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Lucignano R, Bologna A, Gramazio S, Wang PH, Taxis C, Essen LO, Picone D, Spadaccini R. Unravelling the amyloid aggregation mechanism of the sweet protein Monellin: Insights from circular permutated mutants. Int J Biol Macromol 2025; 308:142239. [PMID: 40118405 DOI: 10.1016/j.ijbiomac.2025.142239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2024] [Revised: 03/14/2025] [Accepted: 03/16/2025] [Indexed: 03/23/2025]
Abstract
Protein amyloid aggregates, once regarded solely as pathological hallmarks of human neurodegenerative diseases, have recently gained attention for their potential in biotechnological applications. Among others, MNEI and its variants, initially developed as single-chain derivatives of the sweet protein monellin, also serve as valuable models for studying protein fibrillary aggregation. In this work, we have characterized three circular permutated mutants of MNEI obtained joining the N- and C-termini of MNEI with linkers of different length and restoring the splitting of the polypeptide chain of native monellin. All proteins are well folded but have a different propensity to form oligomeric structures in solution and aggregation rates comparable to or faster than MNEI, as indicated by Thioflavin-T binding assays. Transmission Electron Microscopy (TEM) studies indicate that only Perm1, the mutant with the longest linker, forms fibrillar aggregates. X-ray structures of the mutants show that they crystallize as domain-swapped dimers. Molecular dynamics study highlights potential hot spots controlling the ordered aggregation process of Perm1. Our data support the idea that the formation of a domain-swapped dimer does not favour the formation of fibrillar aggregates and highlight circular permutation as a valuable tool to build nanostructured biomaterials.
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Affiliation(s)
- Rosanna Lucignano
- Department of Chemical Sciences, University of Naples Federico II, Naples, Campania, Italy
| | - Andrea Bologna
- Department of Science and Technology, University of Sannio, Benevento, Campania, Italy
| | - Simona Gramazio
- Department of Science and Technology, University of Sannio, Benevento, Campania, Italy
| | - Po-Hsun Wang
- Structural Biochemistry Unit, Department of Chemistry, Philipps Marburg University, Marburg, Hesse, Germany
| | | | - Lars-Oliver Essen
- Structural Biochemistry Unit, Department of Chemistry, Philipps Marburg University, Marburg, Hesse, Germany
| | - Delia Picone
- Department of Chemical Sciences, University of Naples Federico II, Naples, Campania, Italy.
| | - Roberta Spadaccini
- Department of Science and Technology, University of Sannio, Benevento, Campania, Italy; Structural Biochemistry Unit, Department of Chemistry, Philipps Marburg University, Marburg, Hesse, Germany.
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Das D, Ainavarapu SRK. Protein engineering using circular permutation - structure, function, stability, and applications. FEBS J 2024; 291:3581-3596. [PMID: 38676939 DOI: 10.1111/febs.17146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 03/13/2024] [Accepted: 04/12/2024] [Indexed: 04/29/2024]
Abstract
Protein engineering is important for creating novel variants from natural proteins, enabling a wide range of applications. Approaches such as rational design and directed evolution are routinely used to make new protein variants. Computational tools like de novo design can introduce new protein folds. Expanding the amino acid repertoire to include unnatural amino acids with non-canonical side chains in vitro by native chemical ligation and in vivo via codon expansion methods broadens sequence and structural possibilities. Circular permutation (CP) is an invaluable approach to redesigning a protein by rearranging the amino acid sequence, where the connectivity of the secondary structural elements is altered without changing the overall structure of the protein. Artificial CP proteins (CPs) are employed in various applications such as biocatalysis, sensing of small molecules by fluorescence, genome editing, ligand-binding protein switches, and optogenetic engineering. Many studies have shown that CP can lead to either reduced or enhanced stability or catalytic efficiency. The effects of CP on a protein's energy landscape cannot be predicted a priori. Thus, it is important to understand how CP can affect the thermodynamic and kinetic stability of a protein. In this review, we discuss the discovery and advancement of techniques to create protein CP, and existing reviews on CP. We delve into the plethora of biological applications for designed CP proteins. We subsequently discuss the experimental and computational reports on the effects of CP on the thermodynamic and kinetic stabilities of proteins of various topologies. An understanding of the various aspects of CP will allow the reader to design robust CP proteins for their specific purposes.
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Affiliation(s)
- Debanjana Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
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Melnik TN, Majorina MA, Vorobeva DE, Nagibina GS, Veselova VR, Glukhova KA, Pak MA, Ivankov DN, Uversky VN, Melnik BS. Design of stable circular permutants of the GroEL chaperone apical domain. Cell Commun Signal 2024; 22:90. [PMID: 38303060 PMCID: PMC10836027 DOI: 10.1186/s12964-023-01426-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/08/2023] [Indexed: 02/03/2024] Open
Abstract
Enhancing protein stability holds paramount significance in biotechnology, therapeutics, and the food industry. Circular permutations offer a distinctive avenue for manipulating protein stability while keeping intra-protein interactions intact. Amidst the creation of circular permutants, determining the optimal placement of the new N- and C-termini stands as a pivotal, albeit largely unexplored, endeavor. In this study, we employed PONDR-FIT's predictions of disorder propensity to guide the design of circular permutants for the GroEL apical domain (residues 191-345). Our underlying hypothesis posited that a higher predicted disorder value would correspond to reduced stability in the circular permutants, owing to the increased likelihood of fluctuations in the novel N- and C-termini. To substantiate this hypothesis, we engineered six circular permutants, positioning glycines within the loops as locations for the new N- and C-termini. We demonstrated the validity of our hypothesis along the set of the designed circular permutants, as supported by measurements of melting temperatures by circular dichroism and differential scanning microcalorimetry. Consequently, we propose a novel computational methodology that rationalizes the design of circular permutants with projected stability. Video Abstract.
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Affiliation(s)
- Tatiana N Melnik
- Institute of Protein Research, Russian Academy of Sciences, Institutskaja Str. 4, Pushchino, Moscow Region, 142290, Russia
| | - Maria A Majorina
- Institute of Protein Research, Russian Academy of Sciences, Institutskaja Str. 4, Pushchino, Moscow Region, 142290, Russia
| | - Daria E Vorobeva
- Institute of Protein Research, Russian Academy of Sciences, Institutskaja Str. 4, Pushchino, Moscow Region, 142290, Russia
| | - Galina S Nagibina
- Institute of Protein Research, Russian Academy of Sciences, Institutskaja Str. 4, Pushchino, Moscow Region, 142290, Russia
| | - Victoria R Veselova
- Institute of Protein Research, Russian Academy of Sciences, Institutskaja Str. 4, Pushchino, Moscow Region, 142290, Russia
| | - Ksenia A Glukhova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Institutskaja Str. 3, Puschino, Moscow Region, 142290, Russia
| | - Marina A Pak
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, Moscow, 121205, Russia
| | - Dmitry N Ivankov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, Moscow, 121205, Russia
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Center and Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
| | - Bogdan S Melnik
- Institute of Protein Research, Russian Academy of Sciences, Institutskaja Str. 4, Pushchino, Moscow Region, 142290, Russia.
- Pushchino Branch, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Prospekt Nauki 6, Pushchino, Moscow Region, 142290, Russia.
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SeqCP: A sequence-based algorithm for searching circularly permuted proteins. Comput Struct Biotechnol J 2022; 21:185-201. [PMID: 36582435 PMCID: PMC9763678 DOI: 10.1016/j.csbj.2022.11.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/10/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Circular permutation (CP) is a protein sequence rearrangement in which the amino- and carboxyl-termini of a protein can be created in different positions along the imaginary circularized sequence. Circularly permutated proteins usually exhibit conserved three-dimensional structures and functions. By comparing the structures of circular permutants (CPMs), protein research and bioengineering applications can be approached in ways that are difficult to achieve by traditional mutagenesis. Most current CP detection algorithms depend on structural information. Because there is a vast number of proteins with unknown structures, many CP pairs may remain unidentified. An efficient sequence-based CP detector will help identify more CP pairs and advance many protein studies. For instance, some hypothetical proteins may have CPMs with known functions and structures that are informative for functional annotation, but existing structure-based CP search methods cannot be applied when those hypothetical proteins lack structural information. Despite the considerable potential for applications, sequence-based CP search methods have not been well developed. We present a sequence-based method, SeqCP, which analyzes normal and duplicated sequence alignments to identify CPMs and determine candidate CP sites for proteins. SeqCP was trained by data obtained from the Circular Permutation Database and tested with nonredundant datasets from the Protein Data Bank. It shows high reliability in CP identification and achieves an AUC of 0.9. SeqCP has been implemented into a web server available at: http://pcnas.life.nthu.edu.tw/SeqCP/.
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Key Words
- AUC, area under the ROC curve
- CE, combinatorial extension
- CE-CP, CE with Circular Permutations
- CP, circular permutation
- CPDB, Circular Permutation Database
- CPMs, circular permutants
- CPSARST, Circular Permutation Search Aided by Ramachandran Sequential Transformation
- Circular permutants
- Circular permutation
- MCC, Matthews correlation coefficient
- Protein sequence analysis
- Protein structure modeling
- RMSD, root-mean-square distance
- ROC, receiver operating characteristic
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