliation(s)
- Reeba S Jacob
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
| | - Edna George
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
| | - Pradeep K Singh
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
| | - Shimul Salot
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
| | - Arunagiri Anoop
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
| | - Narendra Nath Jha
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
| | - Shamik Sen
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
| | - Samir K Maji
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
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87
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Hervás R, Li L, Majumdar A, Fernández-Ramírez MDC, Unruh JR, Slaughter BD, Galera-Prat A, Santana E, Suzuki M, Nagai Y, Bruix M, Casas-Tintó S, Menéndez M, Laurents DV, Si K, Carrión-Vázquez M. Molecular Basis of Orb2 Amyloidogenesis and Blockade of Memory Consolidation. PLoS Biol 2016; 14:e1002361. [PMID: 26812143 PMCID: PMC4727891 DOI: 10.1371/journal.pbio.1002361] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 12/16/2015] [Indexed: 12/03/2022] Open
Abstract
Amyloids are ordered protein aggregates that are typically associated with neurodegenerative diseases and cognitive impairment. By contrast, the amyloid-like state of the neuronal RNA binding protein Orb2 in Drosophila was recently implicated in memory consolidation, but it remains unclear what features of this functional amyloid-like protein give rise to such diametrically opposed behaviour. Here, using an array of biophysical, cell biological and behavioural assays we have characterized the structural features of Orb2 from the monomer to the amyloid state. Surprisingly, we find that Orb2 shares many structural traits with pathological amyloids, including the intermediate toxic oligomeric species, which can be sequestered in vivo in hetero-oligomers by pathological amyloids. However, unlike pathological amyloids, Orb2 rapidly forms amyloids and its toxic intermediates are extremely transient, indicating that kinetic parameters differentiate this functional amyloid from pathological amyloids. We also observed that a well-known anti-amyloidogenic peptide interferes with long-term memory in Drosophila. These results provide structural insights into how the amyloid-like state of the Orb2 protein can stabilize memory and be nontoxic. They also provide insight into how amyloid-based diseases may affect memory processes.
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Affiliation(s)
- Rubén Hervás
- Instituto Cajal, IC-CSIC, Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Madrid, Spain
| | - Liying Li
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Amitabha Majumdar
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- National Brain Research Centre, Manesar, Guragon, Haryana, India
| | | | - Jay R. Unruh
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Brian D. Slaughter
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Albert Galera-Prat
- Instituto Cajal, IC-CSIC, Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Madrid, Spain
| | | | - Mari Suzuki
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Yoshitaka Nagai
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Saitama, Japan
| | - Marta Bruix
- Instituto de Química-Física Rocasolano, IQFR-CSIC, Madrid, Spain
| | | | - Margarita Menéndez
- Instituto de Química-Física Rocasolano, IQFR-CSIC, Madrid, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Respiratorias, Madrid, Spain
| | | | - Kausik Si
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Mariano Carrión-Vázquez
- Instituto Cajal, IC-CSIC, Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Madrid, Spain
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88
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Friedmann MP, Torbeev V, Zelenay V, Sobol A, Greenwald J, Riek R. Towards Prebiotic Catalytic Amyloids Using High Throughput Screening. PLoS One 2015; 10:e0143948. [PMID: 26650386 PMCID: PMC4674085 DOI: 10.1371/journal.pone.0143948] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 11/11/2015] [Indexed: 02/07/2023] Open
Abstract
Enzymes are capable of directing complex stereospecific transformations and of accelerating reaction rates many orders of magnitude. As even the simplest known enzymes comprise thousands of atoms, the question arises as to how such exquisite catalysts evolved. A logical predecessor would be shorter peptides, but they lack the defined structure and size that are apparently necessary for enzyme functions. However, some very short peptides are able to assemble into amyloids, thereby forming a well-defined tertiary structure called the cross-β-sheet, which bestows unique properties upon the peptides. We have hypothesized that amyloids could have been the catalytically active precursor to modern enzymes. To test this hypothesis, we designed an amyloid peptide library that could be screened for catalytic activity. Our approach, amenable to high-throughput methodologies, allowed us to find several peptides and peptide mixtures that form amyloids with esterase activity. These results indicate that amyloids, with their stability in a wide range of conditions and their potential as catalysts with low sequence specificity, would indeed be fitting precursors to modern enzymes. Furthermore, our approach can be efficiently expanded upon in library size, screening conditions, and target activity to yield novel amyloid catalysts with potential applications in aqueous-organic mixtures, at high temperature and in other extreme conditions that could be advantageous for industrial applications.
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Affiliation(s)
- Michael P. Friedmann
- Laboratory of Physical Chemistry, Department of Chemistry, ETH Zürich, Zurich, Switzerland
| | - Vladimir Torbeev
- Laboratory of Organic Chemistry, Department of Chemistry, ETH Zürich, Zurich, Switzerland
| | - Viviane Zelenay
- Laboratory of Physical Chemistry, Department of Chemistry, ETH Zürich, Zurich, Switzerland
| | - Alexander Sobol
- Laboratory of Physical Chemistry, Department of Chemistry, ETH Zürich, Zurich, Switzerland
| | - Jason Greenwald
- Laboratory of Physical Chemistry, Department of Chemistry, ETH Zürich, Zurich, Switzerland
- * E-mail: (JG); (RR)
| | - Roland Riek
- Laboratory of Physical Chemistry, Department of Chemistry, ETH Zürich, Zurich, Switzerland
- * E-mail: (JG); (RR)
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89
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Srivastava A, Balaji PV. Molecular events during the early stages of aggregation of GNNQQNY: An all atom MD simulation study of randomly dispersed peptides. J Struct Biol 2015; 192:376-391. [DOI: 10.1016/j.jsb.2015.09.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 09/26/2015] [Accepted: 09/30/2015] [Indexed: 12/11/2022]
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Peptide-Induced Amyloid-Like Conformational Transitions in Proteins. INTERNATIONAL JOURNAL OF PEPTIDES 2015; 2015:723186. [PMID: 26435719 PMCID: PMC4578744 DOI: 10.1155/2015/723186] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 08/03/2015] [Accepted: 08/04/2015] [Indexed: 12/12/2022]
Abstract
Changes in protein conformation can occur both as part of normal protein functioning and during disease pathogenesis. The most common conformational diseases are amyloidoses. Sometimes the development of a number of diseases which are not traditionally related to amyloidoses is associated with amyloid-like conformational transitions of proteins. Also, amyloid-like aggregates take part in normal physiological processes such as memorization and cell signaling. Several primary structural features of a protein are involved in conformational transitions. Also the protein proteolytic fragments can cause the conformational transitions in the protein. Short peptides which could be produced during the protein life cycle or which are encoded by short open reading frames can affect the protein conformation and function.
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91
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Abstract
Highly sophisticated mechanisms that modulate protein structure and function, which involve synthesis and degradation, have evolved to maintain cellular homeostasis. Perturbations in these mechanisms can lead to protein dysfunction as well as deleterious cell processes. Therefore in recent years the etiology of a great number of diseases has been attributed to failures in mechanisms that modulate protein structure. Interconnections among metabolic and cell signaling pathways are critical for homeostasis to converge on mechanisms associated with protein folding as well as for the preservation of the native structure of proteins. For instance, imbalances in secretory protein synthesis pathways lead to a condition known as endoplasmic reticulum (ER) stress which elicits the adaptive unfolded protein response (UPR). Therefore, taking this into consideration, a key part of this paper is developed around the protein folding phenomenon, and cellular mechanisms which support this pivotal condition. We provide an overview of chaperone protein function, UPR via, spatial compartmentalization of protein folding, proteasome role, autophagy, as well as the intertwining between these processes. Several diseases are known to have a molecular etiology in the malfunction of mechanisms responsible for protein folding and in the shielding of native structure, phenomena which ultimately lead to misfolded protein accumulation. This review centers on our current knowledge about pathways that modulate protein folding, and cell responses involved in protein homeostasis.
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92
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Sikosek T, Chan HS. Biophysics of protein evolution and evolutionary protein biophysics. J R Soc Interface 2015; 11:20140419. [PMID: 25165599 DOI: 10.1098/rsif.2014.0419] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The study of molecular evolution at the level of protein-coding genes often entails comparing large datasets of sequences to infer their evolutionary relationships. Despite the importance of a protein's structure and conformational dynamics to its function and thus its fitness, common phylogenetic methods embody minimal biophysical knowledge of proteins. To underscore the biophysical constraints on natural selection, we survey effects of protein mutations, highlighting the physical basis for marginal stability of natural globular proteins and how requirement for kinetic stability and avoidance of misfolding and misinteractions might have affected protein evolution. The biophysical underpinnings of these effects have been addressed by models with an explicit coarse-grained spatial representation of the polypeptide chain. Sequence-structure mappings based on such models are powerful conceptual tools that rationalize mutational robustness, evolvability, epistasis, promiscuous function performed by 'hidden' conformational states, resolution of adaptive conflicts and conformational switches in the evolution from one protein fold to another. Recently, protein biophysics has been applied to derive more accurate evolutionary accounts of sequence data. Methods have also been developed to exploit sequence-based evolutionary information to predict biophysical behaviours of proteins. The success of these approaches demonstrates a deep synergy between the fields of protein biophysics and protein evolution.
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Affiliation(s)
- Tobias Sikosek
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Department of Physics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Hue Sun Chan
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Department of Physics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
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93
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Knowles TPJ, Vendruscolo M, Dobson CM. The amyloid state and its association with protein misfolding diseases. Nat Rev Mol Cell Biol 2014; 15:384-96. [PMID: 24854788 DOI: 10.1038/nrm3810] [Citation(s) in RCA: 1625] [Impact Index Per Article: 162.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The phenomenon of protein aggregation and amyloid formation has become the subject of rapidly increasing research activities across a wide range of scientific disciplines. Such activities have been stimulated by the association of amyloid deposition with a range of debilitating medical disorders, from Alzheimer's disease to type II diabetes, many of which are major threats to human health and welfare in the modern world. It has become clear, however, that the ability to form the amyloid state is more general than previously imagined, and that its study can provide unique insights into the nature of the functional forms of peptides and proteins, as well as understanding the means by which protein homeostasis can be maintained and protein metastasis avoided.
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Affiliation(s)
- Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Christopher M Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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94
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Daskalov A, Gantner M, Wälti MA, Schmidlin T, Chi CN, Wasmer C, Schütz A, Ceschin J, Clavé C, Cescau S, Meier B, Riek R, Saupe SJ. Contribution of specific residues of the β-solenoid fold to HET-s prion function, amyloid structure and stability. PLoS Pathog 2014; 10:e1004158. [PMID: 24945274 PMCID: PMC4055769 DOI: 10.1371/journal.ppat.1004158] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 04/15/2014] [Indexed: 01/12/2023] Open
Abstract
The [Het-s] prion of the fungus Podospora anserina represents a good model system for studying the structure-function relationship in amyloid proteins because a high resolution solid-state NMR structure of the amyloid prion form of the HET-s prion forming domain (PFD) is available. The HET-s PFD adopts a specific β-solenoid fold with two rungs of β-strands delimiting a triangular hydrophobic core. A C-terminal loop folds back onto the rigid core region and forms a more dynamic semi-hydrophobic pocket extending the hydrophobic core. Herein, an alanine scanning mutagenesis of the HET-s PFD was conducted. Different structural elements identified in the prion fold such as the triangular hydrophobic core, the salt bridges, the asparagines ladders and the C-terminal loop were altered and the effect of these mutations on prion function, fibril structure and stability was assayed. Prion activity and structure were found to be very robust; only a few key mutations were able to corrupt structure and function. While some mutations strongly destabilize the fold, many substitutions in fact increase stability of the fold. This increase in structural stability did not influence prion formation propensity in vivo. However, if an Ala replacement did alter the structure of the core or did influence the shape of the denaturation curve, the corresponding variant showed a decreased prion efficacy. It is also the finding that in addition to the structural elements of the rigid core region, the aromatic residues in the C-terminal semi-hydrophobic pocket are critical for prion propagation. Mutations in the latter region either positively or negatively affected prion formation. We thus identify a region that modulates prion formation although it is not part of the rigid cross-β core, an observation that might be relevant to other amyloid models.
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Affiliation(s)
- Asen Daskalov
- Institut de Biochimie et de Génétique Cellulaire, Unité Mixte de Recherche 5095, Centre National de la Recherche Scientifique Université de Bordeaux, Bordeaux, France
| | - Matthias Gantner
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Marielle Aulikki Wälti
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Thierry Schmidlin
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Celestine N. Chi
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Christian Wasmer
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Anne Schütz
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Johanna Ceschin
- Institut de Biochimie et de Génétique Cellulaire, Unité Mixte de Recherche 5095, Centre National de la Recherche Scientifique Université de Bordeaux, Bordeaux, France
| | - Corinne Clavé
- Institut de Biochimie et de Génétique Cellulaire, Unité Mixte de Recherche 5095, Centre National de la Recherche Scientifique Université de Bordeaux, Bordeaux, France
| | - Sandra Cescau
- Institut de Biochimie et de Génétique Cellulaire, Unité Mixte de Recherche 5095, Centre National de la Recherche Scientifique Université de Bordeaux, Bordeaux, France
| | - Beat Meier
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Sven J. Saupe
- Institut de Biochimie et de Génétique Cellulaire, Unité Mixte de Recherche 5095, Centre National de la Recherche Scientifique Université de Bordeaux, Bordeaux, France
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95
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Are proposed early genetic codes capable of encoding viable proteins? J Mol Evol 2014; 78:263-74. [PMID: 24826911 DOI: 10.1007/s00239-014-9622-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 04/28/2014] [Indexed: 01/10/2023]
Abstract
Proteins are elaborate biopolymers balancing between contradicting intrinsic propensities to fold, aggregate, or remain disordered. Assessing their primary structural preferences observable without evolutionary optimization has been reinforced by the recent identification of de novo proteins that have emerged from previously non-coding sequences. In this paper we investigate structural preferences of hypothetical proteins translated from random DNA segments using the standard genetic code and three of its proposed evolutionarily predecessor models encoding 10, 6, and 4 amino acids, respectively. Our only main assumption is that the disorder, aggregation, and transmembrane helix predictions used are able to reflect the differences in the trends of the protein sets investigated. We found that the 10-residue code encodes proteins that resemble modern proteins in their predicted structural properties. All of the investigated early genetic codes give rise to proteins with enhanced disorder and diminished aggregation propensities. Our results suggest that an ancestral genetic code similar to the proposed 10-residue one is capable of encoding functionally diverse proteins but these might have existed under conditions different from today's common physiological ones. The existence of a protein functional repertoire for the investigated earlier stages which is quite distinct as it is today can be deduced from the presented results.
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96
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Srivastava A, Balaji PV. Interplay of sequence, topology and termini charge in determining the stability of the aggregates of GNNQQNY mutants: a molecular dynamics study. PLoS One 2014; 9:e96660. [PMID: 24817093 PMCID: PMC4015988 DOI: 10.1371/journal.pone.0096660] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 04/11/2014] [Indexed: 01/16/2023] Open
Abstract
This study explores the stabilities of single sheet parallel systems of three sequence variants of 1GNNQQNY7, N2D, N2S and N6D, with variations in aggregate size (5–8) and termini charge (charged or neutral). The aggregates were simulated at 300 and 330 K. These mutations decrease amyloid formation in the yeast prion protein Sup35. The present study finds that these mutations cause instability even in the peptide context. The protonation status of termini is found to be a key determinant of stabilities; other determinants are sequence, position of mutation and aggregate size. All systems with charged termini are unstable, whereas both stable and unstable systems are found when the termini are neutral. When termini are charged, the largest stable aggregate for the N2S and N6D systems has 3 to 4 peptides whereas N2D mutation supports oligomers of larger size (5-and 6-mers) as well. Mutation at 2nd position (N2S and N2D) results in fewer H-bonds at the mutated as well as neighboring (Gly1/Gln4) positions. However, no such effect is found if mutation is at 6th position (N6D). The effect of Asn→Asp mutation depends on the position and termini charge: it is more destabilizing at the 2nd position than at the 6th in case of neutral termini, however, the opposite is true in case of charged termini. Appearance of twist in stable systems and in smaller aggregates formed in unstable systems suggests that twist is integral to amyloid arrangement. Disorder, dissociation or rearrangement of peptides, disintegration or collapse of aggregates and formation of amorphous aggregates observed in these simulations are likely to occur during the early stages of aggregation also. The smaller aggregates formed due to such events have a variety of arrangements of peptides. This suggests polymorphic nature of oligomers and presence of a heterogeneous mixture of oligomers during early stages of aggregation.
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Affiliation(s)
- Alka Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Petety V. Balaji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
- * E-mail:
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97
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Linser R, Sarkar R, Krushelnitzky A, Mainz A, Reif B. Dynamics in the solid-state: perspectives for the investigation of amyloid aggregates, membrane proteins and soluble protein complexes. JOURNAL OF BIOMOLECULAR NMR 2014; 59:1-14. [PMID: 24595988 DOI: 10.1007/s10858-014-9822-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 02/26/2014] [Indexed: 06/03/2023]
Abstract
Aggregates formed by amyloidogenic peptides and proteins and reconstituted membrane protein preparations differ significantly in terms of the spectral quality that they display in solid-state NMR experiments. Structural heterogeneity and dynamics can both in principle account for that observation. This perspectives article aims to point out challenges and limitations, but also potential opportunities in the investigation of these systems.
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Affiliation(s)
- Rasmus Linser
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA, 02115, USA
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98
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Russell MJ, Barge LM, Bhartia R, Bocanegra D, Bracher PJ, Branscomb E, Kidd R, McGlynn S, Meier DH, Nitschke W, Shibuya T, Vance S, White L, Kanik I. The drive to life on wet and icy worlds. ASTROBIOLOGY 2014; 14:308-43. [PMID: 24697642 PMCID: PMC3995032 DOI: 10.1089/ast.2013.1110] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 02/02/2014] [Indexed: 05/22/2023]
Abstract
This paper presents a reformulation of the submarine alkaline hydrothermal theory for the emergence of life in response to recent experimental findings. The theory views life, like other self-organizing systems in the Universe, as an inevitable outcome of particular disequilibria. In this case, the disequilibria were two: (1) in redox potential, between hydrogen plus methane with the circuit-completing electron acceptors such as nitrite, nitrate, ferric iron, and carbon dioxide, and (2) in pH gradient between an acidulous external ocean and an alkaline hydrothermal fluid. Both CO2 and CH4 were equally the ultimate sources of organic carbon, and the metal sulfides and oxyhydroxides acted as protoenzymatic catalysts. The realization, now 50 years old, that membrane-spanning gradients, rather than organic intermediates, play a vital role in life's operations calls into question the idea of "prebiotic chemistry." It informs our own suggestion that experimentation should look to the kind of nanoengines that must have been the precursors to molecular motors-such as pyrophosphate synthetase and the like driven by these gradients-that make life work. It is these putative free energy or disequilibria converters, presumably constructed from minerals comprising the earliest inorganic membranes, that, as obstacles to vectorial ionic flows, present themselves as the candidates for future experiments. Key Words: Methanotrophy-Origin of life. Astrobiology 14, 308-343. The fixation of inorganic carbon into organic material (autotrophy) is a prerequisite for life and sets the starting point of biological evolution. (Fuchs, 2011 ) Further significant progress with the tightly membrane-bound H(+)-PPase family should lead to an increased insight into basic requirements for the biological transport of protons through membranes and its coupling to phosphorylation. (Baltscheffsky et al., 1999 ).
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99
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Cámara-Artigas A, Martínez-Rodríguez S, Ortiz-Salmerón E, Martín-García JM. 3D domain swapping in a chimeric c-Src SH3 domain takes place through two hinge loops. J Struct Biol 2014; 186:195-203. [DOI: 10.1016/j.jsb.2014.02.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Revised: 02/10/2014] [Accepted: 02/11/2014] [Indexed: 11/29/2022]
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Rufo CM, Moroz YS, Moroz OV, Stöhr J, Smith TA, Hu X, DeGrado WF, Korendovych IV. Short peptides self-assemble to produce catalytic amyloids. Nat Chem 2014; 6:303-9. [PMID: 24651196 PMCID: PMC3996680 DOI: 10.1038/nchem.1894] [Citation(s) in RCA: 461] [Impact Index Per Article: 46.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 02/12/2014] [Indexed: 12/22/2022]
Abstract
Enzymes fold into unique three-dimensional structures, which underlie their remarkable catalytic properties. The requirement to adopt a stable, folded conformation is likely to contribute to their relatively large size (>10,000 Da). However, much shorter peptides can achieve well-defined conformations through the formation of amyloid fibrils. To test whether short amyloid-forming peptides might in fact be capable of enzyme-like catalysis, we designed a series of seven-residue peptides that act as Zn(2+)-dependent esterases. Zn(2+) helps stabilize the fibril formation, while also acting as a cofactor to catalyse acyl ester hydrolysis. These results indicate that prion-like fibrils are able to not only catalyse their own formation, but they can also catalyse chemical reactions. Thus, they might have served as intermediates in the evolution of modern-day enzymes. These results also have implications for the design of self-assembling nanostructured catalysts including ones containing a variety of biological and non-biological metal ions.
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Affiliation(s)
- Caroline M. Rufo
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Yurii S. Moroz
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Olesia V. Moroz
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Jan Stöhr
- Institute for Neurodegenerative Diseases and Department of Neurology, University of California – San Francisco, San Francisco, CA 94143, USA
| | - Tyler A. Smith
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Xiaozhen Hu
- Department of Pharmaceutical Chemistry, University of California – San Francisco, San Francisco, CA 94158, USA
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry, University of California – San Francisco, San Francisco, CA 94158, USA
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