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Horváth G, Biczók L, Majer Z, Kovács M, Micsonai A, Kardos J, Toke O. Structural insight into a partially unfolded state preceding aggregation in an intracellular lipid-binding protein. FEBS J 2017; 284:3637-3661. [DOI: 10.1111/febs.14264] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 08/15/2017] [Accepted: 09/05/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Gergő Horváth
- Laboratory for NMR Spectroscopy; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest Hungary
| | - László Biczók
- Institute of Materials and Environmental Chemistry; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest Hungary
| | - Zsuzsa Majer
- Institute of Chemistry; Eötvös Loránd University; Budapest Hungary
| | - Mihály Kovács
- Department of Biochemistry; ELTE-MTA ‘Momentum’ Motor Enzymology Research Group; Eötvös Loránd University; Budapest Hungary
| | - András Micsonai
- Department of Biochemistry; MTA-ELTE NAP B Neuroimmunology Research Group; Institute of Biology; Eötvös Loránd University; Budapest Hungary
| | - József Kardos
- Department of Biochemistry; MTA-ELTE NAP B Neuroimmunology Research Group; Institute of Biology; Eötvös Loránd University; Budapest Hungary
| | - Orsolya Toke
- Laboratory for NMR Spectroscopy; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest Hungary
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2
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Structural coalescence underlies the aggregation propensity of a β-barrel protein motif. PLoS One 2017; 12:e0170607. [PMID: 28187186 PMCID: PMC5302452 DOI: 10.1371/journal.pone.0170607] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 01/07/2017] [Indexed: 02/07/2023] Open
Abstract
A clear understanding of the structural foundations underlying protein aggregation is an elusive goal of central biomedical importance. A step toward this aim is exemplified by the β-barrel motif represented by the intestinal fatty acid binding protein (IFABP) and two abridged all-β sheet forms (Δ98Δ and Δ78Δ). At odds with the established notion that a perturbation of the native fold should necessarily favor a buildup of intermediate forms with an enhanced tendency to aggregate, the intrinsic stability (ΔG°H2O) of these proteins does not bear a straightforward correlation with their trifluoroethanol (TFE)-induced aggregation propensity. In view of this fact, we found it more insightful to delve into the connection between structure and stability under sub-aggregating conditions (10% TFE). In the absence of the co-solvent, the abridged variants display a common native-like region decorated with a disordered C-terminal stretch. Upon TFE addition, an increase in secondary structure content is observed, assimilating them to the parent protein. In this sense, TFE perturbs a common native like region while exerting a global compaction effect. Importantly, in all cases, fatty acid binding function is preserved. Interestingly, energetic as well as structural diversity in aqueous solution evolves into a common conformational ensemble more akin in stability. These facts reconcile apparent paradoxical findings related to stability and rates of aggregation. This scenario likely mimics the accrual of aggregation-prone species in the population, an early critical event for the development of fibrillation.
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Sarkar-Banerjee S, Chowdhury S, Paul SS, Dutta D, Ghosh A, Chattopadhyay K. The Non-native Helical Intermediate State May Accumulate at Low pH in the Folding and Aggregation Landscape of the Intestinal Fatty Acid Binding Protein. Biochemistry 2016; 55:4457-68. [DOI: 10.1021/acs.biochem.6b00390] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Suparna Sarkar-Banerjee
- Protein Folding and Dynamics
Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Sourav Chowdhury
- Protein Folding and Dynamics
Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Simanta Sarani Paul
- Protein Folding and Dynamics
Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Debashis Dutta
- Protein Folding and Dynamics
Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Anisa Ghosh
- Protein Folding and Dynamics
Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Krishnananda Chattopadhyay
- Protein Folding and Dynamics
Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
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Angelani CR, Curto LM, Cabanas IS, Caramelo JJ, Uversky VN, Delfino JM. Toward a common aggregation mechanism for a β-barrel protein family: Insights derived from a stable dimeric species. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1599-607. [DOI: 10.1016/j.bbapap.2014.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 05/30/2014] [Accepted: 06/02/2014] [Indexed: 10/25/2022]
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5
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Curto LM, Angelani CR, Caramelo JJ, Delfino JM. Truncation of a β-barrel scaffold dissociates intrinsic stability from its propensity to aggregation. Biophys J 2013. [PMID: 23199921 DOI: 10.1016/j.bpj.2012.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Δ98Δ is a functional all-β sheet variant of intestinal fatty acid binding protein (IFABP) that was generated by controlled proteolysis. This framework is useful to study the molecular determinants related to aggregation of β-barrel proteins. Albeit displaying increased conformational plasticity, Δ98Δ exhibits a nativelike β-barrel topology and is able to support a cooperative folding behavior. Here we present a comparative study of IFABP and Δ98Δ regarding their conformational perturbation and aggregation propensity triggered by trifluoroethanol. Both proteins share a common nucleation-elongation mechanism, whereby the rate-limiting step is the formation of stable dimeric nuclei followed by the association of monomers to the growing aggregates. Despite leading to a less stable structure, the extensive truncation of IFABP yields a form exhibiting a somewhat lower tendency to aggregate. This finding appears at odds with the established notion that a perturbation of the native compact fold should necessarily favor the population of aggregation-prone species. In addition to the aggregation propensity dictated by a given amino-acid sequence, our contention holds that long-range interactions might also play a major role in determining the overall aggregation propensity.
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Affiliation(s)
- Lucrecia M Curto
- Department of Biological Chemistry and Institute of Biochemistry and Biophysics, School of Pharmacy and Biochemistry, University of Buenos Aires, Buenos Aires, Argentina
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6
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de Brevern AG, Bornot A, Craveur P, Etchebest C, Gelly JC. PredyFlexy: flexibility and local structure prediction from sequence. Nucleic Acids Res 2012; 40:W317-22. [PMID: 22689641 PMCID: PMC3394303 DOI: 10.1093/nar/gks482] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Protein structures are necessary for understanding protein function at a molecular level. Dynamics and flexibility of protein structures are also key elements of protein function. So, we have proposed to look at protein flexibility using novel methods: (i) using a structural alphabet and (ii) combining classical X-ray B-factor data and molecular dynamics simulations. First, we established a library composed of structural prototypes (LSPs) to describe protein structure by a limited set of recurring local structures. We developed a prediction method that proposes structural candidates in terms of LSPs and predict protein flexibility along a given sequence. Second, we examine flexibility according to two different descriptors: X-ray B-factors considered as good indicators of flexibility and the root mean square fluctuations, based on molecular dynamics simulations. We then define three flexibility classes and propose a method based on the LSP prediction method for predicting flexibility along the sequence. This method does not resort to sophisticate learning of flexibility but predicts flexibility from average flexibility of predicted local structures. The method is implemented in PredyFlexy web server. Results are similar to those obtained with the most recent, cutting-edge methods based on direct learning of flexibility data conducted with sophisticated algorithms. PredyFlexy can be accessed at http://www.dsimb.inserm.fr/dsimb_tools/predyflexy/.
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7
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Basehore HK, Ropson IJ. Residual interactions in unfolded bile acid-binding protein by 19F NMR. Protein Sci 2011; 20:327-35. [PMID: 21280124 DOI: 10.1002/pro.563] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The folding initiation mechanism of human bile acid-binding protein (BABP) has been examined by (19) F NMR. Equilibrium unfolding studies of BABP labeled with fluorine at all eight of its phenylalanine residues showed that at least two sites experience changes in solvent exposure at high denaturant concentrations. Peak assignments were made by site-specific 4FPhe incorporation. The resonances for proteins specifically labeled at Phe17, Phe47, and Phe63 showed changes in chemical shift at denaturant concentrations at which the remaining five phenylalanine residues appear to be fully solvent-exposed. Phe17 is a helical residue that was not expected to participate in a folding initiation site. Phe47 and Phe63 form part of a hydrophobic core region that may be conserved as a site for folding initiation in the intracellular lipid-binding protein family.
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Affiliation(s)
- H Kenney Basehore
- Department of Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17022, USA
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8
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Franchini GR, Curto LM, Caramelo JJ, Delfino JM. Dissection of a beta-barrel motif leads to a functional dimer: the case of the intestinal fatty acid binding protein. Protein Sci 2010; 18:2592-602. [PMID: 19844951 DOI: 10.1002/pro.273] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A lingering issue in the area of protein engineering is the optimal design of beta motifs. In this regard, the framework provided by intestinal fatty acid binding protein (IFABP) was successfully chosen to explore the consequences on structure and function of the redesign of natural motifs. A truncated form of IFABP (Delta 98 Delta) served to illustrate the nonintuitive notion that the integrity of the beta-barrel can indeed be compromised with no effect on the ability to attain a native-like fold. This is most likely the outcome of the key role played by the preservation of essential core residues. In the search for the minimal structural determinants of this fold, Delta 98 Delta offered room for further intervention. A dissection of this protein leads to a new abridged variant, Delta 78 Delta, containing 60% of the amino acids of IFABP. Spectroscopic analyses indicate that Delta 78 Delta retains substantial beta-sheet content and preserves tertiary interactions, displaying cooperative unfolding and binding activity. Most strikingly, this construct adopts a remarkably stable dimeric structure in solution. This phenomenon takes advantage of the inherent structural plasticity of this motif, likely profitting from edge-to-edge interactions between beta-sheets, whereas avoiding the most commonly occurring outcome represented by aggregation.
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Affiliation(s)
- Gisela R Franchini
- Department of Biological Chemistry and Institute of Biochemistry and Biophysics (IQUIFIB), School of Pharmacy and Biochemistry, University of Buenos Aires, C1113AAD, Buenos Aires, Argentina
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9
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Dosztanyi Z, Meszaros B, Simon I. Bioinformatical approaches to characterize intrinsically disordered/unstructured proteins. Brief Bioinform 2009; 11:225-43. [DOI: 10.1093/bib/bbp061] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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10
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Curto LM, Caramelo JJ, Franchini GR, Delfino JM. Delta98Delta, a minimalist model of antiparallel beta-sheet proteins based on intestinal fatty acid binding protein. Protein Sci 2009; 18:735-46. [PMID: 19309727 DOI: 10.1002/pro.71] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The design of beta-barrels has always been a formidable challenge for de novo protein design. For instance, a persistent problem is posed by the intrinsic tendency to associate given by free edges. From the opposite standpoint provided by the redesign of natural motifs, we believe that the intestinal fatty acid binding protein (IFABP) framework allows room for intervention, giving rise to abridged forms from which lessons on beta-barrel architecture and stability could be learned. In this context, Delta98Delta (encompassing residues 29-126 of IFABP) emerges as a monomeric variant that folds properly, retaining functional activity, despite lacking extensive stretches involved in the closure of the beta-barrel. Spectroscopic probes (fluorescence and circular dichroism) support the existence of a form preserving the essential determinants of the parent structure, albeit endowed with enhanced flexibility. Chemical and physical perturbants reveal cooperative unfolding transitions, with evidence of significant population of intermediate species in equilibrium, structurally akin to those transiently observed in IFABP. The recognition by the natural ligand oleic acid exerts a mild stabilizing effect, being of a greater magnitude than that found for IFABP. In summary, Delta98Delta adopts a monomeric state with a compact core and a loose periphery, thus pointing to the nonintuitive notion that the integrity of the beta-barrel can indeed be compromised with no consequence on the ability to attain a native-like and functional fold.
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Affiliation(s)
- Lucrecia María Curto
- Department of Biological Chemistry and Institute of Biochemistry and Biophysics (IQUIFIB), School of Pharmacy and Biochemistry, University of Buenos Aires, C1113AAD Buenos Aires, Argentina
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11
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Adenovirus type 5 E4 Orf3 protein targets promyelocytic leukaemia (PML) protein nuclear domains for disruption via a sequence in PML isoform II that is predicted as a protein interaction site by bioinformatic analysis. J Gen Virol 2009; 90:95-104. [DOI: 10.1099/vir.0.005512-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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12
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Mallam AL, Jackson SE. Use of protein engineering techniques to elucidate protein folding pathways. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2008; 84:57-113. [PMID: 19121700 DOI: 10.1016/s0079-6603(08)00403-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Anna L Mallam
- Department of Chemistry, Cambridge, CB2 1EW, United Kingdom
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13
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Hirose S, Shimizu K, Kanai S, Kuroda Y, Noguchi T. POODLE-L: a two-level SVM prediction system for reliably predicting long disordered regions. Bioinformatics 2007; 23:2046-53. [PMID: 17545177 DOI: 10.1093/bioinformatics/btm302] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
MOTIVATION Recent experimental and theoretical studies have revealed several proteins containing sequence segments that are unfolded under physiological conditions. These segments are called disordered regions. They are actively investigated because of their possible involvement in various biological processes, such as cell signaling, transcriptional and translational regulation. Additionally, disordered regions can represent a major obstacle to high-throughput proteome analysis and often need to be removed from experimental targets. The accurate prediction of long disordered regions is thus expected to provide annotations that are useful for a wide range of applications. RESULTS We developed Prediction Of Order and Disorder by machine LEarning (POODLE-L; L stands for long), the Support Vector Machines (SVMs) based method for predicting long disordered regions using 10 kinds of simple physico-chemical properties of amino acid. POODLE-L assembles the output of 10 two-level SVM predictors into a final prediction of disordered regions. The performance of POODLE-L for predicting long disordered regions, which exhibited a Matthew's correlation coefficient of 0.658, was the highest when compared with eight well-established publicly available disordered region predictors. AVAILABILITY POODLE-L is freely available at http://mbs.cbrc.jp/poodle/poodle-l.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Galzitskaya OV, Garbuzynskiy SO, Lobanov MY. FoldUnfold: web server for the prediction of disordered regions in protein chain. Bioinformatics 2006; 22:2948-9. [PMID: 17021161 DOI: 10.1093/bioinformatics/btl504] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
UNLABELLED Identification of disordered regions in polypeptide chains is very important because such regions are essential for protein function. A new parameter, namely mean packing density of residues has been introduced to detect disordered regions in a protein sequence. We have demonstrated that regions with weak expected packing density would be responsible for the appearance of disordered regions. Our method (FoldUnfold) has been tested on datasets of globular proteins (559 proteins) and long disordered protein segments (129 proteins) and showed improved performance over some other widely used methods, such as DISOPRED, PONDR VL3H, IUPred and GlobPlot. AVAILABILITY The FoldUnfold server is available for users at http://skuld.protres.ru/~mlobanov/ogu/ogu.cgi. There is a link to our server through the web site of DisProt (http://www.disprot.org/predictors.php).
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Affiliation(s)
- Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences 142290, Pushchino, Moscow Region, Russia.
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15
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Chattopadhyay K, Frieden C. Steady-state and time-resolved fluorescence studies of the intestinal fatty acid binding protein. Proteins 2006; 63:327-35. [PMID: 16421929 DOI: 10.1002/prot.20861] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The intestinal fatty acid binding protein contains two tryptophan residues (Trp6 and Trp82) both of which have been shown by X-ray and NMR methods to be buried in hydrophobic clusters. By using a combination of steady-state and time-resolved fluorescence experiments, we have deconvoluted the lifetime weighted contribution of each of the tryptophans to the steady-state fluorescence quantum yield. While Trp82 has been implicated in an intermediate that appears at relatively high denaturant concentrations, the variation of the lifetime weighted contribution of Trp6 with urea or guanidium hydrochloride shows formation of an intermediate state at low concentrations of the denaturant before the actual unfolding starts. Trp82 did not show similar behavior. Fluorescence quenching experiments by acrylamide show that while Trp6 in the native protein is less solvent-exposed, its accessibility is increased significantly at low urea concentration indicating that the early intermediate state is partially unfolded. Time-resolved anisotropy experiments indicate that the volume of the partially unfolded intermediates is larger than the native protein and lead to the speculation that the last step of the protein folding might be the removal of solvent molecules from the protein.
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Affiliation(s)
- Krishnananda Chattopadhyay
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
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