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Goluguri RR, Udgaonkar JB. Microsecond Rearrangements of Hydrophobic Clusters in an Initially Collapsed Globule Prime Structure Formation during the Folding of a Small Protein. J Mol Biol 2016; 428:3102-17. [PMID: 27370109 DOI: 10.1016/j.jmb.2016.06.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 06/17/2016] [Accepted: 06/19/2016] [Indexed: 12/14/2022]
Abstract
Determining how polypeptide chain collapse initiates structure formation during protein folding is a long standing goal. It has been challenging to characterize experimentally the dynamics of the polypeptide chain, which lead to the formation of a compact kinetic molten globule (MG) in about a millisecond. In this study, the sub-millisecond events that occur early during the folding of monellin from the guanidine hydrochloride-unfolded state have been characterized using multiple fluorescence and fluorescence resonance energy transfer probes. The kinetic MG is shown to form in a noncooperative manner from the unfolded (U) state as a result of at least three different processes happening during the first millisecond of folding. Initial chain compaction completes within the first 37μs, and further compaction occurs only after structure formation commences at a few milliseconds of folding. The transient nonnative and native-like hydrophobic clusters with side chains of certain residues buried form during the initial chain collapse and the nonnative clusters quickly disassemble. Subsequently, partial chain desolvation occurs, leading to the formation of a kinetic MG. The initial chain compaction and subsequent chain rearrangement appear to be barrierless processes. The two structural rearrangements within the collapsed globule appear to prime the protein for the actual folding transition.
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Affiliation(s)
- Rama Reddy Goluguri
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India.
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Li M, Liu Z. Dimensions, energetics, and denaturant effects of the protein unstructured state. Protein Sci 2016; 25:734-47. [PMID: 26683260 DOI: 10.1002/pro.2865] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/09/2015] [Accepted: 12/15/2015] [Indexed: 11/09/2022]
Abstract
Determining the energetics of the unfolded state of a protein is essential for understanding the folding mechanics of ordered proteins and the structure-function relation of intrinsically disordered proteins. Here, we adopt a coil-globule transition theory to develop a general scheme to extract interaction and free energy information from single-molecule fluorescence resonance energy transfer spectroscopy. By combining protein stability data, we have determined the free energy difference between the native state and the maximally collapsed denatured state in a number of systems, providing insight on the specific/nonspecific interactions in protein folding. Both the transfer and binding models of the denaturant effects are demonstrated to account for the revealed linear dependence of inter-residue interactions on the denaturant concentration, and are thus compatible under the coil-globule transition theory to further determine the dimension and free energy of the conformational ensemble of the unfolded state. The scaling behaviors and the effective θ-state are also discussed.
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Affiliation(s)
- Maodong Li
- College of Chemistry and Molecular Engineering, Center for Quantitative Biology, and Beijing National Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing, 100871, China
| | - Zhirong Liu
- College of Chemistry and Molecular Engineering, Center for Quantitative Biology, and Beijing National Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing, 100871, China
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Ohtomo H, Ohtomo M, Sato D, Kurobe A, Sunato A, Matsumura Y, Kihara H, Fujiwara K, Ikeguchi M. A Physicochemical and Mutational Analysis of Intersubunit Interactions of Escherichia coli Ferritin A. Biochemistry 2015; 54:6243-51. [PMID: 26399896 DOI: 10.1021/acs.biochem.5b00723] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ferritin A from Escherichia coli (EcFtnA) is 24-meric protein, which forms spherical cagelike structures called nanocages. The nanocage structure is stabilized by the interface around 4-, 3-, and 2-fold symmetric axes. The subunit structure of EcFtnA comprises a four-helix bundle (helices A-D) and an additional helix E, which forms a 4-fold axis. In this study, we examined the contribution of the interface around three symmetric axes. pH-induced dissociation experiments monitored by analytical ultracentrifugation and small-angle X-ray scattering showed that the dimer related by 2-fold symmetry is the most stable unit. Mutations located near the 3-fold axis revealed that the contribution of each interaction was small. A mutant lacking helix E at the 4-fold axis formed a nanocage, suggesting that helix E is not essential for nanocage formation. Further truncation of the C-terminus of helix D abrogated the formation of the nanocage, suggesting that a few residues located at the C-terminus of helix D are critical for this process. These properties are similar to those known for mammalian ferritins and seem to be common principles for nanocage formation. The difference between EcFtnA and mammalian ferritins was that helix E-truncated EcFtnA maintained an iron-incorporating ability, whereas mammalian mutants lost it.
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Affiliation(s)
- Hideaki Ohtomo
- Department of Bioinformatics, Soka University , 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan
| | - Mio Ohtomo
- Department of Bioinformatics, Soka University , 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan
| | - Daisuke Sato
- Department of Bioinformatics, Soka University , 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan
| | - Atsushi Kurobe
- Department of Bioinformatics, Soka University , 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan
| | - Ayumi Sunato
- Department of Bioinformatics, Soka University , 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan
| | - Yoshitaka Matsumura
- Department of Physics, Kansai Medical University , 18-89 Uyama-Higashi, Hirakata 573-1136, Japan
| | - Hiroshi Kihara
- Department of Physics, Kansai Medical University , 18-89 Uyama-Higashi, Hirakata 573-1136, Japan
| | - Kazuo Fujiwara
- Department of Bioinformatics, Soka University , 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan
| | - Masamichi Ikeguchi
- Department of Bioinformatics, Soka University , 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan
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Konuma T, Sakurai K, Yagi M, Goto Y, Fujisawa T, Takahashi S. Highly Collapsed Conformation of the Initial Folding Intermediates of β-Lactoglobulin with Non-Native α-Helix. J Mol Biol 2015; 427:3158-65. [DOI: 10.1016/j.jmb.2015.07.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 07/21/2015] [Accepted: 07/22/2015] [Indexed: 10/23/2022]
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Okabe T, Miyajima T, Nakagawa K, Tsukamoto S, Fujiwara K, Ikeguchi M. Effect of non-native helix destabilization on the folding of equine β-lactoglobulin. J Biochem 2014; 156:291-7. [DOI: 10.1093/jb/mvu043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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6
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Ikeguchi M. Transient non-native helix formation during the folding of β-lactoglobulin. Biomolecules 2014; 4:202-16. [PMID: 24970212 PMCID: PMC4030977 DOI: 10.3390/biom4010202] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 02/05/2014] [Accepted: 02/10/2014] [Indexed: 11/20/2022] Open
Abstract
In ideal proteins, only native interactions are stabilized step-by-step in a smooth funnel-like energy landscape. In real proteins, however, the transient formation of non-native structures is frequently observed. In this review, the transient formation of non-native structures is described using the non-native helix formation during the folding of β-lactoglobulin as a prominent example. Although β-lactoglobulin is a predominantly β-sheet protein, it has been shown to form non-native helices during the early stage of folding. The location of non-native helices, their stabilization mechanism, and their role in the folding reaction are discussed.
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Affiliation(s)
- Masamichi Ikeguchi
- Department of Bioinformatics, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan.
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