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Polańska O, Szulc N, Stottko R, Olek M, Nadwodna J, Gąsior-Głogowska M, Szefczyk M. Challenges in Peptide Solubilization - Amyloids Case Study. CHEM REC 2024; 24:e202400053. [PMID: 39023378 DOI: 10.1002/tcr.202400053] [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: 03/18/2024] [Revised: 05/23/2024] [Indexed: 07/20/2024]
Abstract
Peptide science has been a rapidly growing research field because of the enormous potential application of these biocompatible and bioactive molecules. However, many factors limit the widespread use of peptides in medicine, and low solubility is among the most common problems that hamper drug development in the early stages of research. Solubility is a crucial, albeit poorly understood, feature that determines peptide behavior. Several different solubility predictors have been proposed, and many strategies and protocols have been reported to dissolve peptides, but none of them is a one-size-fits-all method for solubilization of even the same peptide. In this review, we look for the reasons behind the difficulties in dissolving peptides, analyze the factors influencing peptide aggregation, conduct a critical analysis of solubilization strategies and protocols available in the literature, and give some tips on how to deal with the so-called difficult sequences. We focus on amyloids, which are particularly difficult to dissolve and handle such as amyloid beta (Aβ), insulin, and phenol-soluble modulins (PSMs).
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Affiliation(s)
- Oliwia Polańska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Natalia Szulc
- Department of Physics and Biophysics, Wroclaw University of Environmental and Life Sciences, Norwida 25, 50-375, Wrocław, Poland
| | - Rafał Stottko
- Faculty of Chemistry, Wrocław University of Science and Technology, Gdanska 7/9, 50-344, Wrocław, Poland
| | - Mateusz Olek
- Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, Traugutta 2, 41-800 Zabrze, Poland
| | - Julita Nadwodna
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Marlena Gąsior-Głogowska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Monika Szefczyk
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
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Szulc N, Gąsior-Głogowska M, Żyłka P, Szefczyk M, Wojciechowski JW, Żak AM, Dyrka W, Kaczorowska A, Burdukiewicz M, Tarek M, Kotulska M. Structural effects of charge destabilization and amino acid substitutions in amyloid fragments of CsgA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 313:124094. [PMID: 38503257 DOI: 10.1016/j.saa.2024.124094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/21/2024]
Abstract
The most studied functional amyloid is the CsgA, major curli subunit protein, which is produced by numerous strains of Enterobacteriaceae. Although CsgA sequences are highly conserved, they exhibit species diversity, which reflects the specific evolutionary and functional adaptability of the major curli subunit. Herein, we performed bioinformatics analyses to uncover the differences in the amyloidogenic properties of the R4 fragments in Escherichia coli and Salmonella enterica and proposed four mutants for more detailed studies: M1, M2, M3, and M4. The mutated sequences were characterized by various experimental techniques, such as circular dichroism, ATR-FTIR, FT-Raman, thioflavin T, transmission electron microscopy and confocal microscopy. Additionally, molecular dynamics simulations were performed to determine the role of buffer ions in the aggregation process. Our results demonstrated that the aggregation kinetics, fibril morphology, and overall structure of the peptide were significantly affected by the positions of charged amino acids within the repeat sequences of CsgA. Notably, substituting glycine with lysine resulted in the formation of distinctive spherically packed globular aggregates. The differences in morphology observed are attributed to the influence of phosphate ions, which disrupt the local electrostatic interaction network of the polypeptide chains. This study provides knowledge on the preferential formation of amyloid fibrils based on charge states within the polypeptide chain.
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Affiliation(s)
- Natalia Szulc
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland; CNRS, University of Lorraine, F-5400 Nancy, France; Department of Physics and Biophysics, Faculty of Biotechnology and Food Science, Wrocław University of Environmental and Life Sciences, Norwida 25, 50-375 Wrocław, Poland
| | - Marlena Gąsior-Głogowska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Paweł Żyłka
- Department of Electrical Engineering Fundamentals, Faculty of Electrical Engineering, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Monika Szefczyk
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Jakub W Wojciechowski
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Andrzej M Żak
- Institute of Advanced Materials, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Witold Dyrka
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Aleksandra Kaczorowska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland; Laboratory of Cytobiochemistry, Faculty of Biotechnology, University of Wroclaw, F. Joliot-Curie 14a, 50-383 Wroclaw, Poland
| | - Michał Burdukiewicz
- Institute of Biotechnology and Biomedicine, Autonomous University of Barcelona, Campus Universitat Autònoma de Barcelona Plaça Cívica Bellaterra, s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain; Clinical Research Centre, Medical University of Bialystok, Jana Kilinskiego 1, 15-089 Bialystok, Poland
| | - Mounir Tarek
- CNRS, University of Lorraine, F-5400 Nancy, France.
| | - Malgorzata Kotulska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland.
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Garfagnini T, Bemporad F, Harries D, Chiti F, Friedler A. Amyloid Aggregation Is Potently Slowed Down by Osmolytes Due to Compaction of Partially Folded State. J Mol Biol 2023; 435:168281. [PMID: 37734431 DOI: 10.1016/j.jmb.2023.168281] [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: 03/25/2023] [Revised: 07/30/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023]
Abstract
Amyloid aggregation is a key process in amyloidoses and neurodegenerative diseases. Hydrophobicity is one of the major driving forces for this type of aggregation, as an increase in hydrophobicity generally correlates with aggregation susceptibility and rate. However, most experimental systems in vitro and prediction tools in silico neglect the contribution of protective osmolytes present in the cellular environment. Here, we assessed the role of hydrophobic mutations in amyloid aggregation in the presence of osmolytes. To achieve this goal, we used the model protein human muscle acylphosphatase (mAcP) and mutations to leucine that increased its hydrophobicity without affecting its thermodynamic stability. Osmolytes significantly slowed down the aggregation kinetics of the hydrophobic mutants, with an effect larger than that observed on the wild-type protein. The effect increased as the mutation site was closer to the middle of the protein sequence. We propose that the preferential exclusion of osmolytes from mutation-introduced hydrophobic side-chains quenches the aggregation potential of the ensemble of partially unfolded states of the protein by inducing its compaction and inhibiting its self-assembly with other proteins. Our results suggest that including the effect of the cellular environment in experimental setups and predictive softwares, for both mechanistic studies and drug design, is essential in order to obtain a more complete combination of the driving forces of amyloid aggregation.
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Affiliation(s)
- Tommaso Garfagnini
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 9190401, Israel
| | - Francesco Bemporad
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
| | - Daniel Harries
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 9190401, Israel; The Fritz Haber Research Center, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 9190401, Israel
| | - Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
| | - Assaf Friedler
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 9190401, Israel.
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Sahoo BR, Bardwell JCA. SERF, a family of tiny highly conserved, highly charged proteins with enigmatic functions. FEBS J 2023; 290:4150-4162. [PMID: 35694898 DOI: 10.1111/febs.16555] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 11/27/2022]
Abstract
Amyloid formation is a misfolding process that has been linked to age-related diseases, including Alzheimer's and Huntington's. Understanding how cellular factors affect this process in vivo is vital in realizing the dream of controlling this insidious process that robs so many people of their humanity. SERF (small EDRK-rich factor) was initially isolated as a factor that accelerated polyglutamine amyloid formation in a C. elegans model. SERF knockouts inhibit amyloid formation of a number of proteins that include huntingtin, α-synuclein and β-amyloid which are associated with Huntington's, Parkinson's and Alzheimer's disease, respectively, and purified SERF protein speeds their amyloid formation in vitro. SERF proteins are highly conserved, highly charged and conformationally dynamic proteins that form a fuzzy complex with amyloid precursors. They appear to act by specifically accelerating the primary step of amyloid nucleation. Brain-specific SERF knockout mice, though viable, appear to be more prone to deposition of amyloids, and show modified fibril morphology. Whole-body knockouts are perinatally lethal due to an apparently unrelated developmental issue. Recently, it was found that SERF binds RNA and is localized to nucleic acid-rich membraneless compartments. SERF-related sequences are commonly found fused to zinc finger sequences. These results point towards a nucleic acid-binding function. How this function relates to their ability to accelerate amyloid formation is currently obscure. In this review, we discuss the possible biological functions of SERF family proteins in the context of their structural fuzziness, modulation of amyloid pathway, nucleic acid binding and their fusion to folded proteins.
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Affiliation(s)
- Bikash R Sahoo
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | - James C A Bardwell
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
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5
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Suthar SK, Lee SY. Truncation or proteolysis of α-synuclein in Parkinsonism. Ageing Res Rev 2023; 90:101978. [PMID: 37286088 DOI: 10.1016/j.arr.2023.101978] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 05/28/2023] [Accepted: 06/03/2023] [Indexed: 06/09/2023]
Abstract
Posttranslational modifications of α-synuclein, such as truncation or abnormal proteolysis, are implicated in Parkinson's disease (PD), dementia with Lewy bodies (DLB), and multiple system atrophy (MSA). A key focus of this article includes the proteases responsible for inducing truncation, the specific sites susceptible to truncation, and the resultant influence of these truncated species on the seeding and aggregation of endogenous α-synuclein. We also shed light on the unique structural attributes of these truncated species, and how these modifications can lead to distinctive forms of synucleinopathies. In addition, we explore the comparative toxic potentials of various α-synuclein species. An extensive analysis of available evidence of truncated α-synuclein species in human-synucleinopathy brains is also provided. Lastly, we delve into the detrimental impact of truncated species on key cellular structures such as the mitochondria and endoplasmic reticulum. Our article discusses enzymes involved in α-synuclein truncation, including 20 S proteasome, cathepsins, asparagine endopeptidase, caspase-1, calpain-1, neurosin/kallikrein-6, matrix metalloproteinase-1/-3, and plasmin. Truncation patterns impact α-synuclein aggregation - C-terminal truncation accelerates aggregation with larger truncations correlated with shortened aggregation lag times. N-terminal truncation affects aggregation differently based on the truncation location. C-terminally truncated α-synuclein forms compact, shorter fibrils compared to the full-length (FL) protein. N-terminally truncated monomers form fibrils similar in length to FL α-synuclein. Truncated forms show distinct fibril morphologies, increased β-sheet structures, and greater protease resistance. Misfolded α-synuclein can adopt various conformations, leading to unique aggregates and distinct synucleinopathies. Fibrils, with prion-like transmission, are potentially more toxic than oligomers, though this is still debated. Different α-synuclein variants with N- and C-terminal truncations, namely 5-140, 39-140, 65-140, 66-140, 68-140, 71-140, 1-139, 1-135, 1-133, 1-122, 1-119, 1-115, 1-110, and 1-103 have been found in PD, DLB, and MSA patients' brains. In Parkinsonism, excess misfolded α-synuclein overwhelms the proteasome degradation system, resulting in truncated protein production and accumulation in the mitochondria and endoplasmic reticulum.
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Affiliation(s)
| | - Sang-Yoon Lee
- Neuroscience Research Institute, Gachon University, Incheon, South Korea; Department of Neuroscience, College of Medicine, Gachon University, Incheon, South Korea.
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Acquasaliente L, De Filippis V. The Role of Proteolysis in Amyloidosis. Int J Mol Sci 2022; 24:ijms24010699. [PMID: 36614141 PMCID: PMC9820691 DOI: 10.3390/ijms24010699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023] Open
Abstract
Amyloidoses are a group of diseases associated with deposits of amyloid fibrils in different tissues. So far, 36 different types of amyloidosis are known, each due to the misfolding and accumulation of a specific protein. Amyloid deposits can be found in several organs, including the heart, brain, kidneys, and spleen, and can affect single or multiple organs. Generally, amyloid-forming proteins become prone to aggregate due to genetic mutations, acquired environmental factors, excessive concentration, or post-translational modifications. Interestingly, amyloid aggregates are often composed of proteolytic fragments, derived from the degradation of precursor proteins by yet unidentified proteases, which display higher amyloidogenic tendency compared to precursor proteins, thus representing an important mechanism in the onset of amyloid-based diseases. In the present review, we summarize the current knowledge on the proteolytic susceptibility of three of the main human amyloidogenic proteins, i.e., transthyretin, β-amyloid precursor protein, and α-synuclein, in the onset of amyloidosis. We also highlight the role that proteolytic enzymes can play in the crosstalk between intestinal inflammation and amyloid-based diseases.
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Affiliation(s)
- Laura Acquasaliente
- Correspondence: (L.A.); (V.D.F.); Tel.: +39-0498275703 (L.A.); +39-0498275698 (V.D.F.)
| | - Vincenzo De Filippis
- Correspondence: (L.A.); (V.D.F.); Tel.: +39-0498275703 (L.A.); +39-0498275698 (V.D.F.)
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Khan AN, Khan RH. Protein misfolding and related human diseases: A comprehensive review of toxicity, proteins involved, and current therapeutic strategies. Int J Biol Macromol 2022; 223:143-160. [PMID: 36356861 DOI: 10.1016/j.ijbiomac.2022.11.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/02/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022]
Abstract
Most of the cell's chemical reactions and structural components are facilitated by proteins. But proteins are highly dynamic molecules, where numerous modifications or changes in the cellular environment can affect their native conformational fold leading to protein aggregation. Various stress conditions, such as oxidative stress, mutations and metal toxicity may cause protein misfolding and aggregation by shifting the conformational equilibrium towards more aggregation-prone states. Most of the protein misfolding diseases (PMDs) involve aggregation of protein. We have discussed such proteins like Aβ peptide, α-synuclein, amylin and lysozyme involved in Alzheimer's, Parkinson's, type II diabetes and non-neuropathic systemic amyloidosis respectively. Till date, all advances in PMDs therapeutics help symptomatically but do not prevent the root cause of the disease, i.e., the aggregation of protein involved in the diseases. Current efforts focused on developing therapies for PMDs have employed diverse strategies; repositioning pre-existing drugs as it saves time and money; natural compounds that are touted as potential drug candidates have an advantage of being taken in diet normally and will induce lesser side effects. This review also covers recently developed therapeutic strategies like antisense drugs and disaggregases which has yielded therapeutic agents that have transitioned from preclinical studies into human clinical trials.
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Affiliation(s)
- Asra Nasir Khan
- Interdisciplinary Biotechnology Unit, AMU, Aligarh 202002, India
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Wakayama K, Kimura S, Kobatake Y, Kamishina H, Nishii N, Takashima S, Honda R, Kamatari YO. Molecular Mechanisms of Aggregation of Canine SOD1 E40K Amyloidogenic Mutant Protein. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010156. [PMID: 36615350 PMCID: PMC9822309 DOI: 10.3390/molecules28010156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/17/2022] [Accepted: 12/21/2022] [Indexed: 12/29/2022]
Abstract
Canine degenerative myelopathy (DM) is a human amyotrophic lateral sclerosis (ALS)-like neurodegenerative disease. It is a unique, naturally occurring animal model of human ALS. Canine DM is associated with the aggregation of canine superoxide dismutase 1 (cSOD1), which is similar to human ALS. Almost 100% of cases in dogs are familial, and the E40K mutation in cSOD1 is a major causative mutation of DM. Therefore, it is important to understand the molecular mechanisms underlying cSOD1(E40K) aggregation. To address this, we first analyzed the structural model of wild type cSOD1. Interactions were evident between amino acid E40 and K91. Therefore, the mutation at residue E40 causes loss of the interaction and may destabilize the native structure of cSOD1. Differential scanning fluorimetry revealed that the E40K mutant was less stable than the wild type. Moreover, stability could be recovered by the E40K and K91E double mutation. Acceleration of amyloid fibril formation in vitro and aggregate formation in cells of cSOD1(E40K) was also suppressed by the introduction of this double mutation in thioflavin T fluorescence assay results and in transfectant cells, respectively. These results clearly show the importance of the interaction between amino acid residues E40 and K91 in cSOD1 for the stability of the native structure and aggregation.
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Affiliation(s)
- Kento Wakayama
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Shintaro Kimura
- Life Science Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- Neuroprotection Research Laboratory, Departments of Radiology and Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Yui Kobatake
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Hiroaki Kamishina
- Life Science Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- Kyoto AR, 33 Sayama-Nakamichi, Kumiyama, Kuze, Kyoto 613-0036, Japan
| | - Naohito Nishii
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Satoshi Takashima
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Ryo Honda
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Yuji O. Kamatari
- Life Science Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- Institute for Glyco-Core Research (iGCORE), Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- Correspondence: ; Tel.: +81-58-293-3900
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Thu TTM, Li MS. Protein aggregation rate depends on mechanical stability of fibrillar structure . J Chem Phys 2022; 157:055101. [DOI: 10.1063/5.0088689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The formation of the fibrillar structure of amyloid proteins/peptides is believed to be associated with neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, etc. Since the rate of aggregation can influence neurotoxicity, finding the key factors that control this rate is of paramount importance. It was recently found evidence that the rate of protein aggregation is related to the mechanical stability of the fibrillar structure, such that the higher the mechanical stability, the faster the fibril is formed. However, this conclusion was supported by a limited dataset. In this work, we expand the previous study to a larger dataset, including the wild type of Aβ42 peptide and its 20 mutants, the aggregation rate of which was measured experimentally. By using all-atom steered molecular dynamics (SMD) simulations we can access the mechanical stability of the fibril structure, which is characterized by the rupture force, pulling work and unbinding free energy barrier. Our result confirms that mechanical stability is indeed related to the aggregation rate. Since estimation of the aggregation rate using all-atom simulations is almost forbidden by the current computational capabilities, our result is useful for predicting it based on information obtained from fast SMD simulations for fibrils.
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Affiliation(s)
| | - Mai Suan Li
- Theoretical Physics, Institute of Physics, Polish Academy of Sciences, Poland
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Brunori M, Gianni S. An Outlook on the Complexity of Protein Morphogenesis in Health and Disease. Front Mol Biosci 2022; 9:909567. [PMID: 35769915 PMCID: PMC9234464 DOI: 10.3389/fmolb.2022.909567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 04/28/2022] [Indexed: 11/21/2022] Open
Abstract
The study of the mechanisms whereby proteins achieve their native functionally competent conformation has been a key issue in molecular biosciences over the last 6 decades. Nevertheless, there are several debated issues and open problems concerning some aspects of this fundamental problem. By considering the emerging complexity of the so-called “native state,” we attempt hereby to propose a personal account on some of the key topics in the field, ranging from the relationships between misfolding and diseases to the significance of protein disorder. Finally, we briefly describe the recent and exciting advances in predicting protein structures from their amino acid sequence.
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Affiliation(s)
- Maurizio Brunori
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università, Rome, Italy
- Accademia Nazionale dei Lincei, Rome, Italy
- *Correspondence: Maurizio Brunori,
| | - Stefano Gianni
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università, Rome, Italy
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11
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Sturchio A, Dwivedi AK, Malm T, Wood MJ, Cilia R, Sharma JS, Hill EJ, Schneider LS, Graff-Radford NR, Mori H, Nübling G, El Andaloussi S, Svenningsson P, Ezzat K, Espay AJ. High Soluble Amyloid-β42 Predicts Normal Cognition in Amyloid-Positive Individuals with Alzheimer's Disease-Causing Mutations. J Alzheimers Dis 2022; 90:333-348. [PMID: 36120786 PMCID: PMC9661329 DOI: 10.3233/jad-220808] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2022] [Indexed: 12/18/2022]
Abstract
BACKGROUND In amyloid-positive individuals at risk for Alzheimer's disease (AD), high soluble 42-amino acid amyloid-β (Aβ42) levels are associated with normal cognition. It is unknown if this relationship applies longitudinally in a genetic cohort. OBJECTIVE To test the hypothesis that high Aβ42 preserves normal cognition in amyloid-positive individuals with Alzheimer's disease (AD)-causing mutations (APP, PSEN1, or PSEN2) to a greater extent than lower levels of brain amyloid, cerebrospinal fluid (CSF) phosphorylated tau (p-tau), or total tau (t-tau). METHODS Cognitive progression was defined as any increase in Clinical Dementia Rating (CDR = 0, normal cognition; 0.5, very mild dementia; 1, mild dementia) over 3 years. Amyloid-positivity was defined as a standard uptake value ratio (SUVR) ≥1.42 by Pittsburgh compound-B positron emission tomography (PiB-PET). We used modified Poisson regression models to estimate relative risk (RR), adjusted for age at onset, sex, education, APOE4 status, and duration of follow-up. The results were confirmed with multiple sensitivity analyses, including Cox regression. RESULTS Of 232 mutation carriers, 108 were PiB-PET-positive at baseline, with 43 (39.8%) meeting criteria for progression after 3.3±2.0 years. Soluble Aβ42 levels were higher among CDR non-progressors than CDR progressors. Higher Aβ42 predicted a lower risk of progression (adjusted RR, 0.36; 95% confidence interval [CI], 0.19-0.67; p = 0.002) better than lower SUVR (RR, 0.81; 95% CI, 0.68-0.96; p = 0.018). CSF Aβ42 levels predicting lower risk of progression increased with higher SUVR levels. CONCLUSION High CSF Aβ42 levels predict normal cognition in amyloid-positive individuals with AD-causing genetic mutations.
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Affiliation(s)
- Andrea Sturchio
- Department of Neurology, James J. and Joan A. Gardner Family Center for Parkinson’s Disease and Movement Disorders, University of Cincinnati, Cincinnati, OH, USA
- Department of Clinical Neuroscience, Neuro Svenningsson, Karolinska Institutet, Stockholm, Sweden
| | - Alok K. Dwivedi
- Department of Molecular and Translational Medicine, Division of Biostatistics & Epidemiology, Texas Tech University Health Sciences Center, El Paso, TX, USA
| | - Tarja Malm
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Matthew J.A. Wood
- Department of Paediatrics, University of Oxford, Oxford, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
| | - Roberto Cilia
- Department of Clinical Neurosciences, Fondazione IRCCS Istituto Neurologico Carlo Besta, Parkinson and Movement Disorders Unit, Milan, Italy
| | - Jennifer S. Sharma
- Department of Neurology, James J. and Joan A. Gardner Family Center for Parkinson’s Disease and Movement Disorders, University of Cincinnati, Cincinnati, OH, USA
| | - Emily J. Hill
- Department of Neurology, James J. and Joan A. Gardner Family Center for Parkinson’s Disease and Movement Disorders, University of Cincinnati, Cincinnati, OH, USA
| | - Lon S. Schneider
- University of Southern California Keck School of Medicine, Los Angeles, CA, USA
| | | | - Hiroshi Mori
- Department of Clinical Neuroscience, Medical School, Osaka City University, Sutoku University, Abenoku, Osaka, Nagaoka, Japan
| | - Georg Nübling
- German Center for Neurodegenerative Diseases, Site Munich, Germany
- Department of Neurology, Ludwig-Maximilians University Munich, Germany
| | - Samir El Andaloussi
- Department of Laboratory Medicine, Biomolecular and Cellular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Per Svenningsson
- Department of Clinical Neuroscience, Neuro Svenningsson, Karolinska Institutet, Stockholm, Sweden
| | - Kariem Ezzat
- Department of Laboratory Medicine, Biomolecular and Cellular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Alberto J. Espay
- Department of Neurology, James J. and Joan A. Gardner Family Center for Parkinson’s Disease and Movement Disorders, University of Cincinnati, Cincinnati, OH, USA
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12
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The role of intra and inter-molecular disulfide bonds in modulating amyloidogenesis: A review. Arch Biochem Biophys 2021; 716:109113. [PMID: 34958750 DOI: 10.1016/j.abb.2021.109113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/17/2021] [Accepted: 12/22/2021] [Indexed: 11/20/2022]
Abstract
All proteins have the inherent ability to undergo transformation from their native structure to a β sheet rich fibrillar structure, called amyloid when subjected to specific conditions. Proteins with a high propensity to form amyloid fibrils have been implicated in a variety of disorders like Alzheimer's disease, Parkinson's disease, Type II diabetes, Amyotrophic Lateral Sclerosis (ALS) and prion diseases. Among the various critical factors that modulate the process of amyloid formation, disulfide bonds have been identified as one of the key determinants of amyloid propensity in proteins. Studies have shown that intra-molecular disulfide bonds impart stability to the native structure of a protein and decrease the tendency for amyloid aggregation, whereas intermolecular disulfide bonds aid in the process of aggregation. In this review, we will analyze the varying effects of both intra as well as inter-molecular disulfide bonds on the amyloid aggregation propensities of a few proteins associated with amyloid disorders.
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13
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The role of amyloids in Alzheimer's and Parkinson's diseases. Int J Biol Macromol 2021; 190:44-55. [PMID: 34480905 DOI: 10.1016/j.ijbiomac.2021.08.197] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 11/23/2022]
Abstract
With varying clinical symptoms, most neurodegenerative diseases are associated with abnormal loss of neurons. They share the same common pathogenic mechanisms involving misfolding and aggregation, and these visible aggregates of proteins are deposited in the central nervous system. Amyloid formation is thought to arise from partial unfolding of misfolded proteins leading to the exposure of hydrophobic surfaces, which interact with other similar structures and give rise to form dimers, oligomers, protofibrils, and eventually mature fibril aggregates. Accumulating evidence indicates that amyloid oligomers, not amyloid fibrils, are the most toxic species that causes Alzheimer's disease (AD) and Parkinson's disease (PD). AD has recently been recognized as the 'twenty-first century plague', with an incident rate of 1% at 60 years of age, which then doubles every fifth year. Currently, 5.3 million people in the US are afflicted with this disease, and the number of cases is expected to rise to 13.5 million by 2050. PD, a disorder of the brain, is the second most common form of dementia, characterized by difficulty in walking and movement. Keeping the above views in mind, in this review we have focused on the roles of amyloid in neurodegenerative diseases including AD and PD, the involvement of amyloid in mitochondrial dysfunction leading to neurodegeneration, are also considered in the review.
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14
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Kumar P, Jagtap YA, Patwa SM, Kinger S, Dubey AR, Prajapati VK, Dhiman R, Poluri KM, Mishra A. Autophagy based cellular physiological strategies target oncogenic progression. J Cell Physiol 2021; 237:258-277. [PMID: 34448206 DOI: 10.1002/jcp.30567] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 07/27/2021] [Accepted: 08/16/2021] [Indexed: 12/22/2022]
Abstract
Evidence accumulated from past findings indicates that defective proteostasis may contribute to risk factors for cancer generation. Irregular assembly of abnormal proteins catalyzes the disturbance of cellular proteostasis and induces the ability of abnormal cellular proliferation. The autophagy mechanism plays a key role in the regular clearance of abnormal/poor lipids, proteins, and various cellular organelles. The results of functional and effective autophagy deliver normal cellular homeostasis, which establishes supportive metabolism and avoids unexpected tumorigenesis events. Still, the precise molecular mechanism of autophagy in tumor suppression has not been clear. How autophagy triggers selective or nonselective bulk degradation to dissipate tumor promotion under stress conditions is not clear. Under proteotoxic insults to knockdown the drive of tumorigenesis, it is critical for us to figure out the detailed molecular functions of autophagy in human cancers. The current article summarizes autophagy-based theragnostic strategies targeting various phases of tumorigenesis and suggests the preventive roles of autophagy against tumor progression. A better understanding of various molecular partners of autophagic flux will improve and innovate therapeutic approaches based on autophagic-susceptible effects against cellular oncogenic transformation.
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Affiliation(s)
- Prashant Kumar
- Department of Bioscience & Bioengineering, Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, India
| | - Yuvraj Anandrao Jagtap
- Department of Bioscience & Bioengineering, Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, India
| | - Som Mohanlal Patwa
- Department of Bioscience & Bioengineering, Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, India
| | - Sumit Kinger
- Department of Bioscience & Bioengineering, Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, India
| | - Ankur Rakesh Dubey
- Department of Bioscience & Bioengineering, Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Rohan Dhiman
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela, Odisha, India
| | - Krishna Mohan Poluri
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Amit Mishra
- Department of Bioscience & Bioengineering, Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, India
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15
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Baumer KM, Cook CD, Zahler CT, Beard AA, Chen Z, Koone JC, Dashnaw CM, Villacob RA, Solouki T, Wood JL, Borchelt DR, Shaw BF. Supercharging Prions via Amyloid‐Selective Lysine Acetylation. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Katelyn M. Baumer
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
| | | | - Collin T. Zahler
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
| | | | - Zhijuan Chen
- Department of Neuroscience University of Florida Gainesville FL USA
| | - Jordan C. Koone
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
| | - Chad M. Dashnaw
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
| | - Raul A. Villacob
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
| | - Touradj Solouki
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
| | - John L. Wood
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
| | | | - Bryan F. Shaw
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
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16
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A Conceptual Framework for Integrating Cellular Protein Folding, Misfolding and Aggregation. Life (Basel) 2021; 11:life11070605. [PMID: 34202456 PMCID: PMC8304792 DOI: 10.3390/life11070605] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/16/2021] [Accepted: 06/21/2021] [Indexed: 02/06/2023] Open
Abstract
How proteins properly fold and maintain solubility at the risk of misfolding and aggregation in the cellular environments still remains largely unknown. Aggregation has been traditionally treated as a consequence of protein folding (or misfolding). Notably, however, aggregation can be generally inhibited by affecting the intermolecular interactions leading to aggregation, independently of protein folding and conformation. We here point out that rigorous distinction between protein folding and aggregation as two independent processes is necessary to reconcile and underlie all observations regarding the combined cellular protein folding and aggregation. So far, the direct attractive interactions (e.g., hydrophobic interactions) between cellular macromolecules including chaperones and interacting polypeptides have been widely believed to mainly stabilize polypeptides against aggregation. However, the intermolecular repulsions by large excluded volume and surface charges of cellular macromolecules can play a key role in stabilizing their physically connected polypeptides against aggregation, irrespective of the connection types and induced conformational changes, underlying the generic intrinsic chaperone activity of cellular macromolecules. Such rigorous distinction and intermolecular repulsive force-driven aggregation inhibition by cellular macromolecules could give new insights into understanding the complex cellular protein landscapes that remain uncharted.
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17
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AbsoluRATE: An in-silico method to predict the aggregation kinetics of native proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140682. [PMID: 34102324 DOI: 10.1016/j.bbapap.2021.140682] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/12/2021] [Accepted: 06/04/2021] [Indexed: 12/12/2022]
Abstract
Protein aggregation has two aspects, namely, mechanistic and kinetics. Understanding protein aggregation kinetics is critical for prediction of progression of diseases caused by amyloidosis, accumulation of aggregates in biotherapeutics during storage and engineering commercial nano-biomaterials. In this work, we have collected experimentally determined absolute protein aggregation rates and developed an SVM based regression model to predict absolute rates of protein and peptide aggregation near-physiological conditions. The regression model achieved a correlation coefficient of 0.72 with MAE of 0.91 (natural log of kapp, where kapp is in hour-1) using leave-one-out cross-validation on a dataset of 82 non-redundant proteins/peptides. The model accounts for the experimental conditions (such as temperature, pH, ionic and protein concentration) and sequence-based properties. The amino acid sequence features revealed by this model as being important for aggregation kinetics, are also associated with the aggregation mechanism. In particular, inherent aggregation propensity of the protein/peptide sequence and number of aggregation prone regions (APRs) unpunctuated by the gatekeeping residues, were found to play important roles in the prediction of the absolute aggregation rates. This analysis shows that mechanism and kinetics of protein aggregation are coupled via common sequence attributes. The aggregation kinetic prediction method developed in this work is available at https://web.iitm.ac.in/bioinfo2/absolurate-pred/index.html.
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18
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Baumer KM, Cook CD, Zahler CT, Beard AA, Chen Z, Koone JC, Dashnaw CM, Villacob RA, Solouki T, Wood JL, Borchelt DR, Shaw BF. Supercharging Prions via Amyloid-Selective Lysine Acetylation. Angew Chem Int Ed Engl 2021; 60:15069-15079. [PMID: 33876528 DOI: 10.1002/anie.202103548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Indexed: 11/10/2022]
Abstract
Repulsive electrostatic forces between prion-like proteins are a barrier against aggregation. In neuropharmacology, however, a prion's net charge (Z) is not a targeted parameter. Compounds that selectively boost prion Z remain unreported. Here, we synthesized compounds that amplified the negative charge of misfolded superoxide dismutase-1 (SOD1) by acetylating lysine-NH3 + in amyloid-SOD1, without acetylating native-SOD1. Compounds resembled a "ball and chain" mace: a rigid amyloid-binding "handle" (benzothiazole, stilbene, or styrylpyridine); an aryl ester "ball"; and a triethylene glycol chain connecting ball to handle. At stoichiometric excess, compounds acetylated up to 9 of 11 lysine per misfolded subunit (ΔZfibril =-8100 per 103 subunits). Acetylated amyloid-SOD1 seeded aggregation more slowly than unacetylated amyloid-SOD1 in vitro and organotypic spinal cord (these effects were partially due to compound binding). Compounds exhibited reactivity with other amyloid and non-amyloid proteins (e.g., fibrillar α-synuclein was peracetylated; serum albumin was partially acetylated; carbonic anhydrase was largely unacetylated).
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Affiliation(s)
- Katelyn M Baumer
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Christopher D Cook
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Collin T Zahler
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Alexandra A Beard
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Zhijuan Chen
- Department of Neuroscience, University of Florida, Gainesville, FL, USA
| | - Jordan C Koone
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Chad M Dashnaw
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Raul A Villacob
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Touradj Solouki
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - John L Wood
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - David R Borchelt
- Department of Neuroscience, University of Florida, Gainesville, FL, USA
| | - Bryan F Shaw
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
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19
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Trist BG, Hilton JB, Hare DJ, Crouch PJ, Double KL. Superoxide Dismutase 1 in Health and Disease: How a Frontline Antioxidant Becomes Neurotoxic. Angew Chem Int Ed Engl 2021; 60:9215-9246. [PMID: 32144830 PMCID: PMC8247289 DOI: 10.1002/anie.202000451] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Indexed: 12/11/2022]
Abstract
Cu/Zn superoxide dismutase (SOD1) is a frontline antioxidant enzyme catalysing superoxide breakdown and is important for most forms of eukaryotic life. The evolution of aerobic respiration by mitochondria increased cellular production of superoxide, resulting in an increased reliance upon SOD1. Consistent with the importance of SOD1 for cellular health, many human diseases of the central nervous system involve perturbations in SOD1 biology. But far from providing a simple demonstration of how disease arises from SOD1 loss-of-function, attempts to elucidate pathways by which atypical SOD1 biology leads to neurodegeneration have revealed unexpectedly complex molecular characteristics delineating healthy, functional SOD1 protein from that which likely contributes to central nervous system disease. This review summarises current understanding of SOD1 biology from SOD1 genetics through to protein function and stability.
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Affiliation(s)
- Benjamin G. Trist
- Brain and Mind Centre and Discipline of PharmacologyThe University of Sydney, CamperdownSydneyNew South Wales2050Australia
| | - James B. Hilton
- Department of Pharmacology and TherapeuticsThe University of MelbourneParkvilleVictoria3052Australia
| | - Dominic J. Hare
- Brain and Mind Centre and Discipline of PharmacologyThe University of Sydney, CamperdownSydneyNew South Wales2050Australia
- School of BioSciencesThe University of MelbourneParkvilleVictoria3052Australia
- Atomic Medicine InitiativeThe University of Technology SydneyBroadwayNew South Wales2007Australia
| | - Peter J. Crouch
- Department of Pharmacology and TherapeuticsThe University of MelbourneParkvilleVictoria3052Australia
| | - Kay L. Double
- Brain and Mind Centre and Discipline of PharmacologyThe University of Sydney, CamperdownSydneyNew South Wales2050Australia
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20
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Shahbazi Dastjerdeh M, Shokrgozar MA, Rahimi H, Golkar M. Potential aggregation hot spots in recombinant human keratinocyte growth factor: a computational study. J Biomol Struct Dyn 2021; 40:8169-8184. [PMID: 33843469 DOI: 10.1080/07391102.2021.1908912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The recombinant human keratinocyte growth factor (rhKGF) is a highly aggregation-prone therapeutic protein. The high aggregation liability of rhKGF is manifested by loss of the monomeric state, and accumulation of the aggregated species even at moderate temperatures. Here, we analyzed the rhKGF for its vulnerability toward aggregation by detection of aggregation-prone regions (APRs) using several sequence-based computational tools including TANGO, ZipperDB, AGGRESCAN, Zyggregator, Camsol, PASTA, SALSA, WALTZ, SODA, Amylpred, AMYPDB, and structure-based tools including SolubiS, CamSol structurally corrected, Aggrescan3D and spatial aggregation propensity (SAP) algorithm. The sequence-based prediction of APRs in rhKGF indicated that they are mainly located at positions 10-30, 40-60, 61-66, 88-120, and 130-140. Mapping on the rhKGF structure revealed that most of these residues including F16-R25, I43, E45, R47-I56, F61, Y62, N66, L88-E91, E108-F110, A112, N114, T131, and H133-T140 are surface-exposed in the native state which can promote aggregation without major unfolding event, or the conformational change may occur in the oligomers. The other regions are buried in the native state and their contribution to non-native aggregation is mediated by a preceding unfolding event. The structure-based prediction of APRs using the SAP tool limited the number of identified APRs to the dynamically-exposed hydrophobic residues including V12, A50, V51, L88, I89, L90, I118, L135, and I139 mediating the native-state aggregation. Our analysis of APRs in rhKGF identified the regions determining the intrinsic aggregation propensity of the rhKGF which are the candidate positions for engineering the rhKGF to reduce its aggregation tendency.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Hamzeh Rahimi
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Majid Golkar
- Department of Parasitology, Pasteur Institute of Iran, Tehran, Iran
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21
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The concept of protein folding/unfolding and its impacts on human health. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021. [PMID: 34090616 DOI: 10.1016/bs.apcsb.2021.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Proteins have evolved in specific 3D structures and play different functions in cells and determine various reactions and pathways. The newly synthesized amino acid chains once depart ribosome must crumple into three-dimensional structures so can be biologically active. This process of protein that makes a functional molecule is called protein folding. The protein folding is both a biological and a physicochemical process that depends on the sequence of it. In fact, this process occurs more complicated and in some cases and in exposure to some molecules like glucose (glycation), mistaken folding leads to amyloid structures and fatal disorders called conformational diseases. Such conditions are detected by the quality control system of the cell and these abnormal proteins undergo renovation or degradation. This scenario takes place by the chaperones, chaperonins, and Ubiquitin-proteasome complex. Understanding of protein folding mechanisms from different views including experimental and computational approaches has revealed some intermediate ensembles such as molten globule and has been subjected to biophysical and molecular biology attempts to know more about prevalent conformational diseases.
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22
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Prabakaran R, Rawat P, Thangakani AM, Kumar S, Gromiha MM. Protein aggregation: in silico algorithms and applications. Biophys Rev 2021; 13:71-89. [PMID: 33747245 PMCID: PMC7930180 DOI: 10.1007/s12551-021-00778-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/01/2021] [Indexed: 01/08/2023] Open
Abstract
Protein aggregation is a topic of immense interest to the scientific community due to its role in several neurodegenerative diseases/disorders and industrial importance. Several in silico techniques, tools, and algorithms have been developed to predict aggregation in proteins and understand the aggregation mechanisms. This review attempts to provide an essence of the vast developments in in silico approaches, resources available, and future perspectives. It reviews aggregation-related databases, mechanistic models (aggregation-prone region and aggregation propensity prediction), kinetic models (aggregation rate prediction), and molecular dynamics studies related to aggregation. With a multitude of prediction models related to aggregation already available to the scientific community, the field of protein aggregation is rapidly maturing to tackle new applications.
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Affiliation(s)
- R. Prabakaran
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu India
| | - Puneet Rawat
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu India
| | - A. Mary Thangakani
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu India
| | - Sandeep Kumar
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT USA
| | - M. Michael Gromiha
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu India
- School of Computing, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa Japan
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23
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Trist BG, Hilton JB, Hare DJ, Crouch PJ, Double KL. Superoxide Dismutase 1 in Health and Disease: How a Frontline Antioxidant Becomes Neurotoxic. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000451] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Benjamin G. Trist
- Brain and Mind Centre and Discipline of Pharmacology The University of Sydney, Camperdown Sydney New South Wales 2050 Australia
| | - James B. Hilton
- Department of Pharmacology and Therapeutics The University of Melbourne Parkville Victoria 3052 Australia
| | - Dominic J. Hare
- Brain and Mind Centre and Discipline of Pharmacology The University of Sydney, Camperdown Sydney New South Wales 2050 Australia
- School of BioSciences The University of Melbourne Parkville Victoria 3052 Australia
- Atomic Medicine Initiative The University of Technology Sydney Broadway New South Wales 2007 Australia
| | - Peter J. Crouch
- Department of Pharmacology and Therapeutics The University of Melbourne Parkville Victoria 3052 Australia
| | - Kay L. Double
- Brain and Mind Centre and Discipline of Pharmacology The University of Sydney, Camperdown Sydney New South Wales 2050 Australia
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24
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Kimura S, Kamatari YO, Kuwahara Y, Hara H, Yamato O, Maeda S, Kamishina H, Honda R. Canine SOD1 harboring E40K or T18S mutations promotes protein aggregation without reducing the global structural stability. PeerJ 2020; 8:e9512. [PMID: 32742795 PMCID: PMC7368427 DOI: 10.7717/peerj.9512] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/18/2020] [Indexed: 11/20/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive and fatal neurodegenerative disease associated with aggregation of superoxide dismutase 1 (SOD1) protein. More than 160 mutations in human SOD1 have been identified in familial ALS and extensively characterized in previous studies. Here, we investigated the effects of T18S and E40K mutations on protein aggregation of canine SOD1. These two mutations are exclusively found in canine degenerative myelopathy (an ALS-like neurodegenerative disease in dogs), whose phenotype is unknown at the level of protein folding. Interestingly, the T18S and E40K mutations did not alter far-UV CD spectrum, enzymatic activity, or global structural stability of canine SOD1. However, thioflavin-T assay and transmission electron microscopy analysis revealed that these mutations promote formation of fibrous aggregates, in particular in the Cu2+/Zn2+-unbound state. These evidence suggested that the T18S and E40K mutations promote protein aggregation through a unique mechanism, possibly involving destabilization of the local structure, reduction of net negative charge, or production of disulfide-linked oligomers.
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Affiliation(s)
- Shintaro Kimura
- The United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan
| | | | - Yukina Kuwahara
- Joint Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Hideaki Hara
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, Gifu, Japan
| | - Osamu Yamato
- Laboratory of Veterinary Clinical Pathology, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Sadatoshi Maeda
- The United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan
| | - Hiroaki Kamishina
- The United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan.,Center for Highly Advanced Integration of Nano and Life Sciences, Gifu University, Gifu, Japan
| | - Ryo Honda
- The United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
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25
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Gil-Garcia M, Navarro S, Ventura S. Coiled-coil inspired functional inclusion bodies. Microb Cell Fact 2020; 19:117. [PMID: 32487230 PMCID: PMC7268670 DOI: 10.1186/s12934-020-01375-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/25/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Recombinant protein expression in bacteria often leads to the formation of intracellular insoluble protein deposits, a major bottleneck for the production of soluble and active products. However, in recent years, these bacterial protein aggregates, commonly known as inclusion bodies (IBs), have been shown to be a source of stable and active protein for biotechnological and biomedical applications. The formation of these functional IBs is usually facilitated by the fusion of aggregation-prone peptides or proteins to the protein of interest, leading to the formation of amyloid-like nanostructures, where the functional protein is embedded. RESULTS In order to offer an alternative to the classical amyloid-like IBs, here we develop functional IBs exploiting the coiled-coil fold. An in silico analysis of coiled-coil and aggregation propensities, net charge, and hydropathicity of different potential tags identified the natural homo-dimeric and anti-parallel coiled-coil ZapB bacterial protein as an optimal candidate to form assemblies in which the native state of the fused protein is preserved. The protein itself forms supramolecular fibrillar networks exhibiting only α-helix secondary structure. This non-amyloid self-assembly propensity allows generating innocuous IBs in which the recombinant protein of interest remains folded and functional, as demonstrated using two different fluorescent proteins. CONCLUSIONS Here, we present a proof of concept for the use of a natural coiled-coil domain as a versatile tool for the production of functional IBs in bacteria. This α-helix-based strategy excludes any potential toxicity drawback that might arise from the amyloid nature of β-sheet-based IBs and renders highly active and homogeneous submicrometric particles.
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Affiliation(s)
- Marcos Gil-Garcia
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Susanna Navarro
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
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Malmberg M, Malm T, Gustafsson O, Sturchio A, Graff C, Espay AJ, Wright AP, El Andaloussi S, Lindén A, Ezzat K. Disentangling the Amyloid Pathways: A Mechanistic Approach to Etiology. Front Neurosci 2020; 14:256. [PMID: 32372895 PMCID: PMC7186396 DOI: 10.3389/fnins.2020.00256] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 03/06/2020] [Indexed: 12/23/2022] Open
Abstract
Amyloids are fibrillar protein aggregates associated with diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), type II diabetes and Creutzfeldt-Jakob disease. The process of amyloid polymerization involves three pathological protein transformations; from natively folded conformation to the cross-β conformation, from biophysically soluble to insoluble, and from biologically functional to non-functional. While amyloids share a similar cross-β conformation, the biophysical transformation can either take place spontaneously via a homogeneous nucleation mechanism (HON) or catalytically on an exogenous surface via a heterogeneous nucleation mechanism (HEN). Here, we postulate that the different nucleation pathways can serve as a mechanistic basis for an etiological classification of amyloidopathies, where hereditary forms generally follow the HON pathway, while sporadic forms follow seed-induced (prions) or surface-induced (including microbially induced) HEN pathways. Critically, the conformational and biophysical amyloid transformation results in loss-of-function (LOF) of the original natively folded and soluble protein. This LOF can, at least initially, be the mechanism of amyloid toxicity even before amyloid accumulation reaches toxic levels. By highlighting the important role of non-protein species in amyloid formation and LOF mechanisms of toxicity, we propose a generalized mechanistic framework that could help better understand the diverse etiology of amyloid diseases and offer new opportunities for therapeutic interventions, including replacement therapies.
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Affiliation(s)
- Maja Malmberg
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
- SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Tarja Malm
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Oskar Gustafsson
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Stockholm, Sweden
| | - Andrea Sturchio
- Department of Neurology and Rehabilitation Medicine, James J and Joan A Gardner Center for Parkinson Disease and Movement Disorders, University of Cincinnati, Cincinnati, OH, United States
| | - Caroline Graff
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Solna, Sweden
- Unit for Hereditary Dementias, Theme Aging, Karolinska University Hospital, Solna, Sweden
| | - Alberto J. Espay
- Department of Neurology and Rehabilitation Medicine, James J and Joan A Gardner Center for Parkinson Disease and Movement Disorders, University of Cincinnati, Cincinnati, OH, United States
| | - Anthony P. Wright
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Stockholm, Sweden
| | - Samir El Andaloussi
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Stockholm, Sweden
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Anders Lindén
- Unit for Lung and Airway Research, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Respiratory Medicine and Allergy, Karolinska University Hospital, Stockholm, Sweden
| | - Kariem Ezzat
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Stockholm, Sweden
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Bigman LS, Levy Y. Proteins: molecules defined by their trade-offs. Curr Opin Struct Biol 2020; 60:50-56. [DOI: 10.1016/j.sbi.2019.11.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/07/2019] [Accepted: 11/11/2019] [Indexed: 12/30/2022]
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28
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Choi SI. A Simple Principle for Understanding the Combined Cellular Protein Folding and Aggregation. Curr Protein Pept Sci 2020; 21:3-21. [DOI: 10.2174/1389203720666190725114550] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/09/2019] [Accepted: 07/10/2019] [Indexed: 12/27/2022]
Abstract
Proteins can undergo kinetic/thermodynamic partitioning between folding and aggregation. Proper protein folding and thermodynamic stability are crucial for aggregation inhibition. Thus, proteinfolding principles have been widely believed to consistently underlie aggregation as a consequence of conformational change. However, this prevailing view appears to be challenged by the ubiquitous phenomena that the intrinsic and extrinsic factors including cellular macromolecules can prevent aggregation, independently of (even with sacrificing) protein folding rate and stability. This conundrum can be definitely resolved by ‘a simple principle’ based on a rigorous distinction between protein folding and aggregation: aggregation can be controlled by affecting the intermolecular interactions for aggregation, independently of the intramolecular interactions for protein folding. Aggregation is beyond protein folding. A unifying model that can conceptually reconcile and underlie the seemingly contradictory observations is described here. This simple principle highlights, in particular, the importance of intermolecular repulsive forces against aggregation, the magnitude of which can be correlated with the size and surface properties of molecules. The intermolecular repulsive forces generated by the common intrinsic properties of cellular macromolecules including chaperones, such as their large excluded volume and surface charges, can play a key role in preventing the aggregation of their physically connected polypeptides, thus underlying the generic intrinsic chaperone activity of soluble cellular macromolecules. Such intermolecular repulsive forces of bulky cellular macromolecules, distinct from protein conformational change and attractive interactions, could be the puzzle pieces for properly understanding the combined cellular protein folding and aggregation including how proteins can overcome their metastability to amyloid fibrils in vivo.
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Affiliation(s)
- Seong Il Choi
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
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29
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Computational prediction and redesign of aberrant protein oligomerization. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 169:43-83. [DOI: 10.1016/bs.pmbts.2019.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Pallarés I, Ventura S. Advances in the Prediction of Protein Aggregation Propensity. Curr Med Chem 2019; 26:3911-3920. [DOI: 10.2174/0929867324666170705121754] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 04/14/2017] [Accepted: 04/20/2017] [Indexed: 12/29/2022]
Abstract
Background:
Protein aggregation into β-sheet-enriched insoluble assemblies is being
found to be associated with an increasing number of debilitating human pathologies, such as Alzheimer’s
disease or type 2 diabetes, but also with premature aging. Furthermore, protein aggregation
represents a major bottleneck in the production and marketing of proteinbased therapeutics.
Thus, the development of methods to accurately forecast the aggregation propensity of a certain
protein is of much value.
Methods/Results:
A myriad of in vitro and in vivo aggregation studies have shown that the aggregation
propensity of a certain polypeptide sequence is highly dependent on its intrinsic properties
and, in most cases, driven by specific short regions of high aggregation propensity. These observations
have fostered the development of a first generation of algorithms aimed to predict protein
aggregation propensities from the protein sequence. A second generation of programs able to map
protein aggregation on protein structures is emerging. Herein, we review the most representative
online accessible predictive tools, emphasizing their main distinctive features and the range of
applications.
Conclusion:
In this review, we describe representative biocomputational approaches to evaluate
the aggregation properties of protein sequences and structures, while illustrating how they can
become very useful tools to target protein aggregation in biomedicine and biotechnology.
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Affiliation(s)
- Irantzu Pallarés
- Institut de Biotecnologia i Biomedicina, Universitat Autonoma de Barcelona, 08193-Bellaterra (Barcelona), Spain
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina, Universitat Autonoma de Barcelona, 08193-Bellaterra (Barcelona), Spain
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Bouyacoub Y, Falfoul Y, Ouederni M, Sayeb M, Chedli A, Chargui M, Sassi H, Chakroun Chenguel I, Munier FL, El Matri L, Abdelhak S, Cheour M. Granular type I corneal dystrophy in a large consanguineous Tunisian family with homozygous p.R124S mutation in the TGFBI gene. Ophthalmic Genet 2019; 40:329-337. [PMID: 31322463 DOI: 10.1080/13816810.2019.1639202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Purpose: We report the clinical features and the mutational analysis in a large Tunisian family with granular corneal dystrophy type I (GCD1). Patients and Methods: Thirty-three members of the Tunisian family underwent a complete ophthalmologic examination. DNA extraction and direct Sanger sequencing of the exons 4 and 12 of transforming growth factor β Induced (TGFBI) gene was performed for 42 members. For the molecular modeling of TGFBI protein, we used pGenTHREADER method to identify templates, 3D-EXPRESSO program to align sequences, MODELLER to get a homology model for the FAS1 (fasciclin-like) domains and finally NOMAD-ref web server for the energy minimization. Results: The diagnosis of GCD1 was clinically and genetically confirmed. Sequencing of exon 4 of TGFBI gene revealed the p.[R124S] mutation at heterozygous and homozygous states in patients with different clinical severities. Visual acuity was severely affected in the homozygous patients leading to a first penetrating keratoplasty. Recurrence occurred rapidly, began in the seat of the corneal stitches and remained superficial up to 40 years after the graft. For heterozygous cases, visual acuity ranged from 6/10 to 10/10. Corneal opacities were deeper and predominating in the stromal center. According to bioinformatic analysis, this mutation likely perturbs the protein physicochemical properties and reduces its solubility without structural modification. Conclusions: Our study describes for the first time phenotype-genotype correlation in a large Tunisian family with GCDI and illustrates for the first time clinical and histopathological presentation of homozygous p.[R124S] mutation. These results help to understand pathophysiology of the disease.
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Affiliation(s)
- Yosra Bouyacoub
- Laboratory of Biomedical Genetics and Oncogenetics, Université Tunis El Manar, Institut Pasteur de Tunis, LR16IPT05 , Tunis , Tunisia.,Institut Supérieur de Biotechnologie, Université de Monastir , Monastir , Tunisia
| | - Yousra Falfoul
- B Department, Hedi Raies Institute of Ophthalmology , Tunis , Tunisia.,Oculogenetic Laboratory, LR14SP01, Hedi Raies Institute of Ophthalmology , Tunis , Tunisia
| | - Mariem Ouederni
- Department of Ophthalmology, Habib Thameur Hospital , Tunis , Tunisia
| | - Marwa Sayeb
- Laboratory of Biomedical Genetics and Oncogenetics, Université Tunis El Manar, Institut Pasteur de Tunis, LR16IPT05 , Tunis , Tunisia
| | - Aschraf Chedli
- Department of Anatomopathology, Habib Thameur Hospital , Tunis , Tunisia
| | - Mariem Chargui
- Laboratory of Biomedical Genetics and Oncogenetics, Université Tunis El Manar, Institut Pasteur de Tunis, LR16IPT05 , Tunis , Tunisia
| | - Hela Sassi
- Department of Ophthalmology, Habib Thameur Hospital , Tunis , Tunisia
| | | | - Francis L Munier
- Jules-Gonin Eye Hospital, University of Lausanne , Lausanne , Switzerland
| | - Leila El Matri
- B Department, Hedi Raies Institute of Ophthalmology , Tunis , Tunisia.,Oculogenetic Laboratory, LR14SP01, Hedi Raies Institute of Ophthalmology , Tunis , Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genetics and Oncogenetics, Université Tunis El Manar, Institut Pasteur de Tunis, LR16IPT05 , Tunis , Tunisia
| | - Monia Cheour
- Department of Ophthalmology, Habib Thameur Hospital , Tunis , Tunisia
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Navarro S, Ventura S. Computational re-design of protein structures to improve solubility. Expert Opin Drug Discov 2019; 14:1077-1088. [DOI: 10.1080/17460441.2019.1637413] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Susanna Navarro
- Institut de Biotecnologia i de Biomedicina, Parc de Recerca UAB, Mòdul B, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina, Parc de Recerca UAB, Mòdul B, Universitat Autònoma de Barcelona, Barcelona, Spain
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Thu TTM, Co NT, Tu LA, Li MS. Aggregation rate of amyloid beta peptide is controlled by beta-content in monomeric state. J Chem Phys 2019; 150:225101. [PMID: 31202253 DOI: 10.1063/1.5096379] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Understanding the key factors that govern the rate of protein aggregation is of immense interest since protein aggregation is associated with a number of neurodegenerative diseases. Previous experimental and theoretical studies have revealed that the hydrophobicity, charge, and population of the fibril-prone monomeric state control the fibril formation rate. Because the fibril structures consist of cross beta sheets, it is widely believed that those sequences that have a high beta content (β) in the monomeric state should have high aggregation rates as the monomer can serve as a template for fibril growth. However, this important fact has never been explicitly proven, motivating us to carry out this study. Using replica exchange molecular dynamics simulation with implicit water, we have computed β of 19 mutations of amyloid beta peptide of 42 residues (Aβ42) for which the aggregation rate κ has been measured experimentally. We have found that κ depends on β in such a way that the higher the propensity to aggregation, the higher the beta content in the monomeric state. Thus, we have solved a long-standing problem of the dependence of fibril formation time of the β-structure on a quantitative level.
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Affiliation(s)
- Tran Thi Minh Thu
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Nguyen Truong Co
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Ly Anh Tu
- Department of Applied Physics, Faculty of Applied Science, Ho Chi Minh City University of Technology-VNU HCM, 268 Ly Thuong Kiet Street, District 10, Ho Chi Minh City, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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Sengupta I, Udgaonkar J. Monitoring site-specific conformational changes in real-time reveals a misfolding mechanism of the prion protein. eLife 2019; 8:44698. [PMID: 31232689 PMCID: PMC6590988 DOI: 10.7554/elife.44698] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 06/11/2019] [Indexed: 11/25/2022] Open
Abstract
During pathological aggregation, proteins undergo remarkable conformational re-arrangements to anomalously assemble into a heterogeneous collection of misfolded multimers, ranging from soluble oligomers to insoluble amyloid fibrils. Inspired by fluorescence resonance energy transfer (FRET) measurements of protein folding, an experimental strategy to study site-specific misfolding kinetics during aggregation, by effectively suppressing contributions from inter-molecular FRET, is described. Specifically, the kinetics of conformational changes across different secondary and tertiary structural segments of the mouse prion protein (moPrP) were monitored independently, after the monomeric units transformed into large oligomers OL, which subsequently disaggregated reversibly into small oligomers OS at pH 4. The sequence segments spanning helices α2 and α3 underwent a compaction during the formation of OL and elongation into β-sheets during the formation of OS. The β1-α1-β2 and α2-α3 subdomains were separated, and the helix α1 was unfolded to varying extents in both OL and OS.
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Affiliation(s)
- Ishita Sengupta
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India
| | - Jayant Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India
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35
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Pedersen JN, Zhou Y, Guo Z, Pérez B. Genetic and chemical approaches for surface charge engineering of enzymes and their applicability in biocatalysis: A review. Biotechnol Bioeng 2019; 116:1795-1812. [DOI: 10.1002/bit.26979] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 03/10/2019] [Accepted: 03/28/2019] [Indexed: 12/25/2022]
Affiliation(s)
| | - Ye Zhou
- Department of EngineeringAarhus UniversityAarhus Denmark
- Key Laboratory for Molecular Enzymology and Engineering, Ministry of Education, School of Life ScienceJilin UniversityChangchun China
| | - Zheng Guo
- Department of EngineeringAarhus UniversityAarhus Denmark
| | - Bianca Pérez
- AgrotechDanish Technological InstituteAarhus Denmark
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36
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La Manna S, Scognamiglio PL, Roviello V, Borbone F, Florio D, Di Natale C, Bigi A, Cecchi C, Cascella R, Giannini C, Sibillano T, Novellino E, Marasco D. The acute myeloid leukemia-associated Nucleophosmin 1 gene mutations dictate amyloidogenicity of the C-terminal domain. FEBS J 2019; 286:2311-2328. [PMID: 30921500 DOI: 10.1111/febs.14815] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 01/29/2019] [Accepted: 03/21/2019] [Indexed: 01/04/2023]
Abstract
Nucleophosmin 1 (NPM1) is a nucleus-cytoplasm shuttling protein ubiquitously expressed and highly conserved. It is involved in many cellular processes and its gene is mutated in ~ 50-60% of Acute Myeloid Leukemia (AML) patients. These mutations cause its cytoplasmic mislocation and accumulation (referred to as NPM1c+) and open the door to rational targeted therapy for AML diseases with mutated NPM1. Currently, there is limited knowledge on the mechanism of action of NPM1c+ and on structural determinants of the leukemogenic potential of AML mutations. Numerous previous studies outlined an unexpected amyloid-like aggregation tendency of several regions located in the C-terminal domain that, in wild-type form, fold as a three-helical-bundle. Here, using a combination of different techniques including Thioflavin T fluorescence, congo red absorbance, CD spectroscopy, Scanning Electron Microscopy (SEM) and wide-angle X-ray scattering on a series of peptides bearing mutations, we evidence that the amyloidogenicity of NPM1 mutants is directly linked to AML. Noticeably, AML point mutations strongly affect the amyloid cytotoxic effects in neuroblastoma cells and the morphologies of deriving fibrils. This study paves the way to deepen our understanding of AML-associated NPM1 mutants, and could help to break new ground for the identification of novel drugs targeting NPM1c+ for treatment of AML.
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Affiliation(s)
- Sara La Manna
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", Italy
| | - Pasqualina Liana Scognamiglio
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", Italy
| | - Valentina Roviello
- Analytical Chemistry for the Environment and CeSMA (Advanced Metrologic Service Center), University of Naples "Federico II", Italy
| | - Fabio Borbone
- Department of Chemical Sciences, University of Naples "Federico II", Italy
| | - Daniele Florio
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", Italy
| | - Concetta Di Natale
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", Italy
| | - Alessandra Bigi
- Department of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, Italy
| | - Cristina Cecchi
- Department of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, Italy
| | - Roberta Cascella
- Department of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, Italy
| | - Cinzia Giannini
- Institute of Crystallography (IC), National Research Council, Bari, Italy
| | - Teresa Sibillano
- Institute of Crystallography (IC), National Research Council, Bari, Italy
| | - Ettore Novellino
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", Italy
| | - Daniela Marasco
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", Italy
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37
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Evers A, Pfeiffer-Marek S, Bossart M, Heubel C, Stock U, Tiwari G, Gebauer B, Elshorst B, Pfenninger A, Lukasczyk U, Hessler G, Kamm W, Wagner M. Peptide Optimization at the Drug Discovery-Development Interface: Tailoring of Physicochemical Properties Toward Specific Formulation Requirements. J Pharm Sci 2019; 108:1404-1414. [DOI: 10.1016/j.xphs.2018.11.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 11/27/2018] [Indexed: 12/31/2022]
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38
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Patterson-Orazem AC, Hill SE, Wang Y, Dominic IM, Hall CK, Lieberman RL. Differential Misfolding Properties of Glaucoma-Associated Olfactomedin Domains from Humans and Mice. Biochemistry 2019; 58:1718-1727. [PMID: 30802039 DOI: 10.1021/acs.biochem.8b01309] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mutations in myocilin, predominantly within its olfactomedin (OLF) domain, are causative for the heritable form of open angle glaucoma in humans. Surprisingly, mice expressing Tyr423His mutant myocilin, corresponding to a severe glaucoma-causing mutation (Tyr437His) in human subjects, exhibit a weak, if any, glaucoma phenotype. To address possible protein-level discrepancies between mouse and human OLFs, which might lead to this outcome, biophysical properties of mouse OLF were characterized for comparison with those of human OLF. The 1.55 Å resolution crystal structure of mouse OLF reveals an asymmetric 5-bladed β-propeller that is nearly indistinguishable from previous structures of human OLF. Wild-type and selected mutant mouse OLFs mirror thermal stabilities of their human OLF counterparts, including characteristic stabilization in the presence of calcium. Mouse OLF forms thioflavin T-positive aggregates with a similar end-point morphology as human OLF, but amyloid aggregation kinetic rates of mouse OLF are faster than human OLF. Simulations and experiments support the interpretation that kinetics of mouse OLF are faster because of a decreased charge repulsion arising from more neutral surface electrostatics. Taken together, phenotypic differences observed in mouse and human studies of mutant myocilin could be a function of aggregation kinetics rates, which would alter the lifetime of putatively toxic protofibrillar intermediates.
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Affiliation(s)
- Athéna C Patterson-Orazem
- School of Chemistry & Biochemistry , Georgia Institute of Technology , Atlanta , Georgia 30332-0400 , United States
| | - Shannon E Hill
- School of Chemistry & Biochemistry , Georgia Institute of Technology , Atlanta , Georgia 30332-0400 , United States
| | - Yiming Wang
- Department of Chemical & Biomolecular Engineering , North Carolina State University , Raleigh , North Carolina 27695-7905 , United States
| | - Iramofu M Dominic
- School of Chemistry & Biochemistry , Georgia Institute of Technology , Atlanta , Georgia 30332-0400 , United States
| | - Carol K Hall
- Department of Chemical & Biomolecular Engineering , North Carolina State University , Raleigh , North Carolina 27695-7905 , United States
| | - Raquel L Lieberman
- School of Chemistry & Biochemistry , Georgia Institute of Technology , Atlanta , Georgia 30332-0400 , United States
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An in-silico method for identifying aggregation rate enhancer and mitigator mutations in proteins. Int J Biol Macromol 2018; 118:1157-1167. [DOI: 10.1016/j.ijbiomac.2018.06.102] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 06/19/2018] [Accepted: 06/20/2018] [Indexed: 12/27/2022]
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40
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Mechanism of aggregation and membrane interactions of mammalian prion protein. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018. [DOI: 10.1016/j.bbamem.2018.02.031] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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41
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Effects of allantoin and dimethyl sulfoxide on the thermal aggregation of lysozyme. Int J Biol Macromol 2018; 119:180-185. [PMID: 30009897 DOI: 10.1016/j.ijbiomac.2018.07.043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 07/02/2018] [Accepted: 07/11/2018] [Indexed: 11/24/2022]
Abstract
Allantoin is used to suppress protein aggregation without decreasing the melting temperature. However, the solubility of allantoin in water or buffer solutions is too low (approximately 30 mM at ambient temperature) to be used as a protein aggregation suppressor in various situations. Here we show that a high-concentration solution of allantoin in neat dimethyl sulfoxide (DMSO) is useful as a stock solution for the additive that controls protein aggregation. The allantoin concentration from 10 to 100 mM in 10% (v/v) DMSO significantly suppressed the thermal aggregation of hen egg white lysozyme as a model protein, with increasing allantoin concentration. The residual activity of lysozyme in 10% DMSO and 100 mM allantoin after heating at 90 °C for 10 min was increased >3-fold compared to that without allantoin. Thus, it was concluded that allantoin in DMSO is an effective stock solution for practical application in enhancing the recovery of enzymatic activity and suppressing the formation of small aggregate of protein.
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42
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Haimov B, Srebnik S. The Relation between α-Helical Conformation and Amyloidogenicity. Biophys J 2018; 114:1869-1877. [PMID: 29653837 DOI: 10.1016/j.bpj.2018.03.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/23/2018] [Accepted: 03/20/2018] [Indexed: 01/23/2023] Open
Abstract
Amyloid fibrils are stable aggregates of misfolded proteins and polypeptides that are insoluble and resistant to protease activity. Abnormal formation of amyloid fibrils in vivo may lead to neurodegenerative disorders and other systemic amyloidosis, such as Alzheimer's, Parkinson's, and atherosclerosis. Because of their clinical importance, amyloids are under intense scientific research. It is believed that short polypeptide segments within proteins are responsible for the transformation of correctly folded proteins into parts of larger amyloid fibrils and that this transition is modulated by environmental factors, such as pH, salt concentration, interaction with the cell membrane, and interaction with metal ions. Most studies on amyloids focus on the amyloidogenic sequences. The focus of this study is on the structure of the amyloidogenic α-helical segments because the α-helical secondary structure has been recognized to be a key player in different stages of the amyloidogenesis process. We have previously shown that the α-helical conformation may be expressed by two parameters (θ and ρ) that form orthogonal coordinates based on the Ramachandran dihedrals (φ and ψ) and provide an illuminating interpretation of the α-helical conformation. By performing statistical analysis on α-helical conformations found in the Protein Data Bank, an apparent relation between α-helical conformation, as expressed by θ and ρ, and amyloidogenicity is revealed. Remarkably, random amino acid sequences, whose helical structures were obtained from the most probable dihedral angles, revealed the same dependency of amyloidogenicity, suggesting the importance of α-helical structure as opposed to sequence.
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Affiliation(s)
- Boris Haimov
- Russell Berrie Nanotechnology Institute, Technion - Israel Institute of Technology, Haifa, Israel
| | - Simcha Srebnik
- Russell Berrie Nanotechnology Institute, Technion - Israel Institute of Technology, Haifa, Israel; Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, Israel.
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Nishinami S, Yoshizawa S, Arakawa T, Shiraki K. Allantoin and hydantoin as new protein aggregation suppressors. Int J Biol Macromol 2018; 114:497-503. [PMID: 29505874 DOI: 10.1016/j.ijbiomac.2018.03.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 02/21/2018] [Accepted: 03/02/2018] [Indexed: 01/08/2023]
Abstract
Allantoin is widely used in pharmaceutical and cosmetic products, and is composed of a hydantoin ring and a ureido group. Recent reports showed that allantoin suppresses thermal aggregation of hen egg white lysozyme (LYZ). However, structural insight into the properties of allantoin on protein aggregation and whether allantoin controls the aggregation of other proteins under different stress conditions remain unclear. Here we studied the structural properties of allantoin in terms of its effects on protein aggregation by comparing allantoin with urea and hydantoin. Furthermore, we analyzed the effects of allantoin and its derivatives on the aggregation of LYZ, carbonic anhydrase from bovine erythrocytes (BCA), albumin from chicken egg white (OVA), and immunoglobulin G (IgG) by various stresses in comparison with arginine. These four proteins are widely different in charged state and molecular size. Allantoin suppressed the aggregation and inactivation of LYZ comparing to arginine without affecting the melting temperature of proteins, and was responsible for the slightly improved formation of soluble oligomers and insoluble aggregates of IgG with thermal and acidic stresses. In contrast, hydantoin increased the solubility of aromatic amino acids more effectively than arginine and allantoin. The structural properties underlying the observed effects of allantoin as an aggregation suppressor include hydrophobic interactions between hydantoin moiety and aromatic ring on the surface of proteins, which is reflected on the difference between allantoin and arginine. These results show that the backbone of hydantoin ring may be a new category of additives for development of small aggregation suppressors.
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Affiliation(s)
- Suguru Nishinami
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
| | - Shunsuke Yoshizawa
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
| | - Tsutomu Arakawa
- Alliance Protein Laboratories, San Diego, CA 92121, United States
| | - Kentaro Shiraki
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan.
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Cheng B, Li Y, Ma L, Wang Z, Petersen RB, Zheng L, Chen Y, Huang K. Interaction between amyloidogenic proteins and biomembranes in protein misfolding diseases: Mechanisms, contributors, and therapy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1876-1888. [PMID: 29466701 DOI: 10.1016/j.bbamem.2018.02.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 02/12/2018] [Accepted: 02/13/2018] [Indexed: 12/14/2022]
Abstract
The toxic deposition of misfolded amyloidogenic proteins is associated with more than fifty protein misfolding diseases (PMDs), including Alzheimer's disease, Parkinson's disease and type 2 diabetes mellitus. Protein deposition is a multi-step process modulated by a variety of factors, in particular by membrane-protein interaction. The interaction results in permeabilization of biomembranes contributing to the cytotoxicity that leads to PMDs. Different biological and physiochemical factors, such as protein sequence, lipid composition, and chaperones, are known to affect the membrane-protein interaction. Here, we provide a comprehensive review of the mechanisms and contributing factors of the interaction between biomembranes and amyloidogenic proteins, and a summary of the therapeutic approaches to PMDs that target this interaction. This article is part of a Special Issue entitled: Protein Aggregation and Misfolding at the Cell Membrane Interface edited by Ayyalusamy Ramamoorthy.
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Affiliation(s)
- Biao Cheng
- Department of Pharmacy, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430023, China; Key Laboratory for Molecular Diagnosis of Hubei Province, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430023, China
| | - Yang Li
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Liang Ma
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhuoyi Wang
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Robert B Petersen
- Foundational Sciences, Central Michigan University College of Medicine, Mt. Pleasant, MI 48858, USA
| | - Ling Zheng
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan 430072, China
| | - Yuchen Chen
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Kun Huang
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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Katina NS, Balobanov VA, Ilyina NB, Vasiliev VD, Marchenkov VV, Glukhov AS, Nikulin AD, Bychkova VE. sw ApoMb Amyloid Aggregation under Nondenaturing Conditions: The Role of Native Structure Stability. Biophys J 2017; 113:991-1001. [PMID: 28877500 DOI: 10.1016/j.bpj.2017.07.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 07/19/2017] [Accepted: 07/20/2017] [Indexed: 12/17/2022] Open
Abstract
Investigation of the molecular mechanisms underlying amyloid-related human diseases attracts close attention. These diseases, the number of which currently is above 40, are characterized by formation of peptide or protein aggregates containing a cross-β structure. Most of the amyloidogenesis mechanisms described so far are based on experimental studies of aggregation of short peptides, intrinsically disordered proteins, or proteins under denaturing conditions, and studies of amyloid aggregate formations by structured globular proteins under conditions close to physiological ones are still in the initial stage. We investigated the effect of amino acid substitutions on propensity of the completely helical protein sperm whale apomyoglobin (sw ApoMb) for amyloid formation from its structured state in the absence of denaturing agents. Stability and aggregation of mutated sw ApoMb were studied using circular dichroism, Fourier transform infrared spectroscopy, x-ray diffraction, native electrophoresis, and electron microscopy techniques. Here, we demonstrate that stability of the protein native state determines both protein aggregation propensity and structural peculiarities of formed aggregates. Specifically, structurally stable mutants show low aggregation propensity and moderately destabilized sw ApoMb variants form amyloids, whereas their strongly destabilized mutants form both amyloids and nonamyloid aggregates.
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Affiliation(s)
- Natalya S Katina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Vitalii A Balobanov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Nelly B Ilyina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Victor D Vasiliev
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Victor V Marchenkov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Anatoly S Glukhov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Alexey D Nikulin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Valentina E Bychkova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
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46
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Salt-regulated reversible fibrillation of Mycobacterium tuberculosis isocitrate lyase: Concurrent restoration of structure and activity. Int J Biol Macromol 2017; 104:89-96. [DOI: 10.1016/j.ijbiomac.2017.06.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 05/30/2017] [Accepted: 06/02/2017] [Indexed: 02/03/2023]
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Abstract
Protein aggregation is an active area of research in recent decades, since it is the most common and troubling indication of protein instability. Understanding the mechanisms governing protein aggregation and amyloidogenesis is a key component to the aetiology and pathogenesis of many devastating disorders, including Alzheimer's disease or type 2 diabetes. Protein aggregation data are currently found "scattered" in an increasing number of repositories, since advances in computational biology greatly influence this field of research. This review exploits the various resources of aggregation data and attempts to distinguish and analyze the biological knowledge they contain, by introducing protein-based, fragment-based and disease-based repositories, related to aggregation. In order to gain a broad overview of the available repositories, a novel comprehensive network maps and visualizes the current association between aggregation databases and other important databases and/or tools and discusses the beneficial role of community annotation. The need for unification of aggregation databases in a common platform is also addressed.
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Affiliation(s)
- Paraskevi L Tsiolaki
- a Section of Cell Biology and Biophysics, Department of Biology, School of Sciences , National and Kapodistrian University of Athens , Athens , Greece
| | - Katerina C Nastou
- a Section of Cell Biology and Biophysics, Department of Biology, School of Sciences , National and Kapodistrian University of Athens , Athens , Greece
| | - Stavros J Hamodrakas
- a Section of Cell Biology and Biophysics, Department of Biology, School of Sciences , National and Kapodistrian University of Athens , Athens , Greece
| | - Vassiliki A Iconomidou
- a Section of Cell Biology and Biophysics, Department of Biology, School of Sciences , National and Kapodistrian University of Athens , Athens , Greece
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48
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Nguyen PT, Zottig X, Sebastiao M, Bourgault S. Role of Site-Specific Asparagine Deamidation in Islet Amyloid Polypeptide Amyloidogenesis: Key Contributions of Residues 14 and 21. Biochemistry 2017; 56:3808-3817. [PMID: 28665109 DOI: 10.1021/acs.biochem.7b00209] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Deamidation of an asparagine residue is a spontaneous non-enzymatic post-translational modification that results in the conversion of asparagine into a mixture of aspartic acid and isoaspartic acid. This chemical conversion modulates protein conformation and physicochemical properties, which could lead to protein misfolding and aggregation. In this study, we investigated the effects of site-specific Asn deamidation on the amyloidogenicity of the aggregation-prone peptide islet amyloid polypeptide (IAPP). IAPP is a 37-residue peptidic hormone whose deposition as insoluble amyloid fibrils is closely associated with type 2 diabetes. Asn residues were successively substituted with an Asp or isoAsp, and amyloid formation was evaluated by a thioflavin T fluorescence assay, circular dichroism spectroscopy, atomic force microscopy, and transmission electron microscopy. Whereas deamidation at position 21 inhibited IAPP conformational conversion and amyloid formation, the N14D mutation accelerated self-assembly and led to the formation of long and thick amyloid fibrils. In contrast, IAPP was somewhat tolerant to the successive deamidation of Asn residues 22, 31, and 35. Interestingly, a small molar ratio of IAPP deamidated at position 14 promoted the formation of nucleating species and the elongation from unmodified IAPP. Besides, using the rat pancreatic β cell line INS-1E, we observed that site-specific deamidation did not significantly alter IAPP-induced toxicity. These data indicate that Asn deamidation can modulate IAPP amyloid formation and fibril morphology and that the site of modification plays a critical role. Above all, this study reinforces the notion that IAPP amyloidogenesis is governed by precise intermolecular interactions involving specific Asn side chains.
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Affiliation(s)
- Phuong Trang Nguyen
- Department of Chemistry, University of Québec in Montreal , C.P. 8888, Succursale Centre-Ville, Montreal H3C 3P8, Canada.,Quebec Network for Research on Protein Function, Engineering, and Applications, PROTEO
| | - Ximena Zottig
- Department of Chemistry, University of Québec in Montreal , C.P. 8888, Succursale Centre-Ville, Montreal H3C 3P8, Canada.,Quebec Network for Research on Protein Function, Engineering, and Applications, PROTEO
| | - Mathew Sebastiao
- Department of Chemistry, University of Québec in Montreal , C.P. 8888, Succursale Centre-Ville, Montreal H3C 3P8, Canada.,Quebec Network for Research on Protein Function, Engineering, and Applications, PROTEO
| | - Steve Bourgault
- Department of Chemistry, University of Québec in Montreal , C.P. 8888, Succursale Centre-Ville, Montreal H3C 3P8, Canada.,Quebec Network for Research on Protein Function, Engineering, and Applications, PROTEO
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49
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Smith DJ, Shell MS. Can Simple Interaction Models Explain Sequence-Dependent Effects in Peptide Homodimerization? J Phys Chem B 2017; 121:5928-5943. [PMID: 28537734 DOI: 10.1021/acs.jpcb.7b03186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The development of rapid methods to explain and predict peptide interactions, aggregation, and self-assembly has become important to understanding amyloid disease pathology, the shelf stability of peptide therapeutics, and the design of novel peptide materials. Although experimental aggregation databases have been used to develop correlative and statistical models, molecular simulations offer atomic-level details that potentially provide greater physical insight and allow one to single out the most explanatory simple models. Here, we outline one such approach using a case study that develops homodimerization models for serine-glycine peptides with various hydrophobic leucine mutations. Using detailed all-atom simulations, we calculate reference dimerization free energy profiles and binding constants for a small peptide library. We then use statistical methods to systematically assess whether simple interaction models, which do not require expensive simulations and free energy calculation, can capture them. Surprisingly, some combinations of a few simple scaling laws well recapitulate the detailed, all-atom results with high accuracy. Specifically, we find that a recently proposed phenomenological hydrophobic force law and coarse measures of entropic effects in binding offer particularly high explanatory power, underscoring the physical relevance to association that these driving forces can play.
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Affiliation(s)
- David J Smith
- Department of Chemical Engineering, University of California, Santa Barbara , Santa Barbara, California 93106, United States
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara , Santa Barbara, California 93106, United States
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50
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Sengupta I, Bhate SH, Das R, Udgaonkar JB. Salt-Mediated Oligomerization of the Mouse Prion Protein Monitored by Real-Time NMR. J Mol Biol 2017; 429:1852-1872. [DOI: 10.1016/j.jmb.2017.05.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 05/05/2017] [Accepted: 05/07/2017] [Indexed: 12/11/2022]
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