1
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Sønderby TV, Najarzadeh Z, Otzen DE. Functional Bacterial Amyloids: Understanding Fibrillation, Regulating Biofilm Fibril Formation and Organizing Surface Assemblies. Molecules 2022; 27:4080. [PMID: 35807329 PMCID: PMC9268375 DOI: 10.3390/molecules27134080] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 02/01/2023] Open
Abstract
Functional amyloid is produced by many organisms but is particularly well understood in bacteria, where proteins such as CsgA (E. coli) and FapC (Pseudomonas) are assembled as functional bacterial amyloid (FuBA) on the cell surface in a carefully optimized process. Besides a host of helper proteins, FuBA formation is aided by multiple imperfect repeats which stabilize amyloid and streamline the aggregation mechanism to a fast-track assembly dominated by primary nucleation. These repeats, which are found in variable numbers in Pseudomonas, are most likely the structural core of the fibrils, though we still lack experimental data to determine whether the repeats give rise to β-helix structures via stacked β-hairpins (highly likely for CsgA) or more complicated arrangements (possibly the case for FapC). The response of FuBA fibrillation to denaturants suggests that nucleation and elongation involve equal amounts of folding, but protein chaperones preferentially target nucleation for effective inhibition. Smart peptides can be designed based on these imperfect repeats and modified with various flanking sequences to divert aggregation to less stable structures, leading to a reduction in biofilm formation. Small molecules such as EGCG can also divert FuBA to less organized structures, such as partially-folded oligomeric species, with the same detrimental effect on biofilm. Finally, the strong tendency of FuBA to self-assemble can lead to the formation of very regular two-dimensional amyloid films on structured surfaces such as graphite, which strongly implies future use in biosensors or other nanobiomaterials. In summary, the properties of functional amyloid are a much-needed corrective to the unfortunate association of amyloid with neurodegenerative disease and a testimony to nature's ability to get the best out of a protein fold.
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Affiliation(s)
- Thorbjørn Vincent Sønderby
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark; (T.V.S.); (Z.N.)
- Sino-Danish Center (SDC), Eastern Yanqihu Campus, University of Chinese Academy of Sciences, 380 Huaibeizhuang, Huairou District, Beijing 101400, China
| | - Zahra Najarzadeh
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark; (T.V.S.); (Z.N.)
| | - Daniel Erik Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark; (T.V.S.); (Z.N.)
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2
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Catalini S, Rossi B, Tortora M, Foggi P, Gessini A, Masciovecchio C, Bruni F. Hydrogen Bonding and Solvation of a Proline-Based Peptide Model in Salt Solutions. Life (Basel) 2021; 11:824. [PMID: 34440568 PMCID: PMC8400059 DOI: 10.3390/life11080824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/07/2021] [Accepted: 08/09/2021] [Indexed: 12/24/2022] Open
Abstract
The hydrogen bonding of water and water/salt mixtures around the proline-based tripeptide model glycyl-l-prolyl-glycinamide·HCl (GPG-NH2) is investigated here by multi-wavelength UV resonance Raman spectroscopy (UVRR) to clarify the role of ion-peptide interactions in affecting the conformational stability of this peptide. The unique sensitivity and selectivity of the UVRR technique allow us to efficiently probe the hydrogen bond interaction between water molecules and proline residues in different solvation conditions, along with its influence on trans to cis isomerism in the hydrated tripeptide. The spectroscopic data suggest a relevant role played by the cations in altering the solvation shell at the carbonyl site of proline., while the fluoride and chloride anions were found to promote the establishment of the strongest interactions on the C=O site of proline. This latter effect is reflected in the greater stabilization of the trans conformers of the tripeptide in the presence of these specific ions. The molecular view provided by UVRR experiments was complemented by the results of circular dichroism (CD) measurements that show a strong structural stabilizing effect on the β-turn motif of GPG-NH2 observed in the presence of KF as a co-solute.
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Affiliation(s)
- Sara Catalini
- European Laboratory for Non-Linear Spectroscopy, LENS, Via Nello Carrara, 1, 50019 Sesto Fiorentino, Italy; (S.C.); (P.F.)
| | - Barbara Rossi
- Elettra-Sincrotrone Trieste, S.S. 114 km 163.5, Basovizza, 34149 Trieste, Italy; (M.T.); (A.G.); (C.M.)
| | - Mariagrazia Tortora
- Elettra-Sincrotrone Trieste, S.S. 114 km 163.5, Basovizza, 34149 Trieste, Italy; (M.T.); (A.G.); (C.M.)
- Area Science Park, Padriciano, 99, 34149 Trieste, Italy
| | - Paolo Foggi
- European Laboratory for Non-Linear Spectroscopy, LENS, Via Nello Carrara, 1, 50019 Sesto Fiorentino, Italy; (S.C.); (P.F.)
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto, 8, 06123 Perugia, Italy
| | - Alessandro Gessini
- Elettra-Sincrotrone Trieste, S.S. 114 km 163.5, Basovizza, 34149 Trieste, Italy; (M.T.); (A.G.); (C.M.)
| | - Claudio Masciovecchio
- Elettra-Sincrotrone Trieste, S.S. 114 km 163.5, Basovizza, 34149 Trieste, Italy; (M.T.); (A.G.); (C.M.)
| | - Fabio Bruni
- Dipartimento di Scienze, Università degli Studi Roma Tre, Via della Vasca Navale, 84, 00146 Roma, Italy;
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3
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Walther R, Monge P, Pedersen AB, Benderoth A, Pedersen JN, Farzadfard A, Mandrup OA, Howard KA, Otzen DE, Zelikin AN. Per-glycosylation of the Surface-Accessible Lysines: One-Pot Aqueous Route to Stabilized Proteins with Native Activity. Chembiochem 2021; 22:2478-2485. [PMID: 33998129 DOI: 10.1002/cbic.202100228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Indexed: 11/11/2022]
Abstract
Chemical glycosylation of proteins is a powerful tool applied widely in biomedicine and biotechnology. However, it is a challenging undertaking and typically relies on recombinant proteins and site-specific conjugations. The scope and utility of this nature-inspired methodology would be broadened tremendously by the advent of facile, scalable techniques in glycosylation, which are currently missing. In this work, we investigated a one-pot aqueous protocol to achieve indiscriminate, surface-wide glycosylation of the surface accessible amines (lysines and/or N-terminus). We reveal that this approach afforded minimal if any change in the protein activity and recognition events in biochemical and cell culture assays, but at the same time provided a significant benefit of stabilizing proteins against aggregation and fibrillation - as demonstrated on serum proteins (albumins and immunoglobulin G, IgG), an enzyme (uricase), and proteins involved in neurodegenerative disease (α-synuclein) and diabetes (insulin). Most importantly, this highly advantageous result was achieved via a one-pot aqueous protocol performed on native proteins, bypassing the use of complex chemical methodologies and recombinant proteins.
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Affiliation(s)
- Raoul Walther
- Department of Chemistry, Aarhus University, Aarhus, 8000, Denmark
| | - Pere Monge
- Department of Chemistry, Aarhus University, Aarhus, 8000, Denmark
| | | | - Anja Benderoth
- Department of Chemistry, Aarhus University, Aarhus, 8000, Denmark
| | | | - Azad Farzadfard
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, 8000, Denmark
| | - Ole A Mandrup
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, 8000, Denmark
| | - Kenneth A Howard
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, 8000, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, 8000, Denmark
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, 8000, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, 8000, Denmark
| | - Alexander N Zelikin
- Department of Chemistry, Aarhus University, Aarhus, 8000, Denmark
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, 8000, Denmark
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4
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Krainer G, Hartmann A, Bogatyr V, Nielsen J, Schlierf M, Otzen DE. SDS-induced multi-stage unfolding of a small globular protein through different denatured states revealed by single-molecule fluorescence. Chem Sci 2020; 11:9141-9153. [PMID: 34123163 PMCID: PMC8163379 DOI: 10.1039/d0sc02100h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 08/07/2020] [Indexed: 12/03/2022] Open
Abstract
Ionic surfactants such as sodium dodecyl sulfate (SDS) unfold proteins in a much more diverse yet effective way than chemical denaturants such as guanidium chloride (GdmCl). But how these unfolding processes compare on a molecular level is poorly understood. Here, we address this question by scrutinising the unfolding pathway of the globular protein S6 in SDS and GdmCl with single-molecule Förster resonance energy transfer (smFRET) spectroscopy. We show that the unfolding mechanism in SDS is strikingly different and convoluted in comparison to denaturation in GdmCl. In contrast to the reversible two-state unfolding behaviour in GdmCl characterised by kinetics on the timescale of seconds, SDS demonstrated not one, but four distinct regimes of interactions with S6, dependent on the surfactant concentration. At ≤1 mM SDS, S6 and surfactant molecules form quasi-micelles on a minute timescale; at millimolar [SDS], the protein denatures through an unfolded/denatured ensemble of highly heterogeneous states on a multi-second timescale; at tens of millimolar of SDS, the protein unfolds into a micelle-packed conformation on the second timescale; and >50 mM SDS, the protein unfolds with millisecond timescale dynamics. We propose a detailed model for multi-stage unfolding of S6 in SDS, which involves at least three different types of denatured states with different level of compactness and dynamics and a continually changing landscape of interactions between protein and surfactant. Our results highlight the great potential of single-molecule fluorescence as a direct probe of nanoscale protein structure and dynamics in chemically complex surfactant environments.
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Affiliation(s)
- Georg Krainer
- B CUBE - Center for Molecular Bioengineering, TU Dresden Tatzberg 41 01307 Dresden Germany
| | - Andreas Hartmann
- B CUBE - Center for Molecular Bioengineering, TU Dresden Tatzberg 41 01307 Dresden Germany
| | - Vadim Bogatyr
- B CUBE - Center for Molecular Bioengineering, TU Dresden Tatzberg 41 01307 Dresden Germany
| | - Janni Nielsen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University Gustav Wieds Vej 14 8000 Aarhus Denmark
| | - Michael Schlierf
- B CUBE - Center for Molecular Bioengineering, TU Dresden Tatzberg 41 01307 Dresden Germany
- Cluster of Excellence Physics of Life, TU Dresden 01062 Dresden Germany
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University Gustav Wieds Vej 14 8000 Aarhus Denmark
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5
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Hidden kinetic traps in multidomain folding highlight the presence of a misfolded but functionally competent intermediate. Proc Natl Acad Sci U S A 2020; 117:19963-19969. [PMID: 32747559 PMCID: PMC7443948 DOI: 10.1073/pnas.2004138117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Much of our current knowledge on protein folding is based on work focused on isolated domains. In this study, using a combination of NMR and kinetic experiments, we depict the folding pathway of a multidomain construct comprising two PDZ domains in tandem, belonging to the protein Whirlin. We demonstrate the presence of a misfolded intermediate that competes with productive folding. Interestingly, we show that, unexpectedly, this misfolded state retains the native-like functional ability to bind its physiological ligand, representing a clear example of a functionally competent misfolded state. On the basis of these results and a comparative analysis of the amino acidic sequences of Whirlin from different species, we propose a possible physiological role of the misfolded intermediate. Although more than 75% of the proteome is composed of multidomain proteins, current knowledge of protein folding is based primarily on studies of isolated domains. In this work, we describe the folding mechanism of a multidomain tandem construct comprising two distinct covalently bound PDZ domains belonging to a protein called Whirlin, a scaffolding protein of the hearing apparatus. In particular, via a synergy between NMR and kinetic experiments, we demonstrate the presence of a misfolded intermediate that competes with productive folding. In agreement with the view that tandem domain swapping is a potential source of transient misfolding, we demonstrate that such a kinetic trap retains native-like functional activity, as shown by the preserved ability to bind its physiological ligand. Thus, despite the general knowledge that protein misfolding is intimately associated with dysfunction and diseases, we provide a direct example of a functionally competent misfolded state. Remarkably, a bioinformatics analysis of the amino acidic sequence of Whirlin from different species suggests that the tendency to perform tandem domain swapping between PDZ1 and PDZ2 is highly conserved, as demonstrated by their unexpectedly high sequence identity. On the basis of these observations, we discuss on a possible physiological role of such misfolded intermediate.
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6
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Koopman MB, Rüdiger SG. Behind closed gates - chaperones and charged residues determine protein fate. EMBO J 2020; 39:e104939. [PMID: 32350912 DOI: 10.15252/embj.2020104939] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Charged residues flanking aggregation-prone regions play a role in protein folding and prevention of aggregation. In this issue of The EMBO Journal, Houben et al exploit the role of such charged gatekeepers in aggregation suppression and find that negative charges are more effective than positive ones. Strikingly, the prominent Hsp70 chaperone has a strong preference for the less effective, basic gate keepers. This implies co-adaptation of chaperone specificity and composition of protein sequences in evolution.
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Affiliation(s)
- Margreet B Koopman
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, The Netherlands.,Science for Life, Utrecht University, Utrecht, The Netherlands
| | - Stefan Gd Rüdiger
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, The Netherlands.,Science for Life, Utrecht University, Utrecht, The Netherlands
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7
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Clark PL, Plaxco KW, Sosnick TR. Water as a Good Solvent for Unfolded Proteins: Folding and Collapse are Fundamentally Different. J Mol Biol 2020; 432:2882-2889. [PMID: 32044346 DOI: 10.1016/j.jmb.2020.01.031] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 12/30/2022]
Abstract
The argument that the hydrophobic effect is the primary effect driving the folding of globular proteins is nearly universally accepted (including by the authors). But does this view also imply that water is a "poor" solvent for the unfolded states of these same proteins? Here we argue that the answer is "no," that is, folding to a well-packed, extensively hydrogen-bonded native structure differs fundamentally from the nonspecific chain collapse that defines a poor solvent. Thus, the observation that a protein folds in water does not necessitate that water is a poor solvent for its unfolded state. Indeed, chain-solvent interactions that are marginally more favorable than nonspecific intrachain interactions are beneficial to protein function because they destabilize deleterious misfolded conformations and inter-chain interactions.
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Affiliation(s)
- Patricia L Clark
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA.
| | - Kevin W Plaxco
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA.
| | - Tobin R Sosnick
- Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA.
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8
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Theoretical and computational advances in protein misfolding. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 118:1-31. [PMID: 31928722 DOI: 10.1016/bs.apcsb.2019.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Misfolded proteins escape the cellular quality control mechanism and fail to fold properly or remain correctly folded leading to a loss in their functional specificity. Thus misfolding of proteins cause a large number of very different diseases ranging from errors in metabolism to various types of complex neurodegenerative diseases. A theoretical and computational perspective of protein misfolding is presented with a special emphasis on its salient features, mechanism and consequences. These insights quantitatively analyze different determinants of misfolding, that may be applied to design disease specific molecular targets.
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9
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Xu Q, Hong H, Yu W, Jiang X, Yan X, Wu J. Sodium Chloride Suppresses the Bitterness of Protein Hydrolysates by Decreasing Hydrophobic Interactions. J Food Sci 2018; 84:86-91. [PMID: 30561810 DOI: 10.1111/1750-3841.14419] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/22/2018] [Accepted: 11/17/2018] [Indexed: 12/12/2022]
Abstract
The formation of bitter off-flavor is a long-existing issue during food protein hydrolysis. The aim of this study is to determine the mechanism of sodium chloride (NaCl) suppressing the bitterness of protein hydrolysates. In this study, the bitterness of egg white hydrolysate (EWH) and hen meat hydrolysate (HPH) was determined using an electronic tongue. The results showed that the bitterness intensity of quinine hydrochloride, EWH, and HPH was suppressed significantly by NaCl in a concentration-dependent manner (P < 0.05). The particle sizes, turbidity, zeta potentials, and surface hydrophobicity of EWH and HPH were also significantly decreased by NaCl at concentrations of 0.05, 0.1, 0.3, and 0.5 M (P < 0.05). These results indicated that adding NaCl at certain concentrations led to a salting-in effect, burying hydrophobic groups and decreasing the surface hydrophobicity of peptides, resulting in the decrease of bitterness. Using NaCl is an alternative, effective, and cheap strategy to suppress protein hydrolysate bitterness by decreasing hydrophobic interactions in food industry. PRACTICAL APPLICATION: NaCl can be used as an effective bitterness masker for food protein hydrolysates by decreasing hydrophobic interactions of peptides.
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Affiliation(s)
- Qingbiao Xu
- Coll. of Animal Sciences and Technology, Huazhong Agricultural Univ., Wuhan, 430070, China.,Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China.,Hubei Provincial Engineering Lab. for Pig Precision Feeding and Feed Safety Technology, Wuhan, 430070, China.,Dept. of Agricultural, Food and Nutritional Science, Univ. of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Hui Hong
- Dept. of Agricultural, Food and Nutritional Science, Univ. of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Wenlin Yu
- Dept. of Agricultural, Food and Nutritional Science, Univ. of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Xu Jiang
- Dept. of Agricultural, Food and Nutritional Science, Univ. of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Xianghua Yan
- Coll. of Animal Sciences and Technology, Huazhong Agricultural Univ., Wuhan, 430070, China.,Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China.,Hubei Provincial Engineering Lab. for Pig Precision Feeding and Feed Safety Technology, Wuhan, 430070, China
| | - Jianping Wu
- Dept. of Agricultural, Food and Nutritional Science, Univ. of Alberta, Edmonton, Alberta, T6G 2P5, Canada
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10
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Size and topology modulate the effects of frustration in protein folding. Proc Natl Acad Sci U S A 2018; 115:9234-9239. [PMID: 30150375 DOI: 10.1073/pnas.1801406115] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The presence of conflicting interactions, or frustration, determines how fast biomolecules can explore their configurational landscapes. Recent experiments have provided cases of systems with slow reconfiguration dynamics, perhaps arising from frustration. While it is well known that protein folding speed and mechanism are strongly affected by the protein native structure, it is still unknown how the response to frustration is modulated by the protein topology. We explore the effects of nonnative interactions in the reconfigurational and folding dynamics of proteins with different sizes and topologies. We find that structural correlations related to the folded state size and topology play an important role in determining the folding kinetics of proteins that otherwise have the same amount of nonnative interactions. In particular, we find that the reconfiguration dynamics of α-helical proteins are more susceptible to frustration than β-sheet proteins of the same size. Our results may explain recent experimental findings and suggest that attempts to measure the degree of frustration due to nonnative interactions might be more successful with α-helical proteins.
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11
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Liu Z, Thirumalai D. Denaturants Alter the Flux through Multiple Pathways in the Folding of PDZ Domain. J Phys Chem B 2018; 122:1408-1416. [PMID: 29303586 DOI: 10.1021/acs.jpcb.7b11408] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although we understand many aspects of how small proteins (number of residues less than about hundred) fold, it is a major challenge to quantitatively describe how large proteins self-assemble. To partially overcome this challenge, we performed simulations using the self-organized polymer model with side chains (SOP-SC) in guanidinium chloride (GdmCl), using the molecular transfer model (MTM), to describe the folding of the 110-residue PDZ3 domain. The simulations reproduce the folding thermodynamics accurately including the melting temperature (Tm), the stability of the folded state with respect to the unfolded state. We show that the calculated dependence of ln kobs (kobs is the relaxation rate) has the characteristic chevron shape. The slopes of the chevron plots are in good agreement with experiments. We show that PDZ3 folds by four major pathways populating two metastable intermediates, in accord with the kinetic partitioning mechanism. The structure of one of the intermediates, populated after polypeptide chain collapse, is structurally similar to an equilibrium intermediate. Surprisingly, the connectivities between the intermediates and hence, the fluxes through the pathways depend on the concentration of GdmCl. The results are used to predict possible outcomes for unfolding of PDZ domain subject to mechanical forces. Our study demonstrates that, irrespective of the size or topology, simulations based on MTM and SOP-SC offer a theoretical framework for describing the folding of proteins, mimicking precisely the conditions used in experiments.
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Affiliation(s)
- Zhenxing Liu
- Department of Physics, Beijing Normal University , Beijing 100875, China
| | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
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12
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Metola A, Bouchet AM, Alonso-Mariño M, Diercks T, Mäler L, Goñi FM, Viguera AR. Purification and characterization of the colicin A immunity protein in detergent micelles. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2181-2192. [PMID: 28803731 DOI: 10.1016/j.bbamem.2017.08.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 08/06/2017] [Accepted: 08/09/2017] [Indexed: 11/18/2022]
Abstract
The immunity proteins against pore-forming colicins represent a family of integral membrane proteins that reside in the inner membrane of producing cells. Cai, the colicin A immunity protein, was characterized here in detergent micelles by circular dichroism (CD), size exclusion chromatography, chemical cross-linking, nuclear magnetic resonance (NMR) spectroscopy, cysteine accessibility, and colicin A binding in detergent micelles. Bile-salt derivatives induced extensive protein polymerization that precluded further investigation. The physical characterization of detergent-solubilized protein indicates that phosphate-containing detergents are more efficient in extracting, solubilizing and maintaining Cai in a monomeric state. Yet, their capacity to ensure protein activity, reconstitution, helix packing, and high-quality NMR spectra was inferior to that of milder detergents. Solvent ionic strength and composition greatly modified the solubilizing capacity of milder detergents. Most importantly, binding to the colicin A pore-forming domain (pf-ColA) occurred almost exclusively in sugar-derived detergents. The relative performance of the different detergents in each experiment depends on their impact not only on Cai structure, solubility and oligomerization state, but also on other reaction components and technical aspects. Thus, proteoliposomes were best obtained from protein in LDAO micelles, possibly also due to indirect effects on the lipidic bilayer. The compatibility of a detergent with Cai/pf-ColA complex formation is influenced by its effect on the conformational landscape of each protein, where detergent-mediated pf-ColA denaturation could also lead to negative results. The NMR spectra were greatly affected by the solubility, monodispersity, fold and dynamics of the protein-detergent complexes, and none of those tested here provided NMR spectra of sufficient quality to allow for peak assignment. Cai function could be proven in alkyl glycosides and not in those detergents that afforded the best solubility, reconstitution efficiency or spectral quality indicating that these criteria cannot be taken as unambiguous proof of nativeness without the support of direct activity measurements.
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Affiliation(s)
- Ane Metola
- Instituto Biofisika (CSIC, UPV/EHU), Parque Científico de la UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Bizkaia, Spain
| | - Ana M Bouchet
- Instituto Biofisika (CSIC, UPV/EHU), Parque Científico de la UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Bizkaia, Spain
| | - Marian Alonso-Mariño
- Instituto Biofisika (CSIC, UPV/EHU), Parque Científico de la UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Bizkaia, Spain
| | - Tammo Diercks
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia Ed. 800, 48160 Derio, Spain
| | - Lena Mäler
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, The Arrhenius Laboratory, Stockholm University, 10691 Stockholm, Sweden
| | - Félix M Goñi
- Instituto Biofisika (CSIC, UPV/EHU), Parque Científico de la UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Bizkaia, Spain; Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa. Spain
| | - Ana R Viguera
- Instituto Biofisika (CSIC, UPV/EHU), Parque Científico de la UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Bizkaia, Spain.
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13
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Andersen KK, Vad B, Omer S, Otzen DE. Concatemers of Outer Membrane Protein A Take Detours in the Folding Landscape. Biochemistry 2016; 55:7123-7140. [PMID: 27973779 DOI: 10.1021/acs.biochem.6b01153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Outer membrane protein A (OmpA) is the most abundant protein in the outer membrane of Escherichia coli. The N-terminal domain forms an eight-stranded membrane-embedded β-barrel that is widely used as a model protein for in vitro folding into the membrane and into surfactant micelles. Under conditions that include a low surfactant concentration, OmpA can form stable higher-order structures by intermolecular association. Other β-barrel membrane proteins also associate to form noncovalently linked trimers in vivo. This inspired us to test how topological constraints imposed by intramolecular links between individual OmpA molecules affect this process. Here we report on the properties of concatemers consisting of two and three copies of the transmembrane part of OmpA. Both concatemers could be folded to a native state in surfactant micelles according to spectroscopy and electrophoretic band shifts. This native state had the same thermodynamic stability against chemical denaturation as the original OmpA. Above 1.5 M GdmCl, concatemerization increased both refolding and unfolding rates, which we attribute to entropic effects. However, below 1.5 M GdmCl, folding kinetics were 2-3 orders of magnitude slower and more complex, involving a greater degree of parallel folding steps and species that could be classified as off-pathway. Only OmpA2 could quantitatively be folded into vesicles (though to an extent lower than that of OmpA), while OmpA3 formed three species with different levels of folding. Thus, close spatial and sequential proximity of OmpA domains on the same polypeptide chain have a strong tendency to trap the protein in different misfolded states.
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Affiliation(s)
- Kell K Andersen
- iNANO and Department of Molecular Biology and Genetics, Aarhus University , Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Brian Vad
- iNANO and Department of Molecular Biology and Genetics, Aarhus University , Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Sahar Omer
- iNANO and Department of Molecular Biology and Genetics, Aarhus University , Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Daniel E Otzen
- iNANO and Department of Molecular Biology and Genetics, Aarhus University , Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
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14
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Wang H, Lang L, Logan DT, Danielsson J, Oliveberg M. Tricking a Protein To Swap Strands. J Am Chem Soc 2016; 138:15571-15579. [DOI: 10.1021/jacs.6b05151] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Huabing Wang
- Arrhenius
Laboratories of Natural Sciences, Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Lisa Lang
- Arrhenius
Laboratories of Natural Sciences, Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Derek T. Logan
- Division
of Biochemistry and Structural Biology, Department of Chemistry, Lund University, Box
124, 221 00 Lund, Sweden
| | - Jens Danielsson
- Arrhenius
Laboratories of Natural Sciences, Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Mikael Oliveberg
- Arrhenius
Laboratories of Natural Sciences, Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
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15
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Bemporad F, Ramazzotti M. From the Evolution of Protein Sequences Able to Resist Self-Assembly to the Prediction of Aggregation Propensity. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 329:1-47. [PMID: 28109326 DOI: 10.1016/bs.ircmb.2016.08.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Folding of polypeptide chains into biologically active entities is an astonishingly complex process, determined by the nature and the sequence of residues emerging from ribosomes. While it has been long believed that evolution has pressed genomes so that specific sequences could adopt unique, functional three-dimensional folds, it is now clear that complex protein machineries act as quality control system and supervise folding. Notwithstanding that, events such as erroneous folding, partial folding, or misfolding are frequent during the life of a cell or a whole organism, and they can escape controls. One of the possible outcomes of this misbehavior is cross-β aggregation, a super secondary structure which represents the hallmark of self-assembled, well organized, and extremely ordered structures termed amyloid fibrils. What if evolution would have not taken into account such possibilities? Twenty years of research point toward the idea that, in fact, evolution has constantly supervised the risk of errors and minimized their impact. In this review we tried to survey the major findings in the amyloid field, trying to describe what the real pitfalls of protein folding are-from an evolutionary perspective-and how sequence and structural features have evolved to balance the need for perfect, dynamic, functionally efficient structures, and the detrimental effects implicit in the dangerous process of folding. We will discuss how the knowledge obtained from these studies has been employed to produce computational methods able to assess, predict, and discriminate the aggregation properties of protein sequences.
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Affiliation(s)
- F Bemporad
- Università degli Studi di Firenze, Firenze, Italy.
| | - M Ramazzotti
- Università degli Studi di Firenze, Firenze, Italy.
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16
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Kurland CG, Harish A. The phylogenomics of protein structures: The backstory. Biochimie 2015; 119:284-302. [DOI: 10.1016/j.biochi.2015.07.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 07/28/2015] [Indexed: 12/11/2022]
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17
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Hutton RD, Wilkinson J, Faccin M, Sivertsson EM, Pelizzola A, Lowe AR, Bruscolini P, Itzhaki LS. Mapping the Topography of a Protein Energy Landscape. J Am Chem Soc 2015; 137:14610-25. [PMID: 26561984 DOI: 10.1021/jacs.5b07370] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein energy landscapes are highly complex, yet the vast majority of states within them tend to be invisible to experimentalists. Here, using site-directed mutagenesis and exploiting the simplicity of tandem-repeat protein structures, we delineate a network of these states and the routes between them. We show that our target, gankyrin, a 226-residue 7-ankyrin-repeat protein, can access two alternative (un)folding pathways. We resolve intermediates as well as transition states, constituting a comprehensive series of snapshots that map early and late stages of the two pathways and show both to be polarized such that the repeat array progressively unravels from one end of the molecule or the other. Strikingly, we find that the protein folds via one pathway but unfolds via a different one. The origins of this behavior can be rationalized using the numerical results of a simple statistical mechanics model that allows us to visualize the equilibrium behavior as well as single-molecule folding/unfolding trajectories, thereby filling in the gaps that are not accessible to direct experimental observation. Our study highlights the complexity of repeat-protein folding arising from their symmetrical structures; at the same time, however, this structural simplicity enables us to dissect the complexity and thereby map the precise topography of the energy landscape in full breadth and remarkable detail. That we can recapitulate the key features of the folding mechanism by computational analysis of the native structure alone will help toward the ultimate goal of designed amino-acid sequences with made-to-measure folding mechanisms-the Holy Grail of protein folding.
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Affiliation(s)
- Richard D Hutton
- Hutchison/MRC Research Centre , Hills Road, Cambridge CB2 0XZ, U.K
| | - James Wilkinson
- Hutchison/MRC Research Centre , Hills Road, Cambridge CB2 0XZ, U.K
| | - Mauro Faccin
- ICTEAM, Université Catholique de Lovain , Euler Building 4, Avenue Lemaître, B-1348 Louvain-la-Neuve, Belgium
| | - Elin M Sivertsson
- Department of Pharmacology, University of Cambridge , Tennis Court Road, Cambridge CB2 1PD, U.K
| | - Alessandro Pelizzola
- Dipartimento di Scienza Applicata e Tecnologia, CNISM, and Center for Computational Studies, Politecnico di Torino , Corso Duca degli Abruzzi 24, I-10129 Torino, Italy.,INFN, Sezione di Torino , via Pietro Giuria 1, I-10125 Torino, Italy.,Human Genetics Foundation (HuGeF) , Via Nizza 52, I-10126 Torino, Italy
| | - Alan R Lowe
- Institute of Structural and Molecular Biology and London Centre for Nanotechnology, University College London and Birkbeck College , London WC1E 7HX, U.K
| | - Pierpaolo Bruscolini
- Departamento de Física Teórica and Instituto de Biocomputacíon y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza , c/Mariano Esquillor s/n, 50018 Zaragoza, Spain
| | - Laura S Itzhaki
- Department of Pharmacology, University of Cambridge , Tennis Court Road, Cambridge CB2 1PD, U.K
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18
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Estrela N, Franquelim HG, Lopes C, Tavares E, Macedo JA, Christiansen G, Otzen DE, Melo EP. Sucrose prevents protein fibrillation through compaction of the tertiary structure but hardly affects the secondary structure. Proteins 2015; 83:2039-51. [DOI: 10.1002/prot.24921] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 08/14/2015] [Accepted: 08/28/2015] [Indexed: 01/30/2023]
Affiliation(s)
- Nídia Estrela
- Centre for Biomedical Research (CBMR); University of Algarve, Campus of Gambelas; Faro 8005-139 Portugal
| | - Henri G. Franquelim
- Instituto De Medicina Molecular; Faculdade De Medicina Da Universidade De Lisboa; Av. Prof. Egas Moniz, Edifício Egas Moniz Lisboa 1649-028 Portugal
| | - Carlos Lopes
- Centre for Biomedical Research (CBMR); University of Algarve, Campus of Gambelas; Faro 8005-139 Portugal
| | - Evandro Tavares
- Centre for Biomedical Research (CBMR); University of Algarve, Campus of Gambelas; Faro 8005-139 Portugal
| | - Joana A. Macedo
- Centre for Biomedical Research (CBMR); University of Algarve, Campus of Gambelas; Faro 8005-139 Portugal
| | | | - Daniel E. Otzen
- Department of Molecular Biology and Genetics; Aarhus University, iNANO (Interdisciplinary Nanoscience Centre); Gustav Wieds Vej 14 Aarhus C 8000 Denmark
| | - Eduardo P. Melo
- Centre for Biomedical Research (CBMR); University of Algarve, Campus of Gambelas; Faro 8005-139 Portugal
- Instituto Superior Técnico, Centro De Química Estrutural; Av. Rovisco Pais Lisboa 1049-001 Portugal
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19
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Tsai MY, Zheng W, Balamurugan D, Schafer NP, Kim BL, Cheung MS, Wolynes PG. Electrostatics, structure prediction, and the energy landscapes for protein folding and binding. Protein Sci 2015; 25:255-69. [PMID: 26183799 DOI: 10.1002/pro.2751] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 07/14/2015] [Indexed: 11/09/2022]
Abstract
While being long in range and therefore weakly specific, electrostatic interactions are able to modulate the stability and folding landscapes of some proteins. The relevance of electrostatic forces for steering the docking of proteins to each other is widely acknowledged, however, the role of electrostatics in establishing specifically funneled landscapes and their relevance for protein structure prediction are still not clear. By introducing Debye-Hückel potentials that mimic long-range electrostatic forces into the Associative memory, Water mediated, Structure, and Energy Model (AWSEM), a transferable protein model capable of predicting tertiary structures, we assess the effects of electrostatics on the landscapes of thirteen monomeric proteins and four dimers. For the monomers, we find that adding electrostatic interactions does not improve structure prediction. Simulations of ribosomal protein S6 show, however, that folding stability depends monotonically on electrostatic strength. The trend in predicted melting temperatures of the S6 variants agrees with experimental observations. Electrostatic effects can play a range of roles in binding. The binding of the protein complex KIX-pKID is largely assisted by electrostatic interactions, which provide direct charge-charge stabilization of the native state and contribute to the funneling of the binding landscape. In contrast, for several other proteins, including the DNA-binding protein FIS, electrostatics causes frustration in the DNA-binding region, which favors its binding with DNA but not with its protein partner. This study highlights the importance of long-range electrostatics in functional responses to problems where proteins interact with their charged partners, such as DNA, RNA, as well as membranes.
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Affiliation(s)
- Min-Yeh Tsai
- Department of Chemistry, Rice University, Houston, Texas, 77005.,Center for Theoretical Biological Physics, Rice University, Houston, Texas, 77005.,Department of Physics, University of Houston, Houston, Texas, 77204
| | - Weihua Zheng
- Department of Chemistry, Rice University, Houston, Texas, 77005.,Center for Theoretical Biological Physics, Rice University, Houston, Texas, 77005
| | - D Balamurugan
- Computation Institute, University of Chicago, Chicago, Illinois, 60637
| | - Nicholas P Schafer
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus C, Denmark
| | - Bobby L Kim
- Department of Chemistry, Rice University, Houston, Texas, 77005.,Center for Theoretical Biological Physics, Rice University, Houston, Texas, 77005
| | - Margaret S Cheung
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, 77005.,Department of Physics, University of Houston, Houston, Texas, 77204
| | - Peter G Wolynes
- Department of Chemistry, Rice University, Houston, Texas, 77005.,Center for Theoretical Biological Physics, Rice University, Houston, Texas, 77005.,Physics and Astronomy, Rice University, Houston, Texas, 77005
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20
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Chekmarev SF. Protein folding as a complex reaction: a two-component potential for the driving force of folding and its variation with folding scenario. PLoS One 2015; 10:e0121640. [PMID: 25848943 PMCID: PMC4388825 DOI: 10.1371/journal.pone.0121640] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 02/11/2015] [Indexed: 11/19/2022] Open
Abstract
The Helmholtz decomposition of the vector field of probability fluxes in a two-dimensional space of collective variables makes it possible to introduce a potential for the driving force of protein folding [Chekmarev, J. Chem. Phys. 139 (2013) 145103]. The potential has two components: one component (Φ) is responsible for the source and sink of the folding flow, which represent, respectively, the unfolded and native state of the protein, and the other (Ψ) accounts for the flow vorticity inherently generated at the periphery of the flow field and provides the canalization of the flow between the source and sink. Both components obey Poisson’s equations with the corresponding source/sink terms. In the present paper, we consider how the shape of the potential changes depending on the scenario of protein folding. To mimic protein folding dynamics projected onto a two-dimensional space of collective variables, the two-dimensional Müller and Brown potential is employed. Three characteristic scenarios are considered: a single pathway from the unfolded to the native state without intermediates, two parallel pathways without intermediates, and a single pathway with an off-pathway intermediate. To determine the probability fluxes, the hydrodynamic description of the folding reaction is used, in which the first-passage folding is viewed as a steady flow of the representative points of the protein from the unfolded to the native state. We show that despite the possible complexity of the folding process, the Φ-component is simple and universal in shape. The Ψ-component is more complex and reveals characteristic features of the process of folding. The present approach is potentially applicable to other complex reactions, for which the transition from the reactant to the product can be described in a space of two (collective) variables.
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Affiliation(s)
- Sergei F. Chekmarev
- Institute of Thermophysics, 630090 Novosibirsk, Russia and Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia
- * E-mail:
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21
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Folding energetics and oligomerization of polytopic α-helical transmembrane proteins. Arch Biochem Biophys 2014; 564:281-96. [DOI: 10.1016/j.abb.2014.07.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 06/26/2014] [Accepted: 07/14/2014] [Indexed: 01/06/2023]
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22
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Visualization of protein folding funnels in lattice models. PLoS One 2014; 9:e100861. [PMID: 25010343 PMCID: PMC4091862 DOI: 10.1371/journal.pone.0100861] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/31/2014] [Indexed: 11/19/2022] Open
Abstract
Protein folding occurs in a very high dimensional phase space with an exponentially large number of states, and according to the energy landscape theory it exhibits a topology resembling a funnel. In this statistical approach, the folding mechanism is unveiled by describing the local minima in an effective one-dimensional representation. Other approaches based on potential energy landscapes address the hierarchical structure of local energy minima through disconnectivity graphs. In this paper, we introduce a metric to describe the distance between any two conformations, which also allows us to go beyond the one-dimensional representation and visualize the folding funnel in 2D and 3D. In this way it is possible to assess the folding process in detail, e.g., by identifying the connectivity between conformations and establishing the paths to reach the native state, in addition to regions where trapping may occur. Unlike the disconnectivity maps method, which is based on the kinetic connections between states, our methodology is based on structural similarities inferred from the new metric. The method was developed in a 27-mer protein lattice model, folded into a 3×3×3 cube. Five sequences were studied and distinct funnels were generated in an analysis restricted to conformations from the transition-state to the native configuration. Consistent with the expected results from the energy landscape theory, folding routes can be visualized to probe different regions of the phase space, as well as determine the difficulty in folding of the distinct sequences. Changes in the landscape due to mutations were visualized, with the comparison between wild and mutated local minima in a single map, which serves to identify different trapping regions. The extension of this approach to more realistic models and its use in combination with other approaches are discussed.
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23
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Knowles TPJ, Vendruscolo M, Dobson CM. The amyloid state and its association with protein misfolding diseases. Nat Rev Mol Cell Biol 2014; 15:384-96. [PMID: 24854788 DOI: 10.1038/nrm3810] [Citation(s) in RCA: 1625] [Impact Index Per Article: 162.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The phenomenon of protein aggregation and amyloid formation has become the subject of rapidly increasing research activities across a wide range of scientific disciplines. Such activities have been stimulated by the association of amyloid deposition with a range of debilitating medical disorders, from Alzheimer's disease to type II diabetes, many of which are major threats to human health and welfare in the modern world. It has become clear, however, that the ability to form the amyloid state is more general than previously imagined, and that its study can provide unique insights into the nature of the functional forms of peptides and proteins, as well as understanding the means by which protein homeostasis can be maintained and protein metastasis avoided.
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Affiliation(s)
- Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Christopher M Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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24
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Exploring the Minimally Frustrated Energy Landscape of Unfolded ACBP. J Mol Biol 2014; 426:722-34. [DOI: 10.1016/j.jmb.2013.10.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 10/23/2013] [Accepted: 10/24/2013] [Indexed: 12/18/2022]
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25
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26
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Kaya H, Uzunoğlu Z, Chan HS. Spatial ranges of driving forces are a key determinant of protein folding cooperativity and rate diversity. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:044701. [PMID: 24229309 DOI: 10.1103/physreve.88.044701] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 08/21/2013] [Indexed: 06/02/2023]
Abstract
The physical basis of two-state-like folding transitions and the tremendous diversity in folding rates is elucidated by directly simulating the folding kinetics of 52 representative proteins. Relative to the results from a common modeling approach, the diversity of the simulated folding rates can be increased from ~10(2.1) to the experimental ~10(6.0) by a modest decrease in the spatial range of the attractive potential. The required theoretical range is consistent with desolvation physics and is notably much more permissive than that needed for two-state-like homopolymer collapse.
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Affiliation(s)
- Hüseyin Kaya
- Department of Biophysics, Faculty of Medicine, University of Gaziantep, 27310 Gaziantep, Turkey
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27
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Aghera N, Udgaonkar JB. The Utilization of Competing Unfolding Pathways of Monellin Is Dictated by Enthalpic Barriers. Biochemistry 2013; 52:5770-9. [DOI: 10.1021/bi400688w] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Nilesh Aghera
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bangalore 560065,
India
| | - Jayant B. Udgaonkar
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bangalore 560065,
India
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28
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Thermodynamic origins of protein folding, allostery, and capsid formation in the human hepatitis B virus core protein. Proc Natl Acad Sci U S A 2013; 110:E2782-91. [PMID: 23824290 DOI: 10.1073/pnas.1308846110] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
HBc, the capsid-forming "core protein" of human hepatitis B virus (HBV), is a multidomain, α-helical homodimer that aggressively forms human HBV capsids. Structural plasticity has been proposed to be important to the myriad functions HBc mediates during viral replication. Here, we report detailed thermodynamic analyses of the folding of the dimeric HBc protomer under conditions that prevented capsid formation. Central to our success was the use of ion mobility spectrometry-mass spectrometry and microscale thermophoresis, which allowed folding mechanisms to be characterized using just micrograms of protein. HBc folds in a three-state transition with a stable, dimeric, α-helical intermediate. Extensive protein engineering showed thermodynamic linkage between different structural domains. Unusual effects associated with mutating some residues suggest structural strain, arising from frustrated contacts, is present in the native dimer. We found evidence of structural gatekeepers that, when mutated, alleviated native strain and prevented (or significantly attenuated) capsid formation by tuning the population of alternative native conformations. This strain is likely an evolved feature that helps HBc access the different structures associated with its diverse essential functions. The subtle balance between native and strained contacts may provide the means to tune conformational properties of HBc by molecular interactions or mutations, thereby conferring allosteric regulation of structure and function. The ability to trap HBc conformers thermodynamically by mutation, and thereby ablate HBV capsid formation, provides proof of principle for designing antivirals that elicit similar effects.
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29
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Folding of outer membrane proteins. Arch Biochem Biophys 2013; 531:34-43. [DOI: 10.1016/j.abb.2012.10.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 10/11/2012] [Accepted: 10/19/2012] [Indexed: 11/18/2022]
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30
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Deva T, Lorenzen N, Vad BS, Petersen SV, Thørgersen I, Enghild JJ, Kristensen T, Otzen DE. Off-pathway aggregation can inhibit fibrillation at high protein concentrations. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:677-87. [PMID: 23313095 DOI: 10.1016/j.bbapap.2012.12.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2012] [Revised: 12/11/2012] [Accepted: 12/28/2012] [Indexed: 11/24/2022]
Abstract
Ribosomal protein S6 fibrillates readily at slightly elevated temperatures and acidic pH. We find that S6 fibrillation is retarded rather than favored when the protein concentration is increased above a threshold concentration of around 3.5mg/mL. We name this threshold concentration C(FR), the concentration at which fibrillation is retarded. Our data are consistent with a model in which this inhibition is due to the formation of an off-pathway oligomeric species with native-like secondary structure. The oligomeric species dominates at high protein concentrations but exists in dynamic equilibrium with the monomer so that seeding with fibrils can overrule oligomer formation and favors fibrillation under C(FR) conditions. Thus, fibrillation competes with formation of off-pathway oligomers, probably due to a monomeric conversion step that is required to commit the protein to the fibrillation pathway. The S6 oligomer is resistant to pepsin digestion. We also report that S6 forms different types of fibrils dependent on protein concentration. Our observations highlight the multitude of conformational states available to proteins under destabilizing conditions.
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Affiliation(s)
- Taru Deva
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, University of Aarhus, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.
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31
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Andersen KK, Wang H, Otzen DE. A Kinetic Analysis of the Folding and Unfolding of OmpA in Urea and Guanidinium Chloride: Single and Parallel Pathways. Biochemistry 2012; 51:8371-83. [DOI: 10.1021/bi300974y] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kell K. Andersen
- Interdisciplinary Nanoscience Centre (iNANO), Centre
for Insoluble Protein Structures (inSPIN), Department of Molecular
Biology and Genetics, University of Aarhus, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Huabing Wang
- Interdisciplinary Nanoscience Centre (iNANO), Centre
for Insoluble Protein Structures (inSPIN), Department of Molecular
Biology and Genetics, University of Aarhus, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Daniel E. Otzen
- Interdisciplinary Nanoscience Centre (iNANO), Centre
for Insoluble Protein Structures (inSPIN), Department of Molecular
Biology and Genetics, University of Aarhus, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
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32
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Ganguly D, Otieno S, Waddell B, Iconaru L, Kriwacki RW, Chen J. Electrostatically accelerated coupled binding and folding of intrinsically disordered proteins. J Mol Biol 2012; 422:674-684. [PMID: 22721951 DOI: 10.1016/j.jmb.2012.06.019] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 06/08/2012] [Accepted: 06/11/2012] [Indexed: 11/25/2022]
Abstract
Intrinsically disordered proteins (IDPs) are now recognized to be prevalent in biology, and many potential functional benefits have been discussed. However, the frequent requirement of peptide folding in specific interactions of IDPs could impose a kinetic bottleneck, which could be overcome only by efficient folding upon encounter. Intriguingly, existing kinetic data suggest that specific binding of IDPs is generally no slower than that of globular proteins. Here, we exploited the cell cycle regulator p27(Kip1) (p27) as a model system to understand how IDPs might achieve efficient folding upon encounter for facile recognition. Combining experiments and coarse-grained modeling, we demonstrate that long-range electrostatic interactions between enriched charges on p27 and near its binding site on cyclin A not only enhance the encounter rate (i.e., electrostatic steering) but also promote folding-competent topologies in the encounter complexes, allowing rapid subsequent formation of short-range native interactions en route to the specific complex. In contrast, nonspecific hydrophobic interactions, while hardly affecting the encounter rate, can significantly reduce the efficiency of folding upon encounter and lead to slower binding kinetics. Further analysis of charge distributions in a set of known IDP complexes reveals that, although IDP binding sites tend to be more hydrophobic compared to the rest of the target surface, their vicinities are frequently enriched with charges to complement those on IDPs. This observation suggests that electrostatically accelerated encounter and induced folding might represent a prevalent mechanism for promoting facile IDP recognition.
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Affiliation(s)
- Debabani Ganguly
- Department of Biochemistry, Kansas State University, Manhattan, KS 66506, USA
| | - Steve Otieno
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Brett Waddell
- The Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Luigi Iconaru
- Departments of Structural Biology and Developmental Neurobiology, St. Jude's Children's Research Hospital, Memphis, TN 38105, USA
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Jianhan Chen
- Department of Biochemistry, Kansas State University, Manhattan, KS 66506, USA.
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33
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Dasgupta A, Udgaonkar JB. Four-State Folding of a SH3 Domain: Salt-Induced Modulation of the Stabilities of the Intermediates and Native State. Biochemistry 2012; 51:4723-34. [DOI: 10.1021/bi300223b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amrita Dasgupta
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bangalore 560065,
India
| | - Jayant B. Udgaonkar
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bangalore 560065,
India
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34
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Morris ER, Searle MS. Overview of protein folding mechanisms: experimental and theoretical approaches to probing energy landscapes. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2012; Chapter 28:28.2.1-28.2.22. [PMID: 22470128 DOI: 10.1002/0471140864.ps2802s68] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We present an overview of the current experimental and theoretical approaches to studying protein folding mechanisms, set against current models of the folding energy landscape. We describe how stability and folding kinetics can be determined experimentally and how this data can be interpreted in terms of the characteristic features of various models from the simplest two-state pathway to a multi-state mechanism. We summarize the pros and cons of a range of spectroscopic methods for measuring folding rates and present a theoretical framework, coupled with protein engineering approaches, for elucidating folding mechanisms and structural features of folding transition states. A series of case studies are used to show how experimental kinetic data can be interpreted in the context of non-native interactions, populated intermediates, parallel folding pathways, and sequential transition states. We also show how computational methods now allow transient species of high energy, such as folding transition states, to be modeled on the basis of experimental Φ-value analysis derived from the effects of point mutations on folding kinetics.
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Affiliation(s)
- Elizabeth R Morris
- Centre for Biomolecular Sciences, School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Mark S Searle
- Centre for Biomolecular Sciences, School of Chemistry, University of Nottingham, Nottingham, United Kingdom
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35
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Abstract
Surface charges of proteins have in several cases been found to function as "structural gatekeepers," which avoid unwanted interactions by negative design, for example, in the control of protein aggregation and binding. The question is then if side-chain charges, due to their desolvation penalties, play a corresponding role in protein folding by avoiding competing, misfolded traps? To find out, we removed all 32 side-chain charges from the 101-residue protein S6 from Thermus thermophilus. The results show that the charge-depleted S6 variant not only retains its native structure and cooperative folding transition, but folds also faster than the wild-type protein. In addition, charge removal unleashes pronounced aggregation on longer timescales. S6 provides thus an example where the bias toward native contacts of a naturally evolved protein sequence is independent of charges, and point at a fundamental difference in the codes for folding and intermolecular interaction: specificity in folding is governed primarily by hydrophobic packing and hydrogen bonding, whereas solubility and binding relies critically on the interplay of side-chain charges.
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36
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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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37
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Ji M, Hartsock RW, Sun Z, Gaffney KJ. Interdependence of Conformational and Chemical Reaction Dynamics during Ion Assembly in Polar Solvents. J Phys Chem B 2011; 115:11399-408. [DOI: 10.1021/jp205660q] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Minbiao Ji
- PULSE Institute, SLAC National Accelerator Laboratory, ‡Department of Physics, and §Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Robert W. Hartsock
- PULSE Institute, SLAC National Accelerator Laboratory, ‡Department of Physics, and §Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Zheng Sun
- PULSE Institute, SLAC National Accelerator Laboratory, ‡Department of Physics, and §Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Kelly J. Gaffney
- PULSE Institute, SLAC National Accelerator Laboratory, ‡Department of Physics, and §Department of Chemistry, Stanford University, Stanford, California 94305, United States
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Sakurai K, Fujioka S, Konuma T, Yagi M, Goto Y. A circumventing role for the non-native intermediate in the folding of β-lactoglobulin. Biochemistry 2011; 50:6498-507. [PMID: 21678970 DOI: 10.1021/bi200241a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Folding experiments have suggested that some proteins have kinetic intermediates with a non-native structure. A simple G ̅o model does not explain such non-native intermediates. Therefore, the folding energy landscape of proteins with non-native intermediates should have characteristic properties. To identify such properties, we investigated the folding of bovine β-lactoglobulin (βLG). This protein has an intermediate with a non-native α-helical structure, although its native form is predominantly composed of β-structure. In this study, we prepared mutants whose α-helical and β-sheet propensities are modified and observed their folding using a stopped-flow circular dichroism apparatus. One interesting finding was that E44L, whose β-sheet propensity was increased, showed a folding intermediate with an amount of β-structure similar to that of the wild type, though its folding took longer. Thus, the intermediate seems to be a trapped intermediate. The high α-helical propensity of the wild-type sequence likely causes the folding pathway to circumvent such time-consuming intermediates. We propose that the role of the non-native intermediate is to control the pathway at the beginning of the folding reaction.
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Affiliation(s)
- Kazumasa Sakurai
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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39
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Abstract
Evidence is growing at an increasing -pace that amyloid fibers are not just the result of aberrant protein folding associated with neurodegenerative diseases, but are widespread in nature for beneficial reasons. Amyloid is an attractive building material because its robust design and simple repetitive structure make for very durable and metabolically cheap material. But this requires that the production of amyloid be put under firm control. This appears to involve the use of four to five chaperones that are expressed under the control of the same promoter as the amyloid proteins. Significant progress has been made in deciphering this process in E. coli's csg operon, also found in Salmonella. Recently, we have discovered a new and unrelated operon (fap) responsible for amyloid production in Pseudomonas, which also confers biofilm-forming properties to E. coli. Intriguingly, this operon shares a number of features with csg, namely two homologous proteins (one of which, FapC, has been shown to be directly involved in amyloid build-up) and a small number of auxiliary proteins. However, FapC seems to be less economically structured than its E. coli counterpart, with a smaller number of repeats and very large and variable linker regions. Furthermore, the putative chaperones are not homologous to their csg counterparts and have intriguing homologies to proteins with other functions. These findings suggest that controlled amyloid production has arisen on many independent occasions due to the usefulness of the product and offers the potential for intriguing insights into how nature disarms and reconstructs a potentially very dangerous weapon.
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Affiliation(s)
- Daniel Otzen
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology, Aarhus University, Aarhus, Denmark.
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40
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Bayro MJ, Maly T, Birkett NR, MacPhee CE, Dobson CM, Griffin RG. High-resolution MAS NMR analysis of PI3-SH3 amyloid fibrils: backbone conformation and implications for protofilament assembly and structure . Biochemistry 2010; 49:7474-84. [PMID: 20707313 PMCID: PMC2932965 DOI: 10.1021/bi100864t] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The SH3 domain of the PI3 kinase (PI3-SH3 or PI3K-SH3) readily aggregates into fibrils in vitro and has served as an important model system in the investigation of the molecular properties and mechanism of formation of amyloid fibrils. We describe the molecular conformation of PI3-SH3 in amyloid fibril form as revealed by magic-angle spinning (MAS) solid-state nuclear magnetic resonance (NMR) spectroscopy. The MAS NMR spectra of these fibrils display excellent resolution, with narrow (13)C and (15)N line widths, representing a high degree of structural order and the absence of extensive molecular motion for the majority of the polypeptide chain. We have identified the spin systems of 82 of the 86 residues in the protein and obtained sequential resonance assignments for 75 of them. Chemical shift analysis indicates that the protein subunits making up the fibril adopt a compact conformation consisting of four well-defined beta-sheet regions and four random-coil elements with varying degrees of local dynamics or disorder. The backbone conformation of PI3-SH3 in fibril form differs significantly from that of the native state of the protein, both in secondary structure and in the location of dynamic or disordered segments. The site-specific MAS NMR analysis of PI3-SH3 fibrils we report here is compared with previously published mechanistic and structural data, resulting in a detailed interpretation of the factors that mediate fibril formation by PI3-SH3 and allowing us to propose a possible model of the core structure of the fibrils. Our results confirm the structural similarities between PI3-SH3 fibrils and amyloid assemblies directly related to degenerative and infectious diseases.
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Affiliation(s)
- Marvin J. Bayro
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Thorsten Maly
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Neil R. Birkett
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Cait E. MacPhee
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH9 3JZ, UK
| | - Christopher M. Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Robert G. Griffin
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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41
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Mutational studies uncover non-native structure in the dimeric kinetic intermediate of the H2A-H2B heterodimer. J Mol Biol 2010; 401:518-31. [PMID: 20600120 DOI: 10.1016/j.jmb.2010.06.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2010] [Revised: 06/15/2010] [Accepted: 06/16/2010] [Indexed: 11/21/2022]
Abstract
The folding pathway of the histone H2A-H2B heterodimer minimally includes an on-pathway, dimeric, burst-phase intermediate, I(2). The partially folded H2A and H2B monomers populated at equilibrium were characterized as potential monomeric kinetic intermediates. Folding kinetics were compared for initiation from isolated, folded monomers and the heterodimer unfolded in 4 M urea. The observed rates were virtually identical above 0.4 M urea, exhibiting a log-linear relationship on the final denaturant concentration. Below approximately 0.4 M urea (concentrations inaccessible from the 4-M urea unfolded state), a rollover in the rates was observed; this suggests that a component of the I(2) ensemble contains non-native structure that rearranges/isomerizes to a more native-like species. The contribution of helix propensity to the stability of the I(2) ensemble was assessed with a set of H2A-H2B mutants containing Ala and Gly replacements at nine sites, focusing mainly on the long, central alpha2 helix. Equilibrium and kinetic folding/unfolding data were collected to determine the effects of the mutations on the stability of I(2) and the transition state between I(2) and N(2). This limited mutational study indicated that residues in the alpha2 helices of H2A and H2B as well as alpha1 of H2B and both the C-terminus of alpha3 and the short alphaC helix of H2A contribute to the stability of the I(2) burst-phase species. Interestingly, at least eight of the nine targeted residues stabilize I(2) by interactions that are non-native to some extent. Given that destabilizing I(2) and these non-native interactions does not accelerate folding, it is concluded that the native and non-native structures present in the I(2) ensemble enable efficient folding of H2A-H2B.
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42
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Hills RD, Kathuria SV, Wallace LA, Day IJ, Brooks CL, Matthews CR. Topological frustration in beta alpha-repeat proteins: sequence diversity modulates the conserved folding mechanisms of alpha/beta/alpha sandwich proteins. J Mol Biol 2010; 398:332-50. [PMID: 20226790 DOI: 10.1016/j.jmb.2010.03.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 02/27/2010] [Accepted: 03/03/2010] [Indexed: 10/19/2022]
Abstract
The thermodynamic hypothesis of Anfinsen postulates that structures and stabilities of globular proteins are determined by their amino acid sequences. Chain topology, however, is known to influence the folding reaction, in that motifs with a preponderance of local interactions typically fold more rapidly than those with a larger fraction of nonlocal interactions. Together, the topology and sequence can modulate the energy landscape and influence the rate at which the protein folds to the native conformation. To explore the relationship of sequence and topology in the folding of beta alpha-repeat proteins, which are dominated by local interactions, we performed a combined experimental and simulation analysis on two members of the flavodoxin-like, alpha/beta/alpha sandwich fold. Spo0F and the N-terminal receiver domain of NtrC (NT-NtrC) have similar topologies but low sequence identity, enabling a test of the effects of sequence on folding. Experimental results demonstrated that both response-regulator proteins fold via parallel channels through highly structured submillisecond intermediates before accessing their cis prolyl peptide bond-containing native conformations. Global analysis of the experimental results preferentially places these intermediates off the productive folding pathway. Sequence-sensitive Gō-model simulations conclude that frustration in the folding in Spo0F, corresponding to the appearance of the off-pathway intermediate, reflects competition for intra-subdomain van der Waals contacts between its N- and C-terminal subdomains. The extent of transient, premature structure appears to correlate with the number of isoleucine, leucine, and valine (ILV) side chains that form a large sequence-local cluster involving the central beta-sheet and helices alpha2, alpha 3, and alpha 4. The failure to detect the off-pathway species in the simulations of NT-NtrC may reflect the reduced number of ILV side chains in its corresponding hydrophobic cluster. The location of the hydrophobic clusters in the structure may also be related to the differing functional properties of these response regulators. Comparison with the results of previous experimental and simulation analyses on the homologous CheY argues that prematurely folded unproductive intermediates are a common property of the beta alpha-repeat motif.
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Affiliation(s)
- Ronald D Hills
- Department of Molecular Biology and Kellogg School of Science and Technology, The Scripps Research Institute, 10550 North Torrey Pines Road TPC6, La Jolla, CA 92037, USA
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43
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Exploring the folding energy landscape of a series of designed consensus tetratricopeptide repeat proteins. Proc Natl Acad Sci U S A 2009; 106:17383-8. [PMID: 19805120 DOI: 10.1073/pnas.0907455106] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Repeat proteins contain short, tandem arrays of simple structural motifs (20-40 aa). These stack together to form nonglobular structures that are stabilized by short-range interactions from residues close in primary sequence. Unlike globular proteins, they have few, if any, long-range nonlocal stabilizing interactions. One ubiquitous repeat is the tetratricopeptide motif (TPR), a 34-aa helix-turn-helix motif. In this article we describe the folding kinetics of a series of 7 designed TPR proteins that are assembled from arraying identical designed consensus repeats (CTPRan). These range from the smallest 2-repeat protein to a large 10-repeat protein (approximately 350 aa). In particular, we describe how the energy landscape changes with the addition of repeat units. The data reveal that although the CTPRa proteins have low local frustration, their highly symmetric, modular native structure is reflected in their multistate kinetics of unfolding and folding. Moreover, although the initial folding of all CTPRan proteins involves a nucleus with similar solvent accessibility, their subsequent folding to the native structure depends directly on repeat number. This corresponds to an increasingly complex landscape that culminates in CTPRa10 populating a misfolded, off-pathway intermediate. These results extend our current understanding of the malleable folding pathways of repeat proteins and highlight the consequences of adding identical repeats to the energy landscape.
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44
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Lindner AB, Demarez A. Protein aggregation as a paradigm of aging. Biochim Biophys Acta Gen Subj 2009; 1790:980-96. [PMID: 19527771 DOI: 10.1016/j.bbagen.2009.06.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Revised: 06/08/2009] [Accepted: 06/09/2009] [Indexed: 12/23/2022]
Abstract
The process of physiological decline leading to death of the individual is driven by the deteriorating capacity to withstand extrinsic and intrinsic hazards, resulting in damage accumulation with age. The dynamic changes with time of the network governing the outcome of misfolded proteins, exemplifying as intrinsic hazards, is considered here as a paradigm of aging. The main features of the network, namely, the non-linear increase of damage and the presence of amplifying feedback loops within the system are presented through a survey of the different components of the network and related cellular processes in aging and disease.
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Affiliation(s)
- Ariel B Lindner
- INSERM U571, Paris Descartes University, Paris, F-75015, France.
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45
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Reumers J, Maurer-Stroh S, Schymkowitz J, Rousseau F. Protein sequences encode safeguards against aggregation. Hum Mutat 2009; 30:431-7. [PMID: 19156839 DOI: 10.1002/humu.20905] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Functional requirements shaped proteins into globular structures. Under these structural constraints, which require both regular secondary structure and a hydrophobic core, protein aggregation is an unavoidable corollary to protein structure. However, as aggregation results in reduced fitness, natural selection will tend to eliminate strongly aggregating sequences. The analysis of distribution and variation of aggregation patterns in the human proteome using the TANGO algorithm confirms the findings of a previous study on several proteomes: the flanks of aggregation-prone regions are enriched with charged residues and proline, the so-called gatekeeper-residues. Moreover, in this study, we observed a widespread redundancy in gatekeeper usage. Interestingly, aggregating regions from key proteins such as p53 or huntingtin are among the most extensive "gatekept" sequences. As a consequence, mutations that remove gatekeepers could therefore result in a strong increase in disease-susceptibility. In a set of disease-associated mutations from the UniProt database, we find a strong enrichment of mutations that disrupt gatekeeper motifs. Closer inspection of a number of case studies indicates clearly that removing gatekeepers may play a determining role in widely varying disorders, such as van der Woude syndrome (VWS), X-linked Fabry disease (FD), and limb-girdle muscular dystrophy.
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Affiliation(s)
- Joke Reumers
- Switch Laboratory, VIB, Vrije Universiteit Brussel, Brussels, Belgium
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46
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Buell AK, Tartaglia GG, Birkett NR, Waudby CA, Vendruscolo M, Salvatella X, Welland ME, Dobson CM, Knowles TPJ. Position-Dependent Electrostatic Protection against Protein Aggregation. Chembiochem 2009; 10:1309-12. [DOI: 10.1002/cbic.200900144] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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47
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Mouillon JM, Eriksson SK, Harryson P. Mimicking the plant cell interior under water stress by macromolecular crowding: disordered dehydrin proteins are highly resistant to structural collapse. PLANT PHYSIOLOGY 2008; 148:1925-37. [PMID: 18849483 PMCID: PMC2593683 DOI: 10.1104/pp.108.124099] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Accepted: 10/01/2008] [Indexed: 05/18/2023]
Abstract
The dehydrins are a class of drought-induced proteins in plants that lack a fixed three-dimensional structure. Their specific molecular action, as well as the reason for their disordered character, is as yet poorly understood. It has been speculated, however, that the dehydrins are tuned to acquire a biologically active structure only under the conditions in which they normally function (i.e. upon dehydration). To test this hypothesis, we here investigate the effect of reduced water content and macromolecular crowding on three dehydrins from Arabidopsis (Arabidopsis thaliana). As a simplistic model for mimicking cellular dehydration, we used polyethylene glycol, glycerol, and sugars that plants naturally employ as compatible solutes (i.e. sucrose and glucose). Macromolecular crowding was induced by the large polysaccharides Ficoll and dextran. The results show that the dehydrins are remarkably stable in their disordered state and are only modestly affected by the solvent alterations. A notable exception is the dehydrin Cor47, which shows a small, intrinsic increase in helical structure at high concentrations of osmolytes. We also examined the effect of phosphorylation but found no evidence that such posttranslational modifications of the dehydrin sequences modulate their structural response to osmolytes and crowding agents. These results suggest that the dehydrins are highly specialized proteins that have evolved to maintain their disordered character under conditions in which unfolded states of several globular proteins would tend to collapse.
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Affiliation(s)
- Jean-Marie Mouillon
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, S-901 87 Umeå, Sweden
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48
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Comparison of successive transition states for folding reveals alternative early folding pathways of two homologous proteins. Proc Natl Acad Sci U S A 2008; 105:19241-6. [PMID: 19033470 DOI: 10.1073/pnas.0804774105] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The energy landscape theory provides a general framework for describing protein folding reactions. Because a large number of studies, however, have focused on two-state proteins with single well-defined folding pathways and without detectable intermediates, the extent to which free energy landscapes are shaped up by the native topology at the early stages of the folding process has not been fully characterized experimentally. To this end, we have investigated the folding mechanisms of two homologous three-state proteins, PTP-BL PDZ2 and PSD-95 PDZ3, and compared the early and late transition states on their folding pathways. Through a combination of Phi value analysis and molecular dynamics simulations we obtained atomic-level structures of the transition states of these homologous three-state proteins and found that the late transition states are much more structurally similar than the early ones. Our findings thus reveal that, while the native state topology defines essentially in a unique way the late stages of folding, it leaves significant freedom to the early events, a result that reflects the funneling of the free energy landscape toward the native state.
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49
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Nordlund A, Oliveberg M. SOD1-associated ALS: a promising system for elucidating the origin of protein-misfolding disease. HFSP JOURNAL 2008; 2:354-64. [PMID: 19436494 DOI: 10.2976/1.2995726] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Indexed: 11/19/2022]
Abstract
Amyotropic lateral sclerosis (ALS) is a neurodegenerative disease linked to misfolding and aggregation of the homodimeric enzyme superoxide dismutase (SOD1). In contrast to the precursors of other neurodegenerative diseases, SOD1 is a soluble and simple-to-study protein with immunoglobulin-like structure. Also, there are more than 120 ALS-provoking SOD1 mutations at the disposal for detailed elucidation of the disease-triggering factors at molecular level. In this article, we review recent progress in the characterization of the folding and assembly pathway of the SOD1 dimer and how this is affected by ALS-provoking mutations. Despite the diverse nature of these mutations, the results offer so far a surprising simplicity. The ALS-provoking mutations decrease either protein stability or net repulsive charge: the classical hallmarks for a disease mechanism triggered by association of non-native protein. In addition, the mutant data identifies immature SOD1 monomers as the species from which the cytotoxic pathway emerges, and point at compromised folding cooperativity as a key disease determinant. The relative ease by which these data can be obtained makes SOD1 a promising model for elucidating also the origin of other neurodegenerative diseases where the precursor proteins are structurally more elusive.
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Affiliation(s)
- Anna Nordlund
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden
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50
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Abstract
Experimental studies show that many proteins fold along sequential pathways defined by folding intermediates. An intermediate may not always be a single population of molecules but may consist of subpopulations that differ in their average structure. These subpopulations are likely to fold via independent pathways. Parallel folding and unfolding pathways appear to arise because of structural heterogeneity. For some proteins, the folding pathways can effectively switch either because different subpopulations of an intermediate get populated under different folding conditions, or because intermediates on otherwise hidden pathways get stabilized, leading to their utilization becoming discernible, or because mutations stabilize different substructures. Therefore, the same protein may fold via different pathways in different folding conditions. Multiple folding pathways make folding robust, and evolution is likely to have selected for this robustness to ensure that a protein will fold under the varying conditions prevalent in different cellular contexts.
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Affiliation(s)
- Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India.
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