1
|
Gupta MN, Uversky VN. Pre-Molten, Wet, and Dry Molten Globules en Route to the Functional State of Proteins. Int J Mol Sci 2023; 24:ijms24032424. [PMID: 36768742 PMCID: PMC9916686 DOI: 10.3390/ijms24032424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
Transitions between the unfolded and native states of the ordered globular proteins are accompanied by the accumulation of several intermediates, such as pre-molten globules, wet molten globules, and dry molten globules. Structurally equivalent conformations can serve as native functional states of intrinsically disordered proteins. This overview captures the characteristics and importance of these molten globules in both structured and intrinsically disordered proteins. It also discusses examples of engineered molten globules. The formation of these intermediates under conditions of macromolecular crowding and their interactions with nanomaterials are also reviewed.
Collapse
Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Correspondence: ; Tel.: +1-813-494-5816
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
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).
Collapse
|
4
|
Conti S, Li X, Gianni S, Ghadami SA, Buxbaum J, Cecchi C, Chiti F, Bemporad F. A Complex Equilibrium among Partially Unfolded Conformations in Monomeric Transthyretin. Biochemistry 2014; 53:4381-92. [DOI: 10.1021/bi500430w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Simona Conti
- Dipartimento
di Scienze Biomediche Sperimentali e Cliniche “Mario Serio”,
Sezione di Biochimica, Università degli Studi di Firenze, Viale G. B. Morgagni 50, 50134 Firenze, Italy
| | - Xinyi Li
- Department
of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, MEM-230, La
Jolla, California 92037, United States
| | - Stefano Gianni
- Istituto
Pasteur Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche
“A. Rossi Fanelli”, Istituto di Biologia e Patologia
Molecolari del CNR, Università di Roma “La Sapienza”, P. le A. Moro 5, 00185 Roma, Italy
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Seyyed Abolghasem Ghadami
- Dipartimento
di Scienze Biomediche Sperimentali e Cliniche “Mario Serio”,
Sezione di Biochimica, Università degli Studi di Firenze, Viale G. B. Morgagni 50, 50134 Firenze, Italy
| | - Joel Buxbaum
- Department
of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, MEM-230, La
Jolla, California 92037, United States
| | - Cristina Cecchi
- Dipartimento
di Scienze Biomediche Sperimentali e Cliniche “Mario Serio”,
Sezione di Biochimica, Università degli Studi di Firenze, Viale G. B. Morgagni 50, 50134 Firenze, Italy
| | - Fabrizio Chiti
- Dipartimento
di Scienze Biomediche Sperimentali e Cliniche “Mario Serio”,
Sezione di Biochimica, Università degli Studi di Firenze, Viale G. B. Morgagni 50, 50134 Firenze, Italy
| | - Francesco Bemporad
- Dipartimento
di Scienze Biomediche Sperimentali e Cliniche “Mario Serio”,
Sezione di Biochimica, Università degli Studi di Firenze, Viale G. B. Morgagni 50, 50134 Firenze, Italy
| |
Collapse
|
5
|
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.
Collapse
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
| | | |
Collapse
|
6
|
Chong SH, Lee C, Kang G, Park M, Ham S. Structural and thermodynamic investigations on the aggregation and folding of acylphosphatase by molecular dynamics simulations and solvation free energy analysis. J Am Chem Soc 2011; 133:7075-83. [PMID: 21500781 DOI: 10.1021/ja1116233] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein engineering method to study the mutation effects on muscle acylphosphatase (AcP) has been actively applied to describe kinetics and thermodynamics associated with AcP aggregation as well as folding processes. Despite the extensive mutation experiments, the molecular origin and the structural motifs for aggregation and folding kinetics as well as thermodynamics of AcP have not been rationalized at the atomic resolution. To this end, we have investigated the mutation effects on the structures and thermodynamics for the aggregation and folding of AcP by using the combination of fully atomistic, explicit-water molecular dynamics simulations, and three-dimensional reference interaction site model theory. The results indicate that the A30G mutant with the fastest experimental aggregation rate displays considerably decreased α1-helical contents as well as disrupted hydrophobic core compared to the wild-type AcP. Increased solvation free energy as well as hydrophobicity upon A30G mutation is achieved due to the dehydration of hydrophilic side chains in the disrupted α1-helix region of A30G. In contrast, the Y91Q mutant with the slowest aggregation rate shows a non-native H-bonding network spanning the mutation site to hydrophobic core and α1-helix region, which rigidifies the native state protein conformation with the enhanced α1-helicity. Furthermore, Y91Q exhibits decreased solvation free energy and hydrophobicity compared to wild type due to more exposed and solvated hydrophilic side chains in the α1-region. On the other hand, the experimentally observed slower folding rates in both mutants are accompanied by decreased helicity in α2-helix upon mutation. We here provide the atomic-level structures and thermodynamic quantities of AcP mutants and rationalize the structural origin for the changes that occur upon introduction of those mutations along the AcP aggregation and folding processes.
Collapse
Affiliation(s)
- Song-Ho Chong
- Department of Chemistry, Sookmyung Women's University, Hyochangwon-gil 52, Yongsan-gu, Seoul, 140-742, Korea
| | | | | | | | | |
Collapse
|
7
|
Bemporad F, Vannocci T, Varela L, Azuaga AI, Chiti F. A model for the aggregation of the acylphosphatase from Sulfolobus solfataricus in its native-like state. BIOCHIMICA ET BIOPHYSICA ACTA 2008; 1784:1986-96. [PMID: 18832052 DOI: 10.1016/j.bbapap.2008.08.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Revised: 08/19/2008] [Accepted: 08/21/2008] [Indexed: 11/15/2022]
Abstract
Evidence is accumulating that normally folded proteins retain a significant tendency to form amyloid fibrils through a direct assembly of monomers in their native-like conformation. However, the factors promoting such processes are not yet well understood. The acylphosphatase from Sulfolobus solfataricus (Sso AcP) aggregates under conditions in which a native-like state is initially populated and forms, as a first step, aggregates in which the monomers maintain their native-like topology. An unstructured N-terminal segment and an edge beta-strand were previously shown to play a major role in the process. Using kinetic experiments on a set of Sso AcP variants we shall show that the major event of the first step is the establishment of an inter-molecular interaction between the unstructured segment of one Sso AcP molecule and the globular unit of another molecule. This interaction is determined by the primary sequence of the unstructured segment and not by its physico-chemical properties. Moreover, we shall show that the conversion of these initial aggregates into amyloid-like protofibrils is an intra-molecular process in which the Sso AcP molecules undergo conformational modifications. The obtained results allow the formulation of a model for the assembly of Sso AcP into amyloid-like aggregates at a molecular level.
Collapse
Affiliation(s)
- Francesco Bemporad
- Department of Biochemical Sciences, University of Florence, Viale Morgagni 50, Florence 50134, Italy
| | | | | | | | | |
Collapse
|
8
|
Parrini C, Bemporad F, Baroncelli A, Gianni S, Travaglini-Allocatelli C, Kohn JE, Ramazzotti M, Chiti F, Taddei N. The folding process of acylphosphatase from Escherichia coli is remarkably accelerated by the presence of a disulfide bond. J Mol Biol 2008; 379:1107-18. [PMID: 18495159 DOI: 10.1016/j.jmb.2008.04.051] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2007] [Revised: 04/21/2008] [Accepted: 04/23/2008] [Indexed: 11/30/2022]
Abstract
The acylphosphatase from Escherichia coli (EcoAcP) is the first AcP so far studied with a disulfide bond. A mutational variant of the enzyme lacking the disulfide bond has been produced by substituting the two cysteine residues with alanine (EcoAcP mutational variant C5A/C49A, mutEcoAcP). The native states of the two protein variants are similar, as shown by far-UV and near-UV circular dichroism and dynamic light-scattering measurements. From unfolding experiments at equilibrium using intrinsic fluorescence and far-UV circular dichroism as probes, EcoAcP shows an increased conformational stability as compared with mutEcoAcP. The wild-type protein folds according to a two-state model with a very fast rate constant (k(F)(H2O)=72,600 s(-1)), while mutEcoAcP folds ca 1500-fold slower, via the accumulation of a partially folded species. The correlation between the hydrophobicity of the polypeptide chain and the folding rate, found previously in the AcP-like structural family, is maintained only when considering the mutant but not the wild-type protein, which folds much faster than expected from this correlation. Similarly, the correlation between the relative contact order and the folding rate holds only for mutEcoAcP. The correlation also holds for EcoAcP, provided the relative contact order value is recalculated by considering the disulfide bridge as an alternate path for the backbone to determine the shortest sequence separation between contacting residues. These results indicate that the presence of a disulfide bond in a protein is an important determinant of the folding rate and allows its contribution to be determined in quantitative terms.
Collapse
Affiliation(s)
- Claudia Parrini
- Dipartimento di Scienze Biochimiche, Università degli Studi di Firenze, Viale Morgagni 50, 50134 Firenze, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Bemporad F, Gsponer J, Hopearuoho HI, Plakoutsi G, Stati G, Stefani M, Taddei N, Vendruscolo M, Chiti F. Biological function in a non-native partially folded state of a protein. EMBO J 2008; 27:1525-35. [PMID: 18451804 PMCID: PMC2396399 DOI: 10.1038/emboj.2008.82] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Accepted: 03/31/2008] [Indexed: 11/09/2022] Open
Abstract
As structural flexibility is known to be required for enzyme catalysis and pattern recognition and a significant fraction of eukaryotic proteins appear to be unfolded or contain unstructured regions, biological activity of conformational states distinct from fully folded structures could be more common than previously thought. By applying a procedure that allows the recovery of enzymatic activity to be monitored in real time, we show that a non-native state populated transiently during folding of the acylphosphatase from Sulfolobus solfataricus is enzymatically active. The structural characterization of this partially folded state reveals that enzymatic activity is possible even if the catalytic site is structurally heterogeneous, whereas the remainder of the structure acts as a scaffold. These results extend the spectrum of biological functions carried out in the absence of a folded state to include enzyme catalysis.
Collapse
Affiliation(s)
- Francesco Bemporad
- Dipartimento di Scienze Biochimiche, Università degli Studi di Firenze, Firenze, Italy
| | - Joerg Gsponer
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | | | - Georgia Plakoutsi
- Dipartimento di Scienze Biochimiche, Università degli Studi di Firenze, Firenze, Italy
| | - Gianmarco Stati
- Dipartimento di Scienze Biochimiche, Università degli Studi di Firenze, Firenze, Italy
| | - Massimo Stefani
- Dipartimento di Scienze Biochimiche, Università degli Studi di Firenze, Firenze, Italy
| | - Niccolò Taddei
- Dipartimento di Scienze Biochimiche, Università degli Studi di Firenze, Firenze, Italy
| | | | - Fabrizio Chiti
- Dipartimento di Scienze Biochimiche, Università degli Studi di Firenze, Firenze, Italy
| |
Collapse
|
10
|
Soldi G, Bemporad F, Chiti F. The degree of structural protection at the edge beta-strands determines the pathway of amyloid formation in globular proteins. J Am Chem Soc 2008; 130:4295-302. [PMID: 18335927 DOI: 10.1021/ja076628s] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The assembly of proteins into highly organized fibrillar aggregates is a key process in biology, biotechnology, and human disease. It has been shown that proteins retain a small, yet significant propensity to aggregate when they are folded into compact globular structures, and this may be physiologically relevant, particularly when considering that proteins spend most of their lifespan into such compact states. Proteins from the acylphosphatase-like structural family have been shown to aggregate via different mechanisms, with some members forming native-like aggregates as a first step of their aggregation process and others requiring unfolding as a first necessary step. Here we use the acylphosphatase from Sulfolobus solfataricus to show that assembly of folded protein molecules into native-like aggregates is prevented by single-point mutations that introduce structural protections within one of the most flexible region of the protein, the peripheral edge beta-strand 4. The resulting mutants do not form native-like aggregates, but can still form thioflavin T-binding and beta-structured oligomers, albeit more slowly than the wild-type protein. The kinetic data show that formation of the latter species proceeds via an alternative mechanism that is independent of the transient formation of native-like aggregates.
Collapse
Affiliation(s)
- Gemma Soldi
- Dipartimento di Scienze Biochimiche, Università di Firenze, Viale Morgagni 50, 50134 Firenze, Italy
| | | | | |
Collapse
|
11
|
Ramazzotti M, Parrini C, Stefani M, Manao G, Degl'Innocenti D. The intrachain disulfide bridge is responsible of the unusual stability properties of novel acylphosphatase from Escherichia coli. FEBS Lett 2006; 580:6763-8. [PMID: 17134700 DOI: 10.1016/j.febslet.2006.11.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2006] [Revised: 11/13/2006] [Accepted: 11/14/2006] [Indexed: 11/24/2022]
Abstract
Acylphosphatase (AcP) activity in prokaryotes was classically attributed to some aspecific acid phosphatases. We identified an open reading frame for a putative AcP in the b0968 Escherichia coli gene and purified the recombinant enzyme after checking by RT-PCR that it was indeed expressed. EcoAcP has a predicted typical fold of the AcP family but displays a very low specific activity and a high structural stability differently from its mesophilic and similarly to its hyperthermophilic counterparts. Site directed mutagenesis suggests that, together with other structural features, the intrachain S-S bridge in EcoAcP is involved in a remarkable thermal and chemical stabilization of the protein without affecting its catalytic activity.
Collapse
Affiliation(s)
- Matteo Ramazzotti
- Department of Biochemical Sciences, University of Florence, V.le Morgagni 50, 50134 Firenze, Italy
| | | | | | | | | |
Collapse
|
12
|
Pagano K, Ramazzotti M, Viglino P, Esposito G, Degl'Innocenti D, Taddei N, Corazza A. NMR solution structure of the acylphosphatase from Escherichia coli. JOURNAL OF BIOMOLECULAR NMR 2006; 36:199-204. [PMID: 17021943 DOI: 10.1007/s10858-006-9073-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2006] [Revised: 07/14/2006] [Accepted: 07/17/2006] [Indexed: 05/12/2023]
Abstract
The solution structure of Escherichia coli acylphosphatase (E. coli AcP), a small enzyme catalyzing the hydrolysis of acylphosphates, was determined by (1)H and (15)N NMR and restrained modelling calculation. In analogy with the other members of AcP family, E. coli AcP shows an alpha/beta sandwich domain composed of four antiparallel and one parallel beta-strand, assembled in a five-stranded beta-sheet facing two antiparallel alpha-helices. The pairwise RMSD values calculated for the backbone atoms of E. coli and Sulfolobus solfataricus AcP, Bovine common type AcP and Horse muscle AcP are 2.18, 5.31 and 5.12 A, respectively. No significant differences are present in the active site region and the catalytic residue side chains are consistently positioned in the structures.
Collapse
Affiliation(s)
- Katiuscia Pagano
- Department of Biomedical Sciences and Technologies, University of Udine, Udine, Italy
| | | | | | | | | | | | | |
Collapse
|
13
|
Soldi G, Plakoutsi G, Taddei N, Chiti F. Stabilization of a native protein mediated by ligand binding inhibits amyloid formation independently of the aggregation pathway. J Med Chem 2006; 49:6057-64. [PMID: 17004719 DOI: 10.1021/jm0606488] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The acylphosphatases from Sulfolobus solfataricus and Drosophila melanogaster (Sso AcP and AcPDro2) were previously shown to form amyloid-like aggregates without the need to unfold initially. Inorganic phosphate (Pi), a competitive inhibitor binding specifically to the active site of these proteins, was found to stabilize, upon binding, the native state of AcPDro2 and to inhibit its conversion into amyloid-like fibrils. The inhibitory effect of Pi is suppressed only in a variant in which the Arg residue responsible for Pi binding is mutated. The study on Sso AcP shows that Pi retards both the formation of the initial nativelike oligomers and their subsequent conversion into protofibrils. Thus, stabilization of the native structure mediated by specific binding with small molecules can be an effective therapeutic strategy against protein deposition diseases that originate from initially folded proteins, independently of the structure of the protein, its aggregation pathway, and the particular aggregated species responsible for pathogenesis.
Collapse
Affiliation(s)
- Gemma Soldi
- Dipartimento di Scienze Biochimiche, Università di Firenze, Viale Morgagni 50, 50134 Firenze, Italy
| | | | | | | |
Collapse
|
14
|
Abstract
Amyloid formation by globular proteins that normally adopt a compact folded structure is generally induced in vitro under harsh conditions involving low pH, high temperature, high pressure, or in the presence of organic solvents. Under these conditions, folded proteins are generally unfolded, at least partially. The approach described here shows a rationale and two detailed examples as to how the mechanism of aggregation of a globular protein can be probed under conditions in which it is initially in its folded conformation, and hence relevant to a physiological environment.
Collapse
Affiliation(s)
- Giordana Marcon
- Università di Firenze, Dipartimento di Scienze Biochimiche, Firenze, Italy
| | | | | |
Collapse
|
15
|
Corazza A, Rosano C, Pagano K, Alverdi V, Esposito G, Capanni C, Bemporad F, Plakoutsi G, Stefani M, Chiti F, Zuccotti S, Bolognesi M, Viglino P. Structure, conformational stability, and enzymatic properties of acylphosphatase from the hyperthermophile Sulfolobus solfataricus. Proteins 2006; 62:64-79. [PMID: 16287076 DOI: 10.1002/prot.20703] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The structure of AcP from the hyperthermophilic archaeon Sulfolobus solfataricus has been determined by (1)H-NMR spectroscopy and X-ray crystallography. Solution and crystal structures (1.27 A resolution, R-factor 13.7%) were obtained on the full-length protein and on an N-truncated form lacking the first 12 residues, respectively. The overall Sso AcP fold, starting at residue 13, displays the same betaalphabetabetaalphabeta topology previously described for other members of the AcP family from mesophilic sources. The unstructured N-terminal tail may be crucial for the unusual aggregation mechanism of Sso AcP previously reported. Sso AcP catalytic activity is reduced at room temperature but rises at its working temperature to values comparable to those displayed by its mesophilic counterparts at 25-37 degrees C. Such a reduced activity can result from protein rigidity and from the active site stiffening due the presence of a salt bridge between the C-terminal carboxylate and the active site arginine. Sso AcP is characterized by a melting temperature, Tm, of 100.8 degrees C and an unfolding free energy, DeltaG(U-F)H2O, at 28 degrees C and 81 degrees C of 48.7 and 20.6 kJ mol(-1), respectively. The kinetic and structural data indicate that mesophilic and hyperthermophilic AcP's display similar enzymatic activities and conformational stabilities at their working conditions. Structural analysis of the factor responsible for Sso AcP thermostability with respect to mesophilic AcP's revealed the importance of a ion pair network stabilizing particularly the beta-sheet and the loop connecting the fourth and fifth strands, together with increased density packing, loop shortening and a higher alpha-helical propensity.
Collapse
Affiliation(s)
- Alessandra Corazza
- Dipartimento di Scienze e Tecnologie Biomediche, Università di Udine, Udine, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Robinson-Rechavi M, Godzik A. Structural genomics of thermotoga maritima proteins shows that contact order is a major determinant of protein thermostability. Structure 2005; 13:857-60. [PMID: 15939017 DOI: 10.1016/j.str.2005.03.011] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2004] [Revised: 03/17/2005] [Accepted: 03/17/2005] [Indexed: 11/29/2022]
Abstract
Despite numerous studies, understanding the structural basis of protein stability in thermophilic organisms has remained elusive. One of the main reasons is the limited number of thermostable protein structures available for analysis, but also the difficulty in identifying relevant features to compare. Notably, an intuitive feeling of "compactness" of thermostable proteins has eluded quantification. With the unprecedented opportunity to assemble a data set for comparative analyses due to the recent advances in structural genomics, we can now revisit this issue and focus on experimentally determined structures of proteins from the hyperthermophilic bacterium Thermotoga maritima. We find that 73% of T. maritima proteins have higher contact order than their mesophilic homologs. Thus, contact order, a structural feature that was originally introduced to explain differences in folding rates of different protein families, is a significant parameter that can now be correlated with thermostability.
Collapse
Affiliation(s)
- Marc Robinson-Rechavi
- Joint Center for Structural Genomics, University of California, San Diego, La Jolla, California 92093, USA.
| | | |
Collapse
|
17
|
Plakoutsi G, Bemporad F, Calamai M, Taddei N, Dobson CM, Chiti F. Evidence for a mechanism of amyloid formation involving molecular reorganisation within native-like precursor aggregates. J Mol Biol 2005; 351:910-22. [PMID: 16024042 DOI: 10.1016/j.jmb.2005.06.043] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2005] [Revised: 06/16/2005] [Accepted: 06/17/2005] [Indexed: 10/25/2022]
Abstract
The aggregation of the alpha/beta protein acylphosphatase from Sulfolobus solfataricus has been studied under conditions in which the protein maintains a native-like, although destabilised, conformation and that therefore bear resemblance to a physiological medium. Static and dynamic light-scattering measurements indicate that under these conditions the protein aggregates rapidly, within two minutes. The initial aggregates are enzymatically active and have a secondary structure that is not yet characterized by the high content of cross-beta structure typical of amyloid, as inferred from Fourier transform infra-red and circular dichroism measurements. These species then convert slowly into enzymatically inactive aggregates that bind thioflavin T and Congo red, characteristic of amyloid structures, and contain extensive beta-sheet structure. Transmission electron microscopy reveals the presence in the latter aggregates of spherical species and thin, elongated protofibrils, both with diameters of 3-5 nm. Kinetic tests reveal that this process occurs without the need for dissolution and re-nucleation of the aggregates. Formation of thioflavin T-binding and beta-structured aggregates is substantially more rapid than unfolding of the native state, indicating that the initial aggregation process promotes formation of amyloid structures. Taken together, these findings suggest a mechanism of amyloid formation that may have physiological relevance and in which the amyloid structures result from reorganisation of the molecular interactions within the initially formed non-amyloid aggregates.
Collapse
Affiliation(s)
- Georgia Plakoutsi
- Dipartimento di Scienze Biochimiche, Università di Firenze, Viale Morgagni 50, 50134 Firenze, Italy
| | | | | | | | | | | |
Collapse
|