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Ghosh D, Biswas A, Radhakrishna M. Advanced computational approaches to understand protein aggregation. BIOPHYSICS REVIEWS 2024; 5:021302. [PMID: 38681860 PMCID: PMC11045254 DOI: 10.1063/5.0180691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/18/2024] [Indexed: 05/01/2024]
Abstract
Protein aggregation is a widespread phenomenon implicated in debilitating diseases like Alzheimer's, Parkinson's, and cataracts, presenting complex hurdles for the field of molecular biology. In this review, we explore the evolving realm of computational methods and bioinformatics tools that have revolutionized our comprehension of protein aggregation. Beginning with a discussion of the multifaceted challenges associated with understanding this process and emphasizing the critical need for precise predictive tools, we highlight how computational techniques have become indispensable for understanding protein aggregation. We focus on molecular simulations, notably molecular dynamics (MD) simulations, spanning from atomistic to coarse-grained levels, which have emerged as pivotal tools in unraveling the complex dynamics governing protein aggregation in diseases such as cataracts, Alzheimer's, and Parkinson's. MD simulations provide microscopic insights into protein interactions and the subtleties of aggregation pathways, with advanced techniques like replica exchange molecular dynamics, Metadynamics (MetaD), and umbrella sampling enhancing our understanding by probing intricate energy landscapes and transition states. We delve into specific applications of MD simulations, elucidating the chaperone mechanism underlying cataract formation using Markov state modeling and the intricate pathways and interactions driving the toxic aggregate formation in Alzheimer's and Parkinson's disease. Transitioning we highlight how computational techniques, including bioinformatics, sequence analysis, structural data, machine learning algorithms, and artificial intelligence have become indispensable for predicting protein aggregation propensity and locating aggregation-prone regions within protein sequences. Throughout our exploration, we underscore the symbiotic relationship between computational approaches and empirical data, which has paved the way for potential therapeutic strategies against protein aggregation-related diseases. In conclusion, this review offers a comprehensive overview of advanced computational methodologies and bioinformatics tools that have catalyzed breakthroughs in unraveling the molecular basis of protein aggregation, with significant implications for clinical interventions, standing at the intersection of computational biology and experimental research.
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Affiliation(s)
- Deepshikha Ghosh
- Department of Biological Sciences and Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gujarat 382355, India
| | - Anushka Biswas
- Department of Chemical Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gujarat 382355, India
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Aklima J, Onchaiya S, Saotome T, Velmurugan P, Motoichi T, Naima J, Kuroda Y, Ohta Y. Direct Analysis of Mitochondrial Damage Caused by Misfolded/Destabilized Proteins. Int J Mol Sci 2022; 23:ijms23179881. [PMID: 36077279 PMCID: PMC9456338 DOI: 10.3390/ijms23179881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Protein quality control is essential for cellular homeostasis. In this study, we examined the effect of improperly folded proteins that do not form amyloid fibrils on mitochondria, which play important roles in ATP production and cell death. First, we prepared domain 3 of the dengue envelope protein in wild type and four mutants with widely different biophysical properties in misfolded/aggregated or destabilized states. The effects of the different proteins were detected using fluorescence microscopy and Western blotting, which revealed that three of the five proteins disrupted both inner and outer membrane integrity, while the other two proteins, including the wild type, did not. Next, we examined the common characteristics of the proteins that displayed toxicity against mitochondria by measuring oligomer size, molten globule-like properties, and thermal stability. The common feature of all three toxic proteins was thermal instability. Therefore, our data strongly suggest that thermally unstable proteins generated in the cytosol can cause cellular damage by coming into direct contact with mitochondria. More importantly, we revealed that this damage is not amyloid-specific.
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Affiliation(s)
- Jannatul Aklima
- Division of Biotechnology and Life Sciences, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chittagong 4331, Bangladesh
| | - Sawaros Onchaiya
- Division of Biotechnology and Life Sciences, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan
| | - Tomonori Saotome
- Division of Biotechnology and Life Sciences, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan
- Department of Bioengineering, Nagaoka University of Technology, Niigata 940-2188, Japan
| | - Punitha Velmurugan
- Division of Biotechnology and Life Sciences, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan
| | - Taihei Motoichi
- Division of Biotechnology and Life Sciences, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan
| | - Jannatul Naima
- Division of Biotechnology and Life Sciences, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan
| | - Yutaka Kuroda
- Division of Biotechnology and Life Sciences, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan
| | - Yoshihiro Ohta
- Division of Biotechnology and Life Sciences, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan
- Correspondence:
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So M, Hata Y, Naiki H, Goto Y. Heparin-induced amyloid fibrillation of β 2 -microglobulin explained by solubility and a supersaturation-dependent conformational phase diagram. Protein Sci 2017; 26:1024-1036. [PMID: 28249361 DOI: 10.1002/pro.3149] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 02/21/2017] [Accepted: 02/22/2017] [Indexed: 12/19/2022]
Abstract
Amyloid fibrils are fibrillar deposits of denatured proteins associated with amyloidosis and are formed by a nucleation and growth mechanism. We revisited an alternative and classical view of amyloid fibrillation: amyloid fibrils are crystal-like precipitates of denatured proteins formed above solubility upon breaking supersaturation. Various additives accelerate and then inhibit amyloid fibrillation in a concentration-dependent manner, suggesting that the combined effects of stabilizing and destabilizing forces affect fibrillation. Heparin, a glycosaminoglycan and anticoagulant, is an accelerator of fibrillation for various amyloidogenic proteins. By using β2 -microglobulin, a protein responsible for dialysis-related amyloidosis, we herein examined the effects of various concentrations of heparin on fibrillation at pH 2. In contrast to previous studies that focused on accelerating effects, higher concentrations of heparin inhibited fibrillation, and this was accompanied by amorphous aggregation. The two-step effects of acceleration and inhibition were similar to those observed for various salts. The results indicate that the anion effects caused by sulfate groups are one of the dominant factors influencing heparin-dependent fibrillation, although the exact structures of fibrils and amorphous aggregates might differ between those formed by simple salts and matrix-forming heparin. We propose that a conformational phase diagram, accommodating crystal-like amyloid fibrils and glass-like amorphous aggregates, is important for understanding the effects of various additives.
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Affiliation(s)
- Masatomo So
- Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Yasuko Hata
- Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Hironobu Naiki
- Faculty of Medical Sciences, University of Fukui, Fukui, 910-1193, Japan
| | - Yuji Goto
- Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
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Wang L, Cano M, Handa JT. p62 provides dual cytoprotection against oxidative stress in the retinal pigment epithelium. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1843:1248-58. [PMID: 24667411 PMCID: PMC4019388 DOI: 10.1016/j.bbamcr.2014.03.016] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 03/11/2014] [Accepted: 03/17/2014] [Indexed: 02/07/2023]
Abstract
As a signaling hub, p62/sequestosome plays important roles in cell signaling and degradation of misfolded proteins. p62 has been implicated as an adaptor protein to mediate autophagic clearance of insoluble protein aggregates in age-related diseases, including age-related macular degeneration (AMD), which is characterized by dysfunction of the retinal pigment epithelium (RPE). Our previous studies have shown that cigarette smoke (CS) induces oxidative stress and inhibits the proteasome pathway in cultured human RPE cells, suggesting that p62-mediated autophagy may become the major route to remove impaired proteins under such circumstances. In the present studies, we found that all p62 mRNA variants are abundantly expressed and upregulated by CS induced stress in cultured human RPE cells, yet isoform1 is the major translated form. We also show that p62 silencing exacerbated the CS induced accumulation of damaged proteins, both by suppressing autophagy and by inhibiting the Nrf2 antioxidant response, which in turn, increased protein oxidation. These effects of CS and p62 reduction were further confirmed in mice exposed to CS. We found that over-expression of p62 isoform1, but not its S403A mutant, which lacks affinity for ubiquitinated proteins, reduced misfolded proteins, yet simultaneously promoted an Nrf2-mediated antioxidant response. Thus, p62 provides dual, reciprocal enhancing protection to RPE cells from environmental stress induced protein misfolding and aggregation, by facilitating autophagy and the Nrf2 mediated antioxidant response, which might be a potential therapeutic target against AMD.
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Affiliation(s)
- Lei Wang
- Wilmer Eye Institute, Johns Hopkins School of Medicine, USA.
| | - Marisol Cano
- Wilmer Eye Institute, Johns Hopkins School of Medicine, USA.
| | - James T Handa
- Wilmer Eye Institute, Johns Hopkins School of Medicine, USA.
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Distinguishing crystal-like amyloid fibrils and glass-like amorphous aggregates from their kinetics of formation. Proc Natl Acad Sci U S A 2012; 109:14446-51. [PMID: 22908252 DOI: 10.1073/pnas.1208228109] [Citation(s) in RCA: 221] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Amyloid fibrils and amorphous aggregates are two types of aberrant aggregates associated with protein misfolding diseases. Although they differ in morphology, the two forms are often treated indiscriminately. β(2)-microglobulin (β2m), a protein responsible for dialysis-related amyloidosis, forms amyloid fibrils or amorphous aggregates depending on the NaCl concentration at pH 2.5. We compared the kinetics of their formation, which was monitored by measuring thioflavin T fluorescence, light scattering, and 8-anilino-1-naphthalenesulfonate fluorescence. Thioflavin T fluorescence specifically monitors amyloid fibrillation, whereas light scattering and 8-anilino-1-naphthalenesulfonate fluorescence monitor both amyloid fibrillation and amorphous aggregation. The amyloid fibrils formed via a nucleation-dependent mechanism in a supersaturated solution, analogous to crystallization. The lag phase of fibrillation was reduced upon agitation with stirring or ultrasonic irradiation, and disappeared by seeding with preformed fibrils. In contrast, the glass-like amorphous aggregates formed rapidly without a lag phase. Neither agitation nor seeding accelerated the amorphous aggregation. Thus, by monitoring the kinetics, we can distinguish between crystal-like amyloid fibrils and glass-like amorphous aggregates. Solubility and supersaturation will be key factors for further understanding the aberrant aggregation of proteins.
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Prabhu S, Srinivas V, Ramakrishna T, Raman B, Rao CM. Inhibition of Cu2+-mediated generation of reactive oxygen species by the small heat shock protein αB-crystallin: the relative contributions of the N- and C-terminal domains. Free Radic Biol Med 2011; 51:755-62. [PMID: 21658443 DOI: 10.1016/j.freeradbiomed.2011.05.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Revised: 05/18/2011] [Accepted: 05/18/2011] [Indexed: 11/22/2022]
Abstract
Oxidative stress, Cu(2+) homeostasis, and small heat shock proteins (sHsp's) have important implications in several neurodegenerative diseases. The ubiquitous sHsp αB-crystallin is an oligomeric protein that binds Cu(2+). We have investigated the relative contributions of the N- and C-terminal (C-TDαB-crystallin) domains of αB-crystallin to its Cu(2+)-binding and redox-attenuation properties and mapped the Cu(2+)-binding regions. C-TDαB-crystallin binds Cu(2+) with slightly less affinity and inhibits Cu(2+)-catalyzed, ascorbate-mediated generation of ROS to a lesser extent than αB-crystallin. [Cu(2+)]/[subunit] stoichiometries for redox attenuation by αB-crystallin and C-TDαB-crystallin are 5 and 2, respectively. Both αB-crystallin and C-TDαB-crystallin also inhibit the Fenton reaction of hydroxyl radical formation. Trypsinization of αB-crystallin bound to a Cu(2+)-NTA column and MALDI-TOF analysis of column-bound peptides yielded three peptides located in the N-terminal domain, and in-solution trypsinization of αB-crystallin followed by Cu(2+)-NTA column chromatography identified four additional Cu(2+)-binding peptides located in the C-terminal domain. Thus, Cu(2+)-binding regions are distributed in the N- and C-terminal domains. Small-angle X-ray scattering and sedimentation-velocity measurements indicate quaternary structural changes in αB-crystallin upon Cu(2+) binding. Our study indicates that an oligomer of αB-crystallin can sequester a large number (~150) of Cu(2+) ions. It acts like a "Cu(2+) sponge," exhibits redox attenuation of Cu(2+), and has potential roles in Cu(2+) homeostasis and in preventing oxidative stress.
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Affiliation(s)
- Sankaralingam Prabhu
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Hyderabad 500 007, India
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