1
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Martínez-Rodríguez S, Cámara-Artigas A, Gavira JA. First 3-D structural evidence of a native-like intertwined dimer in the acylphosphatase family. Biochem Biophys Res Commun 2023; 682:85-90. [PMID: 37804591 DOI: 10.1016/j.bbrc.2023.09.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 09/20/2023] [Indexed: 10/09/2023]
Abstract
Acylphosphatase (AcP, EC 3.6.1.7) is a small model protein conformed by a ferredoxin-like fold, profoundly studied to get insights into protein folding and aggregation processes. Numerous studies focused on the aggregation and/or amyloidogenic properties of AcPs suggest the importance of edge-β-strands in the process. In this work, we present the first crystallographic structure of Escherichia coli AcP (EcoAcP), showing notable differences with the only available NMR structure for this enzyme. EcoAcP is crystalised as an intertwined dimer formed by replacing a single C-terminal β-strand between two protomers, suggesting a flexible character of the C-terminal edge of EcoAcP. Despite numerous works where AcP from different sources have been used as a model system for protein aggregation, our domain-swapped EcoAcP structure is the first 3-D structural evidence of native-like aggregated species for any AcP reported to date, providing clues on molecular determinants unleashing aggregation.
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Affiliation(s)
- Sergio Martínez-Rodríguez
- Department of Biochemistry and Molecular Biology III and Immunology, University of Granada, Avenida de La Investigación 11, Granada, 18071, Spain; Laboratorio de Estudios Cristalográficos, CSIC-UGR, Avda. de Las Palmeras 4, Armilla, Granada, 18100, Spain.
| | - Ana Cámara-Artigas
- Department of Chemistry and Physics, University of Almería, Agrifood Campus of International Excellence (ceiA3), Centro de Investigación en Agrosistemas Intensivos Mediterráneos y Biotecnología Agroalimentaria (CIAMBITAL), Carretera de Sacramento S/n, Almería, 04120, Spain
| | - Jose Antonio Gavira
- Laboratorio de Estudios Cristalográficos, CSIC-UGR, Avda. de Las Palmeras 4, Armilla, Granada, 18100, Spain
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2
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Fusco G, Bemporad F, Chiti F, Dobson CM, De Simone A. The role of structural dynamics in the thermal adaptation of hyperthermophilic enzymes. Front Mol Biosci 2022; 9:981312. [PMID: 36158582 PMCID: PMC9490001 DOI: 10.3389/fmolb.2022.981312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
Proteins from hyperthermophilic organisms are evolutionary optimised to adopt functional structures and dynamics under conditions in which their mesophilic homologues are generally inactive or unfolded. Understanding the nature of such adaptation is of crucial interest to clarify the underlying mechanisms of biological activity in proteins. Here we measured NMR residual dipolar couplings of a hyperthermophilic acylphosphatase enzyme at 80°C and used these data to generate an accurate structural ensemble representative of its native state. The resulting energy landscape was compared to that obtained for a human homologue at 37°C, and additional NMR experiments were carried out to probe fast (15N relaxation) and slow (H/D exchange) backbone dynamics, collectively sampling fluctuations of the two proteins ranging from the nanosecond to the millisecond timescale. The results identified key differences in the strategies for protein-protein and protein-ligand interactions of the two enzymes at the respective physiological temperatures. These include the dynamical behaviour of a β-strand involved in the protection against aberrant protein aggregation and concerted motions of loops involved in substrate binding and catalysis. Taken together these results elucidate the structure-dynamics-function relationship associated with the strategies of thermal adaptation of protein molecules.
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Affiliation(s)
- Giuliana Fusco
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Francesco Bemporad
- Section of Biochemistry, Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, Florence, Italy
| | - Fabrizio Chiti
- Section of Biochemistry, Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, Florence, Italy
| | | | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Department of Pharmacy, University of Naples “Federico II”, Naples, Italy
- *Correspondence: Alfonso De Simone,
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3
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L. Almeida Z, M. M. Brito R. Structure and Aggregation Mechanisms in Amyloids. Molecules 2020; 25:molecules25051195. [PMID: 32155822 PMCID: PMC7179426 DOI: 10.3390/molecules25051195] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 12/27/2022] Open
Abstract
The aggregation of a polypeptide chain into amyloid fibrils and their accumulation and deposition into insoluble plaques and intracellular inclusions is the hallmark of several misfolding diseases known as amyloidoses. Alzheimer′s, Parkinson′s and Huntington’s diseases are some of the approximately 50 amyloid diseases described to date. The identification and characterization of the molecular species critical for amyloid formation and disease development have been the focus of intense scrutiny. Methods such as X-ray and electron diffraction, solid-state nuclear magnetic resonance spectroscopy (ssNMR) and cryo-electron microscopy (cryo-EM) have been extensively used and they have contributed to shed a new light onto the structure of amyloid, revealing a multiplicity of polymorphic structures that generally fit the cross-β amyloid motif. The development of rational therapeutic approaches against these debilitating and increasingly frequent misfolding diseases requires a thorough understanding of the molecular mechanisms underlying the amyloid cascade. Here, we review the current knowledge on amyloid fibril formation for several proteins and peptides from a kinetic and thermodynamic point of view, the structure of the molecular species involved in the amyloidogenic process, and the origin of their cytotoxicity.
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4
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Lévy E, El Banna N, Baïlle D, Heneman-Masurel A, Truchet S, Rezaei H, Huang ME, Béringue V, Martin D, Vernis L. Causative Links between Protein Aggregation and Oxidative Stress: A Review. Int J Mol Sci 2019; 20:ijms20163896. [PMID: 31405050 PMCID: PMC6719959 DOI: 10.3390/ijms20163896] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 07/30/2019] [Accepted: 08/01/2019] [Indexed: 01/17/2023] Open
Abstract
Compelling evidence supports a tight link between oxidative stress and protein aggregation processes, which are noticeably involved in the development of proteinopathies, such as Alzheimer’s disease, Parkinson’s disease, and prion disease. The literature is tremendously rich in studies that establish a functional link between both processes, revealing that oxidative stress can be either causative, or consecutive, to protein aggregation. Because oxidative stress monitoring is highly challenging and may often lead to artefactual results, cutting-edge technical tools have been developed recently in the redox field, improving the ability to measure oxidative perturbations in biological systems. This review aims at providing an update of the previously known functional links between oxidative stress and protein aggregation, thereby revisiting the long-established relationship between both processes.
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Affiliation(s)
- Elise Lévy
- Molecular Virology and Immunology Unit (VIM-UR892), INRA, Université Paris-Saclay, 78352 Jouy-en-Josas, France
- Institut Curie, PSL Research University, CNRS UMR3348, Université Paris-Sud, Université Paris-Saclay, 91400 Orsay, France
| | - Nadine El Banna
- Institut Curie, PSL Research University, CNRS UMR3348, Université Paris-Sud, Université Paris-Saclay, 91400 Orsay, France
| | - Dorothée Baïlle
- Institut Curie, PSL Research University, CNRS UMR3348, Université Paris-Sud, Université Paris-Saclay, 91400 Orsay, France
| | - Amélie Heneman-Masurel
- Institut Curie, PSL Research University, CNRS UMR3348, Université Paris-Sud, Université Paris-Saclay, 91400 Orsay, France
| | - Sandrine Truchet
- Molecular Virology and Immunology Unit (VIM-UR892), INRA, Université Paris-Saclay, 78352 Jouy-en-Josas, France
| | - Human Rezaei
- Molecular Virology and Immunology Unit (VIM-UR892), INRA, Université Paris-Saclay, 78352 Jouy-en-Josas, France
| | - Meng-Er Huang
- Institut Curie, PSL Research University, CNRS UMR3348, Université Paris-Sud, Université Paris-Saclay, 91400 Orsay, France
| | - Vincent Béringue
- Molecular Virology and Immunology Unit (VIM-UR892), INRA, Université Paris-Saclay, 78352 Jouy-en-Josas, France
| | - Davy Martin
- Molecular Virology and Immunology Unit (VIM-UR892), INRA, Université Paris-Saclay, 78352 Jouy-en-Josas, France.
| | - Laurence Vernis
- Institut Curie, PSL Research University, CNRS UMR3348, Université Paris-Sud, Université Paris-Saclay, 91400 Orsay, France.
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5
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Charlton T, Shah V, Lynch T, Candreva J, Chau E, Yang Y, Kim H, Wood A, Kim JR. Amyloid Aggregation of Bacillus circulans Xylanase under Native Conditions and its Modulation by β-Amyloid-Derived Peptide Fragments. Chembiochem 2018; 19:2566-2574. [PMID: 30332530 DOI: 10.1002/cbic.201800472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/13/2018] [Indexed: 12/31/2022]
Abstract
The aggregation of intrinsically disordered proteins into fibrils is implicated in many neurodegenerative diseases. Amyloid aggregation is a generic property of proteins as evidenced by globular proteins that often form amyloid aggregates under partially denaturing conditions. Recently, multiple lines of evidence have suggested that the amyloid aggregation of globular proteins can also occur under native conditions. Unfortunately, amyloid aggregation under native conditions has been demonstrated in only a handful of cases. Engineering a globular protein's amyloid aggregation might benefit from its fusion to an amyloid-derived fragment with reduced aggregation propensity. Unfortunately, the impacts of such fragments on the amyloid aggregation under native conditions have yet to be examined. In this study, we show that a globular protein, Bacillus circulans xylanase (BCX), can aggregate to form amyloid fibrils under native conditions. When BCX was mixed with or fused to the non-self-aggregating fragments, KLVFWAK and ELVFWAE-which were derived from β-amyloid (Aβ)-they modulated the BCX amyloid aggregation to differing extents. This study also provides insight into a correlation between the kinetic stability and amyloid aggregation of BCX, and supports a view that Aβ-derived fragments can be useful for the modulating amyloid aggregation of some, though not all, proteins.
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Affiliation(s)
- Timothy Charlton
- Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY, 11201, USA
| | - Vandan Shah
- Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY, 11201, USA
| | - Tonianna Lynch
- Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY, 11201, USA
| | - Jason Candreva
- Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY, 11201, USA
| | - Edward Chau
- Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY, 11201, USA
| | - YanXi Yang
- Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY, 11201, USA
| | - Hyunjoo Kim
- Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY, 11201, USA
| | - Amy Wood
- Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY, 11201, USA
| | - Jin Ryoun Kim
- Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY, 11201, USA
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6
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Elia F, Cantini F, Chiti F, Dobson CM, Bemporad F. Direct Conversion of an Enzyme from Native-like to Amyloid-like Aggregates within Inclusion Bodies. Biophys J 2017; 112:2540-2551. [PMID: 28636911 PMCID: PMC5479110 DOI: 10.1016/j.bpj.2017.05.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 05/02/2017] [Accepted: 05/08/2017] [Indexed: 01/29/2023] Open
Abstract
The acylphosphatase from Sulfolobus solfataricus (Sso AcP) is a globular protein able to aggregate in vitro from a native-like conformational ensemble without the need for a transition across the major unfolding energy barrier. This process leads to the formation of assemblies in which the protein retains its native-like structure, which subsequently convert into amyloid-like aggregates. Here, we investigate the mechanism by which Sso AcP aggregates in vivo to form bacterial inclusion bodies after expression in E. coli. Shortly after the initiation of expression, Sso AcP is incorporated into inclusion bodies as a native-like protein, still exhibiting small but significant enzymatic activity. Additional experiments revealed that this overall process of aggregation is enhanced by the presence of the unfolded N-terminal region of the sequence and by destabilization of the globular segment of the protein. At later times, the Sso AcP molecules in the inclusion bodies lose their native-like properties and convert into β-sheet-rich amyloid-like structures, as indicated by their ability to bind thioflavin T and Congo red. These results show that the aggregation behavior of this protein is similar in vivo to that observed in vitro, and that, at least for a predominant part of the protein population, the transition from a native to an amyloid-like structure occurs within the aggregate state.
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Affiliation(s)
- Francesco Elia
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio," University of Florence, Firenze, Italy
| | - Francesca Cantini
- Centro Risonanze Magnetiche (CERM) and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio," University of Florence, Firenze, Italy
| | | | - Francesco Bemporad
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio," University of Florence, Firenze, Italy.
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7
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Bemporad F, Ramazzotti M. From the Evolution of Protein Sequences Able to Resist Self-Assembly to the Prediction of Aggregation Propensity. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 329:1-47. [PMID: 28109326 DOI: 10.1016/bs.ircmb.2016.08.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Folding of polypeptide chains into biologically active entities is an astonishingly complex process, determined by the nature and the sequence of residues emerging from ribosomes. While it has been long believed that evolution has pressed genomes so that specific sequences could adopt unique, functional three-dimensional folds, it is now clear that complex protein machineries act as quality control system and supervise folding. Notwithstanding that, events such as erroneous folding, partial folding, or misfolding are frequent during the life of a cell or a whole organism, and they can escape controls. One of the possible outcomes of this misbehavior is cross-β aggregation, a super secondary structure which represents the hallmark of self-assembled, well organized, and extremely ordered structures termed amyloid fibrils. What if evolution would have not taken into account such possibilities? Twenty years of research point toward the idea that, in fact, evolution has constantly supervised the risk of errors and minimized their impact. In this review we tried to survey the major findings in the amyloid field, trying to describe what the real pitfalls of protein folding are-from an evolutionary perspective-and how sequence and structural features have evolved to balance the need for perfect, dynamic, functionally efficient structures, and the detrimental effects implicit in the dangerous process of folding. We will discuss how the knowledge obtained from these studies has been employed to produce computational methods able to assess, predict, and discriminate the aggregation properties of protein sequences.
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Affiliation(s)
- F Bemporad
- Università degli Studi di Firenze, Firenze, Italy.
| | - M Ramazzotti
- Università degli Studi di Firenze, Firenze, Italy.
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8
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Lim KH, Dasari AKR, Hung I, Gan Z, Kelly JW, Wright PE, Wemmer DE. Solid-State NMR Studies Reveal Native-like β-Sheet Structures in Transthyretin Amyloid. Biochemistry 2016; 55:5272-8. [PMID: 27589034 DOI: 10.1021/acs.biochem.6b00649] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Structural characterization of amyloid rich in cross-β structures is crucial for unraveling the molecular basis of protein misfolding and amyloid formation associated with a wide range of human disorders. Elucidation of the β-sheet structure in noncrystalline amyloid has, however, remained an enormous challenge. Here we report structural analyses of the β-sheet structure in a full-length transthyretin amyloid using solid-state NMR spectroscopy. Magic-angle-spinning (MAS) solid-state NMR was employed to investigate native-like β-sheet structures in the amyloid state using selective labeling schemes for more efficient solid-state NMR studies. Analyses of extensive long-range (13)C-(13)C correlation MAS spectra obtained with selectively (13)CO- and (13)Cα-labeled TTR reveal that the two main β-structures in the native state, the CBEF and DAGH β-sheets, remain intact after amyloid formation. The tertiary structural information would be of great use for examining the quaternary structure of TTR amyloid.
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Affiliation(s)
- Kwang Hun Lim
- Department of Chemistry, East Carolina University , Greenville, North Carolina 27858, United States
| | - Anvesh K R Dasari
- Department of Chemistry, East Carolina University , Greenville, North Carolina 27858, United States
| | - Ivan Hung
- Center of Interdisciplinary Magnetic Resonance (CIMAR), National High Magnetic Field Laboratory (NHMFL) , 1800 East, Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Zhehong Gan
- Center of Interdisciplinary Magnetic Resonance (CIMAR), National High Magnetic Field Laboratory (NHMFL) , 1800 East, Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | | | | | - David E Wemmer
- Department of Chemistry, University of California , Berkeley, California 94720, United States
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9
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Protein Aggregation and Its Prediction. MULTIFACETED ROLES OF CRYSTALLOGRAPHY IN MODERN DRUG DISCOVERY 2015. [DOI: 10.1007/978-94-017-9719-1_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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10
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Li GP, Jiang L, Ni JZ, Liu Q, Zhang Y. Computational identification of a new SelD-like family that may participate in sulfur metabolism in hyperthermophilic sulfur-reducing archaea. BMC Genomics 2014; 15:908. [PMID: 25326317 PMCID: PMC4210487 DOI: 10.1186/1471-2164-15-908] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 10/07/2014] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Selenium (Se) and sulfur (S) are closely related elements that exhibit similar chemical properties. Some genes related to S metabolism are also involved in Se utilization in many organisms. However, the evolutionary relationship between the two utilization traits is unclear. RESULTS In this study, we conducted a comparative analysis of the selenophosphate synthetase (SelD) family, a key protein for all known Se utilization traits, in all sequenced archaea. Our search showed a very limited distribution of SelD and Se utilization in this kingdom. Interestingly, a SelD-like protein was detected in two orders of Crenarchaeota: Sulfolobales and Thermoproteales. Sequence and phylogenetic analyses revealed that SelD-like protein contains the same domain and conserved functional residues as those of SelD, and might be involved in S metabolism in these S-reducing organisms. Further genome-wide analysis of patterns of gene occurrence in different thermoproteales suggested that several genes, including SirA-like, Prx-like and adenylylsulfate reductase, were strongly related to SelD-like gene. Based on these findings, we proposed a simple model wherein SelD-like may play an important role in the biosynthesis of certain thiophosphate compound. CONCLUSIONS Our data suggest novel genes involved in S metabolism in hyperthermophilic S-reducing archaea, and may provide a new window for understanding the complex relationship between Se and S metabolism in archaea.
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Affiliation(s)
| | | | | | | | - Yan Zhang
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, P, R, China.
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11
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Garcia-Pardo J, Graña-Montes R, Fernandez-Mendez M, Ruyra A, Roher N, Aviles FX, Lorenzo J, Ventura S. Amyloid formation by human carboxypeptidase D transthyretin-like domain under physiological conditions. J Biol Chem 2014; 289:33783-96. [PMID: 25294878 DOI: 10.1074/jbc.m114.594804] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein aggregation is linked to a growing list of diseases, but it is also an intrinsic property of polypeptides, because the formation of functional globular proteins comes at the expense of an inherent aggregation propensity. Certain proteins can access aggregation-prone states from native-like conformations without the need to cross the energy barrier for unfolding. This is the case of transthyretin (TTR), a homotetrameric protein whose dissociation into its monomers initiates the aggregation cascade. Domains with structural homology to TTR exist in a number of proteins, including the M14B subfamily carboxypeptidases. We show here that the monomeric transthyretin-like domain of human carboxypeptidase D aggregates under close to physiological conditions into amyloid structures, with the population of folded but aggregation-prone states being controlled by the conformational stability of the domain. We thus confirm that the TTR fold keeps a generic residual aggregation propensity upon folding, resulting from the presence of preformed amyloidogenic β-strands in the native state. These structural elements should serve for functional/structural purposes, because they have not been purged out by evolution, but at the same time they put proteins like carboxypeptidase D at risk of aggregation in biological environments and thus can potentially lead to deposition diseases.
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Affiliation(s)
- Javier Garcia-Pardo
- From the Institut de Biotecnologia i Biomedicina, Departaments de Bioquimica i Biologia Molecular and
| | - Ricardo Graña-Montes
- From the Institut de Biotecnologia i Biomedicina, Departaments de Bioquimica i Biologia Molecular and
| | - Marc Fernandez-Mendez
- From the Institut de Biotecnologia i Biomedicina, Departaments de Bioquimica i Biologia Molecular and
| | - Angels Ruyra
- From the Institut de Biotecnologia i Biomedicina
| | - Nerea Roher
- From the Institut de Biotecnologia i Biomedicina, Biologia Cel·lular, Immunologia i Fisiologia Animal, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Francesc X Aviles
- From the Institut de Biotecnologia i Biomedicina, Departaments de Bioquimica i Biologia Molecular and
| | - Julia Lorenzo
- From the Institut de Biotecnologia i Biomedicina, Departaments de Bioquimica i Biologia Molecular and
| | - Salvador Ventura
- From the Institut de Biotecnologia i Biomedicina, Departaments de Bioquimica i Biologia Molecular and
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12
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de Rosa M, Bemporad F, Pellegrino S, Chiti F, Bolognesi M, Ricagno S. Edge strand engineering prevents native-like aggregation in Sulfolobus solfataricus acylphosphatase. FEBS J 2014; 281:4072-84. [PMID: 24893801 DOI: 10.1111/febs.12861] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 05/19/2014] [Accepted: 05/23/2014] [Indexed: 01/09/2023]
Abstract
β-proteins are constantly threatened by the risk of aggregation because β-sheets are inherently structured for edge-to-edge interactions. To avoid native-like aggregation, evolution has resulted in a set of strategies that prevent intermolecular β-interactions. Acylphosphatase from Sulfolobus solfataricus (Sso AcP) represents a suitable model for the study of such a process. Under conditions promoting aggregation, Sso AcP acquires a native-like conformational state whereby an unstructured N-terminal segment interacts with the edge β-strand B4 of an adjacent Sso AcP molecule. Because B4 is poorly protected against aggregation, this interaction triggers the aggregation cascade without the need for unfolding. Recently, three single Sso AcP mutants (V84D, Y86E and V84P) were designed to engineer additional protection against aggregation in B4 and were observed to successfully impair native-like aggregation in all three variants at the expense of a lower stability. To understand the structural basis of the reduced aggregation propensity and lower stability, the crystal structures of the Sso AcP variants were determined in the present study. Structural analysis reveals that the V84D and Y86E mutations exert protection by the insertion of an edge negative charge. A conformationally less regular B4 underlies protection against aggregation in the V84P mutant. The thermodynamic basis of instability is discussed. Moreover, kinetic experiments indicate that aggregation of the three mutants is not native-like and is independent of the interaction between B4 and the unstructured N-terminal segment. The reported data rationalize previous evidence regarding Sso AcP native-like aggregation and provide a basis for the design of aggregation-free proteins. DATABASE The atomic coordinates and related experimental data for the Sso AcP mutants V84P, V84D, ΔN11 Y86E have been deposited in the Protein Data Bank under accession numbers 4OJ3, 4OJG and 4OJH, respectively. STRUCTURED DIGITAL ABSTRACT • Sso AcP and Sso AcP bind by fluorescence technology (View interaction).
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13
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Salvatella X. Structural aspects of amyloid formation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 117:73-101. [PMID: 23663966 DOI: 10.1016/b978-0-12-386931-9.00004-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Amyloid fibrils are highly organized and generally insoluble protein aggregates rich in β secondary structure that can be formed by a wide range of sequences. They have been the object of intense scrutiny because their formation has been associated with a number of neurodegenerative disorders such as Alzheimer's, Parkinson's, Huntington's, and Creutzfeldt-Jakob's diseases. As a consequence of these efforts, much is now known about the properties of proteins that render them prone to form amyloid fibrils, about the mechanism of fibrillation, about the molecular structures of the fibrils, and about the forces that stabilize them. The relationship between the structural properties of the monomeric protein and those of the corresponding aggregate has been, in particular, intensively studied. In this chapter, we will provide an account of current knowledge on this intriguing relationship and provide the reader with key references about this topic.
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14
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Raghunathan G, Soundrarajan N, Sokalingam S, Yun H, Lee SG. Deletional protein engineering based on stable fold. PLoS One 2012; 7:e51510. [PMID: 23240034 PMCID: PMC3519881 DOI: 10.1371/journal.pone.0051510] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 11/01/2012] [Indexed: 12/14/2022] Open
Abstract
Diversification of protein sequence-structure space is a major concern in protein engineering. Deletion mutagenesis can generate a protein sequence-structure space different from substitution mutagenesis mediated space, but it has not been widely used in protein engineering compared to substitution mutagenesis, because it causes a relatively huge range of structural perturbations of target proteins which often inactivates the proteins. In this study, we demonstrate that, using green fluorescent protein (GFP) as a model system, the drawback of the deletional protein engineering can be overcome by employing the protein structure with high stability. The systematic dissection of N-terminal, C-terminal and internal sequences of GFPs with two different stabilities showed that GFP with high stability (s-GFP), was more tolerant to the elimination of amino acids compared to a GFP with normal stability (n-GFP). The deletion studies of s-GFP enabled us to achieve three interesting variants viz. s-DL4, s-N14, and s-C225, which could not been obtained from n-GFP. The deletion of 191–196 loop sequences led to the variant s-DL4 that was expressed predominantly as insoluble form but mostly active. The s-N14 and s-C225 are the variants without the amino acid residues involving secondary structures around N- and C-terminals of GFP fold respectively, exhibiting comparable biophysical properties of the n-GFP. Structural analysis of the variants through computational modeling study gave a few structural insights that can explain the spectral properties of the variants. Our study suggests that the protein sequence-structure space of deletion mutants can be more efficiently explored by employing the protein structure with higher stability.
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Affiliation(s)
- Govindan Raghunathan
- Department of Chemical Engineering, Pusan National University, Busan, South Korea
| | | | - Sriram Sokalingam
- Department of Chemical Engineering, Pusan National University, Busan, South Korea
| | - Hyungdon Yun
- School of Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Sun-Gu Lee
- Department of Chemical Engineering, Pusan National University, Busan, South Korea
- * E-mail:
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15
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Xie JB, Cao Y, Pan H, Qin M, Yan ZQ, Xiong X, Wang W. Photoinduced fibrils formation of chicken egg white lysozyme under native conditions. Proteins 2012; 80:2501-13. [DOI: 10.1002/prot.24132] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 05/09/2012] [Accepted: 05/25/2012] [Indexed: 11/06/2022]
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16
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Bemporad F, De Simone A, Chiti F, Dobson C. Characterizing intermolecular interactions that initiate native-like protein aggregation. Biophys J 2012; 102:2595-604. [PMID: 22713575 PMCID: PMC3368139 DOI: 10.1016/j.bpj.2012.03.057] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 02/28/2012] [Accepted: 03/14/2012] [Indexed: 10/28/2022] Open
Abstract
Folded proteins can access aggregation-prone states without the need for transitions that cross the energy barriers for unfolding. In this study we characterized the initial steps of aggregation from a native-like state of the acylphosphatase from Sulfolobus solfataricus (Sso AcP). Using computer simulations restrained by experimental hydrogen/deuterium (H/D) exchange data, we provide direct evidence that under aggregation-promoting conditions Sso AcP populates a conformational ensemble in which native-like structure is retained throughout the sequence in the absence of local unfolding (N∗), although the protein exhibits an increase in hydrodynamic radius and dynamics. This transition leads an edge strand to experience an increased affinity for a specific unfolded segment of the protein. Direct measurements by means of H/D exchange rates, isothermal titration calorimetry, and intermolecular relaxation enhancements show that after formation of N∗, an intermolecular interaction with an antiparallel arrangement is established between the edge strand and the unfolded segment of the protein. However, under conditions that favor the fully native state of Sso AcP, such an interaction is not established. Thus, these results reveal a novel (to our knowledge) self-assembly mechanism for a folded protein that is based on the increased flexibility of highly aggregation-prone segments in the absence of local unfolding.
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Affiliation(s)
- Francesco Bemporad
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Alfonso De Simone
- Division of Molecular Biosciences, Imperial College London, London, United Kingdom
| | - Fabrizio Chiti
- Dipartimento di Scienze Biochimiche, Università degli Studi di Firenze, Firenze, Italy
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17
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Kamal MZ, Ahmad S, Molugu TR, Vijayalakshmi A, Deshmukh MV, Sankaranarayanan R, Rao NM. In vitro evolved non-aggregating and thermostable lipase: structural and thermodynamic investigation. J Mol Biol 2011; 413:726-41. [PMID: 21925508 DOI: 10.1016/j.jmb.2011.09.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2011] [Revised: 08/02/2011] [Accepted: 09/02/2011] [Indexed: 11/27/2022]
Abstract
Rational and in vitro evolutionary approaches to improve either protein stability or aggregation resistance were successful, but empirical rules for simultaneous improvement of both stability and aggregation resistance under denaturing conditions are still to be ascertained. We have created a robust variant of a lipase from Bacillus subtilis named "6B" using multiple rounds of in vitro evolution. T(m) and optimum activity temperature of 6B is 78 °C and 65 °C, respectively, which is ~22 °C and 30 °C higher than that of wild-type lipase. Most significantly, 6B does not aggregate upon heating. Physical basis of remarkable thermostability and non-aggregating behavior of 6B was explored using X-ray crystallography, NMR and differential scanning calorimetry. Our structural investigations highlight the importance of tightening of mobile regions of the molecule such as loops and helix termini to attain higher thermostability. Accordingly, NMR studies suggest a very rigid structure of 6B lipase. Further investigation suggested that reduction/perturbation of the large hydrophobic patches present in the wild-type protein structure, decreased propensity of amino acid sequence for aggregation and absence of aggregation-prone intermediate during thermal unfolding of 6B can account for its resistance to aggregation. Overall, our study suggest that better anchoring of the loops with the rest of the protein molecule through mutations particularly on the sites that perturb/disturb the exposed hydrophobic patches can simultaneously increase protein stability and aggregation resistance.
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Affiliation(s)
- Md Zahid Kamal
- Centre for Cellular and Molecular Biology (Council of Scientific and Industrial Research), Hyderabad 500007, India
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18
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Pagano K, Bemporad F, Fogolari F, Esposito G, Viglino P, Chiti F, Corazza A. Structural and dynamics characteristics of acylphosphatase from Sulfolobus solfataricus in the monomeric state and in the initial native-like aggregates. J Biol Chem 2010; 285:14689-700. [PMID: 20223823 PMCID: PMC2863212 DOI: 10.1074/jbc.m109.082156] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Revised: 03/08/2010] [Indexed: 02/04/2023] Open
Abstract
It has previously been shown that the acylphosphatase from Sulfolobus solfataricus is capable of forming amyloid-like aggregates under conditions in which the native structure is maintained and via the transient formation of native-like aggregates. Based on the previously determined NMR structure of the native protein, showing a ferredoxin-like fold and the peculiar presence of an unstructured N-terminal segment, we show here, at a molecular level using NMR spectroscopy, that indeed S. solfataricus acylphosphatase remains in a native-like conformation when placed in aggregating conditions and that such a native-like structure persists when the protein forms the initial aggregates, at least within the low molecular weight species. The analysis carried out under different solution conditions, based on the measurement of the combined (1)H and (15)N chemical shifts and hydrogen/deuterium exchange rates, enabled the most significant conformational changes to be monitored upon transfer of the monomeric state into aggregating conditions and upon formation of the initial native-like aggregates. Important increases of the hydrogen/deuterium exchange rates throughout the native protein, accompanied by small and localized structural changes, in the monomeric protein were observed. The results also allow the identification of the intermolecular interaction regions within the native-like aggregates, that involve, in particular, the N-terminal unstructured segment, the apical region including strands S4 and S5 with the connecting loop, and the opposite active site.
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Affiliation(s)
- Katiuscia Pagano
- From the Department of Biomedical Sciences and Technologies, University of Udine, Piazzale Kolbe 4, 33100 Udine, Italy
| | - Francesco Bemporad
- the Department of Biochemical Sciences, University of Firenze, Viale Morgagni 50, 50134, Firenze, Italy, and
| | - Federico Fogolari
- From the Department of Biomedical Sciences and Technologies, University of Udine, Piazzale Kolbe 4, 33100 Udine, Italy
- the Consorzio Interuniversitario Istituto Nazionale di Biostrutture e Biosistemi, Viale Medaglie d'Oro 305, 00136 Rome, Italy
| | - Gennaro Esposito
- From the Department of Biomedical Sciences and Technologies, University of Udine, Piazzale Kolbe 4, 33100 Udine, Italy
- the Consorzio Interuniversitario Istituto Nazionale di Biostrutture e Biosistemi, Viale Medaglie d'Oro 305, 00136 Rome, Italy
| | - Paolo Viglino
- From the Department of Biomedical Sciences and Technologies, University of Udine, Piazzale Kolbe 4, 33100 Udine, Italy
- the Consorzio Interuniversitario Istituto Nazionale di Biostrutture e Biosistemi, Viale Medaglie d'Oro 305, 00136 Rome, Italy
| | - Fabrizio Chiti
- the Department of Biochemical Sciences, University of Firenze, Viale Morgagni 50, 50134, Firenze, Italy, and
- the Consorzio Interuniversitario Istituto Nazionale di Biostrutture e Biosistemi, Viale Medaglie d'Oro 305, 00136 Rome, Italy
| | - Alessandra Corazza
- From the Department of Biomedical Sciences and Technologies, University of Udine, Piazzale Kolbe 4, 33100 Udine, Italy
- the Consorzio Interuniversitario Istituto Nazionale di Biostrutture e Biosistemi, Viale Medaglie d'Oro 305, 00136 Rome, Italy
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19
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Bemporad F, Chiti F. "Native-like aggregation" of the acylphosphatase from Sulfolobus solfataricus and its biological implications. FEBS Lett 2009; 583:2630-8. [PMID: 19595999 DOI: 10.1016/j.febslet.2009.07.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 07/07/2009] [Accepted: 07/09/2009] [Indexed: 11/23/2022]
Abstract
Studies in vitro show that globular proteins can experience the formation of native-like conformational states able to self-assemble with no need of transitions across the energy barrier for unfolding, and that such processes can lead eventually to the formation of amyloid-like species. Circumstantial evidence collected in vivo suggests that aggregation of native-like states can be a concrete possibility for living organisms and thus more relevant than previously thought. In this review we summarize the key observations collected on the "native-like aggregation" of the acylphosphatase from Sulfolobus solfataricus, a protein that has allowed the direct monitoring and analysis of native-like aggregates for its propensity to form rapidly native-like aggregates and their slow conversion into amyloid-like aggregates.
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Affiliation(s)
- Francesco Bemporad
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.
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20
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Abstract
The conversion of proteins from their soluble states into well-organized fibrillar aggregates is associated with a wide range of pathological conditions, including neurodegenerative diseases and systemic amyloidoses. In this review, we discuss the mechanism of aggregation of globular proteins under conditions in which they are initially folded. Although a conformational change of the native state is generally necessary to initiate aggregation, we show that a transition across the major energy barrier for unfolding is not essential and that aggregation may well be initiated from locally unfolded states that become accessible, for example, via thermal fluctuations occurring under physiological conditions. We review recent evidence on this topic and discuss its significance for understanding the onset and potential inhibition of protein aggregation in the context of diseases.
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Affiliation(s)
- Fabrizio Chiti
- Dipartimento di Scienze Biochimiche, Università degli Studi di Firenze, Viale Morgagni 50, I-50134 Firenze, Italy.
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