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Horváth G, Biczók L, Majer Z, Kovács M, Micsonai A, Kardos J, Toke O. Structural insight into a partially unfolded state preceding aggregation in an intracellular lipid-binding protein. FEBS J 2017; 284:3637-3661. [DOI: 10.1111/febs.14264] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 08/15/2017] [Accepted: 09/05/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Gergő Horváth
- Laboratory for NMR Spectroscopy; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest Hungary
| | - László Biczók
- Institute of Materials and Environmental Chemistry; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest Hungary
| | - Zsuzsa Majer
- Institute of Chemistry; Eötvös Loránd University; Budapest Hungary
| | - Mihály Kovács
- Department of Biochemistry; ELTE-MTA ‘Momentum’ Motor Enzymology Research Group; Eötvös Loránd University; Budapest Hungary
| | - András Micsonai
- Department of Biochemistry; MTA-ELTE NAP B Neuroimmunology Research Group; Institute of Biology; Eötvös Loránd University; Budapest Hungary
| | - József Kardos
- Department of Biochemistry; MTA-ELTE NAP B Neuroimmunology Research Group; Institute of Biology; Eötvös Loránd University; Budapest Hungary
| | - Orsolya Toke
- Laboratory for NMR Spectroscopy; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest Hungary
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Sugita M, Matsuoka M, Kikuchi T. Topological and sequence information predict that foldons organize a partially overlapped and hierarchical structure. Proteins 2015; 83:1900-13. [PMID: 26248725 DOI: 10.1002/prot.24874] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 06/23/2015] [Accepted: 07/29/2015] [Indexed: 11/09/2022]
Abstract
It has been suggested that proteins have substructures, called foldons, which can cooperatively fold into the native structure. However, several prior investigations define foldons in various ways, citing different foldon characteristics, thereby making the concept of a foldon ambiguous. In this study, we perform a Gō model simulation and analyze the characteristics of substructures that cooperatively fold into the native-like structure. Although some results do not agree well with the experimental evidence due to the simplicity of our coarse-grained model, our results strongly suggest that cooperatively folding units sometimes organize a partially overlapped and hierarchical structure. This view makes us easy to interpret some different proposal about the foldon as a difference of the hierarchical structure. On the basis of this finding, we present a new method to assign foldons and their hierarchy, using structural and sequence information. The results show that the foldons assigned by our method correspond to the intermediate structures identified by some experimental techniques. The new method makes it easy to predict whether a protein folds sequentially into the native structure or whether some foldons fold into the native structure in parallel.
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Affiliation(s)
- Masatake Sugita
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Masanari Matsuoka
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Takeshi Kikuchi
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
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4
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Vu DM, Brewer SH, Dyer RB. Early turn formation and chain collapse drive fast folding of the major cold shock protein CspA of Escherichia coli. Biochemistry 2012; 51:9104-11. [PMID: 23098216 DOI: 10.1021/bi301296y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The folding mechanism of the β-sheet protein CspA, the major cold shock protein of Escherichia coli, was previously reported to be a concerted, two-state process. We have reexamined the folding of CspA using multiple spectroscopic probes of the equilibrium transition and laser-induced temperature jump (T-jump) to achieve better time resolution of the kinetics. Equilibrium temperature-dependent Fourier transform infrared (1634 cm(-1)) and tryptophan fluorescence measurements reveal probe-dependent thermal transitions with midpoints (T(m)) of 66 ± 1 and 61 ± 1 °C, respectively. Singular-value decomposition analysis with global fitting of the temperature-dependent infrared (IR) difference spectra reveals two spectral components with distinct melting transitions with different midpoints. T-jump relaxation measurements of CspA probed by IR and fluorescence spectroscopy show probe-dependent multiexponential kinetics characteristic of non-two-state folding. The frequency-dependent IR transients all show biphasic relaxation with average time constants of 50 ± 7 and 225 ± 25 μs at a T(f) of 77 °C and almost equal amplitudes. Similar biphasic kinetics are observed using Trp fluorescence of the wild-type protein and the Y42W and T68W mutants, with comparable lifetimes. All of these observations support a model for the folding of CspA through a compact intermediate state. The transient IR and fluorescence spectra are consistent with a diffuse intermediate having β-turns and substantial β-sheet structure. The loop β3-β4 structure is likely not folded in the intermediate state, allowing substantial solvent penetration into the barrel structure.
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Affiliation(s)
- Dung M Vu
- Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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Bosch A, Bertran SP, Lu Y, Garcia A, Jones AM, Dawson MI, Farias EF. Reversal by RARα agonist Am580 of c-Myc-induced imbalance in RARα/RARγ expression during MMTV-Myc tumorigenesis. Breast Cancer Res 2012; 14:R121. [PMID: 22920668 PMCID: PMC3680916 DOI: 10.1186/bcr3247] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 07/13/2012] [Accepted: 08/03/2012] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION Retinoic acid signaling plays key roles in embryonic development and in maintaining the differentiated status of adult tissues. Recently, the nuclear retinoic acid receptor (RAR) isotypes α, β and γ were found to play specific functions in the expansion and differentiation of the stem compartments of various tissues. For instance, RARγ appears to be involved in stem cell compartment expansion, while RARα and RARβ are implicated in the subsequent cell differentiation. We found that over-expressing c-Myc in normal mouse mammary epithelium and in a c-Myc-driven transgenic model of mammary cancer, disrupts the balance between RARγ and RARα/β in favor of RARγ. METHODS The effects of c-Myc on RAR isotype expression were evaluated in normal mouse mammary epithelium, mammary tumor cells obtained from the MMTV-Myc transgenic mouse model as well as human normal immortalized breast epithelial and breast cancer cell lines. The in vivo effect of the RARα-selective agonist 4-[(5,6,7,8-tetrahydro-5,5,8,8-tetramethyl-2-naphthyl)carboxamido]benzoic acid (Am580) was examined in the MMTV-Myc mouse model of mammary tumorigenesis. RESULTS Modulation of the RARα/β to RARγ expression in mammary glands of normal mice, oncomice, and human mammary cell lines through the alteration of RAR-target gene expression affected cell proliferation, survival and tumor growth. Treatment of MMTV-Myc mice with the RARα-selective agonist Am580 led to significant inhibition of mammary tumor growth (~90%, P<0.001), lung metastasis (P<0.01) and extended tumor latency in 63% of mice. Immunocytochemical analysis showed that in these mice, RARα responsive genes such as Cyp26A1, E-cadherin, cellular retinol-binding protein 1 (CRBP1) and p27, were up-regulated. In contrast, the mammary gland tumors of mice that responded poorly to Am580 treatment (37%) expressed significantly higher levels of RARγ. In vitro experiments indicated that the rise in RARγ was functionally linked to promotion of tumor growth and inhibition of differentiation. Thus, activation of the RARα pathway is linked to tumor growth inhibition, differentiation and cell death. CONCLUSIONS The functional consequence of the interplay between c-Myc oncogene expression and the RARγ to RARα/β balance suggests that prevalence of RARγ over-RARα/β expression levels in breast cancer accompanied by c-Myc amplification or over-expression in breast cancer should be predictive of response to treatment with RARα-isotype-specific agonists and warrant monitoring during clinical trials.
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MESH Headings
- Animals
- Benzoates/pharmacology
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Cell Line, Tumor
- Cell Proliferation
- Cell Survival/genetics
- Cell Transformation, Neoplastic/drug effects
- Cell Transformation, Neoplastic/genetics
- Disease Models, Animal
- Female
- Gene Expression Regulation, Neoplastic/drug effects
- Genes, myc
- Heterografts
- Humans
- Lung Neoplasms/secondary
- Mice
- RNA, Small Interfering/genetics
- Receptors, Retinoic Acid/agonists
- Receptors, Retinoic Acid/genetics
- Receptors, Retinoic Acid/metabolism
- Retinoic Acid Receptor alpha
- Retinol-Binding Proteins/genetics
- Tetrahydronaphthalenes/pharmacology
- Transcription, Genetic
- Retinoic Acid Receptor gamma
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Affiliation(s)
- Almudena Bosch
- Mount Sinai School of Medicine, Department of Medicine, The Tisch Cancer Institute, Division of Hematology and Medical Oncology, One Gustave L Levy Place, New York, NY 10029, USA
| | - Silvina P Bertran
- Mount Sinai School of Medicine, Department of Medicine, The Tisch Cancer Institute, Division of Hematology and Medical Oncology, One Gustave L Levy Place, New York, NY 10029, USA
| | - Yongke Lu
- Mount Sinai School of Medicine, Department of Medicine, The Tisch Cancer Institute, Division of Hematology and Medical Oncology, One Gustave L Levy Place, New York, NY 10029, USA
| | - Avalon Garcia
- Mount Sinai School of Medicine, Department of Medicine, The Tisch Cancer Institute, Division of Hematology and Medical Oncology, One Gustave L Levy Place, New York, NY 10029, USA
| | - Alexis M Jones
- Mount Sinai School of Medicine, Department of Medicine, The Tisch Cancer Institute, Division of Hematology and Medical Oncology, One Gustave L Levy Place, New York, NY 10029, USA
| | - Marcia I Dawson
- Cancer Center, Sanford-Burnham Medical Research Institute, 10901, North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Eduardo F Farias
- Mount Sinai School of Medicine, Department of Medicine, The Tisch Cancer Institute, Division of Hematology and Medical Oncology, One Gustave L Levy Place, New York, NY 10029, USA
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Ropson IJ, Boyer JA, Schaeffer BA, Dalessio PM. Comparison of the folding mechanism of highly homologous proteins in the lipid-binding protein family. Proteins 2009; 75:799-806. [PMID: 19003989 DOI: 10.1002/prot.22286] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The folding mechanism of two closely related proteins in the intracellular lipid-binding protein family, human bile acid-binding protein (hBABP), and rat bile acid-binding protein (rBABP) were examined. These proteins are 77% identical (93% similar) in sequence. Both of these single domain proteins fit well to a two-state model for unfolding by fluorescence and circular dichroism at equilibrium. Three phases were observed during the unfolding of rBABP by fluorescence but only one phase was observed during the unfolding of hBABP, suggesting that at least two kinetic intermediates accumulate during the unfolding of rBABP that are not observed during the unfolding of hBABP. Fluorine NMR was used to examine the equilibrium unfolding behavior of the W49 side chain in 6-fluorotryptophan-labeled rBABP and hBABP. The structure of rBABP appears to be more dynamic than that of hBABP in the vicinity of W49 in the absence of denaturant, and urea has a greater effect on this dynamic behavior for rBABP than for hBABP. As such, the folding behavior of highly sequence related proteins in this family can be quite different. These differences imply that moderately sized proteins with high sequence and structural similarity can still populate quite different structures during folding.
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Affiliation(s)
- Ira J Ropson
- Department of Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania, USA.
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7
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Marcelino AMC, Gierasch LM. Roles of beta-turns in protein folding: from peptide models to protein engineering. Biopolymers 2008; 89:380-91. [PMID: 18275088 PMCID: PMC2904567 DOI: 10.1002/bip.20960] [Citation(s) in RCA: 172] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Reverse turns are a major class of protein secondary structure; they represent sites of chain reversal and thus sites where the globular character of a protein is created. It has been speculated for many years that turns may nucleate the formation of structure in protein folding, as their propensity to occur will favor the approximation of their flanking regions and their general tendency to be hydrophilic will favor their disposition at the solvent-accessible surface. Reverse turns are local features, and it is therefore not surprising that their structural properties have been extensively studied using peptide models. In this article, we review research on peptide models of turns to test the hypothesis that the propensities of turns to form in short peptides will relate to the roles of corresponding sequences in protein folding. Turns with significant stability as isolated entities should actively promote the folding of a protein, and by contrast, turn sequences that merely allow the chain to adopt conformations required for chain reversal are predicted to be passive in the folding mechanism. We discuss results of protein engineering studies of the roles of turn residues in folding mechanisms. Factors that correlate with the importance of turns in folding indeed include their intrinsic stability, as well as their topological context and their participation in hydrophobic networks within the protein's structure.
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8
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Meissburger B, Wolfrum C. The role of retinoids and their receptors in metabolic disorders. EUR J LIPID SCI TECH 2008. [DOI: 10.1002/ejlt.200700291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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9
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Marcelino AMC, Smock RG, Gierasch LM. Evolutionary coupling of structural and functional sequence information in the intracellular lipid-binding protein family. Proteins 2007; 63:373-84. [PMID: 16477649 DOI: 10.1002/prot.20860] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We have mined the evolutionary record for the large family of intracellular lipid-binding proteins (iLBPs) by calculating the statistical coupling of residue variations in a multiple sequence alignment using methods developed by Ranganathan and coworkers (Lockless and Ranganathan, Science 1999:286;295-299). The 213 sequences analyzed have a wide range of ligand-binding functions as well as highly divergent phylogenetic origins, assuring broad sampling of sequence space. Emerging from this analysis were two major clusters of coupled residues, which when mapped onto the structure of a representative iLBP under study in our laboratory, cellular retinoic-acid binding protein I, are largely contiguous and provide useful points of comparison to available data for the folding of this protein. One cluster comprises a predominantly hydrophobic core away from the ligand-binding site and likely represents key structural information for the iLBP fold. The other cluster includes the portal region where ligand enters its binding site, regions of the ligand-binding cavity, and the region where the 10-stranded beta-barrel characteristic of this family closes (between strands 1' and 10). Linkages between these two clusters suggest that evolutionary pressures on this family constrain structural and functional sequence information in an interdependent fashion. The necessity of the structure to wrap around a hydrophobic ligand confounds the typical sequestration of hydrophobic side chains. Additionally, ligand entry and exit require these structures to have a capacity for specific conformational change during binding and release. We conclude that an essential and structurally apparent separation of local and global sequence information is conserved throughout the iLBP family.
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10
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Nakajima S, Alvarez-Salgado E, Kikuchi T, Arredondo-Peter R. Prediction of folding pathway and kinetics among plant hemoglobins using an average distance map method. Proteins 2006; 61:500-6. [PMID: 16184600 DOI: 10.1002/prot.20658] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Computational methods, such as the ADM (average distance map) method, have been developed to predict folding of homologous proteins. In this work we used the ADM method to predict the folding pathway and kinetics among selected plant nonsymbiotic (nsHb), symbiotic (Lb), and truncated (tHb) hemoglobins (Hbs). Results predicted that (1) folding of plant Hbs occurs throughout the formation of compact folding modules mostly formed by helices A, B, and C, and E, F, G, and H (folding modules A/C and E/H, respectively), and (2) primitive (moss) nsHbs fold in the C-->N direction, evolved (monocot and dicot) nsHbs fold either in the C-->N or N-->C direction, and Lbs and plant tHbs fold in the C-->N direction. We also predicted relative folding rates of plant Hbs from qualitative analyses of the stability of subdomains and classified plant Hbs into fast and moderate folding. ADM analysis of nsHbs predicted that prehelix A plays a role during folding of the N-terminal domain of Ceratodon nsHb, and that CD-loop plays a role in folding of primitive (Physcomitrella and Ceratodon) but not evolved nsHbs. Modeling of the rice Hb1 A/C and E/H modules showed that module E/H overlaps to the Mycobacterium tuberculosis HbO two-on-two folding. This observation suggests that module E/H is an ancient tertiary structure in plant Hbs.
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Affiliation(s)
- Shunsuke Nakajima
- Department of Bioscience and Bioinformatics, College of Information Science and Engineering, Ritsumeikan University, Shiga, Japan
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11
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Junker M, Schuster CC, McDonnell AV, Sorg KA, Finn MC, Berger B, Clark PL. Pertactin beta-helix folding mechanism suggests common themes for the secretion and folding of autotransporter proteins. Proc Natl Acad Sci U S A 2006; 103:4918-23. [PMID: 16549796 PMCID: PMC1458770 DOI: 10.1073/pnas.0507923103] [Citation(s) in RCA: 174] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Many virulence factors secreted from pathogenic Gram-negative bacteria are autotransporter proteins. The final step of autotransporter secretion is C --> N-terminal threading of the passenger domain through the outer membrane (OM), mediated by a cotranslated C-terminal porin domain. The native structure is formed only after this final secretion step, which requires neither ATP nor a proton gradient. Sequence analysis reveals that, despite size, sequence, and functional diversity among autotransporter passenger domains, >97% are predicted to form parallel beta-helices, indicating this structural topology may be important for secretion. We report the folding behavior of pertactin, an autotransporter passenger domain from Bordetella pertussis. The pertactin beta-helix folds reversibly in isolation, but folding is much slower than expected based on size and native-state topology. Surprisingly, pertactin is not prone to aggregation during folding, even though folding is extremely slow. Interestingly, equilibrium denaturation results in the formation of a partially folded structure, a stable core comprising the C-terminal half of the protein. Examination of the pertactin crystal structure does not reveal any obvious reason for the enhanced stability of the C terminus. In vivo, slow folding would prevent premature folding of the passenger domain in the periplasm, before OM secretion. Moreover, the extra stability of the C-terminal rungs of the beta-helix might serve as a template for the formation of native protein during OM secretion; hence, vectorial folding of the beta-helix could contribute to the energy-independent translocation mechanism. Coupled with the sequence analysis, the results presented here suggest a general mechanism for autotransporter secretion.
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Affiliation(s)
- Mirco Junker
- *Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556-5670; and
| | - Christopher C. Schuster
- *Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556-5670; and
| | - Andrew V. McDonnell
- Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Kelli A. Sorg
- *Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556-5670; and
| | - Mary C. Finn
- *Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556-5670; and
| | - Bonnie Berger
- Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Patricia L. Clark
- *Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556-5670; and
- To whom correspondence should be addressed at:
Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556. E-mail:
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12
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Dalessio PM, Fromholt SE, Ropson IJ. The role of Trp-82 in the folding of intestinal fatty acid binding protein. Proteins 2005; 61:176-83. [PMID: 16080148 DOI: 10.1002/prot.20463] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Multiple phases have been observed during the folding and unfolding of intestinal fatty acid binding protein (WT-IFABP) by stopped-flow fluorescence. Site-directed mutagenesis has been used to examine the role of each of the two tryptophans of this protein in these processes. The unfolding and refolding kinetics of the mutant protein containing only tryptophan 82 (W6Y-IFABP) showed that the tryptophan at this location was critical to the fluorescence signal changes observed throughout the unfolding reaction and early in the refolding reaction. However, the kinetic patterns of the mutant protein containing only tryptophan 6 (W82Y-IFABP) indicated that the tryptophan at this location participated in the fluorescence signal changes observed early in the unfolding reaction and late in the refolding reaction. Together, these data suggest that native-like structure was formed first in the vicinity of tryptophan 82, near the center of the hydrophobic core of this beta-sheet protein, prior to formation of native-like structure in the periphery of the protein.
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Affiliation(s)
- Paula M Dalessio
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, USA
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13
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Kamagata K, Arai M, Kuwajima K. Unification of the Folding Mechanisms of Non-two-state and Two-state Proteins. J Mol Biol 2004; 339:951-65. [PMID: 15165862 DOI: 10.1016/j.jmb.2004.04.015] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2003] [Revised: 04/01/2004] [Accepted: 04/01/2004] [Indexed: 11/15/2022]
Abstract
We have collected the kinetic folding data for non-two-state and two-state globular proteins reported in the literature, and investigated the relationships between the folding kinetics and the native three-dimensional structure of these proteins. The rate constants of formation of both the intermediate and the native state of non-two-state folders were found to be significantly correlated with protein chain length and native backbone topology, which is represented by the absolute contact order and sequence-distant native pairs. The folding rate of two-state folders, which is known to be correlated with the native backbone topology, apparently does not correlate significantly with protein chain length. On the basis of a comparison of the folding rates of the non-two-state and two-state folders, it was found that they are similarly dependent on the parameters that reflect the native backbone topology. This suggests that the mechanisms behind non-two-state and two-state folding are essentially identical. The present results lead us to propose a unified mechanism of protein folding, in which folding occurs in a hierarchical manner, reflecting the hierarchy of the native three-dimensional structure, as embodied in the case of non-two-state folding with an accumulation of the intermediate. Apparently, two-state folding is merely a simplified version of hierarchical folding caused either by an alteration in the rate-limiting step of folding or by destabilization of the intermediate.
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Affiliation(s)
- Kiyoto Kamagata
- Department of Physics, School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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14
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Burns-Hamuro LL, Dalessio PM, Ropson IJ. Replacement of proline with valine does not remove an apparent proline isomerization-dependent folding event in CRABP I. Protein Sci 2004; 13:1670-6. [PMID: 15152096 PMCID: PMC2279983 DOI: 10.1110/ps.03317804] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2003] [Revised: 09/30/2003] [Accepted: 09/30/2003] [Indexed: 10/26/2022]
Abstract
Site-directed mutagenesis has frequently been used to replace proline with other amino acids in order to determine if proline isomerization is responsible for a slow phase during refolding. Replacement of Pro 85 with alanine in cellular retinoic acid binding protein I (CRABP-I) abolished the slowest refolding phase, suggesting that this phase is due to proline isomerization in the unfolded state. To further test this assumption, we mutated Pro 85 to valine, which is the conservative replacement in the two most closely related proteins in the family (cellular retinoic acid binding protein II and cellular retinol binding protein I). The mutant protein was about 1 kcal/mole more stable than wild type. Retinoic acid bound equally well to wild type and P85V-CRABP I, confirming the functional integrity of this mutation. The refolding and unfolding kinetics of the wild-type and mutant proteins were characterized by stopped flow fluorescence and circular dichroism. The mutant P85V protein refolded with three kinetic transitions, the same number as wild-type protein. This result conflicts with the P85A mutant, which lost the slowest refolding rate. The P85V mutation also lacked a kinetic unfolding intermediate found for wild-type protein. These data suggest that proline isomerization may not be responsible for the slowest folding phase of CRABP I. As such, the loss of a slow refolding phase upon mutation of a proline residue may not be diagnostic for proline isomerization effects on protein folding.
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Affiliation(s)
- Lora L Burns-Hamuro
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, College of Medicine, Hershey, PA 17033, USA
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15
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Calloni G, Taddei N, Plaxco KW, Ramponi G, Stefani M, Chiti F. Comparison of the folding processes of distantly related proteins. Importance of hydrophobic content in folding. J Mol Biol 2003; 330:577-91. [PMID: 12842473 DOI: 10.1016/s0022-2836(03)00627-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The N-terminal domain of HypF from Escherichia coli (HypF-N) is a 91 residue protein module sharing the same folding topology and a significant sequence identity with two extensively studied human proteins, muscle and common-type acylphosphatases (mAcP and ctAcP). With the aim of learning fundamental aspects of protein folding from the close comparison of so similar proteins, the folding process of HypF-N has been studied using stopped-flow fluorescence. While mAcP and ctAcP fold in a two-state fashion, HypF-N was found to collapse into a partially folded intermediate before reaching the fully folded conformation. Formation of a burst-phase intermediate is indicated by the roll over in the Chevron plot at low urea concentrations and by the large jump of intrinsic and 8-anilino-1-naphtalenesulphonic acid-derived fluorescence immediately after removal of denaturant. Furthermore, HypF-N was found to fold rapidly with a rate constant that is approximately two and three orders of magnitudes faster than ctAcP and mAcP, respectively. Differences between the bacterial protein and the two human counterparts were also found as to the involvement of proline isomerism in their respective folding processes. The results clearly indicate that features that are often thought to be relevant in protein folding are not highly conserved in the evolution of the acylphosphatase superfamily. The large difference in folding rate between mAcP and HypF-N cannot be entirely accounted for by the difference in relative contact order or related topological metrics. The analysis shows that the higher folding rate of HypF-N is in part due to the relatively high hydrophobic content of this protein. This conclusion, which is also supported by the highly significant correlation found between folding rate and hydrophobic content within a group of proteins displaying the topology of HypF-N and AcPs, suggests that the average hydrophobicity of a protein sequence is an important determinant of its folding rate.
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Affiliation(s)
- Giulia Calloni
- Dipartimento di Scienze Biochimiche, Università di Firenze, Viale Morgagni 50, 50134 Florence, Italy
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16
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Ichimaru T, Kikuchi T. Analysis of the differences in the folding kinetics of structurally homologous proteins based on predictions of the gross features of residue contacts. Proteins 2003; 51:515-30. [PMID: 12784211 DOI: 10.1002/prot.10378] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
It is a general notion that proteins with very similar three-dimensional structures would show very similar folding kinetics. However, recent studies reveal that the folding kinetic properties of some proteins contradict this thought (i.e., the members in a same protein family fold through different pathways). For example, it has been reported that some beta-proteins in the intracellular lipid-binding protein family fold through quite different pathways (Burns et al., Proteins 1998;33:107-118). Similar differences in folding kinetics are also observed in the members of the globin family (Nishimura et al., Nat Struct Biol 2000;7:679-686). In our study, we examine the possibility of predicting qualitative differences in folding kinetics of the intracellular lipid-binding proteins and two globin proteins (i.e., myoglobin and leghemoglobin). The problem is tackled by means of a contact map based on the average distance statistics between residues, the Average Distance Map (ADM), as constructed from sequence. The ADMs for the three proteins show overall similarity, but some local differences among maps are also observed. Our results demonstrate that some properties of the protein folding kinetics are consistent with local differences in the ADMs. We also discuss the general possibility of predicting folding kinetics from sequence information.
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Affiliation(s)
- Takehiro Ichimaru
- Department of Chemistry and Bioscience, College of Industrial Technology, Kurashiki University of Science and the Arts, Kurashiki, Okayama, Japan
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Forsyth WR, Matthews CR. Folding mechanism of indole-3-glycerol phosphate synthase from Sulfolobus solfataricus: a test of the conservation of folding mechanisms hypothesis in (beta(alpha))(8) barrels. J Mol Biol 2002; 320:1119-33. [PMID: 12126630 DOI: 10.1016/s0022-2836(02)00557-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
As a test of the hypothesis that folding mechanisms are better conserved than sequences in TIM barrels, the equilibrium and kinetic folding mechanisms of indole-3-glycerol phosphate synthase (sIGPS) from the thermoacidophilic archaebacterium Sulfolobus solfataricus were compared to the well-characterized models of the alpha subunit of tryptophan synthase (alphaTS) from Escherichia coli. A multifaceted approach combining urea denaturation and far-UV circular dichroism, tyrosine fluorescence total intensity, and tyrosine fluorescence anisotropy was employed. Despite a sequence identity of only 13%, a stable intermediate (I) in sIGPS was found to be similar to a stable intermediate in alphaTS in terms of its thermodynamic properties and secondary structure. Kinetic experiments revealed that the fastest detectable folding event for sIGPS involves a burst-phase (<5ms) reaction that leads directly to the stable intermediate. The slower of two subsequent phases reflects the formation/disruption of an off-pathway dimeric form of I. The faster phase reflects the conversion of I to the native state and is limited by folding under marginally stable conditions and by isomerization or rearrangement under strongly folding conditions. By contrast, alphaTS is thought to fold via an off-pathway burst-phase intermediate whose unfolding controls access to a set of four on-pathway intermediates that comprise the stable equilibrium intermediate. At least three proline isomerization reactions are known to limit their interconversions and lead to a parallel channel mechanism. The simple sequential mechanism deduced for sIGPS reflects the dominance of the on-pathway burst-phase intermediate and the absence of prolyl residues that partition the stable intermediate into kinetically distinguishable species. Comparison of the results for sIGPS and alphaTS demonstrates that the thermodynamic properties and the final steps of the folding reaction are better conserved than the early events. The initial events in folding appear to be more sensitive to the sequence differences between the two TIM barrel proteins.
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Affiliation(s)
- William R Forsyth
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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