1
|
Zhao N, Zhang Q, Yu F, Yao X, Liu H. The α-Synuclein Monomer May Have Different Misfolding Mechanisms in the Induction of α-Synuclein Fibrils with Different Polymorphs. Biomolecules 2023; 13:biom13040682. [PMID: 37189428 DOI: 10.3390/biom13040682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/19/2023] [Accepted: 04/12/2023] [Indexed: 05/17/2023] Open
Abstract
The aggregation of alpha-synuclein (α-Syn) is closely related to the occurrence of some neurodegenerative diseases such as Parkinson's disease. The misfolding of α-Syn monomer plays a key role in the formation of aggregates and extension of fibril. However, the misfolding mechanism of α-Syn remains elusive. Here, three different α-Syn fibrils (isolated from a diseased human brain, generated by in vitro cofactor-tau induction, and obtained by in vitro cofactor-free induction) were selected for the study. The misfolding mechanisms of α-Syn were uncovered by studying the dissociation of the boundary chains based on the conventional molecular dynamics (MD) and Steered MD simulations. The results showed that the dissociation paths of the boundary chains in the three systems were different. According to the reverse process of dissociation, we concluded that in the human brain system, the binding of the monomer and template starts from the C-terminal and gradually misfolds toward the N-terminal. In the cofactor-tau system, the monomer binding starts from residues 58-66 (contain β3), followed by the C-terminal coil (residues 67-79). Then, the N-terminal coil (residues 36-41) and residues 50-57 (contain β2) bind to the template, followed by residues 42-49 (contain β1). In the cofactor-free system, two misfolding paths were found. One is that the monomer binds to the N/C-terminal (β1/β6) and then binds to the remaining residues. The other one is that the monomer binds sequentially from the C- to N-terminal, similar to the human brain system. Furthermore, in the human brain and cofactor-tau systems, electrostatic interactions (especially from residues 58-66) are the main driving force during the misfolding process, whereas in the cofactor-free system, the contributions of electrostatic and van der Waals interactions are comparable. These results may provide a deeper understanding for the misfolding and aggregation mechanism of α-Syn.
Collapse
Affiliation(s)
- Nannan Zhao
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Qianqian Zhang
- Faculty of Applied Sciences, Macao Polytechnic University, Macao SAR, China
| | - Fansen Yu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Xiaojun Yao
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
- Faculty of Applied Sciences, Macao Polytechnic University, Macao SAR, China
| |
Collapse
|
2
|
Abstract
BACKGROUND For insulins in commercial formulations, degradation can be observed within the certified shelf life when not stored at recommended conditions. Elevated temperatures and exposure to shear forces can cause changes in the secondary structure of the hormone, leading to a decrease in pharmaceutical potency. International pharmacopoeia recommendations for insulin quality monitoring assays mainly rely on liquid chromatography methods. These methods are unable to distinguish between active and inactive forms, both of which may exist in pharmaceutical insulins exposed to stress conditions. METHOD Infrared attenuated total reflection spectroscopy has been used for the analysis of insulin dry film preparations using affordable instrumentation. This method can be applied to either formulated insulin specimens or pure insulins obtained by ultrafiltration. Such samples have been stored under different temperatures (0°C, 20°C, and 37°C), and degradation processes have been monitored up to a period of a few months. RESULTS By analyzing specific shifts of absorption bands in the infrared spectra, which are sensitive to the protein secondary structure, even small structural changes in the hormone become evident. Another option is amide I band deconvolution into individual bands, which can be attributed to secondary structure subunits that are part of the insulin tertiary structure. CONCLUSION A novel and innovative method based on infrared attenuated total reflection spectroscopy of insulin dry films is a promising analytical tool for quantifying the degree of insulin degradation, as it provides information on indicating a decrease in biological potency. The established methods for insulin potency assays require animal testing or clamp experiments on people with diabetes.
Collapse
Affiliation(s)
- Sven Delbeck
- Interdisciplinary Center for Life Sciences, South-Westphalia University of Applied Sciences, Iserlohn, Germany
| | - H. Michael Heise
- Interdisciplinary Center for Life Sciences, South-Westphalia University of Applied Sciences, Iserlohn, Germany
- H. Michael Heise, PhD, Interdisciplinary Center for Life Sciences, South-Westphalia University of Applied Sciences, Frauenstuhlweg 31, D-58644 Iserlohn, Germany.
| |
Collapse
|
3
|
Chinnasamy K, Saravanan M, Poomani K. Investigation of binding mechanism and downregulation of elacestrant for wild and L536S mutant estrogen receptor-α through molecular dynamics simulation and binding free energy analysis. J Comput Chem 2020; 41:97-109. [PMID: 31602686 DOI: 10.1002/jcc.26076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 06/22/2019] [Accepted: 08/31/2019] [Indexed: 12/11/2022]
Abstract
The selective estrogen receptor downregulators (SERDs) are the new emerging class of drugs that are used for the treatment of endocrine resistance breast cancer. Elacestrant (ELA) is a new SERD, currently it is in phase II clinical trial. To understand the ELA-ERα interactions, the molecular docking analysis has been carried out. The ELA molecule binds with the helices H3, H5, H6, and H11 and forms important intermolecular interactions. In addition to this, the tetrahydronapthalene and phenyl rings of ELA are forming T-shaped π···π interactions with the Phe404 and Trp383 residues. Further to understand the stability and flexibility of ELA molecule in the active site of wild and mutated L536S ERα, 100ns molecular dynamics (MD) simulation was performed for both complexes. Interestingly, the MD analysis of wild complex revealed an interaction between ELA and the Asn532 of H11, which is an essential interaction for the downregulation/degradation of ERα, whereas this interaction is not observed in the mutated complex. The drug binding mechanism and H12 dynamics have been elucidated from the analysis of hydrogen bonding interactions and the secondary structure analysis. To explore the binding affinity of ELA molecule, the binding free energy and normal mode analyses were carried out. The per residue decomposition analysis also performed, which shows the contribution of individual amino acids. The principal component analysis and residue interaction network analysis were used to identify the modifications and the interaction between the residues. From the results of different analysis, the inhibition mechanism and downregulation of ERα-ELA complex has been investigated. © 2019 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Kalaiarasi Chinnasamy
- Laboratory of Biocrystallography and Computational molecular Biology, Department of Physics, Periyar University, Salem, 636 011, India
| | - Manjula Saravanan
- Laboratory of Biocrystallography and Computational molecular Biology, Department of Physics, Periyar University, Salem, 636 011, India
| | - Kumaradhas Poomani
- Laboratory of Biocrystallography and Computational molecular Biology, Department of Physics, Periyar University, Salem, 636 011, India
| |
Collapse
|
4
|
Colarusso A, Caterino M, Fabbri A, Fiorentini C, Vergara A, Sica F, Parrilli E, Tutino ML. High yield purification and first structural characterization of the full-length bacterial toxin CNF1. Biotechnol Prog 2017; 34:150-159. [PMID: 29063721 DOI: 10.1002/btpr.2574] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 09/12/2017] [Indexed: 11/10/2022]
Abstract
The Cytotoxic Necrotizing Factor 1 (CNF1) is a bacterial toxin secreted by certain Escherichia coli strains causing severe pathologies, making it a protein of pivotal interest in toxicology. In parallel, the CNF1 capability to influence important neuronal processes, like neuronal arborization, astrocytic support, and efficient ATP production, has been efficiently used in the treatment of neurological diseases, making it a promising candidate for therapy. Nonetheless, there are still some unsolved issues about the CNF1 mechanism of action and structuration probably caused by the difficulty to achieve sufficient amounts of the full-length protein for further studies. Here, we propose an efficient strategy for the production and purification of this toxin as a his-tagged recombinant protein from E. coli extracts (CNF1-H8). CNF1-H8 was expressed at the low temperature of 15°C to diminish its characteristic degradation. Then, its purification was achieved using an immobilized metal affinity chromatography (IMAC) and a size exclusion chromatography so as to collect up to 8 mg of protein per liter of culture in a highly pure form. Routine dynamic light scattering (DLS) experiments showed that the recombinant protein preparations were homogeneous and preserved this state for a long time. Furthermore, CNF1-H8 functionality was confirmed by testing its activity on purified RhoA and on HEp-2 cultured cells. Finally, a first structural characterization of the full-length toxin in terms of secondary structure and thermal stability was performed by circular dichroism (CD). These studies demonstrate that our system can be used to produce high quantities of pure recombinant protein for a detailed structural analysis. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 34:150-159, 2018.
Collapse
Affiliation(s)
- Andrea Colarusso
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte Sant'Angelo, Via Cinthia, Napoli, 80126, Italy
| | - Marco Caterino
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte Sant'Angelo, Via Cinthia, Napoli, 80126, Italy
| | - Alessia Fabbri
- Italian Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena, 299, Roma, 00161, Italy
| | - Carla Fiorentini
- Italian Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena, 299, Roma, 00161, Italy
| | - Alessandro Vergara
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte Sant'Angelo, Via Cinthia, Napoli, 80126, Italy.,CEINGE Biotecnologie Avanzate scarl, Via G. Salvatore, Napoli, 80100, Italy.,Institute of Biostructures and Biomaging, CNR, Napoli, Italia Via Mezzocannone 16, Napoli, 80134, Italy
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte Sant'Angelo, Via Cinthia, Napoli, 80126, Italy.,Institute of Biostructures and Biomaging, CNR, Napoli, Italia Via Mezzocannone 16, Napoli, 80134, Italy
| | - Ermenegilda Parrilli
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte Sant'Angelo, Via Cinthia, Napoli, 80126, Italy
| | - Maria Luisa Tutino
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte Sant'Angelo, Via Cinthia, Napoli, 80126, Italy
| |
Collapse
|
5
|
Mou TC, Sreerama N, Terwilliger TC, Woody RW, Gray DM. Independent tyrosyl contributions to the CD of Ff gene 5 protein and the distinctive effects of Y41H and Y41F mutants on protein-protein cooperative interactions. Protein Sci 2002; 11:601-13. [PMID: 11847282 PMCID: PMC2373458 DOI: 10.1110/ps.30002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
The gene 5 protein (g5p) of the Ff virus contains five Tyr, individual mutants of which have now all been characterized by CD spectroscopy. The protein has a dominant tyrosyl 229-nm L(a) CD band that is shown to be approximately the sum of the five individual Tyr contributions. Tyr41 is particularly important in contributing to the high cooperativity with which the g5p binds to ssDNA, and Y41F and Y41H mutants are known to differ in dimer-dimer packing interactions in crystal structures. We compared the solution structures and binding properties of the Y41F and Y41H mutants using CD spectroscopy. Secondary structures of the mutants were similar by CD analyses and close to those derived from the crystal structures. However, there were significant differences in the binding properties of the two mutant proteins. The Y41H protein had an especially low binding affinity and perturbed the spectrum of poly[d(A)] in 2 mM Na(+) much less than did Y41F and the wild-type gene 5 proteins. Moreover, a change in the Tyr 229 nm band, assigned to the perturbation of Tyr34 at the dimer-dimer interface, was absent in titrations with the Y41H mutant under low salt conditions. In contrast, titrations with the Y41H mutant in 50 mM Na(+) exhibited typical CD changes of both the nucleic acid and the Tyr 229-nm band. Thus, protein-protein and g5p-ssDNA interactions appeared to be mutually influenced by ionic strength, indicative of correlated changes in the ssDNA binding and cooperativity loops of the protein or of indirect structural constraints.
Collapse
Affiliation(s)
- Tung-Chung Mou
- Department of Molecular and Cell Biology, The University of Texas at Dallas, Richardson, Texas 75083-0688, USA
| | | | | | | | | |
Collapse
|