51
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Ghasriani H, Kwok JKC, Sherratt AR, Foo ACY, Qureshi T, Goto NK. Micelle-Catalyzed Domain Swapping in the GlpG Rhomboid Protease Cytoplasmic Domain. Biochemistry 2014; 53:5907-15. [DOI: 10.1021/bi500919v] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Houman Ghasriani
- Department of Chemistry and ‡Department of Biochemistry, Microbiology
and
Immunology, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5
| | - Jason K. C. Kwok
- Department of Chemistry and ‡Department of Biochemistry, Microbiology
and
Immunology, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5
| | - Allison R. Sherratt
- Department of Chemistry and ‡Department of Biochemistry, Microbiology
and
Immunology, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5
| | - Alexander C. Y. Foo
- Department of Chemistry and ‡Department of Biochemistry, Microbiology
and
Immunology, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5
| | - Tabussom Qureshi
- Department of Chemistry and ‡Department of Biochemistry, Microbiology
and
Immunology, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5
| | - Natalie K. Goto
- Department of Chemistry and ‡Department of Biochemistry, Microbiology
and
Immunology, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5
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52
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Haque MM, Kim D, Yu YH, Lim S, Kim DJ, Chang YT, Ha HH, Kim YK. Inhibition of tau aggregation by a rosamine derivative that blocks tau intermolecular disulfide cross-linking. Amyloid 2014; 21:185-90. [PMID: 24919397 DOI: 10.3109/13506129.2014.929103] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Abnormal tau aggregates are presumed to be neurotoxic and are an important therapeutic target for multiple neurodegenerative disorders including Alzheimer's disease. Growing evidence has shown that tau intermolecular disulfide cross-linking is critical in generating tau oligomers that serve as a building block for higher-order aggregates. Here we report that a small molecule inhibitor prevents tau aggregation by blocking the generation of disulfide cross-linked tau oligomers. Among the compounds tested, a rosamine derivative bearing mild thiol reactivity selectively labeled tau and effectively inhibited oligomerization and fibrillization processes in vitro. Our data suggest that controlling tau oxidation status could be a new therapeutic strategy for prevention of abnormal tau aggregation.
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Affiliation(s)
- Md Mamunul Haque
- Center for Neuro-medicine, Brain Science Institute, Korea Institute of Science and Technology (KIST) , Seoul , Republic of Korea
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53
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Brumshtein B, Esswein SR, Landau M, Ryan CM, Whitelegge JP, Phillips ML, Cascio D, Sawaya MR, Eisenberg DS. Formation of amyloid fibers by monomeric light chain variable domains. J Biol Chem 2014; 289:27513-25. [PMID: 25138218 DOI: 10.1074/jbc.m114.585638] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Systemic light chain amyloidosis is a lethal disease characterized by excess immunoglobulin light chains and light chain fragments composed of variable domains, which aggregate into amyloid fibers. These fibers accumulate and damage organs. Some light chains induce formation of amyloid fibers, whereas others do not, making it unclear what distinguishes amyloid formers from non-formers. One mechanism by which sequence variation may reduce propensity to form amyloid fibers is by shifting the equilibrium toward an amyloid-resistant quaternary structure. Here we identify the monomeric form of the Mcg immunoglobulin light chain variable domain as the quaternary unit required for amyloid fiber assembly. Dimers of Mcg variable domains remain stable and soluble, yet become prone to assemble into amyloid fibers upon disassociation into monomers.
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Affiliation(s)
- Boris Brumshtein
- From the Departments of Biological Chemistry and Chemistry and Biochemistry, Howard Hughes Medical Institute, UCLA-Department of Energy (DOE) Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095 and
| | - Shannon R Esswein
- From the Departments of Biological Chemistry and Chemistry and Biochemistry, Howard Hughes Medical Institute, UCLA-Department of Energy (DOE) Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095 and
| | - Meytal Landau
- From the Departments of Biological Chemistry and Chemistry and Biochemistry, Howard Hughes Medical Institute, UCLA-Department of Energy (DOE) Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095 and
| | - Christopher M Ryan
- the Pasarow Mass Spectrometry Laboratory, NPI-Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, California 90025
| | - Julian P Whitelegge
- the Pasarow Mass Spectrometry Laboratory, NPI-Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, California 90025
| | - Martin L Phillips
- From the Departments of Biological Chemistry and Chemistry and Biochemistry, Howard Hughes Medical Institute, UCLA-Department of Energy (DOE) Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095 and
| | - Duilio Cascio
- From the Departments of Biological Chemistry and Chemistry and Biochemistry, Howard Hughes Medical Institute, UCLA-Department of Energy (DOE) Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095 and
| | - Michael R Sawaya
- From the Departments of Biological Chemistry and Chemistry and Biochemistry, Howard Hughes Medical Institute, UCLA-Department of Energy (DOE) Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095 and
| | - David S Eisenberg
- From the Departments of Biological Chemistry and Chemistry and Biochemistry, Howard Hughes Medical Institute, UCLA-Department of Energy (DOE) Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095 and
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54
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Smadbeck J, Chan KH, Khoury GA, Xue B, Robinson RC, Hauser CAE, Floudas CA. De novo design and experimental characterization of ultrashort self-associating peptides. PLoS Comput Biol 2014; 10:e1003718. [PMID: 25010703 PMCID: PMC4091692 DOI: 10.1371/journal.pcbi.1003718] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 05/31/2014] [Indexed: 12/19/2022] Open
Abstract
Self-association is a common phenomenon in biology and one that can have positive and negative impacts, from the construction of the architectural cytoskeleton of cells to the formation of fibrils in amyloid diseases. Understanding the nature and mechanisms of self-association is important for modulating these systems and in creating biologically-inspired materials. Here, we present a two-stage de novo peptide design framework that can generate novel self-associating peptide systems. The first stage uses a simulated multimeric template structure as input into the optimization-based Sequence Selection to generate low potential energy sequences. The second stage is a computational validation procedure that calculates Fold Specificity and/or Approximate Association Affinity (K*association) based on metrics that we have devised for multimeric systems. This framework was applied to the design of self-associating tripeptides using the known self-associating tripeptide, Ac-IVD, as a structural template. Six computationally predicted tripeptides (Ac-LVE, Ac-YYD, Ac-LLE, Ac-YLD, Ac-MYD, Ac-VIE) were chosen for experimental validation in order to illustrate the self-association outcomes predicted by the three metrics. Self-association and electron microscopy studies revealed that Ac-LLE formed bead-like microstructures, Ac-LVE and Ac-YYD formed fibrillar aggregates, Ac-VIE and Ac-MYD formed hydrogels, and Ac-YLD crystallized under ambient conditions. An X-ray crystallographic study was carried out on a single crystal of Ac-YLD, which revealed that each molecule adopts a β-strand conformation that stack together to form parallel β-sheets. As an additional validation of the approach, the hydrogel-forming sequences of Ac-MYD and Ac-VIE were shuffled. The shuffled sequences were computationally predicted to have lower K*association values and were experimentally verified to not form hydrogels. This illustrates the robustness of the framework in predicting self-associating tripeptides. We expect that this enhanced multimeric de novo peptide design framework will find future application in creating novel self-associating peptides based on unnatural amino acids, and inhibitor peptides of detrimental self-aggregating biological proteins.
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Affiliation(s)
- James Smadbeck
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, United States of America
| | - Kiat Hwa Chan
- Institute of Bioengineering and Nanotechnology, Singapore, Singapore
| | - George A. Khoury
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, United States of America
| | - Bo Xue
- Institute of Molecular and Cell Biology, A*STAR (Agency of Science, Technology and Research), Biopolis, Singapore, Singapore
| | - Robert C. Robinson
- Institute of Molecular and Cell Biology, A*STAR (Agency of Science, Technology and Research), Biopolis, Singapore, Singapore
| | | | - Christodoulos A. Floudas
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, United States of America
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55
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Estácio SG, Krobath H, Vila-Viçosa D, Machuqueiro M, Shakhnovich EI, Faísca PFN. A simulated intermediate state for folding and aggregation provides insights into ΔN6 β2-microglobulin amyloidogenic behavior. PLoS Comput Biol 2014; 10:e1003606. [PMID: 24809460 PMCID: PMC4014404 DOI: 10.1371/journal.pcbi.1003606] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 03/16/2014] [Indexed: 01/26/2023] Open
Abstract
A major component of ex vivo amyloid plaques of patients with dialysis-related amyloidosis (DRA) is a cleaved variant of β2-microglobulin (ΔN6) lacking the first six N-terminal residues. Here we perform a computational study on ΔN6, which provides clues to understand the amyloidogenicity of the full-length β2-microglobulin. Contrary to the wild-type form, ΔN6 is able to efficiently nucleate fibrillogenesis in vitro at physiological pH. This behavior is enhanced by a mild acidification of the medium such as that occurring in the synovial fluid of DRA patients. Results reported in this work, based on molecular simulations, indicate that deletion of the N-terminal hexapeptide triggers the formation of an intermediate state for folding and aggregation with an unstructured strand A and a native-like core. Strand A plays a pivotal role in aggregation by acting as a sticky hook in dimer assembly. This study further predicts that the detachment of strand A from the core is maximized at pH 6.2 resulting into higher aggregation efficiency. The structural mapping of the dimerization interface suggests that Tyr10, His13, Phe30 and His84 are hot-spot residues in ΔN6 amyloidogenesis. Dialysis-related amyloidosis (DRA) is a conformational disease that affects individuals undergoing long-term haemodialysis. In DRA the progressive accumulation of protein human β2-microglobulin (Hβ2m) in the osteoarticular system, followed by its assembly into amyloid fibrils, eventually leads to tissue erosion and destruction. Disclosing the aggregation mechanism of Hβ2m under physiologically relevant conditions represents a major challenge due to the inability of the protein to efficiently nucleate fibrillogenesis in vitro at physiological pH. On the other hand, ΔN6, a truncated variant of Hβ2m, which is also a major component of ex vivo amyloid deposits extracted from DRA patients, is able to efficiently form amyloid fibrils de novo in physiological conditions. This amyloidogenic behavior is dramatically enhanced in a slightly more acidic pH (6.2) compatible with the mild acidification that occurs in the synovial fluid of DRA patients. In this work, an innovative three-stage methodological approach, relying on an array of molecular simulations, spanning different levels of resolution is used to investigate the initial stage of the de novo aggregation mechanism of ΔN6 in a physiologically relevant pH range. We identify an intermediate state for folding and aggregation, whose potential to dimerize is enhanced at pH 6.2. Our results provide rationalizations for previous experimental observations and new insights into the molecular basis of DRA.
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Affiliation(s)
- Sílvia G. Estácio
- Centro de Física da Matéria Condensada & Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Heinrich Krobath
- Centro de Física da Matéria Condensada & Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Diogo Vila-Viçosa
- Centro de Química e Bioquímica & Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Miguel Machuqueiro
- Centro de Química e Bioquímica & Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Eugene I. Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail: (EIS); (PFNF)
| | - Patrícia F. N. Faísca
- Centro de Física da Matéria Condensada & Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- * E-mail: (EIS); (PFNF)
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56
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Whelly S, Serobian G, Borchardt C, Powell J, Johnson S, Hakansson K, Lindstrom V, Abrahamson M, Grubb A, Cornwall GA. Fertility defects in mice expressing the L68Q variant of human cystatin C: a role for amyloid in male infertility. J Biol Chem 2014; 289:7718-29. [PMID: 24500719 DOI: 10.1074/jbc.m113.515759] [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
Hereditary cystatin C amyloid angiopathy is an autosomal dominant disorder in which a variant form of cystatin C (L68Q) readily forms amyloid deposits in cerebral arteries in affected individuals resulting in early death. L68Q protein deposits in human cystatin C amyloid angiopathy patients have also been found in tissues outside of the brain including the testis, suggesting possible effects on fertility. Heterozygous transgenic mice (L68Q) that express the human L68Q variant of cystatin C under the control of the mouse cystatin C promoter were unable to generate offspring, suggesting the presence of L68Q cystatin C amyloid affected sperm function. In vitro studies showed that epididymal spermatozoa from L68Q mice were unable to fertilize oocytes and exhibited poor sperm motility. Furthermore, spermatozoa from L68Q mice exhibited reduced cell viability compared with wild type (WT) spermatozoa and often were detected in large agglutinated clumps. Examination of the epididymal fluid and spermatozoa from L68Q mice showed increased levels and distinct forms of cystatin C amyloid that were not present in WT mice. The addition of epididymal fluid from L68Q mice to WT spermatozoa resulted in a recapitulation of the L68Q phenotype in that WT spermatozoa showed reduced cell viability and motility compared with WT spermatozoa incubated in epididymal fluid from WT mice. L68Q epididymal fluid that was depleted of cystatin C amyloids, however, did not impair the motility of WT spermatozoa. Taken together these studies suggest that amyloids in the epididymal fluid can be cytotoxic to the maturing spermatozoa resulting in male infertility.
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Affiliation(s)
- Sandra Whelly
- From the Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas 79430 and
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57
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Functional analysis of the accessory protein TapA in Bacillus subtilis amyloid fiber assembly. J Bacteriol 2014; 196:1505-13. [PMID: 24488317 DOI: 10.1128/jb.01363-13] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus subtilis biofilm formation relies on the assembly of a fibrous scaffold formed by the protein TasA. TasA polymerizes into highly stable fibers with biochemical and morphological features of functional amyloids. Previously, we showed that assembly of TasA fibers requires the auxiliary protein TapA. In this study, we investigated the roles of TapA sequences from the C-terminal and N-terminal ends and TapA cysteine residues in its ability to promote the assembly of TasA amyloid-like fibers. We found that the cysteine residues are not essential for the formation of TasA fibers, as their replacement by alanine residues resulted in only minor defects in biofilm formation. Mutating sequences in the C-terminal half had no effect on biofilm formation. However, we identified a sequence of 8 amino acids in the N terminus that is key for TasA fiber formation. Strains expressing TapA lacking these 8 residues were completely defective in biofilm formation. In addition, this TapA mutant protein exhibited a dominant negative effect on TasA fiber formation. Even in the presence of wild-type TapA, the mutant protein inhibited fiber assembly in vitro and delayed biofilm formation in vivo. We propose that this 8-residue sequence is crucial for the formation of amyloid-like fibers on the cell surface, perhaps by mediating the interaction between TapA or TapA and TasA molecules.
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58
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Parui PP, Deshpande MS, Nagao S, Kamikubo H, Komori H, Higuchi Y, Kataoka M, Hirota S. Formation of Oligomeric Cytochrome c during Folding by Intermolecular Hydrophobic Interaction between N- and C-Terminal α-Helices. Biochemistry 2013; 52:8732-44. [DOI: 10.1021/bi400986g] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Partha Pratim Parui
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
- Department
of Chemistry, Jadavpur University, Kolkata 700032, India
| | - Megha Subhash Deshpande
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Satoshi Nagao
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Hironari Kamikubo
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Hirofumi Komori
- Department
of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1
Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshiki Higuchi
- Department
of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1
Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Mikio Kataoka
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Shun Hirota
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
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59
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Pica A, Merlino A, Buell AK, Knowles TPJ, Pizzo E, D'Alessio G, Sica F, Mazzarella L. Three-dimensional domain swapping and supramolecular protein assembly: insights from the X-ray structure of a dimeric swapped variant of human pancreatic RNase. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2116-23. [PMID: 24100329 DOI: 10.1107/s0907444913020507] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 07/23/2013] [Indexed: 11/10/2022]
Abstract
The deletion of five residues in the loop connecting the N-terminal helix to the core of monomeric human pancreatic ribonuclease leads to the formation of an enzymatically active domain-swapped dimer (desHP). The crystal structure of desHP reveals the generation of an intriguing fibril-like aggregate of desHP molecules that extends along the c crystallographic axis. Dimers are formed by three-dimensional domain swapping. Tetramers are formed by the aggregation of swapped dimers with slightly different quaternary structures. The tetramers interact in such a way as to form an infinite rod-like structure that propagates throughout the crystal. The observed supramolecular assembly captured in the crystal predicts that desHP fibrils could form in solution; this has been confirmed by atomic force microscopy. These results provide new evidence that three-dimensional domain swapping can be a mechanism for the formation of elaborate large assemblies in which the protein, apart from the swapping, retains its original fold.
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Affiliation(s)
- Andrea Pica
- Department of Chemical Sciences, University of Naples `Federico II', Via Cintia, 80126 Naples, Italy
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60
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Thakkar SV, Sahni N, Joshi SB, Kerwin BA, He F, Volkin DB, Middaugh CR. Understanding the relevance of local conformational stability and dynamics to the aggregation propensity of an IgG1 and IgG2 monoclonal antibodies. Protein Sci 2013; 22:1295-305. [PMID: 23893936 DOI: 10.1002/pro.2316] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 06/27/2013] [Accepted: 07/15/2013] [Indexed: 12/22/2022]
Abstract
Aggregation of monoclonal antibodies is often a multi-step process involving structural alterations in monomeric proteins and subsequent formation of soluble or insoluble oligomers. The role of local conformational stability and dynamics of native and/or partially altered structures in determining the aggregation propensity of monoclonal antibodies, however, is not well understood. Here, we investigate the role of conformational stability and dynamics of regions with distinct solvent exposure in determining the aggregation propensity of an IgG1 and IgG2 monoclonal antibody. The temperatures employed span the pre-unfolding range (10-40°C) and the onset temperatures (T onset ) for exposure of apolar residues (≈ 50°C), alterations in secondary structures (≈ 60°C) and initiation of visible aggregate formation (≈ 60°C). Solvent-exposed regions were found to precede solvent-shielded regions in an initiation of aggregation for both proteins. Such a process was observed upon alterations in overall tertiary structure while retaining the secondary structures in both the proteins. In addition, a greater dynamic nature of solvent-shielded regions in potential intermediates of IgG1 and the improved conformational stability increased its resistance to aggregation when compared to IgG2. These results suggest that local conformational stability and fluctuations of partially altered structures can influence the aggregation propensity of immunoglobulins.
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Affiliation(s)
- Santosh V Thakkar
- Department of Pharmaceutical Chemistry, Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas, 66047, USA
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61
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Fabian H, Gast K, Laue M, Jetzschmann KJ, Naumann D, Ziegler A, Uchanska-Ziegler B. IR spectroscopic analyses of amyloid fibril formation of β2-microglobulin using a simplified procedure for its in vitro generation at neutral pH. Biophys Chem 2013; 179:35-46. [PMID: 23727989 DOI: 10.1016/j.bpc.2013.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 04/29/2013] [Accepted: 05/01/2013] [Indexed: 11/16/2022]
Abstract
β2-microglobulin (β2m) is known to be the major component of fibrillar deposits in the joints of patients suffering from dialysis-related amyloidosis. We have developed a simplified procedure to convert monomeric recombinant β2m into amyloid fibrils at physiological pH by a combination of stirring and heating, enabling us to follow conformational changes associated with the assembly by infrared spectroscopy and electron microscopy. Our studies reveal that fibrillogenesis begins with the formation of relatively large aggregates, with secondary structure not significantly altered by the stirring-induced association. In contrast, the conversion of the amorphous aggregates into amyloid fibrils is associated with a profound re-organization at the level of the secondary and tertiary structures, leading to non-native like parallel arrangements of the β-strands in the fully formed amyloid structure of β2m. This study highlights the power of an approach to investigate the formation of β2m fibrils by a combination of biophysical techniques including IR spectroscopy.
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Affiliation(s)
- Heinz Fabian
- Robert Koch-Institut, ZBS 6, Nordufer 20, D-13353 Berlin, Germany.
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62
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Östner G, Lindström V, Hjort Christensen P, Kozak M, Abrahamson M, Grubb A. Stabilization, characterization, and selective removal of cystatin C amyloid oligomers. J Biol Chem 2013; 288:16438-16450. [PMID: 23629649 PMCID: PMC3675580 DOI: 10.1074/jbc.m113.469593] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The pathophysiological process in amyloid disorders usually involves the transformation of a functional monomeric protein via potentially toxic oligomers into amyloid fibrils. The structure and properties of the intermediary oligomers have been difficult to study due to their instability and dynamic equilibrium with smaller and larger species. In hereditary cystatin C amyloid angiopathy, a cystatin C variant is deposited in arterial walls and cause brain hemorrhage in young adults. In the present investigation, we use redox experiments of monomeric cystatin C, stabilized against domain swapping by an intramolecular disulfide bond, to generate stable oligomers (dimers, trimers, tetramers, decamers, and high molecular weight oligomers). These oligomers were characterized concerning size by gel filtration, polyacrylamide gel electrophoresis, and mass spectrometry, shape by electron and atomic force microscopy, and, function by assays of their capacity to inhibit proteases. The results showed the oligomers to be highly ordered, domain-swapped assemblies of cystatin C and that the oligomers could not build larger oligomers, or fibrils, without domain swapping. The stabilized oligomers were used to induce antibody formation in rabbits. After immunosorption, using immobilized monomeric cystatin C, and elution from columns with immobilized cystatin C oligomers, oligomer-specific antibodies were obtained. These could be used to selectively remove cystatin C dimers from biological fluids containing both dimers and monomers.
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Affiliation(s)
- Gustav Östner
- Department of Clinical Chemistry, Lund University Hospital, S-22185 Lund, Sweden
| | - Veronica Lindström
- Department of Clinical Chemistry, Lund University Hospital, S-22185 Lund, Sweden
| | | | - Maciej Kozak
- Department of Macromolecular Physics, Adam Mickiewicz University in Poznań, 61-614 Poznań, Poland
| | - Magnus Abrahamson
- Department of Clinical Chemistry, Lund University Hospital, S-22185 Lund, Sweden
| | - Anders Grubb
- Department of Clinical Chemistry, Lund University Hospital, S-22185 Lund, Sweden.
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63
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Orlikowska M, Szymańska A, Borek D, Otwinowski Z, Skowron P, Jankowska E. Structural characterization of V57D and V57P mutants of human cystatin C, an amyloidogenic protein. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:577-86. [PMID: 23519666 PMCID: PMC3976269 DOI: 10.1107/s0907444912051657] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 12/21/2012] [Indexed: 11/10/2022]
Abstract
Wild-type human cystatin C (hCC wt) is a low-molecular-mass protein (120 amino-acid residues, 13,343 Da) that is found in all nucleated cells. Physiologically, it functions as a potent regulator of cysteine protease activity. While the biologically active hCC wt is a monomeric protein, all crystallization efforts to date have resulted in a three-dimensional domain-swapped dimeric structure. In the recently published structure of a mutated hCC, the monomeric fold was preserved by a stabilization of the conformationally constrained loop L1 caused by a single amino-acid substitution: Val57Asn. Additional hCC mutants were obtained in order to elucidate the relationship between the stability of the L1 loop and the propensity of human cystatin C to dimerize. In one mutant Val57 was substituted by an aspartic acid residue, which is favoured in β-turns, and in the second mutant proline, a residue known for broadening turns, was substituted for the same Val57. Here, 2.26 and 3.0 Å resolution crystal structures of the V57D andV57P mutants of hCC are reported and their dimeric architecture is discussed in terms of the stabilization and destabilization effects of the introduced mutations.
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Affiliation(s)
- Marta Orlikowska
- Department of Medicinal Chemistry, Faculty of Chemistry, University of Gdansk, Sobieskiego 18/19, 80-952 Gdansk, Poland
| | - Aneta Szymańska
- Department of Medicinal Chemistry, Faculty of Chemistry, University of Gdansk, Sobieskiego 18/19, 80-952 Gdansk, Poland
| | - Dominika Borek
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA
| | - Zbyszek Otwinowski
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA
| | - Piotr Skowron
- Division of Environmental Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Sobieskiego 18/19, 80-952 Gdansk, Poland
| | - Elżbieta Jankowska
- Department of Medicinal Chemistry, Faculty of Chemistry, University of Gdansk, Sobieskiego 18/19, 80-952 Gdansk, Poland
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64
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The how’s and why’s of protein folding intermediates. Arch Biochem Biophys 2013; 531:14-23. [DOI: 10.1016/j.abb.2012.10.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 10/05/2012] [Accepted: 10/11/2012] [Indexed: 12/13/2022]
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65
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Leukocyte cell-derived chemotaxin 2 is a zinc-binding protein. FEBS Lett 2013; 587:404-9. [DOI: 10.1016/j.febslet.2013.01.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 12/08/2012] [Accepted: 01/09/2013] [Indexed: 11/24/2022]
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66
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Sarell CJ, Woods LA, Su Y, Debelouchina GT, Ashcroft AE, Griffin RG, Stockley PG, Radford SE. Expanding the repertoire of amyloid polymorphs by co-polymerization of related protein precursors. J Biol Chem 2013; 288:7327-37. [PMID: 23329840 PMCID: PMC3591641 DOI: 10.1074/jbc.m112.447524] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Amyloid fibrils can be generated from proteins with diverse sequences and folds. Although amyloid fibrils assembled in vitro commonly involve a single protein precursor, fibrils formed in vivo can contain more than one protein sequence. How fibril structure and stability differ in fibrils composed of single proteins (homopolymeric fibrils) from those generated by co-polymerization of more than one protein sequence (heteropolymeric fibrils) is poorly understood. Here we compare the structure and stability of homo and heteropolymeric fibrils formed from human β2-microglobulin and its truncated variant ΔN6. We use an array of approaches (limited proteolysis, magic angle spinning NMR, Fourier transform infrared spectroscopy, and fluorescence) combined with measurements of thermodynamic stability to characterize the different fibril types. The results reveal fibrils with different structural properties, different side-chain packing, and strikingly different stabilities. These findings demonstrate how co-polymerization of related precursor sequences can expand the repertoire of structural and thermodynamic polymorphism in amyloid fibrils to an extent that is greater than that obtained by polymerization of a single precursor alone.
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Affiliation(s)
- Claire J Sarell
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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67
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Liu C, Zhao M, Jiang L, Cheng PN, Park J, Sawaya MR, Pensalfini A, Gou D, Berk AJ, Glabe CG, Nowick J, Eisenberg D. Out-of-register β-sheets suggest a pathway to toxic amyloid aggregates. Proc Natl Acad Sci U S A 2012; 109:20913-8. [PMID: 23213214 PMCID: PMC3529048 DOI: 10.1073/pnas.1218792109] [Citation(s) in RCA: 158] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Although aberrant protein aggregation has been conclusively linked to dozens of devastating amyloid diseases, scientists remain puzzled about the molecular features that render amyloid fibrils or small oligomers toxic. Here, we report a previously unobserved type of amyloid fibril that tests as cytotoxic: one in which the strands of the contributing β-sheets are out of register. In all amyloid fibrils previously characterized at the molecular level, only in-register β-sheets have been observed, in which each strand makes its full complement of hydrogen bonds with the strands above and below it in the fibril. In out-of-register sheets, strands are sheared relative to one another, leaving dangling hydrogen bonds. Based on this finding, we designed out-of-register β-sheet amyloid mimics, which form both cylindrin-like oligomers and fibrils, and these mimics are cytotoxic. Structural and energetic considerations suggest that out-of-register fibrils can readily convert to toxic cylindrins. We propose that out-of-register β-sheets and their related cylindrins are part of a toxic amyloid pathway, which is distinct from the more energetically favored in-register amyloid pathway.
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Affiliation(s)
- Cong Liu
- aUCLA-DOE Institute for Genomics and Proteomics, The Howard Hughes Medical Institute, Molecular Biology Institute and
| | - Minglei Zhao
- aUCLA-DOE Institute for Genomics and Proteomics, The Howard Hughes Medical Institute, Molecular Biology Institute and
| | - Lin Jiang
- aUCLA-DOE Institute for Genomics and Proteomics, The Howard Hughes Medical Institute, Molecular Biology Institute and
| | | | - Jiyong Park
- aUCLA-DOE Institute for Genomics and Proteomics, The Howard Hughes Medical Institute, Molecular Biology Institute and
| | - Michael R. Sawaya
- aUCLA-DOE Institute for Genomics and Proteomics, The Howard Hughes Medical Institute, Molecular Biology Institute and
| | - Anna Pensalfini
- cMolecular Biology and Biochemistry, University of California, Irvine, CA 92697-2025
| | - Dawei Gou
- dMolecular Biology Institute and Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095; and
| | - Arnold J. Berk
- dMolecular Biology Institute and Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095; and
| | - Charles G. Glabe
- cMolecular Biology and Biochemistry, University of California, Irvine, CA 92697-2025
| | - James Nowick
- Departments of bChemistry and
- 3To whom correspondence may be addressed. E-mail: or
| | - David Eisenberg
- aUCLA-DOE Institute for Genomics and Proteomics, The Howard Hughes Medical Institute, Molecular Biology Institute and
- 3To whom correspondence may be addressed. E-mail: or
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68
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Cassou CA, Sterling HJ, Susa AC, Williams ER. Electrothermal supercharging in mass spectrometry and tandem mass spectrometry of native proteins. Anal Chem 2012. [PMID: 23194134 DOI: 10.1021/ac302256d] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Electrothermal supercharging of protein ions formed by electrospray ionization from buffered aqueous solutions results in significant increases to both the maximum and average charge states compared to native mass spectrometry in which ions are formed from the same solutions but with lower spray potentials. For eight of the nine proteins investigated, the maximum charge states of protonated ions formed from native solutions with electrothermal supercharging is greater than those obtained from conventional denaturing solutions consisting of water/methanol/acid, although the average charging is slightly lower owing to contributions of small populations of more folded low charge-state structures. Under these conditions, electrothermal supercharging is slightly less effective for anions than for cations. Equivalent sequence coverage (80%) is obtained with electron transfer dissociation of the same high charge-state ion of cytochrome c formed by electrothermal supercharging from native solutions and from denaturing solutions. Electrothermal supercharging should be advantageous for combining structural studies of proteins in native environments with mass spectrometers that have limited high m/z capabilities and for significantly improving tandem mass spectrometry performance for protein ions formed from solutions in which the molecules have native structures and activities.
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Affiliation(s)
- Catherine A Cassou
- Department of Chemistry, University of California, Berkeley, 94720-1460, United States
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69
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Hayashi Y, Nagao S, Osuka H, Komori H, Higuchi Y, Hirota S. Domain Swapping of the Heme and N-Terminal α-Helix in Hydrogenobacter thermophilus Cytochrome c552 Dimer. Biochemistry 2012; 51:8608-16. [DOI: 10.1021/bi3011303] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Yugo Hayashi
- Graduate School
of Materials
Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Satoshi Nagao
- Graduate School
of Materials
Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Hisao Osuka
- Department of Life Science,
Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Hirofumi Komori
- Department of Life Science,
Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshiki Higuchi
- Department of Life Science,
Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Shun Hirota
- Graduate School
of Materials
Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
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70
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Ou HD, Kwiatkowski W, Deerinck TJ, Noske A, Blain KY, Land HS, Soria C, Powers CJ, May AP, Shu X, Tsien RY, Fitzpatrick JA, Long JA, Ellisman MH, Choe S, O’Shea CC. A structural basis for the assembly and functions of a viral polymer that inactivates multiple tumor suppressors. Cell 2012; 151:304-19. [PMID: 23063122 PMCID: PMC3681303 DOI: 10.1016/j.cell.2012.08.035] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 05/10/2012] [Accepted: 08/16/2012] [Indexed: 12/21/2022]
Abstract
Evolution of minimal DNA tumor virus' genomes has selected for small viral oncoproteins that hijack critical cellular protein interaction networks. The structural basis for the multiple and dominant functions of adenovirus oncoproteins has remained elusive. E4-ORF3 forms a nuclear polymer and simultaneously inactivates p53, PML, TRIM24, and MRE11/RAD50/NBS1 (MRN) tumor suppressors. We identify oligomerization mutants and solve the crystal structure of E4-ORF3. E4-ORF3 forms a dimer with a central β core, and its structure is unrelated to known polymers or oncogenes. E4-ORF3 dimer units coassemble through reciprocal and nonreciprocal exchanges of their C-terminal tails. This results in linear and branched oligomer chains that further assemble in variable arrangements to form a polymer network that partitions the nuclear volume. E4-ORF3 assembly creates avidity-driven interactions with PML and an emergent MRN binding interface. This reveals an elegant structural solution whereby a small protein forms a multivalent matrix that traps disparate tumor suppressors.
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Affiliation(s)
- Horng D. Ou
- Molecular and Cell Biology Laboratory Salk Institute for Biological Studies 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Witek Kwiatkowski
- Structural Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Thomas J. Deerinck
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Andrew Noske
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Katie Y. Blain
- Structural Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Hannah S. Land
- Plant Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Conrado Soria
- Molecular and Cell Biology Laboratory Salk Institute for Biological Studies 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Colin J. Powers
- Molecular and Cell Biology Laboratory Salk Institute for Biological Studies 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Andrew P. May
- Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, CA 94080, USA
| | - Xiaokun Shu
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California at San Francisco, 555 Mission Bay Blvd South, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Department of Pharmacology, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Roger Y. Tsien
- Howard Hughes Medical Institute, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Department of Pharmacology, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Departments of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - James A.J. Fitzpatrick
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jeff A. Long
- Plant Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Mark H. Ellisman
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Department of Neurosciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Senyon Choe
- Structural Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Clodagh C. O’Shea
- Molecular and Cell Biology Laboratory Salk Institute for Biological Studies 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
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71
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Double domain swapping in bovine seminal RNase: formation of distinct N- and C-swapped tetramers and multimers with increasing biological activities. PLoS One 2012; 7:e46804. [PMID: 23071641 PMCID: PMC3469567 DOI: 10.1371/journal.pone.0046804] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 09/10/2012] [Indexed: 12/24/2022] Open
Abstract
Bovine seminal (BS) RNase, the unique natively dimeric member of the RNase super-family, represents a special case not only for its additional biological actions but also for the singular features of 3D domain swapping. The native enzyme is indeed a mixture of two isoforms: M = M, a dimer held together by two inter-subunit disulfide bonds, and MxM, 70% of the total, which, besides the two mentioned disulfides, is additionally stabilized by the swapping of its N-termini. When lyophilized from 40% acetic acid, BS-RNase oligomerizes as the super-family proto-type RNase A does. In this paper, we induced BS-RNase self-association and analyzed the multimers by size-exclusion chromatography, cross-linking, electrophoresis, mutagenesis, dynamic light scattering, molecular modelling. Finally, we evaluated their enzymatic and cytotoxic activities. Several BS-RNase domain-swapped oligomers were detected, including two tetramers, one exchanging only the N-termini, the other being either N- or C-swapped. The C-swapping event, confirmed by results on a BS-K113N mutant, has been firstly seen in BS-RNase here, and probably stabilizes also multimers larger than tetramers. Interestingly, all BS-RNase oligomers are more enzymatically active than the native dimer and, above all, they display a cytotoxic activity that definitely increases with the molecular weight of the multimers. This latter feature, to date unknown for BS-RNase, suggests again that the self-association of RNases strongly modulates their biological and potentially therapeutic properties.
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72
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Yanagi K, Sakurai K, Yoshimura Y, Konuma T, Lee YH, Sugase K, Ikegami T, Naiki H, Goto Y. The Monomer–Seed Interaction Mechanism in the Formation of the β2-Microglobulin Amyloid Fibril Clarified by Solution NMR Techniques. J Mol Biol 2012; 422:390-402. [DOI: 10.1016/j.jmb.2012.05.034] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 04/30/2012] [Accepted: 05/29/2012] [Indexed: 11/15/2022]
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73
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Hirota S, Ueda M, Hayashi Y, Nagao S, Kamikubo H, Kataoka M. Maintenance of the secondary structure of horse cytochrome c during the conversion process of monomers to oligomers by addition of ethanol. ACTA ACUST UNITED AC 2012; 152:521-9. [DOI: 10.1093/jb/mvs098] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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74
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Mitomi Y, Nomura T, Kurosawa M, Nukina N, Furukawa Y. Post-aggregation oxidation of mutant huntingtin controls the interactions between aggregates. J Biol Chem 2012; 287:34764-75. [PMID: 22891249 DOI: 10.1074/jbc.m112.387035] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Aggregation of protein molecules is a pathological hallmark of many neurodegenerative diseases. Abnormal modifications have often been observed in the aggregated proteins, supporting the aggregation mechanism regulated by post-translational modifications on proteins. Modifications are in general assumed to occur in soluble proteins before aggregation, but actually it remains quite obscure when proteins are modified in the course of the aggregation. Here we focus upon aggregation of huntingtin (HTT), which causes a neurodegenerative disorder, Huntington disease, and we show that oxidation of a methionine residue in HTT occurs in vitro and also in vivo. Copper ions as well as added hydrogen peroxide are found to oxidize the methionine residue, but notably, this oxidative modification occurs only in the aggregated HTT but not in the soluble state. Furthermore, the methionine oxidation creates additional interactions among HTT aggregates and alters overall morphologies of the aggregates. We thus reveal that protein aggregates can be a target of oxidative modifications and propose that such a "post-aggregation" modification is a relevant factor to regulate properties of protein aggregates.
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Affiliation(s)
- Yasushi Mitomi
- Laboratory for Mechanistic Chemistry of Biomolecules, Department of Chemistry, Keio University, Yokohama, Kanagawa 223-8522, Japan
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75
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Ma B, Nussinov R. Selective molecular recognition in amyloid growth and transmission and cross-species barriers. J Mol Biol 2012; 421:172-84. [PMID: 22119878 PMCID: PMC6407624 DOI: 10.1016/j.jmb.2011.11.023] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Revised: 11/10/2011] [Accepted: 11/13/2011] [Indexed: 11/23/2022]
Abstract
Mutual conformational selection and population shift followed by minor induced-fit optimization is the key mechanism in biomolecular recognition, and monomers and small oligomers binding to amyloid seeds in fibril growth is a molecular recognition event. Here, we describe amyloid aggregation, preferred species, cross-species barriers and transmission within the broad framework of molecular recognition. Cross-seeding of amyloid species is governed by conformational selection of compatible (complementary) states. If the dominant conformations of two species are similar, they can cross-seed each other; on the other hand, if they are sufficiently different, they will grow into different fibrils, reflecting species barriers. Such a scenario has recently been observed for the tau protein, which has four repeats. While a construct consisting of repeats 1, 3 and 4 can serve as a seed for the entire four-repeat tau segment, the inverse does not hold. On the other hand, the tau protein repeats with the characteristic U-turn shape can cross-seed Alzheimer's amyloid β and, similarly, the islet amyloid polypeptide. Within this framework, we suggest that the so-called "central dogma" of amyloid formation, where aggregation takes place through nonspecific backbone hydrogen bonding interactions, which are common to all peptides and proteins, is a simple reflection of the heterogeneous, polymorphic free-energy landscape of amyloid species. Here, we review available data and make some propositions addressing this key problem. In particular, we argue that recent theoretical and experimental observations support the key role of selective molecular recognition in amyloidosis and in determining cross-species barriers and transmission.
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Affiliation(s)
- Buyong Ma
- Basic Science Program, SAIC-Frederick, Inc. Center for Cancer Research Nanobiology Program NCI-Frederick, Frederick, MD 21702
| | - Ruth Nussinov
- Basic Science Program, SAIC-Frederick, Inc. Center for Cancer Research Nanobiology Program NCI-Frederick, Frederick, MD 21702
- Sackler Inst. of Molecular Medicine Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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76
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Abstract
For several different proteins an apparent correlation has been observed between the propensity for dimerization by domain-swapping and the ability to aggregate into amyloid-like fibrils. Examples include the disease-related proteins β 2-microglobulin and transthyretin. This has led to proposals that the amyloid-formation pathway may feature extensive domain swapping. One possible consequence of such an aggregation pathway is that the resulting fibrils would incorporate structural elements that resemble the domain-swapped forms of the protein and, thus, reflect certain native-like structures or domain-interactions. In magic angle spinning solid-state NMR-based and other structural studies of such amyloid fibrils, it appears that many of these proteins form fibrils that are not native-like. Several fibrils, instead, have an in-register, parallel conformation, which is a common amyloid structural motif and is seen, for instance, in various prion fibrils. Such a lack of native structure in the fibrils suggests that the apparent connection between domain-swapping ability and amyloid-formation may be more subtle or complex than may be presumed at first glance.
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Affiliation(s)
- Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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77
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Disulfide bridges remain intact while native insulin converts into amyloid fibrils. PLoS One 2012; 7:e36989. [PMID: 22675475 PMCID: PMC3365881 DOI: 10.1371/journal.pone.0036989] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Accepted: 04/11/2012] [Indexed: 11/19/2022] Open
Abstract
Amyloid fibrils are β-sheet-rich protein aggregates commonly found in the organs and tissues of patients with various amyloid-associated diseases. Understanding the structural organization of amyloid fibrils can be beneficial for the search of drugs to successfully treat diseases associated with protein misfolding. The structure of insulin fibrils was characterized by deep ultraviolet resonance Raman (DUVRR) and Nuclear Magnetic Resonance (NMR) spectroscopy combined with hydrogen-deuterium exchange. The compositions of the fibril core and unordered parts were determined at single amino acid residue resolution. All three disulfide bonds of native insulin remained intact during the aggregation process, withstanding scrambling. Three out of four tyrosine residues were packed into the fibril core, and another aromatic amino acid, phenylalanine, was located in the unordered parts of insulin fibrils. In addition, using all-atom MD simulations, the disulfide bonds were confirmed to remain intact in the insulin dimer, which mimics the fibrillar form of insulin.
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78
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Chen KE, Richards AA, Ariffin JK, Ross IL, Sweet MJ, Kellie S, Kobe B, Martin JL. The mammalian DUF59 protein Fam96a forms two distinct types of domain-swapped dimer. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:637-48. [DOI: 10.1107/s0907444912006592] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 02/14/2012] [Indexed: 11/10/2022]
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79
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Abstract
Although amyloid fibers are found in neurodegenerative diseases, evidence points to soluble oligomers of amyloid-forming proteins as the cytotoxic species. Here, we establish that our preparation of toxic amyloid-β(1-42) (Abeta42) fibrillar oligomers (TABFOs) shares with mature amyloid fibrils the cross-β structure, in which adjacent β-sheets adhere by interpenetration of protein side chains. We study the structure and properties of TABFOs by powder X-ray diffraction, EM, circular dichroism, FTIR spectroscopy, chromatography, conformational antibodies, and celluar toxicity. In TABFOs, Abeta42 molecules stack into short protofilaments consisting of pairs of helical β-sheets that wrap around each other to form a superhelix. Wrapping results in a hole along the superhelix axis, providing insight into how Abeta may form pathogenic amyloid pores. Our model is consistent with numerous properties of Abeta42 fibrillar oligomers, including heterogenous size, ability to seed new populations of fibrillar oligomers, and fiber-like morphology.
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80
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Three-dimensional domain swapping in the protein structure space. Proteins 2012; 80:1610-9. [DOI: 10.1002/prot.24055] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 01/16/2012] [Accepted: 01/19/2012] [Indexed: 01/15/2023]
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81
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Colombo M, de Rosa M, Bellotti V, Ricagno S, Bolognesi M. A recurrent D-strand association interface is observed in β-2 microglobulin oligomers. FEBS J 2012; 279:1131-43. [DOI: 10.1111/j.1742-4658.2012.08510.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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82
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Self-assembly of functional, amphipathic amyloid monolayers by the fungal hydrophobin EAS. Proc Natl Acad Sci U S A 2012; 109:E804-11. [PMID: 22308366 DOI: 10.1073/pnas.1114052109] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The hydrophobin EAS from the fungus Neurospora crassa forms functional amyloid fibrils called rodlets that facilitate spore formation and dispersal. Self-assembly of EAS into fibrillar rodlets occurs spontaneously at hydrophobic:hydrophilic interfaces and the rodlets further associate laterally to form amphipathic monolayers. We have used site-directed mutagenesis and peptide experiments to identify the region of EAS that drives intermolecular association and formation of the cross-β rodlet structure. Transplanting this region into a nonamyloidogenic hydrophobin enables it to form rodlets. We have also determined the structure and dynamics of an EAS variant with reduced rodlet-forming ability. Taken together, these data allow us to pinpoint the conformational changes that take place when hydrophobins self-assemble at an interface and to propose a model for the amphipathic EAS rodlet structure.
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83
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Nagao S, Osuka H, Yamada T, Uni T, Shomura Y, Imai K, Higuchi Y, Hirota S. Structural and oxygen binding properties of dimeric horse myoglobin. Dalton Trans 2012; 41:11378-85. [DOI: 10.1039/c2dt30893b] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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84
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Rousseau F, Schymkowitz J, Itzhaki LS. Implications of 3D domain swapping for protein folding, misfolding and function. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 747:137-52. [PMID: 22949116 DOI: 10.1007/978-1-4614-3229-6_9] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Three-dimensional domain swapping is the process by which two identical protein chains exchange a part of their structure to form an intertwined dimer or higher-order oligomer. The phenomenon has been observed in the crystal structures of a range of different proteins. In this chapter we review the experiments that have been performed in order to understand the sequence and structural determinants of domain-swapping and these show how the general principles obtained can be used to engineer proteins to domain swap. We discuss the role of domain swapping in regulating protein function and as one possible mechanism of protein misfolding that can lead to aggregation and disease. We also review a number of interesting pathways of macromolecular assembly involving β-strand insertion or complementation that are related to the domain-swapping phenomenon.
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Affiliation(s)
- Frederic Rousseau
- VIB Switch Laboratory, Department of Molecular Cell Biology, Katholieke Universiteit Leuven, Leuven, Belgium
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85
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Buck PM, Kumar S, Wang X, Agrawal NJ, Trout BL, Singh SK. Computational methods to predict therapeutic protein aggregation. Methods Mol Biol 2012; 899:425-451. [PMID: 22735968 DOI: 10.1007/978-1-61779-921-1_26] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Protein based biotherapeutics have emerged as a successful class of pharmaceuticals. However, these macromolecules endure a variety of physicochemical degradations during manufacturing, shipping, and storage, which may adversely impact the drug product quality. Of these degradations, the irreversible self-association of therapeutic proteins to form aggregates is a major challenge in the formulation of these molecules. Tools to predict and mitigate protein aggregation are, therefore, of great interest to biopharmaceutical research and development. In this chapter, a number of such computational tools developed to understand and predict the various steps involved in protein aggregation are described. These tools can be grouped into three general classes: unfolding kinetics and native state thermal stability, colloidal stability, and sequence/structure based aggregation liabilities. Chapter sections introduce each class by discussing how these predictive tools provide insight into the molecular events leading to protein aggregation. The computational methods are then explained in detail along with their advantages and limitations.
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Affiliation(s)
- Patrick M Buck
- Biotherapeutics Pharmaceutical Research and Development, Pfizer, Inc, St. Louis, MO, USA
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86
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Abstract
Dialysis-related amyloidosis (DRA) is a clinical syndrome of pain, loss of function and other symptoms due to the deposition of amyloid consisting of β(2)-microglobulin (β(2)m) in the musculoskeletal system. The condition is seen in patients who suffer from chronic kidney disease and are treated with hemodialysis for a long time. Even though β(2)m easily can be manipulated to form amyloid in laboratory experiments under non-physiological conditions the precise mechanisms involved in the formation of β(2)m-amyloid in patients with DRA have been difficult to unravel. The current knowledge which is reviewed here indicates that conformational fluctuations centered around the D-strand, the DE-loop, and around the cis-configured Pro32 peptide bond are involved in β(2)m amyloidosis. Also required are highly increased concentrations of circulating β(2)m and possibly various post-translational modifications mediated by the pro-inflammatory environment in uremic blood, together with the influence of divalent metal ions (specifically Cu(2 +)), uremic toxins, and dialysis-enhanced redox-processes. It seems plausible that domain-swapped β(2)m dimers act as building blocks of β-spine cross-β -sheet fibrils consisting of otherwise globular, roughly natively folded protein. An activated complement system and cellular activation perpetuate these reactions which due to the affinity of β(2)m-amyloid for the collagen of synovial surfaces result in the DRA syndrome.
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Affiliation(s)
- Dorthe B Corlin
- Department of Clinical Biochemistry and Immunology, Division of Microbiology and Diagnostics, Statens Serum Institut, Bldg. 85/240, Artillerivej 5, 2300, Copenhagen S, Denmark,
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87
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Teng PK, Anderson NJ, Goldschmidt L, Sawaya MR, Sambashivan S, Eisenberg D. Ribonuclease A suggests how proteins self-chaperone against amyloid fiber formation. Protein Sci 2011; 21:26-37. [PMID: 22095666 DOI: 10.1002/pro.754] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 10/17/2011] [Accepted: 10/17/2011] [Indexed: 11/11/2022]
Abstract
Genomic analyses have identified segments with high fiber-forming propensity in many proteins not known to form amyloid. Proteins are often protected from entering the amyloid state by molecular chaperones that permit them to fold in isolation from identical molecules; but, how do proteins self-chaperone their folding in the absence of chaperones? Here, we explore this question with the stable protein ribonuclease A (RNase A). We previously identified fiber-forming segments of amyloid-related proteins and demonstrated that insertion of these segments into the C-terminal hinge loop of nonfiber-forming RNase A can convert RNase A into the amyloid state through three-dimensional domain-swapping, where the inserted fiber-forming segments interact to create a steric zipper spine. In this study, we convert RNase A into amyloid-like fibers by increasing the loop length and hence conformational freedom of an endogenous fiber-forming segment, SSTSAASS, in the N-terminal hinge loop. This is accomplished by sandwiching SSTSAASS between inserted Gly residues. With these inserts, SSTSAASS is now able to form the steric zipper spine, allowing RNase A to form amyloid-like fibers. We show that these fibers contain RNase A molecules retaining their enzymatic activity and therefore native-like structure. Thus, RNase A appears to prevent fiber formation by limiting the conformational freedom of this fiber-forming segment from entering a steric zipper. Our observations suggest that proteins have evolved to self-chaperone by using similar protective mechanisms.
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Affiliation(s)
- Poh K Teng
- Departments of Chemistry & Biochemistry and Biological Chemistry, Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, University of California-Los Angeles, 611 Charles Young Drive East, CA 90095-1570, USA
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88
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Topping TB, Gloss LM. The impact of solubility and electrostatics on fibril formation by the H3 and H4 histones. Protein Sci 2011; 20:2060-73. [PMID: 21953551 DOI: 10.1002/pro.743] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 09/01/2011] [Accepted: 09/08/2011] [Indexed: 12/15/2022]
Abstract
The goal of this study was to examine fibril formation by the heterodimeric eukaryotic histones (H2A-H2B and H3-H4) and homodimeric archaeal histones (hMfB and hPyA1). The histone fold dimerization motif is an obligatorily domain-swapped structure comprised of two fused helix:β-loop:helix motifs. Domain swapping has been proposed as a mechanism for the evolution of protein oligomers as well as a means to form precursors in the formation of amyloid-like fibrils. Despite sharing a common fold, the eukaryotic histones of the core nucleosome and archaeal histones fold by kinetic mechanisms of differing complexity with transient population of partially folded monomeric and/or dimeric species. No relationship was apparent between fibrillation propensity and equilibrium stability or population of kinetic intermediates. Only H3 and H4, as isolated monomers and as a heterodimer, readily formed fibrils at room temperature, and this propensity correlates with the significantly lower solubility of these polypeptides. The fibrils were characterized by ThT fluorescence, FTIR, and far-UV CD spectroscopies and electron microscopy. The helical histone fold comprises the protease-resistant core of the fibrils, with little or no protease protection of the poorly structured N-terminal tails. The highly charged tails inhibit fibrillation through electrostatic repulsion. Kinetic studies indicate that H3 and H4 form a co-fibril, with simultaneous incorporation of both histones. The potential impact of H3 and H4 fibrillation on the cytotoxicity of extracellular histones and α-synuclein-mediated neurotoxicity and fibrillation is considered.
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Affiliation(s)
- Traci B Topping
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-7520, USA
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89
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Eichner T, Radford SE. Understanding the complex mechanisms of β2-microglobulin amyloid assembly. FEBS J 2011; 278:3868-83. [PMID: 21595827 PMCID: PMC3229708 DOI: 10.1111/j.1742-4658.2011.08186.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Revised: 05/11/2011] [Accepted: 05/13/2011] [Indexed: 11/30/2022]
Abstract
Several protein misfolding diseases are associated with the conversion of native proteins into ordered protein aggregates known as amyloid. Studies of amyloid assemblies have indicated that non-native proteins are responsible for initiating aggregation in vitro and in vivo. Despite the importance of these species for understanding amyloid disease, the structural and dynamic features of amyloidogenic intermediates and the molecular details of how they aggregate remain elusive. This review focuses on recent advances in developing a molecular description of the folding and aggregation mechanisms of the human amyloidogenic protein β(2)-microglobulin under physiologically relevant conditions. In particular, the structural and dynamic properties of the non-native folding intermediate I(T) and its role in the initiation of fibrillation and the development of dialysis-related amyloidosis are discussed.
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Affiliation(s)
- Timo Eichner
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA.
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90
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Eichner T, Radford SE. A diversity of assembly mechanisms of a generic amyloid fold. Mol Cell 2011; 43:8-18. [PMID: 21726806 DOI: 10.1016/j.molcel.2011.05.012] [Citation(s) in RCA: 224] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 04/21/2011] [Accepted: 04/26/2011] [Indexed: 12/28/2022]
Abstract
Protein misfolding and amyloid assembly have long been recognized as being responsible for many devastating human diseases. Recent findings indicate that amyloid assemblies may facilitate crucial biological processes from bacteria to mammals. This review focuses on the mechanistic understanding of amyloid formation, including the transformation of initially innocuous proteins into oligomers and fibrils. The result is a competing folding and assembly energy landscape, which contains a number of routes by which the polypeptide chain can convert its primary sequence into functional structures, dysfunctional assemblies, or epigenetic entities that provide both threats and opportunities in the evolution of life.
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Affiliation(s)
- Timo Eichner
- Astbury Centre for Structural Molecular Biology and Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
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91
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Li J, Hoop CL, Kodali R, Sivanandam VN, van der Wel PCA. Amyloid-like fibrils from a domain-swapping protein feature a parallel, in-register conformation without native-like interactions. J Biol Chem 2011; 286:28988-28995. [PMID: 21715337 PMCID: PMC3190706 DOI: 10.1074/jbc.m111.261750] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 06/21/2011] [Indexed: 11/06/2022] Open
Abstract
The formation of amyloid-like fibrils is characteristic of various diseases, but the underlying mechanism and the factors that determine whether, when, and how proteins form amyloid, remain uncertain. Certain mechanisms have been proposed based on the three-dimensional or runaway domain swapping, inspired by the fact that some proteins show an apparent correlation between the ability to form domain-swapped dimers and a tendency to form fibrillar aggregates. Intramolecular β-sheet contacts present in the monomeric state could constitute intermolecular β-sheets in the dimeric and fibrillar states. One example is an amyloid-forming mutant of the immunoglobulin binding domain B1 of streptococcal protein G, which in its native conformation consists of a four-stranded β-sheet and one α-helix. Under native conditions this mutant adopts a domain-swapped dimer, and it also forms amyloid-like fibrils, seemingly in correlation to its domain-swapping ability. We employ magic angle spinning solid-state NMR and other methods to examine key structural features of these fibrils. Our results reveal a highly rigid fibril structure that lacks mobile domains and indicate a parallel in-register β-sheet structure and a general loss of native conformation within the mature fibrils. This observation contrasts with predictions that native structure, and in particular intermolecular β-strand interactions seen in the dimeric state, may be preserved in "domain-swapping" fibrils. We discuss these observations in light of recent work on related amyloid-forming proteins that have been argued to follow similar mechanisms and how this may have implications for the role of domain-swapping propensities for amyloid formation.
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Affiliation(s)
- Jun Li
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260
| | - Cody L Hoop
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260
| | - Ravindra Kodali
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260
| | - V N Sivanandam
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260
| | - Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260.
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92
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Cabriolu R, Auer S. Amyloid Fibrillation Kinetics: Insight from Atomistic Nucleation Theory. J Mol Biol 2011; 411:275-85. [DOI: 10.1016/j.jmb.2011.05.032] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 03/24/2011] [Accepted: 05/15/2011] [Indexed: 11/25/2022]
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93
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Vottariello F, Giacomelli E, Frasson R, Pozzi N, De Filippis V, Gotte G. RNase A oligomerization through 3D domain swapping is favoured by a residue located far from the swapping domains. Biochimie 2011; 93:1846-57. [PMID: 21771635 DOI: 10.1016/j.biochi.2011.07.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2011] [Accepted: 07/04/2011] [Indexed: 11/27/2022]
Abstract
Bovine pancreatic ribonuclease A forms 3D domain-swapped oligomers by lyophilization from 40% acetic acid solutions or if subjected to various thermally-induced denaturation procedures. Considering that the intrinsic swapping propensity of bovine seminal RNase, the only member of the pancreatic-type RNase super-family that is dimeric in nature, is decreased from 70 to 30% if Arg80 is substituted by Ser (the corresponding residue in native RNase A), we introduced the opposite mutation in position 80 of the pancreatic enzyme. Our aim was to detect if the RNase A tendency to aggregate through domain swapping could increase. Aggregation of the S80R-RNase A mutant was induced either through the 'classic' acetic acid lyophilization, or through a thermally-induced method. The results indicate that the S80R mutant aggregates to a higher extent than the native protein, and that the increase occurs especially through N-terminal swapping. Additional investigations on the dimeric and multimeric species formed indicate that the S80R mutation increases their stability against regression to monomer, and does not significantly change their structural and functional features.
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Affiliation(s)
- Francesca Vottariello
- Dipartimento di Scienze della Vita e della Riproduzione, Sezione di Chimica Biologica, Facoltà di Medicina e Chirurgia, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
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94
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Žerovnik E, Stoka V, Mirtič A, Gunčar G, Grdadolnik J, Staniforth RA, Turk D, Turk V. Mechanisms of amyloid fibril formation--focus on domain-swapping. FEBS J 2011; 278:2263-82. [PMID: 21535473 DOI: 10.1111/j.1742-4658.2011.08149.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Conformational diseases constitute a group of heterologous disorders in which a constituent host protein undergoes changes in conformation, leading to aggregation and deposition. To understand the molecular mechanisms of the process of amyloid fibril formation, numerous in vitro and in vivo studies, including model and pathologically relevant proteins, have been performed. Understanding the molecular details of these processes is of major importance to understand neurodegenerative diseases and could contribute to more effective therapies. Many models have been proposed to describe the mechanism by which proteins undergo ordered aggregation into amyloid fibrils. We classify these as: (a) templating and nucleation; (b) linear, colloid-like assembly of spherical oligomers; and (c) domain-swapping. In this review, we stress the role of domain-swapping and discuss the role of proline switches.
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Affiliation(s)
- Eva Žerovnik
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia.
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