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Zhang Z, Cai Y, Zheng N, Deng Y, Gao L, Wang Q, Xia X. Diverse models of cavity engineering in enzyme modification: Creation, filling, and reshaping. Biotechnol Adv 2024; 72:108346. [PMID: 38518963 DOI: 10.1016/j.biotechadv.2024.108346] [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: 09/08/2023] [Revised: 03/07/2024] [Accepted: 03/19/2024] [Indexed: 03/24/2024]
Abstract
Most enzyme modification strategies focus on designing the active sites or their surrounding structures. Interestingly, a large portion of the enzymes (60%) feature active sites located within spacious cavities. Despite recent discoveries, cavity-mediated enzyme engineering remains crucial for enhancing enzyme properties and unraveling folding-unfolding mechanisms. Cavity engineering influences enzyme stability, catalytic activity, specificity, substrate recognition, and docking. This article provides a comprehensive review of various cavity engineering models for enzyme modification, including cavity creation, filling, and reshaping. Additionally, it also discusses feasible tools for geometric analysis, functional assessment, and modification of cavities, and explores potential future research directions in this field. Furthermore, a promising universal modification strategy for cavity engineering that leverages state-of-the-art technologies and methodologies to tailor cavities according to the specific requirements of industrial production conditions is proposed.
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Affiliation(s)
- Zehua Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Yongchao Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Nan Zheng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Yu Deng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Ling Gao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Qiong Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Xiaole Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China; College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China.
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2
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Sala BM, Le Marchand T, Pintacuda G, Camilloni C, Natalello A, Ricagno S. Conformational Stability and Dynamics in Crystals Recapitulate Protein Behavior in Solution. Biophys J 2020; 119:978-988. [PMID: 32758421 DOI: 10.1016/j.bpj.2020.07.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/08/2020] [Accepted: 07/20/2020] [Indexed: 11/29/2022] Open
Abstract
A growing body of evidences has established that in many cases proteins may preserve most of their function and flexibility in a crystalline environment, and several techniques are today capable to characterize molecular properties of proteins in tightly packed lattices. Intriguingly, in the case of amyloidogenic precursors, the presence of transiently populated states (hidden to conventional crystallographic studies) can be correlated to the pathological fate of the native fold; the low fold stability of the native state is a hallmark of aggregation propensity. It remains unclear, however, to which extent biophysical properties of proteins such as the presence of transient conformations or protein stability characterized in crystallo reflect the protein behavior that is more commonly studied in solution. Here, we address this question by investigating some biophysical properties of a prototypical amyloidogenic system, β2-microglobulin in solution and in microcrystalline state. By combining NMR chemical shifts with molecular dynamics simulations, we confirmed that conformational dynamics of β2-microglobulin native state in the crystal lattice is in keeping with what observed in solution. A comparative study of protein stability in solution and in crystallo is then carried out, monitoring the change in protein secondary structure at increasing temperature by Fourier transform infrared spectroscopy. The increased structural order of the crystalline state contributes to provide better resolved spectral components compared to those collected in solution and crucially, the crystalline samples display thermal stabilities in good agreement with the trend observed in solution. Overall, this work shows that protein stability and occurrence of pathological hidden states in crystals parallel their solution counterpart, confirming the interest of crystals as a platform for the biophysical characterization of processes such as unfolding and aggregation.
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Affiliation(s)
| | - Tanguy Le Marchand
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs (FRE 2034 CNRS, UCBL, ENS Lyon), Université de Lyon, Villeurbanne, France
| | - Guido Pintacuda
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs (FRE 2034 CNRS, UCBL, ENS Lyon), Université de Lyon, Villeurbanne, France
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy.
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy.
| | - Stefano Ricagno
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy.
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3
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Dec R, Koliński M, Kouza M, Dzwolak W. Rapid self-association of highly amyloidogenic H-fragments of insulin: Experiment and molecular dynamics simulations. Int J Biol Macromol 2020; 150:894-903. [DOI: 10.1016/j.ijbiomac.2020.02.153] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 02/14/2020] [Indexed: 01/17/2023]
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4
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Jha V, Rameshwaram NR, Janardhan S, Raman R, Sastry GN, Sharma V, Subba Rao J, Kumar D, Mukhopadhyay S. Uncovering Structural and Molecular Dynamics of ESAT-6:β2M Interaction: Asp53 of Human β2-Microglobulin Is Critical for the ESAT-6:β2M Complexation. THE JOURNAL OF IMMUNOLOGY 2019; 203:1918-1929. [PMID: 31484733 DOI: 10.4049/jimmunol.1700525] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 08/02/2019] [Indexed: 12/12/2022]
Abstract
ESAT-6 is a small secreted protein of Mycobacterium tuberculosis involved in the ESAT-6 secretion system (ESX-1)-mediated virulence and pathogenesis. The protein interacts with β2M, causing downregulation of MHC class I Ag presentation, which could be one of the mechanisms by which it favors increased survival of the bacilli inside the host. In an earlier study, we have shown that the C-terminal region of ESAT-6 is crucial for its interaction with β2M. However, the interface of β2M involved in interaction with ESAT-6 and detailed physicochemical changes associated with ESAT-6:β2M complexation are not fully defined. In this study, using computational and site-directed mutagenesis studies, we demonstrate the presence of strong noncovalent hydrophobic interactions between ESAT-6 and β2M in addition to the vital hydrogen bonding between the aspartate residue (Asp53) of β2M and methionine (Met93) of ESAT-6. Docking-based high-throughput virtual screening followed by 16-point screening on microscale thermophoresis resulted in the identification of two potent inhibitors (SM09 and SM15) that mask the critical Met93 residue of ESAT-6 that is required for ESAT-6:β2M interaction and could rescue cell surface expression of β2M and HLA in human macrophages as well as MHC class I Ag presentation suppressed by ESAT-6 in peritoneal macrophages isolated from C57BL/6 mice. Both SM09 and SM15 significantly inhibited intracellular survival of M. tuberculosis in human macrophages. Further, we characterized the physicochemical properties involved in the ESAT-6:β2M complexation, which may help in understanding host-pathogen interactions.
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Affiliation(s)
- Vishwanath Jha
- Laboratory of Molecular Cell Biology, Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad 500039, Telangana, India.,Graduate Studies, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Nagender Rao Rameshwaram
- Laboratory of Molecular Cell Biology, Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad 500039, Telangana, India
| | - Sridhara Janardhan
- Centre for Molecular Modeling, Council of Scientific and Industrial Research-Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500007, Telangana, India
| | - Rajeev Raman
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Tarnaka, Hyderabad 500007, Telangana, India
| | - G Narahari Sastry
- Centre for Molecular Modeling, Council of Scientific and Industrial Research-Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500007, Telangana, India
| | - Vartika Sharma
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; and
| | - Jasti Subba Rao
- Centre for Chemical Biology and Therapeutics, Institute for Stem Cell Science and Regenerative Medicine, Bangalore 560065, Karnataka, India
| | - Dhiraj Kumar
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; and
| | - Sangita Mukhopadhyay
- Laboratory of Molecular Cell Biology, Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad 500039, Telangana, India;
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Oleuropein aglycone: A polyphenol with different targets against amyloid toxicity. Biochim Biophys Acta Gen Subj 2018; 1862:1432-1442. [DOI: 10.1016/j.bbagen.2018.03.023] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 02/23/2018] [Accepted: 03/20/2018] [Indexed: 12/29/2022]
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6
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HDInsight4PSi: Boosting performance of 3D protein structure similarity searching with HDInsight clusters in Microsoft Azure cloud. Inf Sci (N Y) 2016. [DOI: 10.1016/j.ins.2016.02.029] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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7
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Narang D, Singh A, Mukhopadhyay S. Stepwise unfolding of human β2-microglobulin into a disordered amyloidogenic precursor at low pH. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 46:65-76. [DOI: 10.1007/s00249-016-1138-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 04/20/2016] [Accepted: 05/10/2016] [Indexed: 02/08/2023]
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Camilloni C, Sala BM, Sormanni P, Porcari R, Corazza A, De Rosa M, Zanini S, Barbiroli A, Esposito G, Bolognesi M, Bellotti V, Vendruscolo M, Ricagno S. Rational design of mutations that change the aggregation rate of a protein while maintaining its native structure and stability. Sci Rep 2016; 6:25559. [PMID: 27150430 PMCID: PMC4858664 DOI: 10.1038/srep25559] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 04/20/2016] [Indexed: 01/27/2023] Open
Abstract
A wide range of human diseases is associated with mutations that, destabilizing proteins native state, promote their aggregation. However, the mechanisms leading from folded to aggregated states are still incompletely understood. To investigate these mechanisms, we used a combination of NMR spectroscopy and molecular dynamics simulations to compare the native state dynamics of Beta-2 microglobulin (β2m), whose aggregation is associated with dialysis-related amyloidosis, and its aggregation-resistant mutant W60G. Our results indicate that W60G low aggregation propensity can be explained, beyond its higher stability, by an increased average protection of the aggregation-prone residues at its surface. To validate these findings, we designed β2m variants that alter the aggregation-prone exposed surface of wild-type and W60G β2m modifying their aggregation propensity. These results allowed us to pinpoint the role of dynamics in β2m aggregation and to provide a new strategy to tune protein aggregation by modulating the exposure of aggregation-prone residues.
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Affiliation(s)
- Carlo Camilloni
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.,Department of Chemistry and Institute for Advanced Study, Technische Universität München, Lichtenbergstraße 4, D-85748 Garching, Germany
| | - Benedetta Maria Sala
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Pietro Sormanni
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Riccardo Porcari
- Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins, University College London, London NW3 2PF, UK
| | - Alessandra Corazza
- Dipartimento di Scienze Mediche e Biologiche, Università di Udine, 33100 Udine, Italy
| | - Matteo De Rosa
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Stefano Zanini
- Dipartimento di Scienze Mediche e Biologiche, Università di Udine, 33100 Udine, Italy
| | - Alberto Barbiroli
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università degli Studi di Milano, 20133 Milano, Italy
| | - Gennaro Esposito
- Dipartimento di Scienze Mediche e Biologiche, Università di Udine, 33100 Udine, Italy.,Science and Math Division, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, UAE
| | - Martino Bolognesi
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy.,CIMAINA and CNR Istituto di Biofisica, c/o Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Vittorio Bellotti
- Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins, University College London, London NW3 2PF, UK
| | | | - Stefano Ricagno
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
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de Rosa M, Barbiroli A, Giorgetti S, Mangione PP, Bolognesi M, Ricagno S. Decoding the Structural Bases of D76N ß2-Microglobulin High Amyloidogenicity through Crystallography and Asn-Scan Mutagenesis. PLoS One 2015; 10:e0144061. [PMID: 26625273 PMCID: PMC4666650 DOI: 10.1371/journal.pone.0144061] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 11/12/2015] [Indexed: 11/19/2022] Open
Abstract
D76N is the first natural variant of human β-2 microglobulin (β2m) so far identified. Contrary to the wt protein, this mutant readily forms amyloid fibres in physiological conditions, leading to a systemic and severe amyloidosis. Although the Asp76Asn mutant has been extensively characterized, the molecular bases of its instability and aggregation propensity remain elusive. In this work all Asp residues of human β2m were individually substituted to Asn; D-to-N mutants (D34N, D38N, D53N, D59N, D96N and D98N) were characterised in terms of thermodynamic stability and aggregation propensity. Moreover, crystal structures of the D38N, D53N, D59N and D98N variants were solved at high-resolution (1.24–1.70 Å). Despite showing some significant variations in their thermal stabilities, none showed the dramatic drop in melting temperature (relative to the wt protein) as observed for the pathogenic mutant. Consistently, none of the variants here described displayed any increase in aggregation propensity under the experimental conditions tested. The crystal structures confirmed that D-to-N mutations are generally well tolerated, and lead only to minor reorganization of the side chains in close proximity of the mutated residue. D38N is the only exception, where backbone readjustments and a redistribution of the surface electrostatic charges are observed. Overall, our results suggest that neither removing negative charges at sites 34, 38, 53, 59, 96 and 98, nor the difference in β2m pI, are the cause of the aggressive phenotype observed in D76N. We propose that the dramatic effects of the D76N natural mutation must be linked to effects related to the crucial location of this residue within the β2m fold.
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Affiliation(s)
- Matteo de Rosa
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Alberto Barbiroli
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente, Università di Milano, Via Celoria 2, 20133, Milano, Italy
| | - Sofia Giorgetti
- Dipartimento di Medicina Molecolare, Istituto di Biochimica “A. Castellani”, Università di Pavia, Via Taramelli 3/b, 27100, Pavia, Italy
| | - Patrizia P. Mangione
- Dipartimento di Medicina Molecolare, Istituto di Biochimica “A. Castellani”, Università di Pavia, Via Taramelli 3/b, 27100, Pavia, Italy
| | - Martino Bolognesi
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, 20133, Milano, Italy
- CIMAINA and CNR-Istituto di Biofisica, c/o Università di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Stefano Ricagno
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, 20133, Milano, Italy
- * E-mail:
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Abstract
β2-Microglobulin is responsible for systemic amyloidosis affecting patients undergoing long-term hemodialysis. Its genetic variant D76N causes a very rare form of familial systemic amyloidosis. These two types of amyloidoses differ significantly in terms of the tissue localization of deposits and for major pathological features. Considering how the amyloidogenesis of the β2-microglobulin mechanism has been scrutinized in depth for the last three decades, the comparative analysis of molecular and pathological properties of wild type β2-microglobulin and of the D76N variant offers a unique opportunity to critically reconsider the current understanding of the relation between the protein's structural properties and its pathologic behavior.
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Affiliation(s)
- Monica Stoppini
- From the Department of Molecular Medicine, Institute of Biochemistry, University of Pavia, 27100 Pavia, Italy and
| | - Vittorio Bellotti
- From the Department of Molecular Medicine, Institute of Biochemistry, University of Pavia, 27100 Pavia, Italy and the Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins, Division of Medicine, University College London, London NW3 2PF, United Kingdom
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11
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Gershenson A, Gierasch LM, Pastore A, Radford SE. Energy landscapes of functional proteins are inherently risky. Nat Chem Biol 2014; 10:884-91. [PMID: 25325699 PMCID: PMC4416114 DOI: 10.1038/nchembio.1670] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 09/19/2014] [Indexed: 01/08/2023]
Abstract
Evolutionary pressure for protein function leads to unavoidable sampling of conformational states that are at risk of misfolding and aggregation. The resulting tension between functional requirements and the risk of misfolding and/or aggregation in the evolution of proteins is becoming more and more apparent. One outcome of this tension is sensitivity to mutation, in which only subtle changes in sequence that may be functionally advantageous can tip the delicate balance toward protein aggregation. Similarly, increasing the concentration of aggregation-prone species by reducing the ability to control protein levels or compromising protein folding capacity engenders increased risk of aggregation and disease. In this Perspective, we describe examples that epitomize the tension between protein functional energy landscapes and aggregation risk. Each case illustrates how the energy landscapes for the at-risk proteins are sculpted to enable them to perform their functions and how the risks of aggregation are minimized under cellular conditions using a variety of compensatory mechanisms.
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Affiliation(s)
- Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Lila M Gierasch
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Annalisa Pastore
- Department of Clinical Neurosciences, King’s College London, Denmark Hill Campus, London, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
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12
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Assessing the effect of loop mutations in the folding space of β2-microglobulin with molecular dynamics simulations. Int J Mol Sci 2013; 14:17256-78. [PMID: 23975166 PMCID: PMC3794727 DOI: 10.3390/ijms140917256] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 07/27/2013] [Accepted: 07/30/2013] [Indexed: 12/15/2022] Open
Abstract
We use molecular dynamics simulations of a full atomistic Gō model to explore the impact of selected DE-loop mutations (D59P and W60C) on the folding space of protein human β2-microglobulin (Hβ2m), the causing agent of dialysis-related amyloidosis, a conformational disorder characterized by the deposition of insoluble amyloid fibrils in the osteoarticular system. Our simulations replicate the effect of mutations on the thermal stability that is observed in experiments in vitro. Furthermore, they predict the population of a partially folded state, with 60% of native internal free energy, which is akin to a molten globule. In the intermediate state, the solvent accessible surface area increases up to 40 times relative to the native state in 38% of the hydrophobic core residues, indicating that the identified species has aggregation potential. The intermediate state preserves the disulfide bond established between residue Cys25 and residue Cys80, which helps maintain the integrity of the core region, and is characterized by having two unstructured termini. The movements of the termini dominate the essential modes of the intermediate state, and exhibit the largest displacements in the D59P mutant, which is the most aggregation prone variant. PROPKA predictions of pKa suggest that the population of the intermediate state may be enhanced at acidic pH explaining the larger amyloidogenic potential observed in vitro at low pH for the WT protein and mutant forms.
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Hodkinson JP, Radford SE, Ashcroft AE. The role of conformational flexibility in β2-microglobulin amyloid fibril formation at neutral pH. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:1783-92. [PMID: 22777780 PMCID: PMC3568905 DOI: 10.1002/rcm.6282] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
RATIONALE Amyloid formation is implicated in a number of human diseases. β(2)-Microglobulin (β(2)m) is the precursor protein in dialysis-related amyloidosis and it has been shown that partial, or more complete, unfolding is key to amyloid fibril formation in this pathology. Here the relationship between conformational flexibility and β(2)m amyloid formation at physiological pH has been investigated. METHODS HDX-ESI-MS was used to study the conformational dynamics of β(2)m. Protein engineering, or the addition of Cu(2+) ions, sodium dodecyl sulphate, trifluoroethanol, heparin, or protein stabilisers, was employed to perturb the conformational dynamics of β(2)m. The fibril-forming propensities of the protein variants and the wild-type protein in the presence of additives, which resulted in >5-fold increase in the EX1 rate of HDX, were investigated further. RESULTS ESI-MS revealed that HDX occurs via a mixed EX1/EX2 mechanism under all conditions. Urea denaturation and tryptophan fluorescence indicated that EX1 exchange occurred from a globally unfolded state in wild-type β(2)m. Although >30-fold increase in the HDX exchange rate was observed both for the protein variants and for the wild-type protein in the presence of specific additives, large increases in exchange rate did not necessarily result in extensive de novo fibril formation. CONCLUSIONS The conformational dynamics measured by the EX1 rate of HDX do not predict the ability of β(2)m to form amyloid fibrils de novo at neutral pH. This suggests that the formation of amyloid fibrils from β(2)m at neutral pH is dependent on the generation of one or more specific aggregation-competent species which facilitate self-assembly.
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Affiliation(s)
- John P Hodkinson
- Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of LeedsLeeds, LS2 9JT UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of LeedsLeeds, LS2 9JT UK
- Correspondence S. E. Radford or A. E. Ashcroft, Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK. E-mail: ;
| | - Alison E Ashcroft
- Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of LeedsLeeds, LS2 9JT UK
- Correspondence S. E. Radford or A. E. Ashcroft, Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK. E-mail: ;
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