1
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Loureiro RJS, Faísca PFN. The Early Phase of β2-Microglobulin Aggregation: Perspectives From Molecular Simulations. Front Mol Biosci 2020; 7:578433. [PMID: 33134317 PMCID: PMC7550760 DOI: 10.3389/fmolb.2020.578433] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/08/2020] [Indexed: 11/24/2022] Open
Abstract
Protein β2-microglobulin is the causing agent of two amyloidosis, dialysis related amyloidosis (DRA), affecting the bones and cartilages of individuals with chronic renal failure undergoing long-term hemodialysis, and a systemic amyloidosis, found in one French family, which impairs visceral organs. The protein’s small size and its biomedical significance attracted the attention of theoretical scientists, and there are now several studies addressing its aggregation mechanism in the context of molecular simulations. Here, we review the early phase of β2-microglobulin aggregation, by focusing on the identification and structural characterization of monomers with the ability to trigger aggregation, and initial small oligomers (dimers, tetramers, hexamers etc.) formed in the so-called nucleation phase. We focus our analysis on results from molecular simulations and integrate our views with those coming from in vitro experiments to provide a broader perspective of this interesting field of research. We also outline directions for future computer simulation studies.
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Affiliation(s)
- Rui J S Loureiro
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Lisbon, Portugal
| | - Patrícia F N Faísca
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Lisbon, Portugal.,Department of Physics, Faculty of Sciences, University of Lisboa, Lisbon, Portugal
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2
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Kamaraj B, Al-Subaie AM, Ahmad F, Surapaneni KM, Alsamman K. Effect of novel leukemia mutations (K75E & E222K) on interferon regulatory factor 1 and its interaction with DNA: insights from molecular dynamics simulations and docking studies. J Biomol Struct Dyn 2020; 39:5235-5247. [PMID: 32619131 DOI: 10.1080/07391102.2020.1784790] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Interferon regulatory factor 1 (IRF-1) plays a vital role in cell proliferation and cell differentiation by acting as a tumor suppressor gene and its role is linked to various types of cancers, including leukemia and pre-leukemia myelodysplasia. Mutations in the coding region of the IRF-1 are likely to influence the IRF-1 and its DNA binding affinity. The molecular mechanism of the DNA recognition with the IRF-1 protein upon mutations is still unknown. In this study, we have elucidated the structural and functional behavior of the wild-type and mutant (K75E and E222K) IRF-1 proteins and their corresponding molecular mechanisms with DNA recognition at the molecular level, using molecular dynamics simulations. Furthermore, we also applied the docking approach to examine the binding between the IRF-1 protein and DNA upon mutations. This study evidently explains that, due to mutations, the IRF-1 structure loses its stability and becomes more flexible than the wild-type protein. This structural loss might affect IRF-1-DNA interaction and lead to the inhibition of cancer suppression. Identifying the effects of IRF-1 at the molecular level will be beneficial for designing drugs for IRF-1 associated cancers. These drugs should be designed so that they can help reactivate the IRF-1 function, by increasing the transcriptional activity, to treat leukemia.
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Affiliation(s)
- Balu Kamaraj
- Department of Neuroscience Technology, College of Applied Medical Science in Jubail, Imam Abdulrahman Bin Faisal University, Jubail, Saudi Arabia
| | - Abeer Mohammed Al-Subaie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Fazil Ahmad
- Department of Anesthesia Technology, College of Applied Medical Sciences in Jubail, Imam Abdulrahman Bin Faisal University, Jubail, Saudi Arabia
| | - Krishna Mohan Surapaneni
- Department of Medical Biochemistry, College of Applied Medical Sciences-Jubail (CAMSJ), Imam Abdulrahman Bin Faisal University, Al Jubail, Kingdom of Saudi Arabia (KSA)
| | - Khaldoon Alsamman
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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3
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Hoop CL, Zhu J, Bhattacharya S, Tobita CA, Radford SE, Baum J. Collagen I Weakly Interacts with the β-Sheets of β 2-Microglobulin and Enhances Conformational Exchange To Induce Amyloid Formation. J Am Chem Soc 2020; 142:1321-1331. [PMID: 31875390 PMCID: PMC7135851 DOI: 10.1021/jacs.9b10421] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
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Amyloidogenesis is
significant in both protein function and pathology.
Amyloid formation of folded, globular proteins is commonly initiated
by partial or complete unfolding. However, how this unfolding event
is triggered for proteins that are otherwise stable in their native
environments is not well understood. The accumulation of the immunoglobulin
protein β2-microglobulin (β2m) into
amyloid plaques in the joints of long-term hemodialysis patients is
the hallmark of dialysis-related amyloidosis (DRA). While β2m does not form amyloid unassisted near neutral pH in vitro, the localization of β2m deposits
to joint spaces suggests a role for the local extracellular matrix
(ECM) proteins, specifically collagens, in promoting amyloid formation.
Indeed, collagen and other ECM components have been observed to facilitate
β2m amyloid formation, but the large size and anisotropy
of the complex, combined with the low affinity of these interactions,
have limited atomic-level elucidation of the amyloid-promoting mechanism(s)
by these molecules. Using solution NMR approaches that uniquely probe
weak interactions in large molecular weight complexes, we are able
to map the binding interfaces on β2m for collagen
I and detect collagen I-induced μs–ms time-scale dynamics
in the β2m backbone. By combining solution NMR relaxation
methods and 15N-dark-state exchange saturation transfer
experiments, we propose a model in which weak, multimodal collagen
I−β2m interactions promote exchange with a
minor population of amyloid-competent species to induce fibrillogenesis.
The results portray the intimate role of the environment in switching
an innocuous protein into an amyloid-competent state, rationalizing
the localization of amyloid deposits in DRA.
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Affiliation(s)
- Cody L Hoop
- Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854 , United States
| | - Jie Zhu
- Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854 , United States
| | | | - Caitlyn A Tobita
- Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854 , United States
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences , University of Leeds , Leeds LS2 9JT , U.K
| | - Jean Baum
- Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854 , United States
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4
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Saba Khan N, Verma R, Pradhan D, Nayek A, Bhuyan R, Kumar Sahu T, Kumar Jain A. Analysis of interleukin 23 and 7G10 interactions for computational design of lead antibodies against immune-mediated inflammatory diseases. J Recept Signal Transduct Res 2018; 38:327-334. [PMID: 30481093 DOI: 10.1080/10799893.2018.1511729] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Wealth of structural data on theurapeutic targets in complex with monoclonal antibodies (mAbs) and advances in molecular modeling algorithms present exciting opportunities in the field of novel biologic design. Interleukin 23 (IL23), a well-known drug target for autoimmune diseases, in complex with mAb 7G10 offers prospect to design potent lead antibodies by traversing the complete epitope-paratope interface. Herein, key interactions aiding antibody-based neutralization in IL23-7G10 complex are resolute through PyMOL, LigPlot+, Antibody i-Patch, DiscoTope and FoldX. Six amino acids Ser31, Val33, Asn55, Lys59 in heavy chain and His34, Ser93 in light chain are subjected to in silico mutagenesis with residues Met, Trp, Ile, Leu and Arg. A set of 431 mutant macromolecules are outlined. Binding affinities of these molecules with IL23 are estimated through protein-protein docking by employing ZDOCK, ClusPro and RosettaDock. Subsequently, the macromolecules revealed comparable result with 7G10 are cross validated through binding free-energy calculations by applying Molecular Mechanics/Poisson Boltzman Surface Area method in CHARMM. Thirty nine designed theoretical antibodies showed improved outcome in all evaluations; from these, top 10 molecules showed at least nine unit better binding affinity compared to the known mAb. These molecules have the potential to act as lead antibodies. Subsequent molecular dynamics simulations too favored prospective of best ranked molecule to have therapeutic implications in autoimmune and inflammatory diseases. Abbreviations: IL23: interleukin 23; IL17: interleukin17; Ab: antibody; Ag: antigen; mAbs: monoclonal antibodies; STAT3: signal transducer and activator of transcription 3; STAT4: signal transducer and activator of transcription 4; PDB: protein databank; MM/PBSA: molecular mechanics Poisson-Boltzmann surface area; Ag-Ab: antigen- antibody complex; SPC/E: extended simple point charge; SD: steepest descents; PME: particle mesh ewald; dG: binding free energies; Fv: variable fragment.
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Affiliation(s)
- Noor Saba Khan
- a Biomedical Informatics Centre , ICMR-National Institute of Pathology , New Delhi , India
| | - Rashi Verma
- a Biomedical Informatics Centre , ICMR-National Institute of Pathology , New Delhi , India
| | - Dibyabhaba Pradhan
- a Biomedical Informatics Centre , ICMR-National Institute of Pathology , New Delhi , India.,b ICMR-AIIMS Computational Genomics Centre , Indian Council of Medical Research , New Delhi , India
| | - Arnab Nayek
- a Biomedical Informatics Centre , ICMR-National Institute of Pathology , New Delhi , India
| | - Rajabrata Bhuyan
- c Bioinformatics Infrastructure Facility , University of Kalyani , West Bengal , India
| | - Tanmaya Kumar Sahu
- d Centre for Agricultural Bioinformatics , ICAR-ISARI , New Delhi , India
| | - Arun Kumar Jain
- a Biomedical Informatics Centre , ICMR-National Institute of Pathology , New Delhi , India
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5
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Dongmo Foumthuim CJ, Corazza A, Esposito G, Fogolari F. Molecular dynamics simulations of β2-microglobulin interaction with hydrophobic surfaces. MOLECULAR BIOSYSTEMS 2018; 13:2625-2637. [PMID: 29051937 DOI: 10.1039/c7mb00464h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Hydrophobic surfaces are known to adsorb and unfold proteins, a process that has been studied only for a few proteins. Here we address the interaction of β2-microglobulin, a paradigmatic protein for the study of amyloidogenesis, with hydrophobic surfaces. A system with 27 copies of the protein surrounded by a model cubic hydrophobic box is studied by implicit solvent molecular dynamics simulations. Most proteins adsorb on the walls of the box without major distortions in local geometry, whereas free molecules maintain proper structures and fluctuations as observed in explicit solvent molecular dynamics simulations. The major conclusions from the simulations are as follows: (i) the adopted implicit solvent model is adequate to describe protein dynamics and thermodynamics; (ii) adsorption occurs readily and is irreversible on the simulated timescale; (iii) the regions most involved in molecular encounters and stable interactions with the walls are the same as those that are important in protein-protein and protein-nanoparticle interactions; (iv) unfolding following adsorption occurs at regions found to be flexible by both experiments and simulations; (v) thermodynamic analysis suggests a very large contribution from van der Waals interactions, whereas unfavorable electrostatic interactions are not found to contribute much to adsorption energy. Surfaces with different degrees of hydrophobicity may occur in vivo. Our simulations show that adsorption is a fast and irreversible process which is accompanied by partial unfolding. The results and the thermodynamic analysis presented here are consistent with and rationalize previous experimental work.
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6
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Childers MC, Daggett V. Insights from molecular dynamics simulations for computational protein design. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2017; 2:9-33. [PMID: 28239489 PMCID: PMC5321087 DOI: 10.1039/c6me00083e] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures.
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Affiliation(s)
| | - Valerie Daggett
- Corresponding author: , Phone: 1.206.685.7420, Fax: 1.206.685.3300
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7
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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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8
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Carrillo-Parramon O, Brancolini G, Corni S. A dynamical coarse-grained model to disclose allosteric control of misfolding β2-microglobulin. RSC Adv 2016. [DOI: 10.1039/c6ra15491c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Development of a novel Coarse-Grained (CG) model to study β2-microglobulin dynamical features related to fibrillation: our one CG bead model is able to indicate propensities in the deformation behavior of the protein via investigation of the protein motion correlations.
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Affiliation(s)
| | | | - S. Corni
- CNR Institute of Nanoscience
- 41125 Modena
- Italy
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9
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Estácio SG, Krobath H, Vila-Viçosa D, Machuqueiro M, Shakhnovich EI, Faísca PFN. A simulated intermediate state for folding and aggregation provides insights into ΔN6 β2-microglobulin amyloidogenic behavior. PLoS Comput Biol 2014; 10:e1003606. [PMID: 24809460 PMCID: PMC4014404 DOI: 10.1371/journal.pcbi.1003606] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 03/16/2014] [Indexed: 01/26/2023] Open
Abstract
A major component of ex vivo amyloid plaques of patients with dialysis-related amyloidosis (DRA) is a cleaved variant of β2-microglobulin (ΔN6) lacking the first six N-terminal residues. Here we perform a computational study on ΔN6, which provides clues to understand the amyloidogenicity of the full-length β2-microglobulin. Contrary to the wild-type form, ΔN6 is able to efficiently nucleate fibrillogenesis in vitro at physiological pH. This behavior is enhanced by a mild acidification of the medium such as that occurring in the synovial fluid of DRA patients. Results reported in this work, based on molecular simulations, indicate that deletion of the N-terminal hexapeptide triggers the formation of an intermediate state for folding and aggregation with an unstructured strand A and a native-like core. Strand A plays a pivotal role in aggregation by acting as a sticky hook in dimer assembly. This study further predicts that the detachment of strand A from the core is maximized at pH 6.2 resulting into higher aggregation efficiency. The structural mapping of the dimerization interface suggests that Tyr10, His13, Phe30 and His84 are hot-spot residues in ΔN6 amyloidogenesis. Dialysis-related amyloidosis (DRA) is a conformational disease that affects individuals undergoing long-term haemodialysis. In DRA the progressive accumulation of protein human β2-microglobulin (Hβ2m) in the osteoarticular system, followed by its assembly into amyloid fibrils, eventually leads to tissue erosion and destruction. Disclosing the aggregation mechanism of Hβ2m under physiologically relevant conditions represents a major challenge due to the inability of the protein to efficiently nucleate fibrillogenesis in vitro at physiological pH. On the other hand, ΔN6, a truncated variant of Hβ2m, which is also a major component of ex vivo amyloid deposits extracted from DRA patients, is able to efficiently form amyloid fibrils de novo in physiological conditions. This amyloidogenic behavior is dramatically enhanced in a slightly more acidic pH (6.2) compatible with the mild acidification that occurs in the synovial fluid of DRA patients. In this work, an innovative three-stage methodological approach, relying on an array of molecular simulations, spanning different levels of resolution is used to investigate the initial stage of the de novo aggregation mechanism of ΔN6 in a physiologically relevant pH range. We identify an intermediate state for folding and aggregation, whose potential to dimerize is enhanced at pH 6.2. Our results provide rationalizations for previous experimental observations and new insights into the molecular basis of DRA.
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Affiliation(s)
- Sílvia G. Estácio
- Centro de Física da Matéria Condensada & Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Heinrich Krobath
- Centro de Física da Matéria Condensada & Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Diogo Vila-Viçosa
- Centro de Química e Bioquímica & Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Miguel Machuqueiro
- Centro de Química e Bioquímica & Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Eugene I. Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail: (EIS); (PFNF)
| | - Patrícia F. N. Faísca
- Centro de Física da Matéria Condensada & Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- * E-mail: (EIS); (PFNF)
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10
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Ning L, Guo J, Bai Q, Jin N, Liu H, Yao X. Structural diversity and initial oligomerization of PrP106-126 studied by replica-exchange and conventional molecular dynamics simulations. PLoS One 2014; 9:e87266. [PMID: 24586266 PMCID: PMC3929351 DOI: 10.1371/journal.pone.0087266] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 12/24/2013] [Indexed: 12/15/2022] Open
Abstract
Prion diseases are marked by cerebral accumulation of the abnormal isoform of the prion protein. A fragment of prion protein composed of residues 106–126 (PrP106–126) exhibits similar properties to full length prion and plays a key role in the conformational conversion from cellular prion to its pathogenic pattern. Soluble oligomers of PrP106–126 have been proposed to be responsible for neurotoxicity. However, the monomeric conformational space and initial oligomerization of PrP106–126 are still obscure, which are very important for understanding the conformational conversion of PrP106–126. In this study, replica exchange molecular dynamics simulations were performed to investigate monomeric and dimeric states of PrP106–126 in implicit solvent. The structural diversity of PrP106–126 was observed and this peptide did not acquire stable structure. The dimeric PrP106–126 also displayed structural diversity and hydrophobic interaction drove the dimerization. To further study initial oligomerization of PrP106–126, 1 µs conventional molecular dynamics simulations of trimer and tetramer formation were carried out in implicit solvent. We have observed the spontaneous formation of several basic oligomers and stable oligomers with high β-sheet contents were sampled in the simulations of trimer and tetramer formation. The β-hairpin formed in hydrophobic tail of PrP106–126 with residues 118–120 in turn may stabilize these oligomers and seed the formation oligomers. This study can provide insight into the detailed information about the structure of PrP106–126 and the dynamics of aggregation of monomeric PrP106–126 into oligomers in atomic level.
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Affiliation(s)
- Lulu Ning
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | - Jingjing Guo
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Qifeng Bai
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | | | - Huanxiang Liu
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
- School of Pharmacy, Lanzhou University, Lanzhou, China
- * E-mail: (HL); (XY)
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
- State Key Lab for Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
- * E-mail: (HL); (XY)
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11
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Gümral D, Fogolari F, Corazza A, Viglino P, Giorgetti S, Stoppini M, Bellotti V, Esposito G. Reduction of conformational mobility and aggregation in W60G β2-microglobulin: assessment by 15N NMR relaxation. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2013; 51:795-807. [PMID: 24136818 DOI: 10.1002/mrc.4018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 08/20/2013] [Accepted: 09/14/2013] [Indexed: 05/17/2023]
Abstract
The amyloid pathology associated with long-term haemodialysis is due to the deposition of β2-microglobulin, the non-polymorphic light chain of class I major histocompatibility complex, that accumulates at bone joints into amyloid fibrils. Several lines of evidence show the relevance of the tryptophan residue at position 60 for the fibrillogenic transition of the protein. A comparative (15)N NMR relaxation analysis is presented for wild-type human β2-microglobulin and W60G β2-microglobulin, i.e. the mutant with a glycyne replacing the natural tryptophan residue at position 60. The experimental data, collected at 11.4 T and 310 K, were analyzed by means of the reduced spectral density approach. Molecular dynamics (MD) simulations and corresponding thermodynamic integration, together with hydrodynamic calculations were performed to support data interpretation. The analysis results for the mutant protein are consistent with a reduced aggregation with respect to the wild-type counterpart, as a consequence of an increased conformational rigidity probed by either NMR relaxation and MD simulations. Although dynamics in solution is other than fibrillar competence, the assessed properties of the mutant protein can be related with its reduced ability of forming fibrils when seeded in 20% trifluoroethanol.
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Affiliation(s)
- Devrim Gümral
- Dipartimento di Scienze Mediche e Biologiche, Università di Udine, Udine, Italy; Department of Genetics and Bioengineering, Yeditepe University, Istanbul, Turkey
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12
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Rennella E, Cutuil T, Schanda P, Ayala I, Gabel F, Forge V, Corazza A, Esposito G, Brutscher B. Oligomeric States along the Folding Pathways of β2-Microglobulin: Kinetics, Thermodynamics, and Structure. J Mol Biol 2013; 425:2722-36. [DOI: 10.1016/j.jmb.2013.04.028] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 04/23/2013] [Accepted: 04/26/2013] [Indexed: 10/26/2022]
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13
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Rennella E, Brutscher B. Fast Real-Time NMR Methods for Characterizing Short-Lived Molecular States. Chemphyschem 2013; 14:3059-70. [DOI: 10.1002/cphc.201300339] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Indexed: 12/22/2022]
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14
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C. elegans expressing human β2-microglobulin: a novel model for studying the relationship between the molecular assembly and the toxic phenotype. PLoS One 2012; 7:e52314. [PMID: 23284985 PMCID: PMC3528749 DOI: 10.1371/journal.pone.0052314] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 11/15/2012] [Indexed: 01/12/2023] Open
Abstract
Availability of living organisms to mimic key step of amyloidogenesis of human protein has become an indispensable tool for our translation approach aiming at filling the deep gap existing between the biophysical and biochemical data obtained in vitro and the pathological features observed in patients. Human β(2)-microglobulin (β(2)-m) causes systemic amyloidosis in haemodialysed patients. The structure, misfolding propensity, kinetics of fibrillogenesis and cytotoxicity of this protein, in vitro, have been studied more extensively than for any other globular protein. However, no suitable animal model for β(2)-m amyloidosis has been so far reported. We have now established and characterized three new transgenic C. elegans strains expressing wild type human β(2)-m and two highly amyloidogenic isoforms: P32G variant and the truncated form ΔN6 lacking of the 6 N-terminal residues. The expression of human β(2)-m affects the larval growth of C. elegans and the severity of the damage correlates with the intrinsic propensity to self-aggregate that has been reported in previous in vitro studies. We have no evidence of the formation of amyloid deposits in the body-wall muscles of worms. However, we discovered a strict correlation between the pathological phenotype and the presence of oligomeric species recognized by the A11 antibody. The strains expressing human β(2)-m exhibit a locomotory defect quantified with the body bends assay. Here we show that tetracyclines can correct this abnormality confirming that these compounds are able to protect a living organism from the proteotoxicity of human β(2)-m.
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15
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Tanner DE, Phillips JC, Schulten K. GPU/CPU Algorithm for Generalized Born/Solvent-Accessible Surface Area Implicit Solvent Calculations. J Chem Theory Comput 2012; 8:2521-2530. [PMID: 23049488 PMCID: PMC3464051 DOI: 10.1021/ct3003089] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Molecular dynamics methodologies comprise a vital research tool for structural biology. Molecular dynamics has benefited from technological advances in computing, such as multi-core CPUs and graphics processing units (GPUs), but harnessing the full power of hybrid GPU/CPU computers remains difficult. The generalized Born/solvent-accessible surface area implicit solvent model (GB/SA) stands to benefit from hybrid GPU/CPU computers, employing the GPU for the GB calculation and the CPU for the SA calculation. Here, we explore the computational challenges facing GB/SA calculations on hybrid GPU/CPU computers and demonstrate how NAMD, a parallel molecular dynamics program, is able to efficiently utilize GPUs and CPUs simultaneously for fast GB/SA simulations. The hybrid computation principles demonstrated here are generally applicable to parallel applications employing hybrid GPU/CPU calculations.
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Affiliation(s)
- David E. Tanner
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign
- Beckman Institute, University of Illinois at Urbana-Champaign
| | | | - Klaus Schulten
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign
- Beckman Institute, University of Illinois at Urbana-Champaign
- Department of Physics, University of Illinois at Urbana-Champaign
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16
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Colombo M, de Rosa M, Bellotti V, Ricagno S, Bolognesi M. A recurrent D-strand association interface is observed in β-2 microglobulin oligomers. FEBS J 2012; 279:1131-43. [DOI: 10.1111/j.1742-4658.2012.08510.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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17
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Studying interactions by molecular dynamics simulations at high concentration. J Biomed Biotechnol 2012; 2012:303190. [PMID: 22500085 PMCID: PMC3303702 DOI: 10.1155/2012/303190] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 11/23/2011] [Accepted: 11/24/2011] [Indexed: 11/17/2022] Open
Abstract
Molecular dynamics simulations have been used to study molecular encounters and recognition. In recent works, simulations using high concentration of interacting molecules have been performed. In this paper, we consider the practical problems for setting up the simulation and to analyse the results of the simulation. The simulation of beta 2-microglobulin association and the simulation of the binding of hydrogen peroxide by glutathione peroxidase are provided as examples.
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18
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Esposito G, Corazza A, Bellotti V. Pathological self-aggregation of β(2)-microglobulin: a challenge for protein biophysics. Subcell Biochem 2012; 65:165-183. [PMID: 23225003 DOI: 10.1007/978-94-007-5416-4_7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The pathological aggregation of b(2)-microglobulin (b2m) is examined starting from the relevance of some structural aspects of the protein. The systemic deposition of b2m fibrils has been ascribed to several factors, but no conclusive evidence emerged so far. The characterization of b2m aggregates by direct investigation through electron microscopy, atomic force microscopy, solid state NMR and other solid state techniques provides important structural and morphological information on the assembly, but no clues about the mechanism of the aggregation process. The most relevant mechanistic hypotheses are critically reviewed. In addition to the mechanisms exclusively based on structural features, also the recently reported prion-like conversion is analyzed and shown to hardly comply with some established conditions of the fibrillogenic process. An alternative mechanism is recalled that does not require rare events and involves only the full-length protein in proximity of collagen, i.e. the environment that physiologically supports deposition.
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Affiliation(s)
- Gennaro Esposito
- Dipartimento di Scienze Mediche e Biologiche, Università di Udine, P.le Kolbe, 4, 33100, Udine, Italy,
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19
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Eichner T, Radford SE. Understanding the complex mechanisms of β2-microglobulin amyloid assembly. FEBS J 2011; 278:3868-83. [PMID: 21595827 PMCID: PMC3229708 DOI: 10.1111/j.1742-4658.2011.08186.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Revised: 05/11/2011] [Accepted: 05/13/2011] [Indexed: 11/30/2022]
Abstract
Several protein misfolding diseases are associated with the conversion of native proteins into ordered protein aggregates known as amyloid. Studies of amyloid assemblies have indicated that non-native proteins are responsible for initiating aggregation in vitro and in vivo. Despite the importance of these species for understanding amyloid disease, the structural and dynamic features of amyloidogenic intermediates and the molecular details of how they aggregate remain elusive. This review focuses on recent advances in developing a molecular description of the folding and aggregation mechanisms of the human amyloidogenic protein β(2)-microglobulin under physiologically relevant conditions. In particular, the structural and dynamic properties of the non-native folding intermediate I(T) and its role in the initiation of fibrillation and the development of dialysis-related amyloidosis are discussed.
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Affiliation(s)
- Timo Eichner
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA.
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20
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Gee J, Shell MS. Two-dimensional replica exchange approach for peptide–peptide interactions. J Chem Phys 2011; 134:064112. [DOI: 10.1063/1.3551576] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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21
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Giorgetti S, Raimondi S, Pagano K, Relini A, Bucciantini M, Corazza A, Fogolari F, Codutti L, Salmona M, Mangione P, Colombo L, De Luigi A, Porcari R, Gliozzi A, Stefani M, Esposito G, Bellotti V, Stoppini M. Effect of tetracyclines on the dynamics of formation and destructuration of beta2-microglobulin amyloid fibrils. J Biol Chem 2011; 286:2121-31. [PMID: 21068391 PMCID: PMC3023509 DOI: 10.1074/jbc.m110.178376] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 11/03/2010] [Indexed: 12/31/2022] Open
Abstract
The discovery of methods suitable for the conversion in vitro of native proteins into amyloid fibrils has shed light on the molecular basis of amyloidosis and has provided fundamental tools for drug discovery. We have studied the capacity of a small library of tetracycline analogues to modulate the formation or destructuration of β2-microglobulin fibrils. The inhibition of fibrillogenesis of the wild type protein was first established in the presence of 20% trifluoroethanol and confirmed under a more physiologic environment including heparin and collagen. The latter conditions were also used to study the highly amyloidogenic variant, P32G. The NMR analysis showed that doxycycline inhibits β2-microglobulin self-association and stabilizes the native-like species through fast exchange interactions involving specific regions of the protein. Cell viability assays demonstrated that the drug abolishes the natural cytotoxic activity of soluble β2-microglobulin, further strengthening a possible in vivo therapeutic exploitation of this drug. Doxycycline can disassemble preformed fibrils, but the IC(50) is 5-fold higher than that necessary for the inhibition of fibrillogenesis. Fibril destructuration is a dynamic and time-dependent process characterized by the early formation of cytotoxic protein aggregates that, in a few hours, convert into non-toxic insoluble material. The efficacy of doxycycline as a drug against dialysis-related amyloidosis would benefit from the ability of the drug to accumulate just in the skeletal system where amyloid is formed. In these tissues, the doxycycline concentration reaches values several folds higher than those resulting in inhibition of amyloidogenesis and amyloid destructuration in vitro.
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Affiliation(s)
- Sofia Giorgetti
- From the Department of Biochemistry, University of Pavia, via Taramelli 3b, 27100 Pavia
| | - Sara Raimondi
- From the Department of Biochemistry, University of Pavia, via Taramelli 3b, 27100 Pavia
| | - Katiuscia Pagano
- the Department of Biomedical Sciences and Technologies, University of Udine, Piazzale Kolbe 4, 33100 Udine
| | - Annalisa Relini
- the National Institute of Biostructures and Biosystems (INBB), Viale Medaglie d'Oro 305, 00136 Rome
- the Department of Physics, University of Genoa, via Dodecaneso 33, 16146 Genoa
| | - Monica Bucciantini
- the Department of Biochemical Sciences, University of Florence, Viale Morgagni 50, 50134 Florence
| | - Alessandra Corazza
- the Department of Biomedical Sciences and Technologies, University of Udine, Piazzale Kolbe 4, 33100 Udine
- the National Institute of Biostructures and Biosystems (INBB), Viale Medaglie d'Oro 305, 00136 Rome
| | - Federico Fogolari
- the Department of Biomedical Sciences and Technologies, University of Udine, Piazzale Kolbe 4, 33100 Udine
- the National Institute of Biostructures and Biosystems (INBB), Viale Medaglie d'Oro 305, 00136 Rome
| | - Luca Codutti
- the Department of Biomedical Sciences and Technologies, University of Udine, Piazzale Kolbe 4, 33100 Udine
| | - Mario Salmona
- the Department of Molecular Biochemistry and Pharmacology, Mario Negri Institute for Pharmacological Research, Via La Masa, 19, 20156 Milan, and
| | - Palma Mangione
- From the Department of Biochemistry, University of Pavia, via Taramelli 3b, 27100 Pavia
| | - Lino Colombo
- the Department of Pharmaceutical Chemistry, University of Pavia, via Taramelli 12, 27100 Pavia, Italy
| | - Ada De Luigi
- the Department of Molecular Biochemistry and Pharmacology, Mario Negri Institute for Pharmacological Research, Via La Masa, 19, 20156 Milan, and
| | - Riccardo Porcari
- From the Department of Biochemistry, University of Pavia, via Taramelli 3b, 27100 Pavia
| | - Alessandra Gliozzi
- the National Institute of Biostructures and Biosystems (INBB), Viale Medaglie d'Oro 305, 00136 Rome
- the Department of Physics, University of Genoa, via Dodecaneso 33, 16146 Genoa
| | - Massimo Stefani
- the Department of Biochemical Sciences, University of Florence, Viale Morgagni 50, 50134 Florence
| | - Gennaro Esposito
- the Department of Biomedical Sciences and Technologies, University of Udine, Piazzale Kolbe 4, 33100 Udine
- the National Institute of Biostructures and Biosystems (INBB), Viale Medaglie d'Oro 305, 00136 Rome
| | - Vittorio Bellotti
- From the Department of Biochemistry, University of Pavia, via Taramelli 3b, 27100 Pavia
- the National Institute of Biostructures and Biosystems (INBB), Viale Medaglie d'Oro 305, 00136 Rome
| | - Monica Stoppini
- From the Department of Biochemistry, University of Pavia, via Taramelli 3b, 27100 Pavia
- the National Institute of Biostructures and Biosystems (INBB), Viale Medaglie d'Oro 305, 00136 Rome
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22
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Fogolari F, Corazza A, Varini N, Rotter M, Gumral D, Codutti L, Rennella E, Viglino P, Bellotti V, Esposito G. Molecular dynamics simulation of β₂-microglobulin in denaturing and stabilizing conditions. Proteins 2010; 79:986-1001. [PMID: 21287627 DOI: 10.1002/prot.22940] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Revised: 10/22/2010] [Accepted: 11/02/2010] [Indexed: 11/11/2022]
Abstract
β₂-Microglobulin has been a model system for the study of fibril formation for 20 years. The experimental study of β₂-microglobulin structure, dynamics, and thermodynamics in solution, at atomic detail, along the pathway leading to fibril formation is difficult because the onset of disorder and aggregation prevents signal resolution in Nuclear Magnetic Resonance experiments. Moreover, it is difficult to characterize conformers in exchange equilibrium. To gain insight (at atomic level) on processes for which experimental information is available at molecular or supramolecular level, molecular dynamics simulations have been widely used in the last decade. Here, we use molecular dynamics to address three key aspects of β₂-microglobulin, which are known to be relevant to amyloid formation: (1) 60 ns molecular dynamics simulations of β₂-microglobulin in trifluoroethanol and in conditions mimicking low pH are used to study the behavior of the protein in environmental conditions that are able to trigger amyloid formation; (2) adaptive biasing force molecular dynamics simulation is used to force cis-trans isomerization at Proline 32 and to calculate the relative free energy in the folded and unfolded state. The native-like trans-conformer (known as intermediate 2 and determining the slow phase of refolding), is simulated for 10 ns, detailing the possible link between cis-trans isomerization and conformational disorder; (3) molecular dynamics simulation of highly concentrated doxycycline (a molecule able to suppress fibril formation) in the presence of β₂-microglobulin provides details of the binding modes of the drug and a rationale for its effect.
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Affiliation(s)
- Federico Fogolari
- Dipartimento di Scienze e Tecnologie Biomediche, Universita' di Udine, Piazzale Kolbe 4, 33100 Udine, Italy.
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23
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Regazzoni L, Bertoletti L, Vistoli G, Colombo R, Aldini G, Serra M, Carini M, Caccialanza G, De Lorenzi E. A combined high-resolution mass spectrometric and in silico approach for the characterisation of small ligands of beta2-microglobulin. ChemMedChem 2010; 5:1015-25. [PMID: 20544784 DOI: 10.1002/cmdc.201000082] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Beta(2)-microglobulin (beta(2)-m) is a protein responsible for a severe complication of long-term hemodialysis, known as dialysis-related amyloidosis, in which initial beta(2)-m misfolding leads to amyloid fibril deposition, mainly in the skeletal tissue. Whereas much attention is paid to understanding the complex mechanism of amyloid formation, the evaluation of small molecules that may bind beta(2)-m and possibly inhibit the aggregation process is still largely unexplored mainly because the protein lacks a specific active site. Based on our previous findings, we selected a pilot set of sulfonated molecules that are known to either bind or not to the protein, including binders that are anti-amyloidogenic. We show how a complementary approach, using high-resolution mass spectrometry and in silico studies, can offer rapid and precise information on affinity, as well as insight into the structural requisites that favour or disfavour the inhibitory activity. Overall, this approach can be used for predictive purposes and for a rapid screening of fibrillogenesis inhibitors.
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Affiliation(s)
- Luca Regazzoni
- Dipartimento di Scienze Farmaceutiche Pietro Pratesi, Università degli Studi di Milano, Via Mangiagalli 25, Milan, Italy
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24
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Lin EI, Shell MS. Can Peptide Folding Simulations Provide Predictive Information for Aggregation Propensity? J Phys Chem B 2010; 114:11899-908. [DOI: 10.1021/jp104114n] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Edmund I. Lin
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106-5080
| | - M. Scott Shell
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106-5080
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25
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Pagano K, Bemporad F, Fogolari F, Esposito G, Viglino P, Chiti F, Corazza A. Structural and dynamics characteristics of acylphosphatase from Sulfolobus solfataricus in the monomeric state and in the initial native-like aggregates. J Biol Chem 2010; 285:14689-700. [PMID: 20223823 PMCID: PMC2863212 DOI: 10.1074/jbc.m109.082156] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Revised: 03/08/2010] [Indexed: 02/04/2023] Open
Abstract
It has previously been shown that the acylphosphatase from Sulfolobus solfataricus is capable of forming amyloid-like aggregates under conditions in which the native structure is maintained and via the transient formation of native-like aggregates. Based on the previously determined NMR structure of the native protein, showing a ferredoxin-like fold and the peculiar presence of an unstructured N-terminal segment, we show here, at a molecular level using NMR spectroscopy, that indeed S. solfataricus acylphosphatase remains in a native-like conformation when placed in aggregating conditions and that such a native-like structure persists when the protein forms the initial aggregates, at least within the low molecular weight species. The analysis carried out under different solution conditions, based on the measurement of the combined (1)H and (15)N chemical shifts and hydrogen/deuterium exchange rates, enabled the most significant conformational changes to be monitored upon transfer of the monomeric state into aggregating conditions and upon formation of the initial native-like aggregates. Important increases of the hydrogen/deuterium exchange rates throughout the native protein, accompanied by small and localized structural changes, in the monomeric protein were observed. The results also allow the identification of the intermolecular interaction regions within the native-like aggregates, that involve, in particular, the N-terminal unstructured segment, the apical region including strands S4 and S5 with the connecting loop, and the opposite active site.
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Affiliation(s)
- Katiuscia Pagano
- From the Department of Biomedical Sciences and Technologies, University of Udine, Piazzale Kolbe 4, 33100 Udine, Italy
| | - Francesco Bemporad
- the Department of Biochemical Sciences, University of Firenze, Viale Morgagni 50, 50134, Firenze, Italy, and
| | - Federico Fogolari
- From the Department of Biomedical Sciences and Technologies, University of Udine, Piazzale Kolbe 4, 33100 Udine, Italy
- the Consorzio Interuniversitario Istituto Nazionale di Biostrutture e Biosistemi, Viale Medaglie d'Oro 305, 00136 Rome, Italy
| | - Gennaro Esposito
- From the Department of Biomedical Sciences and Technologies, University of Udine, Piazzale Kolbe 4, 33100 Udine, Italy
- the Consorzio Interuniversitario Istituto Nazionale di Biostrutture e Biosistemi, Viale Medaglie d'Oro 305, 00136 Rome, Italy
| | - Paolo Viglino
- From the Department of Biomedical Sciences and Technologies, University of Udine, Piazzale Kolbe 4, 33100 Udine, Italy
- the Consorzio Interuniversitario Istituto Nazionale di Biostrutture e Biosistemi, Viale Medaglie d'Oro 305, 00136 Rome, Italy
| | - Fabrizio Chiti
- the Department of Biochemical Sciences, University of Firenze, Viale Morgagni 50, 50134, Firenze, Italy, and
- the Consorzio Interuniversitario Istituto Nazionale di Biostrutture e Biosistemi, Viale Medaglie d'Oro 305, 00136 Rome, Italy
| | - Alessandra Corazza
- From the Department of Biomedical Sciences and Technologies, University of Udine, Piazzale Kolbe 4, 33100 Udine, Italy
- the Consorzio Interuniversitario Istituto Nazionale di Biostrutture e Biosistemi, Viale Medaglie d'Oro 305, 00136 Rome, Italy
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26
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Corazza A, Rennella E, Schanda P, Mimmi MC, Cutuil T, Raimondi S, Giorgetti S, Fogolari F, Viglino P, Frydman L, Gal M, Bellotti V, Brutscher B, Esposito G. Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic protein beta2-microglobulin revealed by real-time two-dimensional NMR. J Biol Chem 2009; 285:5827-35. [PMID: 20028983 DOI: 10.1074/jbc.m109.061168] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Beta2-microglobulin (beta2m), the light chain of class I major histocompatibility complex, is responsible for the dialysis-related amyloidosis and, in patients undergoing long term dialysis, the full-length and chemically unmodified beta2m converts into amyloid fibrils. The protein, belonging to the immunoglobulin superfamily, in common to other members of this family, experiences during its folding a long-lived intermediate associated to the trans-to-cis isomerization of Pro-32 that has been addressed as the precursor of the amyloid fibril formation. In this respect, previous studies on the W60G beta2m mutant, showing that the lack of Trp-60 prevents fibril formation in mild aggregating condition, prompted us to reinvestigate the refolding kinetics of wild type and W60G beta2m at atomic resolution by real-time NMR. The analysis, conducted at ambient temperature by the band selective flip angle short transient real-time two-dimensional NMR techniques and probing the beta2m states every 15 s, revealed a more complex folding energy landscape than previously reported for wild type beta2m, involving more than a single intermediate species, and shedding new light into the fibrillogenic pathway. Moreover, a significant difference in the kinetic scheme previously characterized by optical spectroscopic methods was discovered for the W60G beta2m mutant.
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Affiliation(s)
- Alessandra Corazza
- Department of Biomedical Science and Technology, University of Udine, Piazzale Kolbe 4, 33100 Udine, Italy.
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27
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Fogolari F, Haridas H, Corazza A, Viglino P, Corà D, Caselle M, Esposito G, Xodo LE. Molecular models for intrastrand DNA G-quadruplexes. BMC STRUCTURAL BIOLOGY 2009; 9:64. [PMID: 19811654 PMCID: PMC2768733 DOI: 10.1186/1472-6807-9-64] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Accepted: 10/07/2009] [Indexed: 11/10/2022]
Abstract
BACKGROUND Independent surveys of human gene promoter regions have demonstrated an overrepresentation of G(3)X(n1)G3X(n2)G(3)X(n3)G(3) motifs which are known to be capable of forming intrastrand quadruple helix structures. In spite of the widely recognized importance of G-quadruplex structures in gene regulation and growing interest around this unusual DNA structure, there are at present only few such structures available in the Nucleic Acid Database. In the present work we generate by molecular modeling feasible G-quadruplex structures which may be useful for interpretation of experimental data. RESULTS We have used all quadruplex DNA structures deposited in the Nucleic Acid Database in order to select a list of fragments entailing a strand of three adjacent G's paired with another strand of three adjacent G's separated by a loop of one to four residues. These fragments were further clustered and representative fragments were finally selected. Further fragments were generated by assemblying the two strands of each fragment with loops from different fragments whenever the anchor G's were superimposable. The fragments were used to assemble G quadruplex based on a superimposability criterion. CONCLUSION Molecular models have been generated for a large number of G(3)X(n1)G(3)X(n2)G3X(n3)G(3) sequences. For a given sequence not all topologies are possible with the available repertoire of fragments due to steric hindrance and low superimposability. Since all molecular models are generated by fragments coming from observed quadruplex structures, molecular models are in principle reliable and may be used for interpretation of experimental data. Some examples of applications are given.
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Affiliation(s)
- Federico Fogolari
- Dipartimento di Scienze e Tecnologie Biomediche, Università di Udine, Piazzale Kolbe 4 - 33100 Udine, Italy.
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28
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Lin YW, Ni FY, Ying TL. Early events in thermal unfolding of apocytochrome b562 and its double-cysteine mutant as revealed by molecular dynamics simulation. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2008.07.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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29
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Ricagno S, Colombo M, Rosa MD, Sangiovanni E, Giorgetti S, Raimondi S, Bellotti V, Bolognesi M. DE loop mutations affect β2-microglobulin stability and amyloid aggregation. Biochem Biophys Res Commun 2008; 377:146-50. [DOI: 10.1016/j.bbrc.2008.09.108] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Accepted: 09/22/2008] [Indexed: 10/21/2022]
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30
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Sakata M, Chatani E, Kameda A, Sakurai K, Naiki H, Goto Y. Kinetic Coupling of Folding and Prolyl Isomerization of β2-Microglobulin Studied by Mutational Analysis. J Mol Biol 2008; 382:1242-55. [DOI: 10.1016/j.jmb.2008.08.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Revised: 07/28/2008] [Accepted: 08/01/2008] [Indexed: 10/21/2022]
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Abstract
Amyloidlike fibrils are found in many fatal diseases, including Alzheimer's disease, type II diabetes mellitus, transmissible spongiform encephalopathies, and prion diseases. These diseases are linked to proteins that have partially unfolded, misfolded, and aggregated into amyloidlike fibrils. The kinetics of amyloidlike fibrils aggregation is still hotly debated and remains an important open question. We have utilized the GNNQQNY crystal structure and high-temperature molecular dynamics simulation in explicit solvent to study the disaggregation mechanism of the GNNQQNY fibrils and to infer its likely aggregation pathways. A hexamer model and a 12-mer model both with two parallel beta-sheets separated by a dry side-chain interface were adopted in our computational analysis. A cumulative time of 1 micros was simulated for the hexamer model at five different temperatures (298 K, 348 K, 398 K, 448 K, and 498 K), and a cumulative time of 2.1 micros was simulated for the 12-mer model at four temperatures (298 K, 398 K, 448 K, and 498 K). Our disaggregation landscape and kinetics analyses indicate that tetramers probably act as the transition state in both the hexamer and the 12-mer simulations. In addition, the 12-mer simulations show that the initial aggregation nucleus is with eight peptides. Furthermore, the landscape is rather flat from 8-mers to 12-mers, indicating the absence of major barriers once the initial aggregation nucleus forms. Thus, the likely aggregation pathway is from monomers to the initial nucleus of 8-mers with tetramers as the transition state. Transition state structure analysis shows that the two dominant transition state conformations are tetramers in the 3-1 and 2-2 arrangements. The predominant nucleus conformations are in peptide arrangements maximizing dry side-chain contacts. Landscape and kinetics analyses also indicate that the parallel beta-sheets form earlier than the dry side-chain contacts during aggregation. These results provide further insights in understanding the early fibrils aggregation.
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Esposito G, Ricagno S, Corazza A, Rennella E, Gümral D, Mimmi MC, Betto E, Pucillo CE, Fogolari F, Viglino P, Raimondi S, Giorgetti S, Bolognesi B, Merlini G, Stoppini M, Bolognesi M, Bellotti V. The Controlling Roles of Trp60 and Trp95 in β2-Microglobulin Function, Folding and Amyloid Aggregation Properties. J Mol Biol 2008; 378:887-97. [DOI: 10.1016/j.jmb.2008.03.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2007] [Revised: 02/28/2008] [Accepted: 03/02/2008] [Indexed: 10/22/2022]
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